Skip to main content

Advertisement

SpringerLink
Log in

Fecal Recovery of Ingested Cellular DNA: Implications for Noninvasive Detection of Upper Gastrointestinal Neoplasms

  • Original Article
  • Published:
Digestive Diseases and Sciences Aims and scope Submit manuscript

Abstract

Background

Stool DNA testing represents a potential noninvasive approach to detect upper gastrointestinal (UGI) neoplasms. However, little is known about fecal recovery efficiency of DNA exfoliated from UGI tumors.

Aims

The purpose of this study was to establish a human ingestion model that quantitatively approximates daily cellular shedding from UGI neoplasms and to estimate fecal DNA marker recovery rates.

Methods

Healthy volunteers (n = 10) ingested two scheduled doses of raw salmon, 0.3 and 30 g, simulating the mass exfoliated daily from 1 to 4.5 cm lesions. To approach a steady-state, each dose was ingested over three consecutive days in randomized order. Following defecation of an indicator dye ingested with test meals, stools were collected over 48 h. Ingested salmon DNA was captured from stools using probes targeting pathognomonic Salmonidae sequences (SlmII). Captured DNA was quantified using PCR primers to generate 178, 138, 88 and 55 bp amplicons.

Results

SlmII sequences were recovered from all stools following salmon ingestion; recovery was proportional to amount ingested (p = 0.004). Fecal recovery of ingested salmon varied inversely with amplicon size targeted; mean recovery rates of SlmII were 0.49, 0.91, 3.63, and 7.31 copies per 100,000 copies ingested for 178, 134, 88, and 55 bp amplicons, respectively (p < 0.0001). Longer oro-anal transit was associated with reduced recovery.

Conclusions

While recovery efficiencies are low, ingested cellular DNA simulating daily amounts shed from UGI tumors can readily be detected in stool. Assay of shorter-fragment analyte increases recovery. This ingestion model has potential value in studying the effects of perturbations relevant to the fecal recovery of DNA exfoliated from UGI tumors.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Ahlquist DA, Zou H, Domanico M, et al. Next-generation stool DNA test accurately detects colorectal cancer and large adenomas. Gastroenterology. 2012;142:248–256.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Ahlquist DA, Taylor WR, Mahoney DW, et al. The stool DNA test is more accurate than the plasma septin 9 test in detecting colorectal neoplasia. Clin Gastroenterol Hepatol. 2012;10:e1.

    Article  PubMed  Google Scholar 

  3. Lidgard GP, Domanico MJ, Bruinsma JJ, et al. Clinical performance of an automated stool DNA assay for detection of colorectal neoplasia. Clin Gastroenterol Hepatol. 2013;11:1313–1318.

    Article  CAS  PubMed  Google Scholar 

  4. Imperiale TF, Ransohoff DF, Itzkowitz SH, et al. Multitarget stool DNA testing for colorectal-cancer screening. N Engl J Med. 2014;370:1287–1297.

    Article  CAS  PubMed  Google Scholar 

  5. Parkin DM, Bray F, Ferlay J, et al. Global cancer statistics, 2002. CA Cancer J Clin. 2005;55:74–108.

    Article  PubMed  Google Scholar 

  6. Jemal A, Center MM, DeSantis C, et al. Global patterns of cancer incidence and mortality rates and trends. Cancer Epidemiol Biomarkers Prev. 2010;19:1893–1907.

    Article  PubMed  Google Scholar 

  7. Hwang C, Kumar S, Yab TC, Taylor WR, et al. Noninvasive detection of intraductal papillary mucinous neoplasms (IPMN) and early stage cancer of the pancreas with stool DNA testing. Gastroenterology. 2011. doi:10.1016/S0016-5085(11)62812-6.

    PubMed Central  Google Scholar 

  8. Zou H, Harrington JJ, Taylor WR, et al. Pan-detection of gastrointestinal neoplasms by stool DNA testing: establishment of feasibility (Abstract #T2036). Gastroenterology. 2009;136:A625.

    Article  Google Scholar 

  9. Zou H, Taylor WR, Harrington JJ, et al. A sensitive method to scan gene mutations in stool: relevance to detection of gastrointestinal neoplasia. Gastroenterology. 2008;134:A485.

    Google Scholar 

  10. Ahlquist DA. Next-generation stool DNA testing: expanding the scope. Gastroenterology. 2009;136:2068–2073.

    Article  CAS  PubMed  Google Scholar 

  11. Kisiel JB, Yab TC, Taylor WR, et al. Stool DNA testing for the detection of pancreatic cancer: assessment of methylation marker candidates. Cancer. 2012;118:2623–2631.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Yang W. Nucleases: diversity of structure, function and mechanism. Q Rev Biophys. 2011;44:1–93.

    Article  PubMed  Google Scholar 

  13. Igney FH, Krammer PH. Immune escape of tumors: apoptosis resistance and tumor counterattack. J Leukoc Biol. 2002;71:907–920.

    CAS  PubMed  Google Scholar 

  14. Schubbert R, Lettmann C, Doerfler W. Ingested foreign (phage M13) DNA survives transiently in the gastrointestinal tract and enters the bloodstream of mice. Mol Gen Genet. 1994;242:495–504.

    Article  CAS  PubMed  Google Scholar 

  15. Netherwood T, Martin-Orue SM, O’Donnell AG, et al. Assessing the survival of transgenic plant DNA in the human gastrointestinal tract. Nat Biotechnol. 2004;22:204–209.

    Article  CAS  PubMed  Google Scholar 

  16. Zou H, Taylor WR, Harrington JJ, et al. High detection rates of colorectal neoplasia by stool DNA testing with a novel digital melt curve assay. Gastroenterology. 2009;136:459–470.

    Article  CAS  PubMed  Google Scholar 

  17. Kisiel JB, Ahlquist DA. Stool DNA screening for colorectal cancer: opportunities to improve value with next generation tests. J Clin Gastroenterol. 2011;45:301–308.

    Article  PubMed  Google Scholar 

  18. Ahlquist DA. Molecular detection of colorectal neoplasia. Gastroenterology. 2010;138:2127–2139.

    Article  CAS  PubMed  Google Scholar 

  19. Zou H, Cao X, Domenico M, et al. Sensitive Quantitation of Methylated Markers with a Novel Methylation-Specific Technology. Los Angeles, CA: In AACC Meeting; 2010.

    Google Scholar 

  20. Taly V, Pekin D, Benhaim L, et al. Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients. Clin Chem. 2013;59:5. doi:10.1373/clinchem.2012.193409.

    Article  Google Scholar 

  21. Diehl F, Schmidt K, Durkee KH, et al. Analysis of mutations in DNA isolated from plasma and stool of colorectal cancer patients. Gastroenterology. 2008;135:489–498.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Matveev V, Okada N. Retroposons of salmonoid fishes (Actinopterygii: Salmonoidei) and their evolution. Gene. 2009;434:16–28.

    Article  CAS  PubMed  Google Scholar 

  23. Blanpain C, Horsley V, Fuchs E. Epithelial stem cells: turning over new leaves. Cell. 2007;128:445–458.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Green DR, Evan GI. A matter of life and death. Cancer Cell. 2002;1:19–30.

    Article  CAS  PubMed  Google Scholar 

  25. Pellettieri J, Sanchez Alvarado A. Cell turnover and adult tissue homeostasis: from humans to planarians. Annu Rev Genet. 2007;41:83–105.

    Article  CAS  PubMed  Google Scholar 

  26. Ng SH, Artieri CG, Bosdet IE, et al. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics. 2005;86:396–404.

    Article  CAS  PubMed  Google Scholar 

  27. Dain JG, Nicoletti J, Ballard F. Biotransformation of clozapine in humans. Drug Metab Dispos. 1997;25:603–609.

    CAS  PubMed  Google Scholar 

  28. Zou H, Harrington JJ, Klatt KK, et al. A sensitive method to quantify human long DNA in stool: relevance to colorectal cancer screening. Cancer Epidemiol Biomark Prev. 2006;15:1115–1119.

    Article  CAS  Google Scholar 

  29. Matveev V, Nishihara H, Okada N. Novel SINE families from salmons validate Parahucho (Salmonidae) as a distinct genus and give evidence that SINEs can incorporate LINE-related 3′-tails of other SINEs. Mol Biol Evol. 2007;24:1656–1666.

    Article  CAS  PubMed  Google Scholar 

  30. Kent WJ. BLAT—the BLAST-like alignment tool. Genome Res. 2002;12:656–664.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Cooper GM. Chromosomes and Chromatin. The Cell: A Molecular Approach. 2nd ed. Sunderland, MA: Sinauer Associates; 2000.

    Google Scholar 

  32. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 2007;35(Web Server issue):W71–4.

  33. Mouliere F, El Messaoudi S, Gongora C, et al. Circulating cell-free DNA from colorectal cancer patients may reveal high KRAS or BRAF mutation load. Transl Oncol. 2013;6:319–328.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Mouliere F, Robert B, Arnau Peyrotte E, et al. High fragmentation characterizes tumour-derived circulating DNA. PLoS One. 2011;6:e23418.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Taguchi T, Miura Y, Krueger D, et al. Utilizing stomach content and faecal DNA analysis techniques to assess the feeding behaviour of largemouth bass Micropterus salmoides and bluegill Lepomis macrochirus. J Fish Biol. 2014;84:1271–1288.

    Article  CAS  PubMed  Google Scholar 

  36. Gausterer C, Penker M, Krisai-Greilhuber I, et al. Rapid genetic detection of ingested Amanita phalloides. Forensic Sci Int Genet. 2014;9:66–71.

    Article  CAS  PubMed  Google Scholar 

  37. Hamad I, Delaporte E, Raoult D, et al. Detection of termites and other insects consumed by African great apes using molecular fecal analysis. Sci Rep. 2014;4:4478.

    PubMed  PubMed Central  Google Scholar 

  38. Gilbert MT, Jenkins DL, Gotherstrom A, et al. DNA from pre-Clovis human coprolites in Oregon, North America. Science. 2008;320:786–789.

    Article  CAS  PubMed  Google Scholar 

  39. Bon C, Berthonaud V, Maksud F, et al. Coprolites as a source of information on the genome and diet of the cave hyena. Proc Biol Sci. 2012;279:2825–2830.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

The authors would like to thank the generous gift from Eugene and Eve Lane, Mayo Foundation.

Author contributions

Strauss: study concept and design; acquisition of data; analysis and interpretation of data; drafting of the manuscript. Yab: study concept and design, acquisition of data, analysis and interpretation of data, administrative and technical support. O’Connor: acquisition of data, analysis and interpretation of data, technical support, critical review of manuscript. Taylor: study concept and design; acquisition of data; analysis and interpretation of data; drafting of the manuscript. Mahoney: analysis and interpretation of data; statistical analyses; critical review of manuscript. Simonson: acquisition of data, technical support. Christensen: acquisition of data, technical support. Chari: critical review of manuscript. Ahlquist: study concept and design; analysis and interpretation of data; drafting of the manuscript; critical revision of the manuscript for important intellectual content; obtained funding; study supervision.

Author information

Authors and Affiliations

  1. Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55901, USA

    Benjamin B. Strauss, Tracy C. Yab, Helen M. O’Connor, William R. Taylor, Julie A. Simonson, John Christensen, Suresh T. Chari & David A. Ahlquist

  2. Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN, USA

    Helen M. O’Connor

  3. Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA

    Douglas W. Mahoney

Authors
  1. Benjamin B. Strauss
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tracy C. Yab
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Helen M. O’Connor
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. William R. Taylor
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Douglas W. Mahoney
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Julie A. Simonson
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. John Christensen
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Suresh T. Chari
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. David A. Ahlquist
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David A. Ahlquist.

Ethics declarations

Conflict of interest

Dr. Ahlquist and T. Yab, W. Taylor, and D. Mahoney are co-inventors on Mayo Clinic technology licensed to Exact Sciences (Madison WI); and Dr. Ahlquist serves a scientific advisor to and receives research support from Exact Sciences. While Exact Sciences did not provide funding for this study and had no role in the design, data analyses, or manuscript preparation, the findings of this research are thematically linked to the Mayo Clinic collaboration with Exact Sciences. Findings were presented in part at Digestive Disease Week, Chicago, IL, May 2014.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Strauss, B.B., Yab, T.C., O’Connor, H.M. et al. Fecal Recovery of Ingested Cellular DNA: Implications for Noninvasive Detection of Upper Gastrointestinal Neoplasms. Dig Dis Sci 61, 117–125 (2016). https://doi.org/10.1007/s10620-015-3845-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10620-015-3845-z

Keywords

Search

Navigation