Intestinal microflora and its combination as biomarkers and detection methods for liver cancer

Abstract

The invention uses intestinal microbial flora and combinations thereof as a liver cancer biomarker and provide a method for detection, in short, the intestinal microbial flora of the invention can be used as a liver cancer biomarker and can be used as a non-invasive method for detecting or predicting liver cancer, combined with conventional blood tests, not only capable of improving the accuracy rate of detection, but also capable of increasing the willingness of patients to participate in detection to achieve the efficacies of early prevention and early treatment.

Claims

1-4. (canceled)

5. A biomarker for auxiliary diagnosis and detection of liver cancer, comprising at least one microorganism, wherein the microorganism comes from the following groups of bacterial genera: Lachnospira, Succinivibrio, Phascolarctobacterium, rc4_4, Sutterella, WAL 1855D, Methanobrevibacter, Bacteroides, Megasphaera, Dialister, Streptococcus, Acidaminococcus, Epulopiscium, Lactobacillus, Enterococcus, Eubacterium, Rothia, Bifidobacterium, Collinsella, Clostridium, Leuconostoc, Ruminococcus, Rhodococcus, Catenibacterium, Mitsuokella, Roseburia, Granulicatella, Citrobacter, Lactococcus, Coprobacillus, Blautia, Klebsiella, Helicobacter, Succiniclasticum, Peptococcus, Megamonas, Peptostreptococcus, Veillonella, Salmonella, Akkermansia, Corynebacterium and Faecalibacterium.

6. The biomarker for auxiliary diagnosis and detection of liver cancer as claimed in claim 5, wherein the biomarker comprises microorganisms of the following five bacterial genera: Phascolarctobacterium, Lachnospira, Megasphaera, Streptococcus and Bifidobacterium.

7. A biomarker for auxiliary diagnosis and detection of liver cancer, comprising at least one microorganism, wherein the microorganism comes from the following groups of bacterial species: Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides barnesiae, Eubacterium biforme, Haemophilus parainfluenzae, Veillonella dispar, Roseburia faecis, Bifidobacterium longum, Collinsella aerofaciens, Lactobacillus mucosae, Helicobacter pylori, Ruminococcus gnavus, Eubacterium dolichum, Rothia mucilaginosa, Mitsuokella multacida, Collinsella stercoris, Lactobacillus zeae, Coprobacillus cateniformis and Rothia aeria.

8. The biomarker for auxiliary diagnosis and detection of liver cancer as claimed in claim 7, wherein the biomarker comprises microorganisms of the following four bacterial species: Bifidobacterium longum, Ruminococcus gnavus, Eubacterium dolichum and Rothia mucilaginosa.

9. A method for increasing an accuracy rate of detecting liver cancer risk in vitro, comprising simultaneously detecting and analyzing manifestations of at least one biomarker as claimed in claim 5 in a stool sample and alpha-fetoprotein (AFP) content in a blood sample.

10. The method for increasing an accuracy rate of detecting liver cancer risk in vitro as claimed in claim 9, wherein the biomarker comprises microorganisms of the following five bacterial genera: Phascolarctobacterium, Lachnospira, Megasphaera, Streptococcus and Bifidobacterium.

11. A method for increasing an accuracy rate of detecting liver cancer risk in vitro, comprising simultaneously detecting and analyzing manifestations of at least one biomarker as claimed in claim 7 in a stool sample and alpha-fetoprotein (AFP) content in a blood sample.

12. The method for increasing an accuracy rate of detecting liver cancer risk in vitro as claimed in claim 11, wherein the biomarker comprises microorganisms of the following four bacterial species: Bifidobacterium longum, Ruminococcus gnavus, Eubacterium dolichum and Rothia mucilaginosa.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0023] FIG. 1 shows relative content distribution of bacterial genera with significant differences between liver cancer patients and healthy individuals;

[0024] FIG. 2 shows relative content distribution of bacterial species with significant differences between liver cancer patients and healthy individuals;

[0025] FIG. 3 shows the ROC curve analysis results of MDI conversion results (MDI), alpha-fetoprotein (AFP) of 42 bacterial genera, and MDI conversion results combined with alpha-fetoprotein (MDI+AFP) of 42 bacterial genera;

[0026] FIG. 4 shows the ROC curve analysis results of MDI conversion results (MDI), alpha-fetoprotein (AFP) of 19 bacterial species, and MDI conversion results combined with alpha-fetoprotein (MDI+AFP) of 19 bacterial species;

[0027] FIG. 5 shows the ROC curve analysis results of genus Lachnospira (MDI), alpha-fetoprotein (AFP), and genus Lachnospira combined with alpha-fetoprotein (MDI+AFP);

[0028] FIG. 6 shows the ROC curve analysis results of genus Phascolarctobacterium (MDI), alpha-fetoprotein (AFP), and genus Phascolarctobacterium combined with alpha-fetoprotein (MDI+AFP);

[0029] FIG. 7 shows the ROC curve analysis results of genus Megasphaera (MDI), alpha-fetoprotein (AFP), and genus Megasphaera combined with alpha-fetoprotein (MDI+AFP);

[0030] FIG. 8 shows the ROC curve analysis results of genus Dialister (MDI), alpha-fetoprotein (AFP), and genus Dialister combined with alpha-fetoprotein (MDI+AFP);

[0031] FIG. 9 shows the ROC curve analysis results of genus Streptococcus (MDI), alpha-fetoprotein (AFP), and genus Streptococcus combined with alpha-fetoprotein (MDI+AFP);

[0032] FIG. 10 shows the ROC curve analysis results of genus Acidaminococcus (MDI), alpha-fetoprotein (AFP), and genus Acidaminococcus combined with alpha-fetoprotein (MDI+AFP);

[0033] FIG. 11 shows the ROC curve analysis results of genus Lactobacillus (MDI), alpha-fetoprotein (AFP), and genus Lactobacillus combined with alpha-fetoprotein (MDI+AFP);

[0034] FIG. 12 shows the ROC curve analysis results of genus Enterococcus (MDI), alpha-fetoprotein (AFP), and genus Enterococcus combined with alpha-fetoprotein (MDI+AFP);

[0035] FIG. 13 shows the ROC curve analysis results of genus Eubacterium (MDI), alpha-fetoprotein (AFP), and genus Eubacterium combined with alpha-fetoprotein (MDI+AFP);

[0036] FIG. 14 shows the ROC curve analysis results of genus Bifidobacterium (MDI), alpha-fetoprotein (AFP), and genus Bifidobacterium combined with alpha-fetoprotein (MDI+AFP);

[0037] FIG. 15 shows the ROC curve analysis results of genus Collinsella (MDI), alpha-fetoprotein (AFP), and genus Collinsella combined with alpha-fetoprotein (MDI+AFP);

[0038] FIG. 16 shows the ROC curve analysis results of genus Clostridium (MDI), alpha-fetoprotein (AFP), and genus Clostridium combined with alpha-fetoprotein (MDI+AFP);

[0039] FIG. 17 shows the ROC curve analysis results of five bacterial genera of Phascolarctobacterium, Lachnospira, Megasphaera, Streptococcus and Bifidobacterium (MDI), alpha-fetoprotein (AFP), and the aforementioned five bacterial genera combined with alpha-fetoprotein (MDI+AFP);

[0040] FIG. 18 shows relative content distribution of five bacterial genera of Phascolarctobacterium, Lachnospira, Megasphaera, Streptococcus and Bifidobacterium;

[0041] FIG. 19 shows the ROC curve analysis results of species Ruminococcus gnavus (MDI), alpha-fetoprotein (AFP), and species Ruminococcus gnavus combined with alpha-fetoprotein (MDI+AFP);

[0042] FIG. 20 shows the ROC curve analysis results of species Bifidobacterium longum (MDI), alpha-fetoprotein (AFP), and species Bifidobacterium longum combined with alpha-fetoprotein (MDI+AFP);

[0043] FIG. 21 shows the ROC curve analysis results of species Rothia mucilaginosa (MDI), alpha-fetoprotein (AFP), and species Rothia mucilaginosa combined with alpha-fetoprotein (MDI+AFP);

[0044] FIG. 22 shows the ROC curve analysis results of species Collinsella aerofaciens (MDI), alpha-fetoprotein (AFP), and species Collinsella aerofaciens combined with alpha-fetoprotein (MDI+AFP);

[0045] FIG. 23 shows the ROC curve analysis results of species Eubacterium dolichum (MDI), alpha-fetoprotein (AFP), and species Eubacterium dolichum combined with alpha-fetoprotein (MDI+AFP);

[0046] FIG. 24 shows the ROC curve analysis results of four bacterial species of Bifidobacterium longum, Ruminococcus gnavus, Eubacterium dolichum and Rothia mucilaginosa (MDI), alpha-fetoprotein (AFP), and the aforementioned four bacterial species combined with alpha-fetoprotein (MDI+AFP); and

[0047] FIG. 25 shows relative content distribution of four bacterial species of Bifidobacterium longum, Ruminococcus gnavus, Eubacterium dolichum and Rothia mucilaginosa.

DETAILED DESCRIPTION OF THE INVENTION

[0048] The objects, features, and achieved efficacies of the invention can be understood from the description and drawings of the following preferred embodiments.

[0049] The “MDI” referred to in the following embodiments is the abbreviation of microbial dysbiosis index, which uses LEfSe (Linear discriminant analysis Effect Size) analysis method to pick out significant bacterial genus and bacterial species-level flora. After the flora is grouped, the following formula (I) is used to calculate the MDI of the specimen, and calculation of the probability of an estimated case is shown in the following formula (II).

[00001]$\begin{array}{cc}MD{I}_i=\log \left(\frac{{.Math.}_{j\in \mathrm{case}}{p}_{\mathrm{ij}}}{{.Math.}_{i\in \mathrm{ctrl}}{p}_{\mathrm{ij}}}\right)& \left(I\right)\end{array}$$\begin{array}{cc}\mathrm{prob}\left(\mathrm{case}.Math.MDI=x\right)=\frac{\mathrm{den}\left(MDI=x.Math.\mathrm{case}\right)}{\mathrm{den}\left(MDI=x.Math.\mathrm{case}\right)=\mathrm{den}\left(MDI=x.Math.\mathrm{ctrl}\right)}& \left(\mathrm{II}\right)\end{array}$

Embodiment 1: Analysis of Microbial Flora (1)

[0050] As shown in table 1, the paired liver cancer patients and healthy individuals are used as two groups of participants. DNA from their stool samples is extracted respectively, the intestinal flora is identified by the 16S next-generation sequencing method, and the LEfSe analysis method is used to analyze the results of the gastrointestinal flora of the two groups of participants, it can be known that the gastrointestinal flora in the stool samples provided by the two groups of participants are different as shown in FIGS. 1 and 2, wherein:

[0051] as can be known from FIG. 1, there are significant differences in the distribution of the following forty-two bacterial genera between the two groups of participants: Lachnospira, Succinivibrio, Phascolarctobacterium, rc4_4, Sutterella, WAL_1855D, Methanobrevibacter, Bacteroides, Megasphaera, Dialister, Streptococcus, Acidaminococcus, Epulopiscium, Lactobacillus, Enterococcus, Eubacterium, Rothia, Bifidobacterium, Collinsella, Clostridium, Leuconostoc, Ruminococcus, Rhodococcus, Catenibacterium, Mitsuokella, Roseburia, Granulicatella, Citrobacter, Lactococcus, Coprobacillus, Blautia, Klebsiella, Helicobacter, Succiniclasticum, Peptococcus, Megamonas, Peptostreptococcus, Veillonella, Salmonella, Akkermansia, Corynebacterium and Faecalibacterium;

[0052] as can be known from FIG. 2, there are significant differences in the distribution of the following nineteen bacterial species between the two groups of participants: Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides barnesiae, Eubacterium biforme, Haemophilus parainfluenzae, Veillonella dispar, Roseburia faecis, Bifidobacterium longum, Collinsella aerofaciens, Lactobacillus mucosae, Helicobacter pylori, Ruminococcus gnavus, Eubacterium dolichum, Rothia mucilaginosa, Mitsuokella multacida, Collinsella stercoris, Lactobacillus zeae, Coprobacillus cateniformis and Rothia aena.

[0053] Further, the results of the above forty-two bacterial genera and nineteen bacterial species are converted by MDI (microbial dysbiosis index), and then the above MD conversion results, alpha-fetoprotein (AFP), and the combination of MDI and AFP are analyzed by ROC curves, and comparing the AUC of MDI, AFP and MDI+AFP to obtain the results shown in FIG. 3 and FIG. 4.

[0054] From the results in FIG. 3, it can be known that the classification correct rate of liver cancer patients is only about 80% by detecting alpha-fetoprotein (AFP) alone, and when alpha-fetoprotein (AFP) is combined with MDI of the forty-two bacterial genera, the correct rate of detecting liver cancer can be significantly improved to about 94%; and the results in FIG. 4 show that when alpha-fetoprotein (AFP) is combined with MDI of the nineteen bacterial species, the correct rate of detecting occurrence of liver cancer can also be improved.

TABLE-US-00001 TABLE 1 Two groups of participants after pairing Liver Status Healthy cancer P Variable [stat] individuals patients value cohort 53 53 NA Gender Female 17 (32.1%) 12 (22.6%) 0.383 Gender Male 36 (67.9%) 41 (77.4%) 0.383 Stage of Healthy 53 (100.0%) NA <.001 liver IA NA 12 (22.6%) <.001 cancer IB NA 15 (28.3%) <.001 II NA 15 (28.3%) <.001 IIIA NA 1 (1.9%) <.001 IIIB NA 10 (18.9%) <.001 Stage of Healthy 53 (100.0%) NA <.001 liver I NA 27 (50.9%) <.001 cancer-1 II NA 15 (28.3%) <.001 III NA 11 (20.8%) <.001 Stage of Healthy 53 (100.0%) NA <.001 liver Early NA 27 (50.9%) <.001 cancer-2 Advanced NA 26 (49.1%) <.001 Liver Healthy 53 (100.0%) NA <.001 cirrhosis NA NA 29 (54.7%) <.001 Yes NA 24 (45.3%) <.001 NA 31 (58.5%) NA <.001 Alcoholic NA 3 (5.7%) <.001 Hepatitis 20 (37.7%) 27 (50.9%) <.001 B Hepatitis NA 4 (7.5%) <.001 B + Hepatitis C Hepatitis 2 (3.8%) 14 (26.4%) <.001 C Non-A NA 5 (9.4%) <.001 non-B hepatitis Age Mean ± 59.5 ± 9.7 62.2 ± 10.4  0.168 standard deviation Median 59.0 (53.0-68.0) 62.0 (54.0-69.0) 0.204 (Q1-Q3) AFP Mean ±  5.3 ± 2.9 3,445.7 ± 12,312.1 0.044 standard deviation AFP Median 4.4 (3.0-6.0) 15.6 (6.6-294.7) <.001 (Q1-Q3)

Embodiment 2: Analysis of Microbial Flora (2)

[0055] From the results obtained in embodiment 1, the bacterial genera with significant differences are selected, MDI conversion is performed respectively, alpha-fetoprotein (AFP) is combined respectively, and then ROC curve analysis is performed. The results are shown in FIGS. 5 to 16.

[0056] From the results in FIG. 5 to FIG. 16, it can be known that compared with the accuracy rate (81.9%) of using alpha-fetoprotein (AFP) alone in the diagnosis of liver cancer, the correct rate of combining alpha-fetoprotein (AFP) with different bacterial genera respectively for liver cancer diagnosis is significantly improved. Specifically, the correct rate of genus Lachnospira combined with alpha-fetoprotein (AFP) is 87.2%; the correct rate of genus Phascolarctobacterium combined with alpha-fetoprotein (AFP) is 85.4%; the correct rate of genus Megasphaera combined with alpha-fetoprotein (AFP) is 94.2%; the correct rate of genus Dialister combined with alpha-fetoprotein (AFP) is 94.0%; the correct rate of genus Streptococcus combined with alpha-fetoprotein (AFP) is 90.8%; the correct rate of genus Acidaminococcus combined with alpha-fetoprotein (AFP) is 91.4%; the correct rate of genus Lactobacillus combined with alpha-fetoprotein (AFP) is 90.6%; the correct rate of genus Enterococcus combined with alpha-fetoprotein (AFP) is 87.6%; the correct rate of genus Eubacterium combined with alpha-fetoprotein (AFP) is 84.6%; the correct rate of genus Bifidobacterium combined with alpha-fetoprotein (AFP) is 89.1%; the correct rate of genus Collinsella combined with alpha-fetoprotein (AFP) is 89.6%; and the correct rate of genus Clostridium combined with alpha-fetoprotein (AFP) is 87.0%.

[0057] Further, five bacterial genera: Phascolarctobacterium, Lachnospira, Megasphaera, Streptococcus and Bifidobacterium are selected from the above results, MDI conversion is performed, and combined with alpha-fetoprotein (AFP) for ROC curve analysis. The results are shown in FIG. 17; and, the relative content distribution of the five bacterial genera is analyzed, as shown in FIG. 18.

[0058] From the results in FIG. 17, it can be known that compared with the accuracy rate (81.9%) of using alpha-fetoprotein (AFP) alone in the diagnosis of liver cancer, the correct rate of combining alpha-fetoprotein (AFP) with the above five bacterial genera respectively for liver cancer diagnosis is significantly improved to 97%.

Embodiment 3: Analysis of Microbial Flora (3)

[0059] From the results obtained in embodiment 1, the bacterial species with significant differences are select, MDI conversion is performed respectively, and then combined with alpha-fetoproteins respectively to perform ROC curve analysis. The results are shown in FIGS. 19 to 23.

[0060] From the results of FIG. 19 to FIG. 23, it can be known that compared with the accuracy rate (81.9%) of using alpha-fetoprotein (AFP) alone in the diagnosis of liver cancer, the correct rate of combining alpha-fetoprotein (AFP) with different bacterial species respectively for liver cancer diagnosis is significantly improved. Specifically, the correct rate of species Ruminococcus gnavus combined with alpha-fetoprotein (AFP) is 93.3%; the correct rate of species Bifidobacterium longum combined with alpha-fetoprotein (AFP) is 88.8%; the correct rate of species Rothia mucilaginosa combined with alpha-fetoprotein (AFP) is 86.5%; the correct rate of species Collinsella aerofaciens combined with alpha-fetoprotein (AFP) is 89.1%; and the correct rate of species Eubacterium dolichum combined with alpha-fetoprotein (AFP) is 83.3%.

[0061] Further, Bifidobacterium longum, Ruminococcus gnavus, Eubacterium dolichum, and Rothia mucilaginosa species are selected from the above results, MDI conversion is performed, and combined with alpha-fetoprotein (AFP) for ROC curve analysis. The results are shown in FIG. 24; and, the relative content distribution of the above bacterial species is analyzed, as shown in FIG. 25.

[0062] From the results in FIG. 24, it can be known that compared with the accuracy rate (81.9%) of using alpha-fetoprotein (AFP) alone in the diagnosis of liver cancer, the correct rate of combining alpha-fetoprotein (AFP) with the above four bacterial species respectively for liver cancer diagnosis is significantly improved to 96.6%.

[0063] It is to be understood that the above description is only embodiments of the invention and is not used to limit the present invention, and changes in accordance with the concepts of the present invention may be made without departing from the spirit of the present invention, for example, the equivalent effects produced by various transformations, variations, modifications and applications made to the configurations or arrangements shall still fall within the scope covered by the appended claims of the present invention.