Patent Application
20220276246
The present invention relates to a kit for predicting or diagnosing nonalcoholic fatty liver disease, and a method for diagnosing thereof.
Nonalcoholic fatty liver disease (NAFLD) is characterized by liver disease of metabolic disorders ranging from simple steatosis, to nonalcoholic steatohepatitis (NASH) which is an aggressive tissue form that ultimately leads to advanced fibrosis and cirrhosis. The global prevalence of NAFLD is estimated to be 24-30% in most epidemiological studies, and is increasing in parallel with obesity and metabolic syndrome. Although NAFLD is commonly associated with obesity, clinical symptoms and pathological severity similar to those observed in obese NAFLD patients may occur in non-obese subjects. Without considering the cut-off of the different body mass index (BMI) defining obesity (Asian ≥25, other races ≥30), it is consistently reported that 3-30% of the non-obese population has NAFLD in both the West and the East. Although visceral fat, food composition and genetic factors may be associated with non-obese NAFLD, additional studies considering other environmental factors are needed to elucidate the pathogenesis of non-obese NAFLD.
Recently, increased interests have focused on identifying and understanding specific roles of the gut microbiota in various metabolic diseases. Gut dysbiosis, which refers to abnormal changes in the gut microbiota compared to the normal microbiota, is associated with a decrease in bacteria producing beneficial short chain fatty acid (SCFA), changes in bile acid composition, activation of immune response against lipopolysaccharide (LPS), an increase of ethanol production by hyperplasia of ethanol producing bacteria, and conversion of phosphatidylcholine into choline and trimethylamine. Changes in the gut microbiome that affects the gut-liver axis contribute to the progression of chronic liver disease such as NAFLD and cirrhosis and advanced fibrosis.
Boursier et al. compared microbiome changes between patients with mild and severs fibrosis, and observed significant intestinal bacterial imbalance and functional changes in patients with severe fibrosis (Non-patent Document 1). Loomba et al. used metagenomic data to identify 37 bacteria that were significantly enriched or significantly reduced in NAFLD patients with advanced fibrosis, and proposed a microbiome-based biomarker to predict fibrosis (Non-patent Document 2). Bajaj et al. defined the gut microbiome profile during the progression of cirrhosis (Non-patent Document 3). A Chinese cohort study observed changes in the gut microbiome of cirrhosis patients (Non-patent Document 4). However, the microbial taxa associated with disease severity and fibrosis stage were not consistent with previous NAFLD studies. This discrepancy may be due to the influence of regional differences (Non-patent Document 5). However, differences in basic BMI status may explain these inconsistent results. Moreover, specific changes in gut microbiome and related metabolites in the non-obese NAFLD group were rarely defined.
Therefore, there is a need for a method for preventing, treating and diagnosing non-obese NAFLD, which determines the histological severity of NAFLD, well-characterizes the gut microbiome changes, and is effective.
The present invention is to solve the above problem, and its purpose is to provide a detection marker of nonalcoholic fatty liver disease comprising one or more of detection markers selected from the group consisting of a microbial biomarker, bile acid and components thereof, and intestinal short chain fatty acid, a kit for predicting or diagnosing a degree of risk of nonalcoholic fatty liver disease using the detection marker, a method for predicting or diagnosing, or a method for providing information for predicting or diagnosing the degree of risk of nonalcoholic fatty liver disease using the detection marker, and a method for screening a therapeutic agent of nonalcoholic fatty liver disease.
In order to achieve the above purpose, the present invention provides a detection marker of nonalcoholic fatty liver disease and a kit for predicting or diagnosing a degree of risk of nonalcoholic fatty liver disease comprising one or more detection means detecting the detection marker.
The kit may be used for predicting or diagnosing a degree of risk of nonalcoholic fatty liver disease by comprising the aforementioned means of detecting a specific subject and specifying the amount, activity, population, and the like of the specific detection subject, or comparing results with other detection subject.
In the present invention, diagnosis comprises confirming the presence or absence of disease, degree of risk of disease, state of disease and prognosis of disease, and comprises all types of analysis used to derive disease state and decision.
In an embodiment of the present invention, the nonalcoholic fatty liver disease may be nonalcoholic fatty liver, nonalcoholic steatohepatitis or cirrhosis.
In an embodiment of the present invention, predicting the degree of risk of the disease may predict the severity of fibrosis. The severity of fibrosis may include F=0 to F=4, and F=0 means no liver fibrosis; F=1 means mild liver fibrosis; F=2 means significant liver fibrosis; F=3 means advanced liver fibrosis; and F=4 means cirrhosis.
In an embodiment of the present invention, the kit may be for a non-obese patient, for example, a non-obese patient with BMI of 25 kg/m2 or less.
The detection marker of nonalcoholic fatty liver disease may comprise one or more kinds among microbial biomarkers, total bile acid and components, and intestinal short chain fatty acid.
In an embodiment of the present invention, the kit may comprise a detection means capable of detecting one or more of detection markers selected from the following:
(a) one or more detection means respectively detecting one or more selected from the group consisting of microbial biomarkers of nonalcoholic fatty liver disease;
(b) one or more detection means respectively detecting one or more selected from the group consisting of total bile acid and components of bile acid; and
(c) one or more detection means respectively detecting one or more selected from the group consisting of intestinal short chain fatty acids.
The kit may comprise for example, (a); (b); (c); (a) and (b); (a) and (c); (b) and (c); or (a), (b), and (c).
In the present specification, the total bile acid and components of bile acid, the short chain fatty acid, and the like are used as a meaning comprising all metabolites thereof.
The microbial biomarkers of nonalcoholic fatty liver disease, at the Family level, may be one or more selected from the group consisting of Enterobacteriaceae, Veillonellaceae, Rikenellaceae, Fusobacteriaceae, Ruminococcaceae, Lachnospiraceae, Actinomycetaceae, Desulfovibrioceae, and Desulfovibrionaceaeat. For example, it may be one or more selected from the group consisting of Enterobacteriaceae, Veillonellaceae, Ruminococcaceae, Lachnospiraceae and Actinomycetaceae, one or more selected from the group consisting of Enterobacteriaceae, Veillonellaceae, Lachnospiraceae and Ruminococcaceae, or one or more selected from the group consisting of Enterobacteriaceae, Veillonellaceae, and Ruminococcaceae.
One example of the Enterobacteriaceae microorganism may be one or more of Citrobacter and Klebsiella, one example of the Veillonellaceae microorganism may be one or more of Veillonella and Megamonas, one example of the Fusobacteriaceae microorganism may be Fusobacterium, one example of the Desulfovibrionaceae microorganism may be Desulfovibrio, the Ruminococcaceae microorganism may be one or more of Ruminococcus, Faecalibacterium and Oscillospira, the Lachnospiraceae microorganism may be one or more of Coprococcus and Lachnospira, and the Actinomycetaceae microorganism may be Actinomyces.
As one example, the (a) may be one or more of detection means each capable of detecting one or more selected from the group consisting of Enterobacteriaceae, Veillonellaceae, Lachnospiraceae and Ruminococcaceae.
The microbial biomarker according to the present invention, at the genus level, may be one or more kinds selected from the group consisting of Citrobacter, Klebsiella, Ruminococcus, Faecalibacterium, Oscillospira, Coprococcus, and Lachnospira, and specifically, it may be one or more kinds selected from the group consisting of Ruminococcus, Faecalibacterium, Oscillospira, Coprococcus, Veillonella, Megamonas, and Lachnospira, and more specifically, it may be one or more kinds selected from the group consisting of Ruminococcus, Faecalibacterium, Oscillospira, Coprococcus, and Lachnospira, or one or more kinds selected from the group consisting of Veillonella and Megamona.
The total bile acid and components of bile acid may be one or more selected from the group consisting of primary bile acid comprising total bile acid, cholic acid and chenodeoxycholic acid; and secondary bile acid comprising ursodeoxycholic acid, lithocholic acid and deoxycholic acid.
As one example, the (b) may be one or more of detection means each capable of detecting one or more selected from the group consisting of total bile acid, cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, lithocholic acid and deoxycholic acid.
As one example, the (c) may be one or more of detection means each capable of detecting one or more selected from the group consisting of acetate, propionate and butyrate.
In an embodiment of the present invention, the kit may comprise one or more selected from combinations of (a) to (h) as follows:
detection means of the (a),
detection means of the (b),
detection means of the (c),
(d) one or more detection means each capable of detecting one or more selected from the group consisting of Enterobacteriaceae, Veillonellaceae, Lachnospiraceae, Ruminococcaceae, cholic acid, chenodeoxycholic acid, ursodeoxycholic acid and propionate;
(e) one or more detection means each capable of detecting one or more selected from the group consisting of Ruminococcus, Faecalibacterium, Oscillospira, Coprococcus, Lachnospira, total bile acid, cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, lithocholic acid and deoxycholic acid;
(f) one or more detection means each capable of detecting one or more selected from the group consisting of Ruminococcus, Faecalibacterium, Oscillospira, Coprococcus, Lachnospira and fecal propionate;
(g) one or more detection means each capable of detecting one or more selected from the group consisting of Veillonella, Megamonas, total bile acid, cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, lithocholic acid and deoxycholic acid; and
(h) one or more detection means each capable of detecting one or more selected from the group consisting of Veillonella, Megamonas and fecal propionate.
The detection means of the (a) may be, for example, one or more detection means each capable of detecting one or more selected from the group consisting of Enterobacteriaceae, Veillonellaceae, Lachnospiraceae and Ruminococcaceae.
The detection means of the (b) may be, for example, one or more detection means each capable of detecting one or more selected from the group consisting of total bile acid, cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, lithocholic acid and deoxycholic acid.
The detection means of the (c) may be, for example, one or more detection means each capable of detecting one or more selected from the group consisting of short chain fatty acid, acetate, propionate and butyrate.
In an embodiment of the present invention, the kit may comprise one or more selected from combinations of (i) to (k) as follows:
(i) one or more detection means each capable of detecting one or more selected from the group consisting of Enterobacteriaceae, Veillonellaceae, Ruminococcaceae, Citrobacter, Klebsiella, Veillonella, Megamonas, Ruminococcus, Faecalibacterium and Oscillospira;
(j) one or more detection means each capable of detecting one or more selected from the group consisting of cholic acid, chenodeoxycholic acid, ursodeoxycholic acid and metabolites thereof; and
(k) one or more detection means each capable of detecting one or more selected from the group consisting of intestinal short chain fatty acids and propionate.
As one example, the detection marker of nonalcoholic fatty liver disease according to the present invention may comprise one or more kinds selected from the group consisting of Enterobacteriaceae, Veillonellaceae, Rikenellaceae, Fusobacteriaceae, Ruminococcaceae, Lachnospiraceae, Actinomycetaceae, Desulfovibrioceae, Desulfovibrionaceae, Citrobacter, Klebsiella, Veillonella, Megamonas, Fusobacterium, Ruminococcus, Faecalibacterium, Oscillospira, Coprococcus, Lachnospira, Actinomyces, Desulfovibrio, total bile acid, cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, lithocholic acid, deoxycholic acid, short chain fatty acid, acetate, propionate and butyrate.
As one specific example, the detection marker of nonalcoholic fatty liver disease according to the present invention may comprise Enterobacteriaceae, Veillonellaceae, and Ruminococcaceae. According to the Examples of the present application, in case of using the three bacterial markers in combination, non-alcoholic fatty liver can be predicted with high accuracy of AUROC 0.8 or higher in a non-obese subject (
As one specific example, the detection marker of nonalcoholic fatty liver disease according to the present invention may comprise Megamonas and Ruminococcus. According to the Examples of the present application, in case of using the two bacterial markers in combination, non-alcoholic fatty liver could be predicted with high accuracy of AUROC 0.7 or higher in a non-obese subject (
As one specific example, the detection marker of nonalcoholic fatty liver disease according to the present invention may comprise cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, and propionate. According to the Examples of the present application, in case of using 4 metabolite markers in combination, non-alcoholic fatty liver could be predicted with high accuracy of AUROC 0.7 or higher in a non-obese subject.
As one specific example, the detection marker of nonalcoholic fatty liver disease according to the present invention may comprise Enterobacteriaceae, Veillonellaceae, Ruminococcaceae, cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, and propionate. According to the Examples of the present application, in case of using the 3 bacterial markers and 4 metabolite markers in combination, non-alcoholic fatty liver could be predicted with high accuracy of AUROC 0.9 or higher in a non-obese subject. Otherwise, the detection marker of nonalcoholic fatty liver disease according to the present invention may comprise Megamonas, Ruminococcus, cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, and propionate. According to the Examples of the present application, in case of using the 2 bacterial markers and 4 metabolite markers in combination, non-alcoholic fatty liver could be predicted with high accuracy of AUROC 0.9 or higher in a non-obese subject. This was significantly higher accuracy than the biomarker of non-alcoholic fatty liver used conventionally, and thus, it could be seen that the biomarker for predicting non-alcoholic fatty liver according to the present invention could predict non-alcoholic fatty liver accurately, and in particular, it could predict non-alcoholic fatty liver of a non-obese subject more accurately.
The present invention provides a method for predicting or diagnosing, or a method for providing information for predicting or diagnosing a degree of risk of nonalcoholic fatty liver disease comprising detecting one or more of detection markers selected from the group consisting of (a) one or more detection markers selected from the group consisting of microbial biomarkers of nonalcoholic fatty liver disease; (b) one or more detection markers selected from the group consisting of total bile acid and components of bile acid; and (c) one or more detection markers selected from the group consisting of intestinal short chain fatty acids.
In an embodiment of the present invention, the nonalcoholic fatty liver disease may be nonalcoholic fatty liver, nonalcoholic steatohepatitis or cirrhosis. In an embodiment of the present invention, predicting the degree of risk may be predicting the severity of fibrosis. In an embodiment of the present invention, the method for diagnosing or method for providing information for diagnosing may be for a non-obese patient with BMI<25 kg/m2.
In an embodiment of the present invention, the method may comprise one or more steps selected from the following:
(i) measuring abundance of microbial biomarkers as one or more detection markers selected from the group consisting of microbial biomarkers of nonalcoholic fatty liver disease;
(ii) measuring the content in feces of one or more detection markers selected from the group consisting of total bile acid and components of bile acid; and
(iii) measuring the content in feces of one or more detection markers selected from the group consisting of intestinal short chain fatty acid, for example, acetate, propionate and butyrate.
In an embodiment of the present invention, the method may comprise comparing the detected values of a subject individual, with a reference value of a healthy individual corresponding thereto, for detection markers (a) to (c), (a) to (h), (i) to (k), or (a) to (k) which can be comprised in the kit.
In an embodiment of the present invention, the method may comprise determining that the severity of fibrosis is high, the detected value of the subject individual compared to the reference value of the healthy individual is increased or decreased according to an increase or decrease of the following detection markers, as the result of comparing the detected values of the subject and reference value of the healthy individual corresponding thereto:
(a) with respect to one or more detection markers selected from the group consisting of microbial biomarkers of nonalcoholic fatty liver disease, the abundance of Enterobacteriaceae is increased, the abundance of Veillonellaceae is increased, or the abundance of Ruminococcaceae is decreased,
(b) with respect to one or more detection markers selected from the group consisting of total bile acid and components of bile acid, the content of cholic acid in feces is increased, the content of chenodeoxycholic acid in feces is increased, or the content of ursodeoxycholic acid in feces is increased, or
(c) with respect to one or more detection markers selected from the group consisting of intestinal short chain fatty acids, for example, in case that the content of one or more selected from the group consisting of acetate, propionate and butyrate in feces is increased, as one example, in case that the content of propionate in feces is increased, it may comprise determining that the severity of fibrosis is high.
The present invention provides a method for screening a therapeutic agent for nonalcoholic fatty liver disease comprising the following steps:
(1) administering a test substance to an experimental animal having nonalcoholic fatty liver disease;
(2) measuring one or more detection markers selected from the group consisting of (a) one or more detection markers selected from the group consisting of microbial biomarkers of nonalcoholic fatty liver disease; (b) one or more detection markers selected from the group consisting of total bile acid and components of bile acid; and (c) one or more detection markers selected from the group consisting of intestinal short chain fatty acids, in the experimental animal untreated with the test substance and the experimental animal treated with the test substance; and
(3) comparing the measured results in a control group untreated with the test substance and an experimental group administered with the test substance.
In an embodiment of the present invention, the nonalcoholic fatty liver disease may be nonalcoholic fatty liver, nonalcoholic steatohepatitis or cirrhosis.
In an embodiment of the present invention, the experimental animal of the step (1) may have one or more characteristics of the following (1) to (5):
(1) A condition in which the blood ALT concentration is increased, for example, a condition in which it is over 1 time, 1.1 times or more, 1.2 times or more, 1.3 times or more, 1.4 times or more, 1.5 times or more, 1.6 times or more, 1.7 times or more, 1.8 times or more, 1.9 times or more, 2 times or more, 2.1 times or more, 2.2 times or more, 2.3 times or more, 2.4 times or more, 2.5 times or more, 2.6 times or more, 2.7 times or more, 2.8 times or more, 2.9 times or more, 3 times or more, 3.5 times or more, 4 times or more, 4.5 times or more, 5 times or more, 5.5 times or more, 6 times or more, 6.5 times or more, 7 times or more, 7.5 times or more, 8 times or more, 8.5 times or more, 9 times or more, 9.5 times or more, or 10 times or more, of the blood ALT concentration of a normal control group.
(2) A condition in which the blood AST concentration is increased, for example, a condition in which it is over 1 time, 1.1 times or more, 1.2 times or more, 1.3 times or more, 1.4 times or more, 1.5 times or more, 1.6 times or more, 1.7 times or more, 1.8 times or more, 1.9 times or more, 2 times or more, 2.1 times or more, 2.2 times or more, 2.3 times or more, 2.4 times or more, 2.5 times or more, 2.6 times or more, 2.7 times or more, 2.8 times or more, 2.9 times or more, 3 times or more, 3.5 times or more, 4 times or more, 4.5 times or more, 5 times or more, 5.5 times or more, 6 times or more, 6.5 times or more, 7 times or more, 7.5 times or more, 8 times or more, 8.5 times or more, 9 times or more, 9.5 times or more, or 10 times or more, of the blood AST concentration of a normal control group.
(3) A condition in which the secondary bile acid concentration in cecum is decreased, for example, a condition in which it is less than 1 time, 0.9 times or less, 0.8 times or less, 0.7 times or less, 0.6 times or less, 0.5 times or less, 0.4 times or less, 0.3 times or less, 0.2 times or less, or 0.1 time or less, of the secondary bile acid concentration in cecum of a normal control group.
(4) A condition in which the fibrosis marker gene expression is increased, for example, a condition in which it is overexpressed more than 1 time, 1.1 times or more, 1.2 times or more, 1.3 times or more, 1.4 times or more, 1.5 times or more, 1.6 times or more, 1.7 times or more, 1.8 times or more, 1.9 times or more, 2 times or more, 2.1 times or more, 2.2 times or more, 2.3 times or more, 2.4 times or more, 2.5 times or more, 2.6 times or more, 2.7 times or more, 2.8 times or more, 2.9 times or more, 3 times or more, 3.5 times or more, 4 times or more, 4.5 times or more, 5 times or more, 5.5 times or more, 6 times or more, 6.5 times or more, 7 times or more, 7.5 times or more, 8 times or more, 8.5 times or more, 9 times or more, 9.5 times or more, 10 times or more, 11 times or more, 12 times or more, 13 times or more, 14 times or more, 15 times or more, 16 times or more, 17 times or more, 18 times or more, 19 times or more, or 20 times or more, of the fibrosis marker gene expression of a normal control group. The fibrosis marker gene may be one or more kinds selected from the group consisting of Col1a1, Timp1, and α-SMA.
(5) A condition in which the liver weight ratio to body weight is increased, for example, a condition in which it is over 1 time, 1.1 times or more, 1.2 times or more, 1.3 times or more, 1.4 times or more, 1.5 times or more, 1.6 times or more, 1.7 times or more, 1.8 times or more, 1.9 times or more, 2 times or more, 2.1 times or more, 2.2 times or more, 2.3 times or more, 2.4 times or more, 2.5 times or more, 2.6 times or more, 2.7 times or more, 2.8 times or more, 2.9 times or more, or 3 times or more, of the liver weight ratio to body weight of a normal control group.
In an embodiment of the present invention, the test substance may comprise a candidate substance of a therapeutic agent for nonalcoholic fatty liver disease, and for example, it may be one or more selected from the group consisting of peptide, protein, nonpeptide compound, active compound, fermented product, cell extract, plant extract, animal tissue extract and plasma.
In an embodiment of the present invention, the method may comprise one or more steps selected in the following:
measuring the content in feces of one or more detection markers selected from the group consisting of
(i) measuring abundance of microbial biomarkers as one or more detection markers selected from the group consisting of microbial biomarkers of nonalcoholic fatty liver disease;
(ii) measuring the content in feces of one or more detection markers selected from the group consisting of total bile acid and components of bile acid; and
(iii) measuring the content in feces of one or more detection markers selected from the group consisting of intestinal short chain fatty acid, for example, acetate, propionate and butyrate.
In an embodiment of the present invention, the method may comprise comparing detection values of an experimental group administered with a test substance and a control group not administered with the test substance for an experimental animal having nonalcoholic fatty liver disease, for detection markers (a) to (c), (a) to (h), (i) to (k), or (a) to (k).
In an embodiment of the present invention, the method may comprise selecting a test substance as a therapeutic agent of nonalcoholic fatty liver disease, according to an increase or decrease result for each detection marker of the detected value of the experimental group compared to a reference value of the control group, as the result of comparing the detected values of an experimental group and the detected value of a control group:
(a) with respect to one or more detection markers selected from the group consisting of microbial biomarkers of nonalcoholic fatty liver disease, the abundance of Enterobacteriaceae is increased, the abundance of Veillonellaceae is increased, or the abundance of Ruminococcaceae is decreased,
(b) with respect to one or more detection markers selected from the group consisting of total bile acid and components of bile acid, the content in feces of cholic acid is increased, the content in feces of chenodeoxycholic acid is increased, or the content in feces of ursodeoxycholic acid is increased, or
(c) with respect to one or more detection markers selected from the group consisting of intestinal short chain fatty acids, for example, in case that the content in feces of one or more selected from the group consisting of acetate, propionate and butyrate is increased, or as one example, the content in feces of propionate is increased, a step of determining that the severity of fibrosis is high may be comprised.
In an embodiment of the present invention, the method may comprise selecting a test substance in which the abundance of Enterobacteriaceae is decreased, the abundance of Veillonellaceae is decreased, the abundance of Ruminococcaceae is increased, the content in feces of cholic acid is decreased, the content in feces of chenodeoxycholic acid is decreased, the content in feces of ursodeoxycholic acid is decreased, or the content in feces of propionate is decreased, compared to the control group untreated with the test substance.
The method for predicting a degree of risk of nonalcoholic fatty liver disease, the method for providing information for prediction, the method for diagnosis, or the method for providing information for diagnosis, according to one example of the present invention may further comprise administering a therapeutic agent of nonalcoholic fatty liver disease to a subject.
Other embodiment of the present invention relates to a method for treatment of nonalcoholic fatty liver disease, comprising administering a therapeutic agent of nonalcoholic fatty liver disease to a subject determined as having risk of nonalcoholic fatty liver disease by the kit for predicting or diagnosing a degree of risk of nonalcoholic fatty liver disease, the method for predicting a degree of risk of nonalcoholic fatty liver disease, the method for providing information for prediction, the method for diagnosis, or the method for providing information for diagnosis, according to the present invention.
The degree of risk of nonalcoholic fatty liver disease can be effectively predicted or diagnosed using the kit for predicting or diagnosing of the present invention, and in particular, the predictability and significance of information provision in non-obese subjects are excellent. Therefore, it can be effectively used to prevent or treat the corresponding disease by providing effective information on nonalcoholic fatty liver disease through this.
Hereinafter, specific Examples are provided to help the understanding of the present invention, but the following Examples are only illustrative of the present invention, and it is apparent to those skilled in the art that various changes and modifications are possible within the scope and spirit of the present invention, and it is also obvious that these changes and modifications fall within the scope of the appended claims. In the following Examples and comparative Examples, “%” and “part” indicating the content are by weight unless otherwise specified.
The values presented in the following experimental Example are expressed as means±standard deviation (S.D.), and the statistical significance of the difference between each treatment group was determined by one-way ANOVA using Graph Pad Prism 4.0 (San Diego. Calif.).
1. Material and Method
1) Experimental Subject
171 subjects demonstrated by biopsy to have NAFLD and 31 subjects without NAFLD were included. When NAFLD was confirmed histologically and BMI was BMI<25 kg/m2, it was classified as the non-obese NAFLD group.
2) Subject Inclusion and Exclusion Criteria
Subjects were enrolled long-term from January 2013 to February 2017, and the inclusion criteria were as follows:
1. An adult at least 18 years of age,
2. Ultrasonic findings confirming fatty infiltration of liver, and
3. An increase of alanine aminotransferase (ALT) level of unknown etiology within the past 6 months.
On the other hand, subjects who met any of the following criteria were excluded:
1. Hepatitis B or C infection,
2. Autoimmune hepatitis, primary biliary cholangitis, or primary sclerosing cholangitis,
3. Gastrointestinal cancers or hepatocellular carcinoma,
4. Drug-induced steatosis or liver damage,
5. Wilson disease or hemochromatosis,
6. Excessive alcohol consumption (male: >210 g/week, female: >140 g/week),
7. Antibiotic use within the previous month,
8. Diagnosis of malignancy in the past year,
9. Human immunodeficiency virus infection, and
10. Chronic disorders related to lipodystrophy or immunosuppression.
Non-obese and obese control groups included subjects without any suspicion of NFALD (a) during evaluation of living donor liver transplantation or (b) during liver biopsy for characterization of solid liver mass suspected for hepatic adenoma or focal nodular hyperplasia based on imaging studies (Koo B K, Joo S K, Kim D, Bae J M, Park J H, Kim J H, et al. Additive effects of PNPLA3 and TM6SF2 on the histological severity of non-alcoholic fatty liver disease. J Gastroenterol Hepatol 2018; 33:1277-1285.).
3) Liver Histology
Liver histology was evaluated by a single liver pathologist using the NASH CRN histological scoring system. NAFLD was defined as the presence of ≥5% macrovesicular steatosis based on histological examination. NASH was defined based on the overall pattern of liver damage consisting of steatosis, lobular inflammation or ballooning of hepatocytes according to the criteria of Brunt et al. (Brunt E M, Janney C G, Di Bisceglie A M, Neuschwander-Tetri B A, Bacon B R. Nonalcoholic steatohepatitis: a proposal for grading and staging the histological lesions. Am J Gastroenterol 1999; 94:2467-2474; Brunt E M, Kleiner D E, Wilson L A, Belt P, Neuschwander-Tetri B A. Nonalcoholic fatty liver disease (NAFLD) activity score and the histopathologic diagnosis in NAFLD: distinct clinicopathologic meanings. Hepatology 2011; 53:810-820). In addition, steatosis, hepatic lobular inflammation and swelling were scored according to the NAFLD activity scoring system, and the severity of fibrosis was evaluated according to the criteria of Kleiner et al. (Kleiner D E, Brunt E M, Van Natta M, Behling C, Contos M J, Cummings O W, et al. Design and validation of a histological scoring system for nonalcoholic fatty liver disease. Hepatology 2005; 41:1313-1321).
4) Microbiome Analysis Using 16S rRNA Sequencing
DNA of the fecal sample was extracted using QIAamp DNA Stool Mini Kit (Qiagen, Hilden, Germany). V4 region sequencing targeting of 16S rRNA was performed using MiSeq platform (Illumina, San Diego, Calif., USA), and additional treatment of raw sequencing data was performed using QIIME pipeline (v 1.8.0) (Caporaso J G, Kuczynski J, Stombaugh J, Bittinger K, Bushman F D, Costello E K, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7:335-336).
5) Measurement of Fecal Metabolites Using GC-FID and Q-TOP System
Fecal SCFA was measured using Agilent Technologies 7890A GC system (Agilent Technologies, Santa Clara, Calif., USA) according to the method of David (David L A, Maurice C F, Carmody R N, Gootenberg D B, Button J E, Wolfe B E, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014; 505:559-563), and the bile acid profile was evaluated using Q-TOF mass spectrometer (Waters Micromass Technologies, Manchester, UK).
6) Bioinformatics Analysis and Statistical Test
Statistical comparison was performed with Kruskal-Wallis test using GraphPad Prism software Ver. 7.0d (GraphPad Software, San Diego, Calif., USA). For rarefaction curves, the OUT table was selected by 12,000 sequences per sample, and Shannon index was measured by QIIME. Nonparametric multi-dimensional scaling (NMDS) plots were represented using Vergan package of R (Oksanen J, Kindt R, Legendre P, O'Hara B, Stevens M H H, Oksanen M J, et al. The vegan package. Community ecology package 2007; 10.), and the distance was measured using Bray-Curtis method. The statistical significance between groups was estimated using Adonis function. Multivariate association analysis using microbiome data was performed using multivariate association using a linear model (MaAsLin) for identification of specific taxa related to the host phenotype without being affected by other metadata (Morgan X C, Tickle T L, Sokol H, Gevers D, Devaney K L, Ward D V, et al. Dysfunction of the gut microbiome in inflammatory bowel disease and treatment. Genome Biol 2012; 13:R79.). In addition, age, gender and BMI or diabetes were designated as fixed variables, and when the p-value adjusted by Benjamini and Hochberg's false discovery rate (FDR) was lower than 0.20, the association rate was considered as significant.
7) Significant Prediction of Fibrosis by ROC Curves
In order to demonstrate the prediction ability of fibrosis of the microbiome-based biomarkers, the area under the receiver operating characteristic curve (AUROC) method was used. The three family-level bacteria, basic characteristics of subjects (age, gender and BMI) and relative abundance of FIB-4 confirmed in the present experiment were used as inputs for AUROC, and the combination of their factors was calculated using binary logistic regression in SPSS Ver. 25.0 (SPSS Inc., Armonk, N.Y., USA). AUROC comparison was performed by DeLong test using MedCalc software Ver. 18.2.1 (MedCalc Software BVBA, Ostend, Belgium).
2. Experimental Result
1) Basic Characteristics
171 subjects demonstrated as NAFLD (NAFL, n=88; NASH, n=83) by biopsy and 31 non-NAFLD subjects were included, and all subjects were divided into two groups (non-obese, BMI<25; obese, BMI≥25), and each subject was divided into three subgroups according to the histological spectrum of NAFLD or fibrosis. In Table 1 and Table 2, the result of detailed characteristics of each group including clinical, metabolic, biochemical and histological profiles was shown.
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
ns
As a result of confirmation, subjects with NASH or significant fibrosis (F2-4) had high levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT) and diabetic markers in all obese and non-obese groups. The subjects with significant fibrosis had higher NAFLD activity scores, and showed more severe liver histology in terms of histological classification of NAFLD (Table 3 and
2) Observation of Changes in Microbiome According to Fibrosis Severity
Depending on the fibrosis severity, changes of the microbiome were shown differently in the non-obese NAFLD subjects and obese NAFLD subjects.
Specifically, the microbial diversity was compared according to the histological spectrum of NAFLD or fibrosis severity (
The subjects were classified into two groups according to their BMI status. In the non-obese group, a significant decrease in microbial diversity was observed between F1 and F0 (p=0.0074), as well as between F2-4 and F0 (p=0.0084) (
The result indicates that the fibrosis severity is more related to gut microbiome change than necroinflammatory activity, and basic BMI status may also be an important factor contributing to gut microbiome change.
3) Observation of Proliferation of Fibrosis-Related Microbial Taxa
Proliferation of the fibrosis-related microbial taxa was remarkably shown in the non-obese NAFLD subjects. Specifically, in the non-obese and obese subjects, the differences of the specific microbial taxa according to the fibrosis severity were compared using univariate and multivariate analyses (
In the univariate analysis, not only gradual proliferation of Veillonellaceae mostly found in the oral cavity and small intestine and large intestine, but also Enterobacteriaceae were observed according to the fibrosis severity of the non-obese subjects. In the obese subjects, Rikenellaceae became gradually enriched. On the contrary, the abundance of Ruminococcaceae was significantly reduced as fibrosis became more severe, and this was found only in the non-obese subjects. This result could be confirmed in correlation plots (
At the genus level, Faecalibacterium (Ruminococcaceae), Ruminococcus (Ruminococcaceae), Coprococcus (Lachnospiraceae), and Lachnospira (Lachnospiraceae) were significantly drastically reduced in the significant fibrosis group, but the abundance of Enterobacteriaceae_Other (Enterobacteriaceae) and Citrobacter was gradually increased according to the fibrosis severity. This change was observed only in the non-obese subjects.
For multivariate analysis, the age, gender and BMI were adjusted using MaAsLin. Enterobacteriaceae was an abundant family significantly related to the fibrosis severity in the non-obese subjects (p=0.0108, q=0.214) (
Adipo-IR and glycosylated hemoglobin (HbA1c) also showed a positive correlation according to the abundance of Veillonellaceae (adipo-IR, q=0.142; HbA1c, q=0.157). On the contrary, the serum FFA level showed an inverse correlation with the abundance of Ruminococcus in all subjects (q=0.0838) and non-obese subjects (q=0.0838), but it did not in the obese subjects (q=1.00).
In order to elucidate whether these remarkable microbiome changes in the non-obese subjects are related to the host gene effect, the association between bacteria and genetic mutations of PNPL3, TM6SF2, MBOAT7-TMC4, and SREBF-2 using MaAsLin was analyzed. However, significant association of the four genetic mutations with three bacteria was not observed. Only Actinomyces enriched the minor allele of TM6SF2 (C/T) (q=0.169) in the non-obese subjects (
In addition to the three variables of age, gender and BMI, the presence of type 2 diabetes mellitus (DM) was well known to affect the general changes in the microbiome (Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012; 490:55-60.). After additional adjustment for DM, it was found that Enterobacteriaceae (p=0.00197, q=0.0616) and Faecalibacterium (p=0.00242, q=0.0707) were related to the presence of DM in all the subjects (
In order to understand the interaction between the microbial components and gut microbiota network characteristics in the obese and non-obese subjects, co-expression of the taxa related to the fibrosis severity was measured, and the relative abundance was shown (
As a result, in the non-obese subjects, Veillonellaceae and Enterobacteriaceae had an inverse correlation with Ruminococcaceae (rho=−0.275 and −0.333, respectively), and Prevotellaceae showed an inverse correlation with Bacteroidaceae (rho=−0.391). However, the strong interaction between Veillonellaceae/Enterobacteriaceae and Ruminococcaceae was not observed in the obese and all subjects. In particular, the correlation of Veillonellaceae and fibrosis severity was not significant in the obese subjects and all subjects, and this suggests its specific role in progression of fibrosis in the non-obese subjects.
In summary, the proliferation of the specific taxa according to the fibrosis severity was more pronounced in the non-obese group than in the obese group.
4) Observation of Fecal Metabolite Level According to Fibrosis Severity of Non-Obese and Obese NAFLD Subjects
The non-obese and obese NAFLD subjects had different fecal metabolite levels according to the fibrosis severity. Specifically, fecal metabolites mainly related to the gut microbiota were evaluated.
The composition of the total bile acid pool between the non-obese and obese subjects was various, and the non-obese subjects had an increased primary bile acid level according to the increased fibrosis stage (
The total fecal bile acid level was 3 times higher in the non-obese subjects having significant fibrosis (F2-4) than the subjects without fibrosis (F0) (
Among three SCFA, the fecal propionate level was gradually increased as fibrosis became severe in the non-obese subjects (non-obese; p=0.0032, obese; p=0.7979), and showed a significantly positive correlation with the amount of Veillonellaceae known as propionate-producing bacteria (p=0.0155) (
On the contrary to the bile acid profile, the correlation between the significant change of fecal SCFA and its bacterial taxa was observed only in the non-obese subjects (
5) Observation of Bacterial Taxa-Metabolite Network Pattern in Non-Obese and Obese NAFLD
A bacterial taxa-metabolite network showed a unique pattern in the non-obese and obese NAFLD. Specifically, when comparing the gut microbiota elements according to the fibrosis severity and obesity status, a clear change in the microbiome was observed only in the non-obese subjects. To investigate its core cause, NAFLD-associated genetic variant and intestinal metabolite analysis was performed.
Based on the result, co-expression of the taxa and metabolites was evaluated, and the interaction network was shown in
Interestingly, primary bile acid had an inverse correlation with Ruminococcaceae and Rikenellaceae known as indexes of healthy intestine in all the non-obese and obese subjects. Veillonellaceae exhibited a positive correlation with propionate, as well as primary bile acid. Bile acid usually has the potential to regulate growth of susceptible bacteria or to propagate relatively resistant bacteria regardless of obesity status. Nevertheless, the correlation of the intestinal bacterial taxa and fecal metabolites with the sever fibrosis was more remarkable in the non-obese NAFLD subjects than the obese subjects.
6) NAFLD Prediction of Non-Obese Subjects by Microbiota and Metabolite Combination
The microbiota-metabolite combination accurately predicted significant fibrosis in the non-obese NAFLD subjects. Specifically, in order to evaluate the usefulness as a fibrosis-predicting biomarker of the gut microbiota and related fecal metabolites, AUROC for predicting significant fibrosis was compared (
Enterobacteriaceae, Veillonellaceae, and Ruminococcaceae were selected as most representative, and significant fibrosis-related bacterial taxa. As shown in
In addition, Megamonas belonging to Veillonellaceae family and Ruminococcus belonging to Ruminococcaceae were selected. As shown in
As fibrosis-related metabolites, four fecal metabolites (cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, and propionate) were selected, and the combination of the four metabolites predicted significant fibrosis as AUROC of 0.758 in the non-obese subjects (0.505 for all subjects; 0.520 for obese subjects).
In case of addition of the intestinal metabolites to the bacterial marker at a family level, as shown in
The result demonstrated that the diagnosis accuracy of the combination of the identified intestinal bacterial taxa and fecal metabolite, for predicting significant fibrosis in NAFLD subjects was significantly higher in the non-obese subjects than the obese subjects, and clear differences of specific bacterial taxa and large intestine metabolite between the obese and non-obese NAFLD groups could be confirmed. This result emphasizes not only the importance of the gut microbiome as a risk factor explaining the pathogenesis of non-obese NAFLD, but also the importance of application in diagnosis of the novel microbiome-metabolite combination as a non-invasive biomarker for significant fibrosis in non-obese NAFLD.
| Number | Date | Country | Kind |
|---|---|---|---|
| 10-2019-0092689 | Jul 2019 | KR | national |
| 10-2020-0087105 | Jul 2020 | KR | national |
| 10-2020-0094922 | Jul 2020 | KR | national |
| 10-2020-0095361 | Jul 2020 | KR | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/KR2020/010092 | 7/30/2020 | WO |
