1Medical Oncology Laboratory, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
2Data Science Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
3St Luke’s Radiation Oncology Network, Dublin, Ireland
© 2021 The Korean Society of Pathologists/The Korean Society for Cytopathology
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Ethics Statement
Tumor samples were obtained from patients enrolled on the TRI-LARC clinical trial (NCT02151019). Historical tumor samples were obtained from tumor banks under the auspices of Institutional Review Board-approved protocols. Informed consent for tumor biobanking and research studies was obtained from all patients.
Availability of Data and Material
The datasets generated or analyzed during the study are available from the corresponding author on reasonable request.
Code Availability
Not applicable.
Author Contributions
Conceptualization: KLFJ, ST, BTH. Data curation: KLFJ, ST. Formal analysis: KLFJ, SM. Funding acquisition: ST, BTH, BDPO. Investigation: KLFJ, ST. Methodology: KLFJ, ST. Supervision: ST, BTH. Validation: KLFJ, ST. Writing—original draft: KLFJ. Writing—review & editing: KLFJ, ST, SM, BTH. Approval of final manuscript: all authors.
Conflicts of Interest
The authors declare that they have no potential conflicts of interest.
Funding Statement
No funding to declare.
Author (year published) | Rate of Fn detection in CRC tumors (%) | Detection method of Fn | Sample form | Sample age |
---|---|---|---|---|
Nosho et al. (2016) [6] | 8.6 | qPCR ΔCT | FFPE | Unclear |
Author’s work | 10.4 | qPCR ΔCT | FFPE | 0–20 yr |
Lee et al. (2018) [7] |
12 in FFPE 98 in methacarn 100 in frozen tissues |
qPCR ΔCT | FFPE, methacarn or frozen | 6–13 yr |
Mima et al. (2015, 2016) [8–10] | 13 | qPCR ΔCT | FFPE | 7–20 yr |
Borowsky et al. (2021) [11] | 13.7 | qPCR ΔCT | FFPE |
8 to > 26 years NB updated same cohort used by Mima et al., may have used FN data from previous analysis in 2015 for older samples |
Shariati et al. (2021) [12] | 23 | qPCR ΔCT | Fresh frozen | 0–2 yr |
Kunzmann et al. (2019) [13] | 31 ‘high’ for FN but unclear % positive | qPCR ΔCT | Fresh frozen | 6–10 yr |
Yan et al. (2017) [14] | 38 | qPCR ΔCT | Frozen | 4–5 yr |
Okita et al. (2020) [15] | 38 | qPCR ΔCT (different human genome control gene) | FFPE | Age unclear |
Yamamoto et al. (2021) [16] | 45 | qPCR ΔCT | FFPE | 3–4 yr |
Tahara et al. (2014) [17] |
52 for FN 73.8 for pan-fusobacterium |
qPCR ΔCT | Unclear | Unclear |
Lee et al. (2020) [18] | 54 | qPCR ΔCT | FFPE | Age unclear |
Chen et al. (2019) [19] | 55 | qPCR ΔCT | FFPE | <2 yr |
Ito et al. (2015) [20] | 56 | qPCR ΔCT | FFPE | 1–13 yr |
Serna et al. (2020) [21] | 57 pre-treatment (rectal cancers only) | FISH for Fn RNA | FFPE | 2–13 yr |
Tunsjo et al. (2019) [22] | 60 | qPCR ΔCT (used B-globin as control gene) | Allprotect tissue reagent, unclear time to DNA extraction or storage before analysis | 2–5 yr |
Yu et al. (2016) [23] | 61.3 overall | FISH for Fn RNA | FFPE | 1–2 yr |
Kashani et al. (2020) [24] | 68 | PCR of Fn and electrophoresis without control gene | Fresh samples |
1–3 years but may have extracted DNA immediately |
Oh et al. (2019) [2] | 68.8 | qPCR ΔCT | FFPE |
5–13 yr Excluded 20% due to poor quality |
Yamaoka et al. (2018) [25] | 75 | ddPCR | Frozen | 10–18 yr |
Kim et al. (2020) [26] | 82 | qPCR relative to other bacterial genes | Fresh samples with immediate DNA extraction | 4–5 yr |
Li et al. (2016) [27] | 87.1 | PCR ΔCT | Frozen | 3–4 yr |
Comparison of Fn detection rates in publications analyzing CRC tumors by detection method, sample storage format and sample age. There is some tendency for older sample cohorts to have lower rates of detection, for frozen or fresh samples to have higher detection rates compared to FFPE, and ddPCR and FISH may be more sensitive methods than the ubiquitous quantitative polymerase chain reaction for Fn relative to control gene (qPCR ΔCT).
Fn, Fusobacterium nucleatum; CRC, colorectal cancer; qPCR ΔCT, ubiquitous quantitative polymerase chain reaction for Fn relative to control gene; FFPE, formalin-fixed paraffin-embedded; ddPCR, digital droplet polymerase chain reaction; FISH, fluorescent in situ hybridization.
Author (year published) | Rate of Fn detection in CRC tumors (%) | Detection method of Fn | Sample form | Sample age |
---|---|---|---|---|
Nosho et al. (2016) [ |
8.6 | qPCR ΔCT | FFPE | Unclear |
Author’s work | 10.4 | qPCR ΔCT | FFPE | 0–20 yr |
Lee et al. (2018) [ |
12 in FFPE 98 in methacarn 100 in frozen tissues |
qPCR ΔCT | FFPE, methacarn or frozen | 6–13 yr |
Mima et al. (2015, 2016) [ |
13 | qPCR ΔCT | FFPE | 7–20 yr |
Borowsky et al. (2021) [ |
13.7 | qPCR ΔCT | FFPE | 8 to > 26 years NB updated same cohort used by Mima et al., may have used FN data from previous analysis in 2015 for older samples |
Shariati et al. (2021) [ |
23 | qPCR ΔCT | Fresh frozen | 0–2 yr |
Kunzmann et al. (2019) [ |
31 ‘high’ for FN but unclear % positive | qPCR ΔCT | Fresh frozen | 6–10 yr |
Yan et al. (2017) [ |
38 | qPCR ΔCT | Frozen | 4–5 yr |
Okita et al. (2020) [ |
38 | qPCR ΔCT (different human genome control gene) | FFPE | Age unclear |
Yamamoto et al. (2021) [ |
45 | qPCR ΔCT | FFPE | 3–4 yr |
Tahara et al. (2014) [ |
52 for FN 73.8 for pan-fusobacterium |
qPCR ΔCT | Unclear | Unclear |
Lee et al. (2020) [ |
54 | qPCR ΔCT | FFPE | Age unclear |
Chen et al. (2019) [ |
55 | qPCR ΔCT | FFPE | <2 yr |
Ito et al. (2015) [ |
56 | qPCR ΔCT | FFPE | 1–13 yr |
Serna et al. (2020) [ |
57 pre-treatment (rectal cancers only) | FISH for Fn RNA | FFPE | 2–13 yr |
Tunsjo et al. (2019) [ |
60 | qPCR ΔCT (used B-globin as control gene) | Allprotect tissue reagent, unclear time to DNA extraction or storage before analysis | 2–5 yr |
Yu et al. (2016) [ |
61.3 overall | FISH for Fn RNA | FFPE | 1–2 yr |
Kashani et al. (2020) [ |
68 | PCR of Fn and electrophoresis without control gene | Fresh samples | 1–3 years but may have extracted DNA immediately |
Oh et al. (2019) [ |
68.8 | qPCR ΔCT | FFPE | 5–13 yr Excluded 20% due to poor quality |
Yamaoka et al. (2018) [ |
75 | ddPCR | Frozen | 10–18 yr |
Kim et al. (2020) [ |
82 | qPCR relative to other bacterial genes | Fresh samples with immediate DNA extraction | 4–5 yr |
Li et al. (2016) [ |
87.1 | PCR ΔCT | Frozen | 3–4 yr |
Comparison of Fn detection rates in publications analyzing CRC tumors by detection method, sample storage format and sample age. There is some tendency for older sample cohorts to have lower rates of detection, for frozen or fresh samples to have higher detection rates compared to FFPE, and ddPCR and FISH may be more sensitive methods than the ubiquitous quantitative polymerase chain reaction for Fn relative to control gene (qPCR ΔCT). Fn,