WO2018036503A1 - Marqueurs bactériens fécaux pour le cancer colorectal - Google Patents

Marqueurs bactériens fécaux pour le cancer colorectal Download PDF

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WO2018036503A1
WO2018036503A1 PCT/CN2017/098592 CN2017098592W WO2018036503A1 WO 2018036503 A1 WO2018036503 A1 WO 2018036503A1 CN 2017098592 W CN2017098592 W CN 2017098592W WO 2018036503 A1 WO2018036503 A1 WO 2018036503A1
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crc
dna
level
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rna
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PCT/CN2017/098592
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Jun Yu
Joseph Jao Yiu Sung
Qiaoyi LIANG
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The Chinese University Of Hong Kong
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Priority claimed from CN201710261558.9A external-priority patent/CN107779505B/zh
Application filed by The Chinese University Of Hong Kong filed Critical The Chinese University Of Hong Kong
Priority to EP17842925.4A priority Critical patent/EP3504346B1/fr
Priority to US16/327,560 priority patent/US11603567B2/en
Publication of WO2018036503A1 publication Critical patent/WO2018036503A1/fr

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57419—Specifically defined cancers of colon
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56911—Bacteria
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/195—Assays involving biological materials from specific organisms or of a specific nature from bacteria
    • G01N2333/33—Assays involving biological materials from specific organisms or of a specific nature from bacteria from Clostridium (G)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/50—Determining the risk of developing a disease

Definitions

  • Colorectal cancer is the third most common cancer worldwide, accounting for about 10%of all cancer cases diagnosed annually. It is a deadly disease with serious impact on human health. During the year of 2012, for instance, 1.4 million new cases of colorectal cancers were diagnosed globally, and nearly 700,000 deaths from the disease were recorded. Incidence of colorectal cancers is substantially higher in developed countries, where more than 65%of cases are found. Men are more likely to suffer from this disease than women.
  • colorectal cancer can be challenging. Although family history may provide useful implications for diagnosis, vast majority of the disease (greater than 75-95%) occurs in people with little or no genetic risk. Symptoms of colorectal cancer also can vary significantly, depending on the location of the cancer in the colon, and whether it has spread elsewhere in the body. Depending on how early colorectal cancer is diagnosed, its prognosis can vary from very good to very grim: it is highly curable with surgery when the cancer mass remains confined within the wall of the colon; on the other hand, once colorectal cancer has spread, it is usually not curable, with medical intervention focusing on improving quality of life and alleviating symptoms. On average, the 5-year survival rate in the United States is around 65%.
  • the present inventors have identified several bacterial species that are significantly correlated with human colorectal cancer (CRC) and therefore can serve as diagnostic markers for early detection of CRC by non-invasive analysis of patient stool samples. More specifically, the inventors show that, compared with normal individuals, certain bacterial species, such as Parvimonas micra, Solobacterium moorei, and Clostridium hathewayi, are significantly enriched in stool samples from CRC patients, whereas the presence of other bacterial species, such as Bacteroides clarus and Roseburia intestinalis, is significantly reduced in CRC patient stool.
  • CRC human colorectal cancer
  • Such increased or decreased presence of these bacterial species results in higher or lower levels of signature DNA, RNA, and protein species unique to these species, which in turn can be used for detection, both qualitatively and quantitatively, the abnormally enriched/suppressed bacteria population in the samples, thus providing critical information relating to the presence of or a heightened risk of CRC in a human subject, including an increased risk of recurrence of CRC after initial treatment (e.g., surgical intervention, chemotherapy, and/or radiation therapy) in a patient who has been diagnosed of the disease.
  • initial treatment e.g., surgical intervention, chemotherapy, and/or radiation therapy
  • specific suppression or activation of these bacterial species can be prophylactically practiced for reducing an individual’s risk of developing CRC at a future time.
  • the present invention provides a method for assessing the risk for colon cancer in a subject, i.e., the likelihood of colon cancer being present in the subject, and/or the likelihood of the subject developing the disease at a later time, and/or the likelihood of a patient having recurring colon cancer (e.g., after initial treatment of the disease when first diagnosed) .
  • the method generally relies on the detection of an increase or decrease in the population of relevant bacterial species (see, e.g., Table S8 of Example 1 and Table 7 of Example 2) , genera (see, e.g., Table S10 of Example 1) , or phyla (see, e.g., Table S11 of Example 1) , or in the level of certain bacterial gene markers indicative of the relevant bacterial species/genera/phyla (see, e.g., Tables S12 and S13 of Example 1) in a patient stool sample when compared with a control value expected in a healthy subject’s stool.
  • the claimed method comprises the steps of: (a) quantitatively determining level of at least one of the bacterial species of Parvimonas micra, Solobacterium moorei, Bacteroides clarus, Roseburia intestinalis, and Clostridium hathewayi in a stool sample taken from the subject; (b) comparing the level obtained in step (a) with a standard control; (c) determining the level obtained in step (a) as increased or decreased from the standard control; and (d) determining the subject as having an increased risk for colon cancer.
  • the level of at least one of Parvimonas micra and Solobacterium moorei is determined in step (a) , and the level of at least one of Parvimonas micra and Solobacterium moorei is determined as increased from the standard control in step (c) .
  • the level of at least one of Bacteroides clarus, Roseburia intestinalis, and Clostridium hathewayi is determined.
  • step (a) comprises determining the level of a DNA, RNA, or protein unique to at least one of Parvimonas micra, Solobacterium moorei, Bacteroides clarus, Roseburia intestinalis, and Clostridium hathewayi. In some embodiments, step (a) comprises determining the level of a DNA unique to at least one of Parvimonas micra, Solobacterium moorei, Bacteroides clarus, Roseburia intestinalis, and Clostridium hathewayi.
  • step comprises determining the level of a DNA unique to each of Bacteroides clarus and Clostridium hathewayi, optionally further comprising determining the level of a DNA unique to Fusobacterium nucleatum.
  • step (a) comprises determining the levels of gene markers m1704941 (Fn) , m2736705 (Ch) , m3246804 (m7) , and m370640 (Bc) , optionally further comprising determining the level of gene marker m181682 (Ri) .
  • step (c) comprises determining the level of gene marker m1696299 (P. micra) , optionally further comprising determining the level of gene marker m1704941 (Fn) .
  • step (a) comprises a polynucleotide amplification reaction, such as a polymerase chain reaction (PCR) , especially a quantitative PCR (qPCR) .
  • PCR polymerase chain reaction
  • qPCR quantitative PCR
  • a repeat of step (a) is performed at a later time using another stool sample from the subject at the later time.
  • an increase is detected in the level obtained at the repeated step (a) as compared to the level from the original step (a) , it indicates a heightened risk of colon cancer; conversely, a decrease indicates a lessened risk for colon cancer.
  • a further step is performed: administering to the subject an effective amount of an inhibitor of at least one of the bacterial species shown to be enriched (such as Parvimonas micra and Solobacterium moorei) and/or an activator for one or more bacterial species shown to have a decreased presence (such as Bacteroides clarus and Roseburia intestinalis) .
  • an inhibitor of at least one of the bacterial species shown to be enriched such as Parvimonas micra and Solobacterium moorei
  • an activator for one or more bacterial species shown to have a decreased presence such as Bacteroides clarus and Roseburia intestinalis
  • an alternative marker for Fusobacterium nucleatum may be used for quantitatively measuring the presence of the bacterium in a sample.
  • Exemplary primer/probe sequences for this marker are provided in Table A of Example 1 (Fn-target 2) and in Table 8 of Example 2.
  • the present invention provides a kit for detecting colon cancer in a subject.
  • the kit includes these components: (1) a standard control that provides an average amount of at least one of Parvimonas micra, Solobacterium moorei, Bacteroides clarus, Roseburia intestinalis, and Clostridium hathewayi in a stool sample; and (2) an agent that specifically and quantitatively identifies a DNA, RNA, or protein unique to at least one of Parvimonas micra, Solobacterium moorei, Bacteroides clarus, Roseburia intestinalis, and Clostridium hathewayi.
  • the agent is a polynucleotide probe that specifically binds the DNA or RNA, or the agent is an antibody that specifically binds the protein.
  • the agent optionally can comprise a detectable moiety.
  • the kit further comprises a set of two oligonucleotide primers for specifically amplifying at least a segment or full length of the DNA or a reverse-transcribed DNA from the RNA or a complement thereof in an amplification reaction. Exemplary sets of oligonucleotide primers are presented in Table S27 of Example 1 and Table 8 of Example 2, as well as in Table A of Example 1.
  • the kit further comprises an instruction manual.
  • the present invention provides a method for prophylactically treating colon cancer or reducing the risk of developing colon cancer in a subject at a later time.
  • the method comprises the step of administering to the subject an effective amount of an inhibitor or activator/enhancer for at least one of the pertinent bacterial species such as Parvimonas micra, Solobacterium moorei, Bacteroides clarus, Roseburia intestinalis, and Clostridium hathewayi, such that a bacterial species found enriched in a CRC patient stool is to be depressed or inhibited, whereas a bacterial species found decreased in a CRC patient stool is to be activated or promoted.
  • the pertinent bacterial species such as Parvimonas micra, Solobacterium moorei, Bacteroides clarus, Roseburia intestinalis, and Clostridium hathewayi
  • the inhibitor is for at least one of Parvimonas micra, Solobacterium moorei, and Clostridium hathewayi, whereas the activator/enhancer is for at least one of Bacteroides clarus and Roseburia intestinalis.
  • the inhibitor is a nucleic acid encoding an antisense RNA, miRNA, or siRNA, for example, a nucleic acid encoding an antisense RNA, miRNA, or siRNA against at least one of the gene markers m1696299 and m2736705.
  • the nusG gene as an alternative marker for Fusobacterium nucleatum, may be used for practicing every aspect of the present invention as described herein.
  • the present invention provides use of a modulator (i.e., inhibitor or activator) of pertinent bacterial species for manufacturing a medicament for prophylactically treating colon cancer in accordance with the description above and herein.
  • a modulator i.e., inhibitor or activator
  • Figure 1 Species involved in gut microbial dysbiosis associated with colorectal cancer (CRC) .
  • CRC colorectal cancer
  • A Differential relative abundance of two CRC-enriched and one control-enriched microbial species consistently identified using three different methods: metagenomic linkage group (MLG) , molecular operational taxonomic unit (mOTU) and Integrated Microbial Genome (IMG) database.
  • MLG metagenomic linkage group
  • mOTU molecular operational taxonomic unit
  • IMG Integrated Microbial Genome
  • B A co-occurrence network deduced from relative abundance of 21 mOTUs significantly associated with CRC. Species are rearranged in two sides based on their enrichment in CRC or control microbiomes. Spearman correlation coefficient values below -0.5 (negative correlation) are indicated as light grey edges, and coefficient values above 0.5 (positive correlation) are indicated as dark grey edges. Node size shows the average relative abundance for each species, and node color shows their taxono
  • Figure 2 Discovering gut microbial gene markers associated with colorectal cancer (CRC) .
  • CRC colorectal cancer
  • A Principal component analysis based on abundances of 20 gene markers separates CRC cases and control individuals in cohort C1. First and second principal components associate with CRC status (PC1 and PC2 explain 31.9%and 13.3%of variance, respectively) . Compare this with Figure 5 based on 2.1 million genes, where no separation can be observed.
  • B CRC index computed using a simple unweighed linear combination of log-abundance of 20 gene markers for patients with CRC and control individuals from this study, shown together with patients and control individuals from earlier studies on type 2 diabetes 25 and IBD.
  • Figure 3 Validating robust gene markers associated with colorectal cancer (CRC) .
  • Quantitative PCR (qPCR) abundance of two gene markers (m1704941: butyryl-CoA dehydrogenase from Fusobacterium nucleatum, m1696299: RNA polymerase subunit ⁇ , rpoB, from Parvimonas micra) were measured in cohort C2 consisting of 47 cases and 109 healthy controls.
  • Combined log-abundance of the two genes clearly separates CRC microbiomes from controls (A) and classifies CRC microbiomes with an area under the receiver operating characteristic curve of 0.84 (B) .
  • the two marker genes show relatively higher incidence and abundance in CRC stages II and III compared with control and stage I microbiomes (C and D) . Abundances are plotted in log10 scale, and zero abundance is plotted as -8. AUC, areas under the receiver-operating curve; FPR, false-positive rate; TPR, true-positive rate.
  • Figure 4 Microbial dysbiosis in colorectal cancer.
  • A Rarefaction curves showing cumulative number of genes sequenced with increasing sample size. The numbers are close to saturation given the current sample sizes for all 128 samples. Inset: colorectal cancer samples have significantly lower gene counts compared to healthy controls. Only the first three points corresponding to sizes of up to 3 samples each are not significant (NS) .
  • B Gene count distribution of 128 CRC case and healthy control individuals. The grey line shown corresponds to 400,000 genes, below which 80%individuals had cancer.
  • C The Shannon index of the CRC case and healthy control microbiomes from gene abundances.
  • D Simpson index of the CRC case and healthy control microbiomes from gene abundances.
  • Figure 5 Principal component analysis using 2, 110, 489 genes identified in cohort C1.
  • PC1 and PC5 show moderate separation between gut microbiomes of CRC patients and control individuals based on gene profiles, and are associated with CRC status. See Figure 7 for comparing a PCA of 140, 455 significant gene markers where a moderate separation is observed, and Figure 2A where a strong separation is observed.
  • Figure 6 Distribution of P-value association statistics of all microbial genes in cohort C1.
  • Figure 7 2-dimensional histogram of abundance-vs-occurrence rate of CRC-associated gene markers.
  • the CRC-associated gene markers selection was based on the significant enrichment in CRC case or healthy control. We computed the occurrence rate and median relative abundance for the CRC-enriched gene makers and healthy control-enriched gene makers in all 128 samples from C1, and generated a 2-Dimensional histogram following previously described methods 20 to show the distribution of all marker genes.
  • Control-enriched gene makers are mostly present in continuous occurrence rate and high relative abundance.
  • CRC-enriched gene makers are mostly present in low occurrence rate and low abundance.
  • Figure 8 Enrichment of Solobacterium moorei and Peptostreptococcus stomatis in CRC patient microbiomes in cohort C1.
  • Figure 9 Significant species network using IMG version 400 and MLG annotation with q-value ⁇ 0.05 in cohort C1.
  • B A co-occurrence network deduced from 28 IMG species significantly associated with colorectal cancer. Node size indicates the average of relative abundance for each species. See legend for panel A for other details.
  • Figure 10 The Receiver-Operator-Curve of CRC specific species marker selection using random forest method and three different species annotation methods.
  • Figure 11 Minimum redundancy maximum relevance (mRMR) method to identify 20 gene markers that differentiate colorectal cancer cases from controls in cohort C1.
  • mRMR Minimum redundancy maximum relevance
  • Incremental search was performed using the mRMR method which generated a sequential number of subsets. For each subset, the error rate was estimated by a leave-one-out cross-validation (LOOCV) of a linear discrimination classifier. The optimum subset with the lowest error rate contained 20 gene markers.
  • LOOCV leave-one-out cross-validation
  • Figure 12 Correlation between quantification by the metagenomic approach versus quantitative polymerase chain reaction (qPCR) for four gene markers.
  • Figure 13 Evaluating CRC index from four markers in Chinese cohort C2 of 156 individuals.
  • Figure 14 Comparison of (A) gene richness (gene count) and (B) alpha-diversity (Shannon index) distribution in cohorts C1 and D.
  • Figure 15 Evaluating CRC index in cohort D consisting of 40 individuals.
  • Figure 16 Assessment of the qPCR assays.
  • (b) Correlation between Cq values of the internal control and DNA quantities (n 29) .
  • (c) The new duplex qPCR assay can stably assess relative target abundance with an appropriate DNA template concentration from fecal samples.
  • Fn abundance was stably assessed in one randomly selected fecal sample with several final DNA concentrations ⁇ 10 ng/ ⁇ L.
  • Fn abundance was stably assessed in samples, known to have low and very low Fn abundance, with final DNA concentrations ⁇ 10 ng/ ⁇ L, but extremely low DNA concentrations may cause false-negative detection in samples of low Fn abundance.
  • Figure 17 Good correlation in the quantification of each marker by metagenomics approach and qPCR assays.
  • Figure 18 Quantitative detection of fecal bacterial markers in the diagnosis of CRC patients.
  • Fn Fusobacterium nucleatum
  • Bc Bacteroides clarus
  • Rh Roseburia intestinalis
  • Ch Clostridium hathewayi
  • m7 Receiver Operating Characteristic
  • Figure 19 Combination of four-markers showed improved diagnostic ability for CRC.
  • Fn Fusobacterium nucleatum
  • Bc Bacteroides clarus
  • Ch Clostridium hathewayi
  • m7 undefined species
  • Figure 20 Sensitivity of the Commercial Fecal Immunochemical Test (FIT) and bacterial markers according to tumor-node-metastasis (TNM) stage subsets. Shown are the sensitivities of FIT, 4-bacteria, and their combination for the detection of colorectal cancer according to tumor stage. The numbers in parentheses are the number of participants in each category.
  • FIT Fecal Immunochemical Test
  • TPM tumor-node-metastasis
  • Figure 22 Contaminant human DNA had little effect on the new qPCR platform.
  • (a) A representative example of qPCR evaluation of the internal control on a mixture of 10 randomly selected fecal samples added with different concentrations of human DNA.
  • (b) A representative example of duplex qPCR evaluation of the internal control and F. nucleatum on a randomly selected fecal sample added with different concentrations of human DNA.
  • SEQ ID NO: 1 is the nucleotide sequence of the gene marker m181682 (Ri) .
  • SEQ ID NO: 2 is the nucleotide sequence of the gene marker m370640 (Bc) .
  • SEQ ID NO: 3 is the nucleotide sequence of m482585.
  • SEQ ID NO: 4 is the nucleotide sequence of m1696299.
  • SEQ ID NO: 5 is the nucleotide sequence of the gene marker m1704941 (Fn) .
  • SEQ ID NO: 6 is the nucleotide sequence of the gene marker m2736705 (Ch) .
  • SEQ ID NO: 7 is the nucleotide sequence of the gene marker m3246804 (m7) .
  • SEQ ID NO: 8 is the nucleotide sequence of m2040133.
  • SEQ ID NO: 9 is the nucleotide sequence of m1559769.
  • SEQ ID NO: 10 is the nucleotide sequence of m1804565.
  • SEQ ID NO: 11 is a nucleotide sequence of m2206475.
  • SEQ ID NO: 12 is the nucleotide sequence of m3319526.
  • SEQ ID NO: 13 is the nucleotide sequence of m3611706.
  • SEQ ID NO: 14 is the nucleotide sequence of m3976414.
  • SEQ ID NO: 15 is the nucleotide sequence of m4171064.
  • SEQ ID NO: 16 is the nucleotide sequence of m4256106.
  • SEQ ID NO: 17 is the nucleotide sequence of m2211919.
  • SEQ ID NO: 18 is the nucleotide sequence of m2361423.
  • SEQ ID NO: 19 is the nucleotide sequence of m3173495.
  • SEQ ID NO: 20 is the nucleotide sequence of m3531210.
  • colon cancer and “colon cancer” have the same meaning and refer to a cancer of the large intestine (colon) , the lower part of human digestive system, although rectal cancer often more specifically refers to a cancer of the last several inches of the colon, the rectum.
  • a “colorectal cancer cell” is a colon epithelial cell possessing characteristics of colon cancer and encompasses a precancerous cell, which is in the early stages of conversion to a cancer cell or which is predisposed for conversion to a cancer cell. Such cells may exhibit one or more phenotypic traits characteristic of the cancerous cells.
  • gene expression is used to refer to the transcription of a DNA to form an RNA molecule encoding a particular protein or the translation of a protein encoded by a polynucleotide sequence.
  • mRNA level and protein level encoded by a gene of interest are encompassed by the term “gene expression level” in this disclosure.
  • isolated nucleic acid molecule means a nucleic acid molecule that is separated from other nucleic acid molecules that are usually associated with the isolated nucleic acid molecule.
  • an "isolated" nucleic acid molecule includes, without limitation, a nucleic acid molecule that is free of nucleotide sequences that naturally flank one or both ends of the nucleic acid in the genome of the organism from which the isolated nucleic acid is derived (e.g., a cDNA or genomic DNA fragment produced by PCR or restriction endonuclease digestion) .
  • an isolated nucleic acid molecule is generally introduced into a vector (e.g., a cloning vector or an expression vector) for convenience of manipulation or to generate a fusion nucleic acid molecule.
  • an isolated nucleic acid molecule can include an engineered nucleic acid molecule such as a recombinant or a synthetic nucleic acid molecule.
  • nucleic acid or “polynucleotide” refers to deoxyribonucleic acids (DNA) or ribonucleic acids (RNA) and polymers thereof in either single-or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides.
  • nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) , alleles, orthologs, single nucleotide polymorphisms (SNPs) , and complementary sequences as well as the sequence explicitly indicated.
  • degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19: 5081 (1991) ; Ohtsuka et al., J. Biol. Chem.
  • nucleic acid is used interchangeably with gene, cDNA, and mRNA encoded by a gene.
  • gene means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) involved in the transcription/translation of the gene product and the regulation of the transcription/translation, as well as intervening sequences (introns) between individual coding segments (exons) .
  • polypeptide, ” “peptide, ” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues.
  • the terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymers.
  • the terms encompass amino acid chains of any length, including full-length proteins (i.e., antigens) , wherein the amino acid residues are linked by covalent peptide bonds.
  • amino acid refers to refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.
  • Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, ⁇ -carboxyglutamate, and O-phosphoserine.
  • amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
  • amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.
  • Amino acids may include those having non-naturally occurring D-chirality, as disclosed in WO01/12654, which may improve the stability (e.g., half-life) , bioavailability, and other characteristics of a polypeptide comprising one or more of such D-amino acids. In some cases, one or more, and potentially all of the amino acids of a therapeutic polypeptide have D-chirality.
  • Amino acids may be referred to herein by either the commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
  • the terms “identical” or percent “identity, ” in the context of describing two or more polynucleotide or amino acid sequences refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that has at least 80%sequence identity, preferably 85%, 90%, 91%, 92%, 93, 94%, 95%, 96%, 97%, 98%, 99%, or 100%identity, to a reference sequence, when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences are then said to be “substantially identical.
  • this definition also refers to the complement of a test sequence.
  • the identity exists over a region that is at least about 50 amino acids or nucleotides in length, or more preferably over a region that is 75-100 amino acids or nucleotides in length.
  • sequence comparison typically one sequence acts as a reference sequence, to which test sequences are compared.
  • test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated.
  • sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. For sequence comparison of nucleic acids and proteins, the BLAST and BLAST 2.0 algorithms and the default parameters discussed below are used.
  • a “comparison window” includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
  • Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith &Waterman, Adv. Appl. Math. 2: 482 (1981) , by the homology alignment algorithm of Needleman &Wunsch, J. Mol. Biol.
  • HSPs high scoring sequence pairs
  • T is referred to as the neighborhood word score threshold (Altschul et al., supra) .
  • These initial neighborhood word hits acts as seeds for initiating searches to find longer HSPs containing them.
  • the word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased.
  • Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always ⁇ 0) .
  • M forward score for a pair of matching residues
  • N penalty score for mismatching residues
  • Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment.
  • the BLASTP program uses as defaults a word size (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89: 10915 (1989)) .
  • the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul, Proc. Nat’ l. Acad. Sci. USA 90: 5873-5787 (1993)) .
  • One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P (N) ) , which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance.
  • P (N) the smallest sum probability
  • a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.
  • nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid, as described below.
  • a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions.
  • Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions, as described below.
  • Yet another indication that two nucleic acid sequences are substantially identical is that the same primers can be used to amplify the sequence.
  • stringent hybridization conditions and “high stringency” refer to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acids, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures.
  • stringent conditions are selected to be about 5-10 °C lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength pH.
  • T m is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50%of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at T m , 50%of the probes are occupied at equilibrium) .
  • Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
  • a positive signal is at least two times background, preferably 10 times background hybridization.
  • Exemplary stringent hybridization conditions can be as following: 50%formamide, 5 x SSC, and 1%SDS, incubating at 42 °C, or, 5 x SSC, 1%SDS, incubating at 65 °C, with wash in 0.2 x SSC, and 0.1%SDS at 65°C.
  • Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions.
  • Exemplary "moderately stringent hybridization conditions" include a hybridization in a buffer of 40%formamide, 1 M NaCl, 1%SDS at 37°C, and a wash in 1x SSC at 45°C. A positive hybridization is at least twice background.
  • Alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency. Additional guidelines for determining hybridization parameters are provided in numerous references, e.g., Current Protocols in Molecular Biology, ed. Ausubel, et al.
  • An “expression cassette” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular polynucleotide sequence in a host cell.
  • An expression cassette may be part of a plasmid, viral genome, or nucleic acid fragment.
  • an expression cassette includes a polynucleotide to be transcribed, operably linked to a promoter.
  • "Operably linked” in this context means two or more genetic elements, such as a polynucleotide coding sequence and a promoter, placed in relative positions that permit the proper biological functioning of the elements, such as the promoter directing transcription of the coding sequence.
  • an expression cassette Other elements that may be present in an expression cassette include those that enhance transcription (e.g., enhancers) and terminate transcription (e.g., terminators) , as well as those that confer certain binding affinity or antigenicity to the recombinant protein produced from the expression cassette.
  • enhancers e.g., enhancers
  • terminate transcription e.g., terminators
  • immunoglobulin refers to an antigen-binding protein having a basic four-polypeptide chain structure consisting of two heavy and two light chains, said chains being stabilized, for example, by interchain disulfide bonds, which has the ability to specifically bind antigen. Both heavy and light chains are folded into domains.
  • antibody also refers to antigen-and epitope-binding fragments of antibodies, e.g., Fab fragments, that can be used in immunological affinity assays.
  • Fab fragments antigen-and epitope-binding fragments of antibodies
  • pepsin digests an antibody C-terminal to the disulfide linkages in the hinge region to produce F (ab) ' 2 , a dimer of Fab which itself is a light chain joined to V H -C H 1 by a disulfide bond.
  • the F (ab) ' 2 can be reduced under mild conditions to break the disulfide linkage in the hinge region thereby converting the (Fab') 2 dimer into an Fab' monomer.
  • the Fab' monomer is essentially a Fab with part of the hinge region (see, e.g., Fundamental Immunology, Paul, ed., Raven Press, N. Y. (1993) , for a more detailed description of other antibody fragments) . While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that fragments can be synthesized de novo either chemically or by utilizing recombinant DNA methodology. Thus, the term antibody also includes antibody fragments either produced by the modification of whole antibodies or synthesized using recombinant DNA methodologies.
  • the specified binding agent e.g., an antibody
  • Specific binding of an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein or a protein but not its similar "sister" proteins.
  • a variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein or in a particular form.
  • solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g., Harlow &Lane, Antibodies, A Laboratory Manual (1988) for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity) .
  • a specific or selective binding reaction will be at least twice background signal or noise and more typically more than 10 to 100 times background.
  • the term “specifically bind” when used in the context of referring to a polynucleotide sequence forming a double-stranded complex with another polynucleotide sequence describes “polynucleotide hybridization” based on the Watson-Crick base-pairing, as provided in the definition for the term “polynucleotide hybridization method. ”
  • an “increase” or a “decrease” refers to a detectable positive or negative change in quantity from a comparison control, e.g., an established standard control (such as an average level of a pertinent bacterial DNA or RNA or protein found in stool sample of a healthy subject not suffering from or at risk of developing CRC) .
  • An increase is a positive change that is typically at least 10%, or at least 20%, or 50%, or 100%, and can be as high as at least 2-fold or at least 5-fold or even 10-fold of the control value.
  • a decrease is a negative change that is typically at least 10%, or at least 20%, 30%, or 50%, or even as high as at least 80%or 90%of the control value.
  • inhibitor refers to any detectable negative effect on a target biological process, such as RNA transcription, protein expression, cell proliferation, cellular signal transduction, cell proliferation, tumorigenicity, metastatic potential, and recurrence of a disease/condition.
  • a target biological process such as RNA transcription, protein expression, cell proliferation, cellular signal transduction, cell proliferation, tumorigenicity, metastatic potential, and recurrence of a disease/condition.
  • an inhibition is reflected in a decrease of at least 10%, 20%, 30%, 40%, or 50%in target process (e.g., level of a pertinent bacterial DNA, RNA, or protein) upon application of an inhibitor, when compared to a control where the inhibitor is not applied.
  • a "polynucleotide hybridization method" as used herein refers to a method for detecting the presence and/or quantity of a pre-determined polynucleotide sequence based on its ability to form Watson-Crick base-pairing, under appropriate hybridization conditions, with a polynucleotide probe of a known sequence. Examples of such hybridization methods include Southern blot, Northern blot, and in situ hybridization.
  • Primers refer to oligonucleotides that can be used in an amplification method, such as a polymerase chain reaction (PCR) , to amplify a nucleotide sequence based on the polynucleotide sequence corresponding to a gene of interest, e.g., the DNA or RNA sequence of a pertinent bacterial species.
  • PCR polymerase chain reaction
  • at least one of the PCR primers for amplification of a polynucleotide sequence is sequence-specific for that polynucleotide sequence. The exact length of the primer will depend upon many factors, including temperature, source of the primer, and the method used.
  • the oligonucleotide primer typically contains at least 10, or 15, or 20, or 25 or more nucleotides, although it may contain fewer nucleotides or more nucleotides.
  • the factors involved in determining the appropriate length of primer are readily known to one of ordinary skill in the art.
  • the primers used in particular embodiments are shown in Table A of the disclosure where their specific applications are indicated.
  • the term "primer pair” means a pair of primers that hybridize to opposite strands a target DNA molecule or to regions of the target DNA which flank a nucleotide sequence to be amplified.
  • primer site means the area of the target DNA or other nucleic acid to which a primer hybridizes.
  • a “label, " “detectable label, “ or “detectable moiety” is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means.
  • useful labels include 32 P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA) , biotin, digoxigenin, or haptens and proteins that can be made detectable, e.g., by incorporating a radioactive component into the peptide or used to detect antibodies specifically reactive with the peptide.
  • a detectable label is attached to a probe or a molecule with defined binding characteristics (e.g., a polypeptide with a known binding specificity or a polynucleotide) , so as to allow the presence of the probe (and therefore its binding target) to be readily detectable.
  • defined binding characteristics e.g., a polypeptide with a known binding specificity or a polynucleotide
  • Standard control refers to a predetermined amount or concentration of a polynucleotide sequence or polypeptide, e.g., a pertinent bacterial DNA, RNA, or protein, that is present in an established disease-free stool sample, e.g., a stool sample from an average healthy individual who has not been diagnosed with CRC or is known to have increased risk of developing CRC.
  • the standard control value is suitable for the use of a method of the present invention, to serve as a basis for comparing the amount of pertinent bacterial DNA, RNA, or protein that is present in a test sample.
  • An established sample serving as a standard control provides an average amount of pertinent bacterial DNA, RNA, or protein that is typical for a stool sample of an average, healthy human without any colon disease especially CRC as conventionally defined, preferably without any increased risk of developing the disease.
  • a standard control value may vary depending on the nature of the sample as well as other factors such as the gender, age, ethnicity of the subjects based on whom such a control value is established.
  • This selected group should comprise a sufficient number of humans such that the average level or amount of the pertinent bacterial DNA, RNA, or protein found in the stool among these individuals reflects, with reasonable accuracy, the corresponding level/amount of these DNA, RNA, or protein in the general population of healthy humans.
  • the selected group of humans generally have a similar age to that of a subject whose stool sample is tested for indication of colon cancer.
  • other factors such as gender, ethnicity, medical history are also considered and preferably closely matching between the profiles of the test subject and the selected group of individuals establishing the "average" value.
  • amount refers to the quantity of a polynucleotide of interest or a polypeptide of interest, e.g., a pertinent bacterial DNA, RNA, or protein, present in a sample. Such quantity may be expressed in the absolute terms, i.e., the total quantity of the polynucleotide or polypeptide in the sample, or in the relative terms, i.e., the concentration of the polynucleotide or polypeptide in the sample.
  • treat or “treating, " as used in this application, describes to an act that leads to the elimination, reduction, alleviation, reversal, or prevention or delay of onset or recurrence of any symptom of a relevant condition.
  • treating a condition encompasses both therapeutic and prophylactic intervention against the condition.
  • an effective amount of an polynucleotide encoding an antisense RNA is the amount of said polynucleotide to achieve a decreased level of a corresponding RNA or protein expression or biological activity in a bacterial species, such that the risk, symptoms, severity, and/or recurrence change of colon cancer are reduced, reversed, eliminated, prevented, or delayed of the onset in a patient who has been given the polynucleotide for therapeutic purposes.
  • An amount adequate to accomplish this is defined as the "therapeutically effective dose.
  • the dosing range varies with the nature of the therapeutic agent being administered and other factors such as the route of administration and the severity of a patient’s condition.
  • subject or “subject in need of treatment, " as used herein, includes individuals who seek medical attention due to risk of, or actual suffering from, colon cancer. Subjects also include individuals currently undergoing therapy that seek manipulation of the therapeutic regimen. Subjects or individuals in need of treatment include those that demonstrate symptoms of colon cancer or are at risk of suffering from colon cancer or its symptoms. For example, a subject in need of treatment includes individuals with a genetic predisposition or family history for colon cancer, those that have suffered relevant symptoms in the past, those that have been exposed to a triggering substance or event, as well as those suffering from chronic or acute symptoms of the condition. A “subject in need of treatment” may be at any age of life.
  • Inhibitors, ” “activators, ” and “modulators” of a bacterial species are used to refer to inhibitory, activating, or modulating molecules, respectively, identified using in vitro and in vivo assays for binding to pertinent bacterial DNA, RNA, or protein or for their effect on bacterial survival or proliferation.
  • modulator includes inhibitors and activators.
  • Inhibitors are agents that, e.g., partially or totally block binding, decrease, prevent, delay activation, inactivate, desensitize, or down regulate the level or amount of the pertinent bacterial DNA, RNA, or protein, potentially by suppressing the growth or survival of the bacterial species.
  • the inhibitor directly or indirectly binds to a bacterial DNA or RNA, such as an antisence molecule.
  • Inhibitors are synonymous with inactivators and antagonists.
  • Activators are agents that, e.g., stimulate, increase, facilitate, enhance activation, sensitize or up regulate the level or amount of a pertinent bacterial DNA, RNA, or protein, potentially by promoting growth or survival of the bacterial species.
  • Inhibitors, activators, and modulators can be macromolecules such as polynucleotides, polypeptides including antibodies and antibody fragments, or they can be small molecules including carbohydrate-containing molecules, siRNAs, RNA aptamers, and the like.
  • Colorectal cancer patients often face a grim prognosis when the disease is detected in its later stages. Early detection of colorectal cancer is therefore critical for improving patient survival rate. While it was previously known that the bacterial population existing in human gut plays a role in the tumorigenesis and progression of colorectal cancer, inadequate information is available for the development of a non-invasive diagnostic tool that allows fast and reliable detection of the disease based on fecal bacterial markers.
  • the present inventors discovered for the first time that increased presence of certain bacterial species in stool, as demonstrated by increased level of pertinent bacterial DNA, RNA, or protein, are correlated with the presence or heightened risk of colorectal cancer in a patient.
  • This discovery of enrichment of pertinent bacterial species in the colon of colorectal cancer patients provides important means for early detection of colorectal cancer in a non-invasive manner, as well as implications in the monitoring or treatment of the disease.
  • a higher than normal level of the pertinent bacterial DNA, RNA, or protein seen in a stool sample from a test subject, who may or may not exhibit any signs of colon disorder or anomaly indicates a high likelihood that the subject already has or will later develop colorectal cancer.
  • the recognition of such heightened risk allows immediate treatment of the patient if further diagnostic methods confirm the presence of the disease, or allows close monitoring and/or preventive measure to be applied to the patient if the disease has not yet occurred.
  • the inventors discovered significant enrichment of novel species, including Parvimonas micra and Solobacterium moorei, and a strong co-occurrence network between them in the fecal microbiomes of patients with CRC. They identified 20 gene markers that significantly differentiate CRC-associated and control microbiomes in a Chinese cohort, and trans-continental validation of four of them in a Danish cohort. The four gene markers were further validated in published cohorts from the French and Austrian cohorts with areas under the receiver-operating curve (AUC) of 0.72 and 0.77. Quantitative PCR abundance of two gene markers (butyryl-CoA dehydrogenase from F. nucleatum, and RNA polymerase subunit ⁇ , rpoB, from P.
  • AUC receiver-operating curve
  • the inventors identified by metagenome sequencing that the abundances of five bacterial candidates, including Fusobacterium nucleatum (Fn) , Bacteroides clarus (Bc) , Roseburia intestinalis (Ri) , Clostridium hathewayi (Ch) , and one undefined species (m7) are significantly different in fecal samples of CRC patients in comparison to healthy controls as shown in duplex-qPCR assays.
  • the value of fecal Fn as a stool-based biomarker for CRC diagnosis is corroborated (sensitivity of 77.7%, specificity of 79.5%) .
  • Fn bacterial marker candidates
  • Bc bacterial marker candidates
  • Ch Ch
  • m7 A simple linear combination of four bacterial marker candidates (Fn, Bc, Ch, and m7) improves the diagnostic ability of Fn alone for CRC.
  • FIT fecal immunochemical test
  • This invention describes a probe-based internal control assay for quantification of bacterial DNA content and further duplex qPCR assays for quantification of our newly identified fecal bacterial markers by metagenome sequencing.
  • the present inventors have established a reliable platform for convenient translational application of new bacterial markers.
  • the stool-based CRC-associated bacteria identified by the metagenome sequencing study described herein can serve as novel biomarkers for the non-invasive diagnosis of CRC patients.
  • nucleic acids sizes are given in either kilobases (kb) or base pairs (bp) . These are estimates derived from agarose or acrylamide gel electrophoresis, from sequenced nucleic acids, or from published DNA sequences.
  • kb kilobases
  • bp base pairs
  • proteins sizes are given in kilodaltons (kDa) or amino acid residue numbers. Protein sizes are estimated from gel electrophoresis, from sequenced proteins, from derived amino acid sequences, or from published protein sequences.
  • Oligonucleotides that are not commercially available can be chemically synthesized, e.g., according to the solid phase phosphoramidite triester method first described by Beaucage and Caruthers, Tetrahedron Lett. 22: 1859-1862 (1981) , using an automated synthesizer, as described in Van Devanter et. al., Nucleic Acids Res. 12: 6159-6168 (1984) . Purification of oligonucleotides is performed using any art-recognized strategy, e.g., native acrylamide gel electrophoresis or anion-exchange high performance liquid chromatography (HPLC) as described in Pearson and Reanier, J. Chrom. 255: 137-149 (1983) .
  • HPLC high performance liquid chromatography
  • sequence of interest used in this invention e.g., the polynucleotide sequence of a pertinent bacterial DNA or RNA, and synthetic oligonucleotides (e.g., primers) can be verified using, e.g., the chain termination method for double-stranded templates of Wallace et al., Gene 16: 21-26 (1981) .
  • the present invention relates to measuring the level or amount of a signature DNA or RNA for one or more bacterial species found in a person’s stool sample as a means to detect the presence, to assess the risk of developing, and/or to monitor the progression or treatment efficacy of colon cancer, including assessing the likelihood of disease recurrence.
  • the first steps of practicing this invention are to obtain a stool sample from a test subject and extract DNA or RNA from the sample.
  • a stool sample is obtained from a person to be tested or monitored for colon cancer using a method of the present invention. Collection of a stool sample from an individual can be easily achieved either in a clinic or at patient’s home. An appropriate amount of stool is collected and may be stored according to standard procedures prior to further preparation. The analysis of bacterial DNA or RNA found in a patient's stool sample according to the present invention may be performed using established techniques. The methods for preparing stool samples for nucleic acid extraction are well-known among those of skill in the art. See, e.g., Yu et al., Gut. 2015 Sep 25. pii: gutjnl-2015-309800. doi: 10.1136/gutjnl-2015-309800.
  • RNA contamination should be eliminated to avoid interference with DNA analysis.
  • mRNA preparations there are numerous methods for extracting mRNA from a biological sample.
  • the general methods of mRNA preparation can be followed, see, e.g., Sambrook and Russell, supra; various commercially available reagents or kits, such as Trizol reagent (Invitrogen, Carlsbad, CA) , Oligotex Direct mRNA Kits (Qiagen, Valencia, CA) , RNeasy Mini Kits (Qiagen, Hilden, Germany) , and Series 9600 TM (Promega, Madison, WI) , may also be used to obtain mRNA from a biological sample from a test subject. Combinations of more than one of these methods may also be used. It is essential that all contaminating DNA be eliminated from the RNA preparations. Thus, careful handling of the samples, thorough treatment with DNase, and proper negative controls in the amplification and quantification steps should be used.
  • DNA or mRNA is extracted from a sample, the amount of a predetermined bacterial DNA or RNA (such as 16s rDNA or RNA encoded by a bacterial gene unique to the bacterial species) may be quantified.
  • the preferred method for determining the DNA or RNA level is an amplification-based method, e.g., by polymerase chain reaction (PCR) , including reverse transcription-polymerase chain reaction (RT-PCR) for RNA quantitative analysis.
  • PCR polymerase chain reaction
  • RT-PCR reverse transcription-polymerase chain reaction
  • bacterial RNA While a bacterial DNA is directly subject to amplification, bacterial RNA must be first reverse transcribed. Prior to the amplification step, a DNA copy (cDNA) of the target RNA must be synthesized. This is achieved by reverse transcription, which can be carried out as a separate step, or in a homogeneous reverse transcription-polymerase chain reaction (RT-PCR) , a modification of the polymerase chain reaction for amplifying RNA.
  • RT-PCR homogeneous reverse transcription-polymerase chain reaction
  • PCR PCR reagents and protocols are also available from commercial vendors, such as Roche Molecular Systems.
  • PCR is most usually carried out as an automated process with a thermostable enzyme. In this process, the temperature of the reaction mixture is cycled through a denaturing region, a primer annealing region, and an extension reaction region automatically. Machines specifically adapted for this purpose are commercially available.
  • PCR amplification of the target bacterial DNA or RNA is typically used in practicing the present invention
  • amplification of these DNA or RNA species in a sample may be accomplished by any known method, such as ligase chain reaction (LCR) , transcription-mediated amplification, and self-sustained sequence replication or nucleic acid sequence-based amplification (NASBA) , each of which provides sufficient amplification.
  • LCR ligase chain reaction
  • NASBA nucleic acid sequence-based amplification
  • More recently developed branched-DNA technology may also be used to quantitatively determining the amount of DNA or mRNA in the sample.
  • the target bacterial DNA or RNA can also be detected using other standard techniques, well known to those of skill in the art. Although the detection step is typically preceded by an amplification step, amplification is not required in the methods of the invention. For instance, the DNA or RNA may be identified by size fractionation (e.g., gel electrophoresis) , whether or not proceeded by an amplification step.
  • size fractionation e.g., gel electrophoresis
  • the presence of a band of the same size as the standard comparison is an indication of the presence of a target DNA or RNA, the amount of which may then be compared to the control based on the intensity of the band.
  • oligonucleotide probes specific to the target bacterial DNA or RNA can be used to detect the presence of such DNA or RNA species and indicate the amount of bacterial DNA or RNA in comparison to the standard comparison, based on the intensity of signal imparted by the probe.
  • Sequence-specific probe hybridization is a well-known method of detecting a particular nucleic acid comprising other species of nucleic acids. Under sufficiently stringent hybridization conditions, the probes hybridize specifically only to substantially complementary sequences. The stringency of the hybridization conditions can be relaxed to tolerate varying amounts of sequence mismatch.
  • hybridization formats well known in the art, including but not limited to, solution phase, solid phase, or mixed phase hybridization assays.
  • the following articles provide an overview of the various hybridization assay formats: Singer et al., Biotechniques 4: 230, 1986; Haase et al., Methods in Virology, pp. 189-226, 1984; Wilkinson, In situ Hybridization, Wilkinson ed., IRL Press, Oxford University Press, Oxford; and Hames and Higgins eds., Nucleic Acid Hybridization: A Practical Approach, IRL Press, 1987.
  • nucleic acid probes capable of specifically hybridizing to a target nucleic acid i.e., a bacterial 16s rDNA
  • One common method of detection is the use of autoradiography using probes labeled with 3 H, 125 I, 35 S, 14 C, or 32 P, or the like.
  • the choice of radioactive isotope depends on research preferences due to ease of synthesis, stability, and half-lives of the selected isotopes.
  • labels include compounds (e.g., biotin and digoxigenin) , which bind to antiligands or antibodies labeled with fluorophores, chemiluminescent agents, and enzymes.
  • probes can be conjugated directly with labels such as fluorophores, chemiluminescent agents or enzymes. The choice of label depends on sensitivity required, ease of conjugation with the probe, stability requirements, and available instrumentation.
  • probes and primers necessary for practicing the present invention can be synthesized and labeled using well-known techniques.
  • Oligonucleotides used as probes and primers may be chemically synthesized according to the solid phase phosphoramidite triester method first described by Beaucage and Caruthers, Tetrahedron Letts., 22: 1859-1862, 1981, using an automated synthesizer, as described in Needham-VanDevanter et al., Nucleic Acids Res. 12: 6159-6168, 1984. Purification of oligonucleotides is by either native acrylamide gel electrophoresis or by anion-exchange HPLC as described in Pearson and Regnier, J. Chrom., 255: 137-149, 1983.
  • Stool sample from a subject is used in the practice of the present invention and can be obtained and processed for analysis according to known methods or as described in the previous section.
  • a protein e.g., one that is indicative of a bacterium’s identity
  • a sandwich assay can be performed by capturing the target protein from a test sample with an antibody having specific binding affinity for the protein. The protein then can be detected with a labeled antibody having specific binding affinity for it.
  • immunological assays can be carried out using microfluidic devices such as microarray protein chips.
  • a protein of interest e.g., a protein unique to a bacterial species
  • gel electrophoresis such as 2-dimensional gel electrophoresis
  • Standard immunohistochemical techniques can be used to detect a target protein, using the appropriate antibodies.
  • Both monoclonal and polyclonal antibodies can be used for specific detection of the target protein.
  • Antibodies and their binding fragments with specific binding affinity to a particular protein can be generated by known techniques.
  • a variety of methods have been developed based on the mass spectrometry technology to rapidly and accurately quantify target proteins even in a large number of samples. These methods involve highly sophisticated equipment such as the triple quadrupole (triple Q) instrument using the multiple reaction monitoring (MRM) technique, matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometer (MALDI TOF/TOF) , an ion trap instrument using selective ion monitoring SIM) mode, and the electrospray ionization (ESI) based QTOP mass spectrometer.
  • MRM multiple reaction monitoring
  • MALDI TOF/TOF matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometer
  • SIM selective ion monitoring SIM
  • ESI electrospray ionization
  • a group of healthy persons free of any colon disease (especially any form of tumor such as colon cancer) as conventionally defined is first selected. These individuals are within the appropriate parameters, if applicable, for the purpose of screening for and/or monitoring colon cancer using the methods of the present invention. Optionally, the individuals are of same gender, similar age, or similar ethnic background.
  • the healthy status of the selected individuals is confirmed by well established, routinely employed methods including but not limited to general physical examination of the individuals and general review of their medical history.
  • the selected group of healthy individuals must be of a reasonable size, such that the average amount/concentration of pertinent bacteria, their DNA, mRNA, or protein in the stool sample obtained from the group can be reasonably regarded as representative of the normal or average level among the general population of healthy people.
  • the selected group comprises at least 10 human subjects.
  • an average value for the bacteria, their marker DNA, mRNA, or protein is established based on the individual values found in each subject of the selected healthy control group, this average or median or representative value or profile is considered a standard control. A standard deviation is also determined during the same process. In some cases, separate standard controls may be established for separately defined groups having distinct characteristics such as age, gender, or ethnic background.
  • the present invention provides a preventive measure for prophylactically treating patients who are at an increased risk of later developing colon cancer: by way of suppressing the pertinent bacterial species and reducing their presence in the patients’ gut.
  • certain other bacterial species have been shown by the present inventors as having a depressed or less than normal population in CRC patient’s colon.
  • a preventive measure can then be devised for prophylactically treating patients who are at an increased risk of later developing colon cancer: by way of promoting the pertinent bacterial species and increasing/restoring their presence in the patients’ colon.
  • prophylactic treatment of colon cancer encompasses preventing or delaying the onset of one or more of the relevant symptoms of the disease, including reducing mortality or likelihood of disease recurrence among patients who have already received initial treatment.
  • Inhibitors of the pertinent bacterial species can be of virtually any chemical and structural nature: they may be polypeptides (e.g., antibody, antibody fragment, aptamer) , polynucleotides (e.g., antisense DNA/RNA, small inhibitory RNA, or micro RNA) , and small molecules.
  • inhibitors may be useful for suppressing development of colon cancer cells in a patient’s gut and therefore useful for treating colon cancer.
  • an activator the pertinent bacterial species can be of virtually any chemical and structural nature, so long as they possess confirmed enhancing effect on the target bacteria (e.g., promoting bacterial proliferation or suppressing death of bacterial cells) .
  • the patient may be subject to subsequent therapies or preventive/monitoring measures, especially those fitting certain profiles, such as those with a family history of colon cancer, such that the symptoms of these conditions may be prevented, eliminated, ameliorated, reduced in severity and/or frequency, or delayed in their onset.
  • a physician may prescribe both pharmacological and non-pharmacological treatments such as lifestyle modification (e.g., reduce body weight by 5%or more, assume a healthier life style including following a high fibre/low salt diet and maintaining a higher level of physical activities such as walking for at least 150 minutes weekly, and undergo regularly scheduled screening/examination such as colonoscopy every 5 years) .
  • lifestyle modification e.g., reduce body weight by 5%or more, assume a healthier life style including following a high fibre/low salt diet and maintaining a higher level of physical activities such as walking for at least 150 minutes weekly, and undergo regularly scheduled screening/examination such as colonoscopy every 5 years
  • aggressive treatment may be used such as surgical intervention as well as radio-and/or chemo-therapy.
  • Suppression of a bacterial species can be achieved through the use of inhibitor nucleic acids targeting specific bacterial genes such as siRNA, microRNA, miniRNA, lncRNA, antisense oligonucleotides, aptamer.
  • Such nucleic acids can be single-stranded nucleic acids (such as mRNA) or double-stranded nucleic acids (such as DNA) that can translate into an active form of inhibitor of target bacterial RNA under appropriate conditions.
  • the inhibitor-encoding nucleic acid is provided in the form of an expression cassette, typically recombinantly produced, having a promoter operably linked to the polynucleotide sequence encoding the inhibitor.
  • the promoter is one that directs expression specifically in selected bacterial cells.
  • Administration of such nucleic acids can suppress target bacterial gene expression and therefore suppress the bacterial population. Since virtually all known bacteria have been fully sequenced and information deposited in data banks, one can devise suitable inhibitor nucleic acids based on the sequence information.
  • Both inhibitors and activators of the pertinent bacterial species can be confirmed in assays where a bacterial culture is exposed to a candidate compound, and the compound’s effect on the culture is analyzed.
  • an inhibitor can be observed to exhibit an inhibitory or suppressing effect on the bacterial culture, resulting in reduced growth and/or increased bacterial cell death.
  • an activator can be observed to exhibit a positive effect on the bacterial culture, promoting the survival and proliferation/growth of the bacterium.
  • An inhibitory effect is detected when a negative effect on the bacterial culture is established in the test group.
  • the negative effect is at least a 10%decrease; more preferably, the decrease is C Similarly, an activator exhibits an effect of at least 10%, 20%, 50%, or higher increase in cell proliferation, more preferably the increase is at least 1 or 2 fold or even 5 fold.
  • an inhibitor or activator can be any small molecule or macromolecule that simply affects the growth or survival of a particular bacterial speces.
  • any chemical compound can be tested as a potential inhibitor or activator.
  • modulators can be identified by screening a combinatorial library containing a large number of potentially effective compounds. Such combinatorial chemical libraries can be screened in one or more assays, as described herein, to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional "lead compounds" or can themselves be used as potential or actual therapeutics.
  • combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Patent 5,010,175, Furka, Int. J. Pept. Prot. Res. 37: 487-493 (1991) and Houghton et al., Nature 354: 84-88 (1991) ) and carbohydrate libraries (see, e.g., Liang et al., Science, 274: 1520-1522 (1996) and U.S. Patent 5,593,853) .
  • Other chemistries for generating chemical diversity libraries can also be used.
  • Such chemistries include, but are not limited to: peptoids (PCT Publication No. WO 91/19735) , encoded peptides (PCT Publication WO 93/20242) , random bio-oligomers (PCT Publication No. WO 92/00091) , benzodiazepines (U.S. Pat. No. 5,288,514) , diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc. Nat. Acad. Sci. USA 90: 6909-6913 (1993) ) , vinylogous polypeptides (Hagihara et al., J. Amer. Chem. Soc.
  • nucleic acid libraries see, Ausubel, Berger and Sambrook, all supra
  • peptide nucleic acid libraries see, e.g., U.S. Patent 5,539,083
  • antibody libraries see, e.g., Vaughn et al., Nature Biotechnology, 14 (3) : 309-314 (1996) and PCT/US96/10287)
  • small organic molecule libraries see, e.g., benzodiazepines, Baum C&EN, Jan 18, page 33 (1993) ; isoprenoids, U.S. Patent 5,569,588; thiazolidinones and metathiazanones, U.S.
  • Patent 5,549,974 pyrrolidines, U.S. Patents 5,525,735 and 5,519,134; morpholino compounds, U.S. Patent 5,506,337; and benzodiazepines, U.S. Patent 5,288,514) .
  • the modulators of pertinent bacterial species are useful in the manufacture of a pharmaceutical composition or a medicament.
  • a pharmaceutical composition or medicament can be administered to a subject for the treatment of colon cancer, especially for prophylaxis.
  • Compounds used in the treatment method of the present invention are useful in the manufacture of a pharmaceutical composition or a medicament comprising an effective amount thereof in conjunction or mixture with excipients or carriers suitable for application.
  • An exemplary pharmaceutical composition for such therapeutic use comprises (i) an express cassette comprising a polynucleotide sequence encoding an inhibitor (e.g., siRNA, microRNA, miniRNA, lncRNA, antisense oligonucleotides) as described herein, and (ii) a pharmaceutically acceptable excipient or carrier.
  • an inhibitor e.g., siRNA, microRNA, miniRNA, lncRNA, antisense oligonucleotides
  • a pharmaceutically acceptable excipient or carrier e.g., a pharmaceutically acceptable excipient or carrier.
  • the expression cassette may be provided in a therapeutically effective dose for use in a method for treatment as described herein.
  • An inhibitor or activator can be administered via liposomes, which serve to target the conjugates to a particular tissue, as well as increase the half-life of the composition.
  • Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like.
  • the inhibitor to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to, e.g., a receptor prevalent among the targeted cells, or with other therapeutic or immunogenic compositions.
  • liposomes filled with a desired modulator of the invention can be directed to the site of treatment, e.g., colon, where the liposomes then deliver the selected inhibitor compositions.
  • Liposomes for use in the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol.
  • the selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream.
  • a variety of methods are available for preparing liposomes, as described in, e.g., Szoka et al. (1980) Ann. Rev. Biophys. Bioeng. 9: 467, U.S. Pat. Nos. 4,235,871, 4,501,728 and 4,837,028.
  • compositions or medicaments for use in the present invention can be formulated by standard techniques using one or more physiologically acceptable carriers or excipients. Suitable pharmaceutical carriers are described herein and in "Remington's Pharmaceutical Sciences” by E.W. Martin. Compounds and agents of the present invention and their physiologically acceptable salts and solvates can be formulated for administration by any suitable route, including via inhalation, topically, nasally, orally, parenterally, or rectally.
  • Typical formulations for topical administration include creams, ointments, sprays, lotions, and patches.
  • the pharmaceutical composition can, however, be formulated for any type of administration, e.g., intradermal, subdermal, intravenous, intramuscular, intranasal, intracerebral, intratracheal, intraarterial, intraperitoneal, intravesical, intrapleural, intracoronary or intratumoral injection, with a syringe or other devices.
  • Formulation for administration by inhalation e.g., aerosol
  • oral, rectal, or vaginal administration is also contemplated.
  • Suitable formulations for topical application are preferably aqueous solutions, ointments, creams or gels well-known in the art. Such may contain solubilizers, stabilizers, tonicity enhancing agents, buffers and preservatives.
  • Suitable formulations for transdermal application include an effective amount of a modulator of the present invention with carrier.
  • Preferred carriers include absorbable pharmacologically acceptable solvents to assist passage through the skin of the host.
  • transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the compound optionally with carriers, optionally a rate controlling barrier to deliver the compound to the skin of the host at a controlled and predetermined rate over a prolonged period of time, and means to secure the device to the skin.
  • Matrix transdermal formulations may also be used.
  • a pharmaceutical composition or a medicament can take the form of, for example, a tablet or a capsule prepared by conventional means with a pharmaceutically acceptable excipient.
  • Liquid preparations for oral administration can take the form of, for example, solutions, syrups, or suspensions, or they can be presented as a dry product for constitution with water or other suitable vehicle before use.
  • Such liquid preparations can be prepared by conventional means with pharmaceutically acceptable additives, for example, suspending agents, for example, sorbitol syrup, cellulose derivatives, or hydrogenated edible fats; emulsifying agents, for example, lecithin or acacia; non-aqueous vehicles, for example, almond oil, oily esters, ethyl alcohol, or fractionated vegetable oils; and preservatives, for example, methyl or propyl-p-hydroxybenzoates or sorbic acid.
  • the preparations can also contain buffer salts, flavoring, coloring, and/or sweetening agents as appropriate. If desired, preparations for oral administration can be suitably formulated to give controlled release of the active compound.
  • compositions for parenteral administration can be presented in unit dosage form, for example, in ampoules or in multi-dose containers, with an added preservative.
  • injectable compositions are preferably aqueous isotonic solutions or suspensions, and suppositories are preferably prepared from fatty emulsions or suspensions.
  • the compositions may be sterilized and/or contain adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure and/or buffers.
  • the active ingredient can be in powder form for constitution with a suitable vehicle, for example, sterile pyrogen-free water, before use.
  • a suitable vehicle for example, sterile pyrogen-free water
  • they may also contain other therapeutically valuable substances.
  • the compositions are prepared according to conventional mixing, granulating or coating methods, respectively, and contain about 0.1 to 75%, preferably about 1 to 50%, of the active ingredient.
  • the active ingredient may be conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, for example, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide, or other suitable gas.
  • a suitable propellant for example, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide, or other suitable gas.
  • the dosage unit can be determined by providing a valve to deliver a metered amount.
  • Capsules and cartridges of, for example, gelatin for use in an inhaler or insufflator can be formulated containing a powder mix of the compound and a suitable powder base, for example, lactose or starch.
  • the modulators can also be formulated in rectal compositions, for example, suppositories or retention enemas, for example, containing conventional suppository bases, for example, cocoa butter or other glycerides.
  • the active ingredient can be formulated as a depot preparation.
  • Such long-acting formulations can be administered by implantation (for example, subcutaneously or intramuscularly) or by intramuscular injection.
  • the active ingredient can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
  • a pharmaceutical composition or medicament of the present invention comprises (i) an effective amount of a compound as described herein that suppresses or promotes the population of one or more of the pertinent bacterial species identified herein, and (ii) another therapeutic agent.
  • a therapeutic agent may be used individually, sequentially, or in combination with one or more other such therapeutic agents (e.g., a first therapeutic agent, a second therapeutic agent, and a modulator of the present invention) .
  • Administration may be by the same or different route of administration or together in the same pharmaceutical formulation.
  • compositions or medicaments can be administered to a subject at a therapeutically effective dose to prevent, treat, or control colon cancer as described herein.
  • the pharmaceutical composition or medicament is administered to a subject in an amount sufficient to elicit an effective therapeutic response in the subject.
  • the dosage of active agents administered is dependent on the subject’s body weight, age, individual condition, surface area or volume of the area to be treated and on the form of administration.
  • the size of the dose also will be determined by the existence, nature, and extent of any adverse effects that accompany the administration of a particular compound in a particular subject. For example, each type of inhibitor or nucleic acid encoding an inhibitor will likely have a unique dosage.
  • a unit dosage for oral administration to a mammal of about 50 to 70 kg may contain between about 5 and 500 mg of the active ingredient.
  • a dosage of the active compounds of the present invention is a dosage that is sufficient to achieve the desired effect.
  • Optimal dosing schedules can be calculated from measurements of agent accumulation in the body of a subject. In general, dosage may be given once or more daily, weekly, or monthly. Persons of ordinary skill in the art can easily determine optimum dosages, dosing methodologies and repetition rates.
  • compounds or agents may be administered for multiple days at the therapeutically effective daily dose.
  • therapeutically effective administration of compounds to treat a pertinent condition or disease described herein in a subject requires periodic (e.g., daily) administration that continues for a period ranging from three days to two weeks or longer.
  • agents will be administered for at least three consecutive days, often for at least five consecutive days, more often for at least ten, and sometimes for 20, 30, 40 or more consecutive days.
  • consecutive daily doses are a preferred route to achieve a therapeutically effective dose
  • a therapeutically beneficial effect can be achieved even if the agents are not administered daily, so long as the administration is repeated frequently enough to maintain a therapeutically effective concentration of the agents in the subject. For example, one can administer the agents every other day, every third day, or, if higher dose ranges are employed and tolerated by the subject, once a week.
  • Optimum dosages, toxicity, and therapeutic efficacy of such compounds or agents may vary depending on the relative potency of individual compounds or agents and can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, for example, by determining the LD 50 (the dose lethal to 50%of the population) and the ED 50 (the dose therapeutically effective in 50%of the population) .
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and can be expressed as the ratio, LD 50 /ED 50 .
  • Agents that exhibit large therapeutic indices are preferred. While agents that exhibit toxic side effects can be used, care should be taken to design a delivery system that targets such agents to the site of affected tissue to minimize potential damage to normal cells and, thereby, reduce side effects.
  • the data obtained from, for example, cell culture assays and animal studies can be used to formulate a dosage range for use in humans.
  • the dosage of such compounds lies preferably within a range of circulating concentrations that include the ED 50 with little or no toxicity.
  • the dosage can vary within this range depending upon the dosage form employed and the route of administration.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC 50 (the concentration of the agent that achieves a half-maximal inhibition of symptoms) as determined in cell culture.
  • IC 50 concentration of the agent that achieves a half-maximal inhibition of symptoms
  • levels in plasma can be measured, for example, by high performance liquid chromatography (HPLC) .
  • HPLC high performance liquid chromatography
  • the dose equivalent of agents is from about 1 ng/kg to 100 mg/kg for a typical subject.
  • Dosage for an inhibitor or a nucleic acid encoding an inhibitor described herein can be between 0.1-0.5 mg with IV administration (e.g., 5-30 mg/kg) .
  • Small organic compounds inhibitors can be administered orally at between 5-1000 mg, or by intravenous infusion at between 10-500 mg/ml.
  • Polypeptide inhibitors can be administered by intravenous injection or infusion at 50-500 mg/ml (over 120 minutes) ; 1-500 mg/kg (over 60 minutes) ; or 1-100 mg/kg (bolus) five times weekly.
  • Modulators can be administered subcutaneously at 10-500 mg; 0.1-500 mg/kg intravenously twice daily, or about 50 mg once weekly, or 25 mg twice weekly.
  • compositions of the present invention can be administered alone or in combination with at least one additional therapeutic compound.
  • additional therapeutic compounds include systemic and topical anti-inflammatories, pain relievers, anti-histamines, anesthetic compounds, and the like.
  • the additional therapeutic compound can be administered at the same time as, or even in the same composition with, main active ingredient.
  • the additional therapeutic compound can also be administered separately, in a separate composition, or a different dosage form from the main active ingredient. Some doses of the main ingredient can be administered at the same time as the additional therapeutic compound, while others are administered separately, depending on the particular findings of gut bacterial population and characteristics of the individual.
  • the dosage of a pharmaceutical composition of the invention can be adjusted throughout treatment, depending on various factors including profile of patient’s gut bacterial population and physiological response to the therapeutic regimen. Those of skill in the art commonly engage in such adjustments in therapeutic regimen.
  • the invention provides compositions and kits for practicing the methods described herein to assess the level of one or more pertinent bacterial species in a stool sample obtained from in a subject.
  • one or more gene markers indicative of the pertinent bacterial species can be analyzed for the purpose of detecting or diagnosing the presence of colon cancer, determining the risk of developing colon cancer, and monitoring the progression of colon cancer in a patient, such that the patient may have been treated, e.g., by surgery, chemotherapy, and/or radiotherapy.
  • a patient who has not yet developed colon cancer but has been deemed to have an increased risk of developing the disease at a later time may receive medicament comprising one or more modulator (inhibitor and/or activator) of the pertinent bacterial species.
  • Kits for carrying out assays for determining a specific bacterial DNA or RNA level typically include at least one oligonucleotide useful for specific hybridization with at least one segment of the target DNA or RAN sequence or its complementary sequence.
  • this oligonucleotide is labeled with a detectable moiety.
  • the kits may include at least two oligonucleotide primers that can be used in the amplification of at least one segment of the target bacterial DNA or RNA by PCR, including by RT-PCR. Table S27 of Example 1 and Table 8 of Example 2 provide some examples of such primers.
  • Kits for carrying out assays for determining a bacterial protein level typically include at least one antibody useful for specific binding to the protein.
  • this antibody is labeled with a detectable moiety.
  • the antibody can be either a monoclonal antibody or a polyclonal antibody.
  • the kits may include at least two different antibodies, one for specific binding to the target bacterial protein (i.e., the primary antibody) and the other for detection of the primary antibody (i.e., the secondary antibody) , which is often attached to a detectable moiety.
  • kits also include an appropriate standard control.
  • the standard controls indicate the average level of a chosen bacterial DNA, RNA, or protein as found in the stool of healthy subjects neither suffering from colon cancer nor having any increased risk of developing colon cancer.
  • standard control may be provided in the form of a set value.
  • the kits of this invention may provide instruction manuals to guide users in analyzing test samples and assessing the presence or risk of colon cancer in a test subject.
  • the present invention can also be embodied in a device or a system comprising one or more such devices, which is capable of carrying out all or some of the method steps described herein.
  • the device or system performs the following steps upon receiving a stool sample, assessing the risk of developing colon cancer, or monitored for progression of the condition: (a) determining in sample the amount or level of a pertinent bacterial species (e.g., by way of measuring the amount or level of a bacterial DNA, RNA or protein indicative of the bacterial species) ; (b) comparing the amount/level with a standard control value; and (c) providing an output indicating whether colon cancer is likely present in the subject or whether the subject is at an increased risk of developing colon cancer in the future, or whether there is a change, i.e., worsening or improvement, in the subject's colon cancer condition, or whether the patient has an increased likelihood of recurrence colon cancer, e.g., after the initial diagnosis and/or treatment.
  • the device or system of the invention performs the task of steps (b) and (c) , after step (a) has been performed and the amount or concentration from (a) has been entered into the device.
  • the device or system is partially or fully automated.
  • the objective of this study is to evaluate the potential for diagnosing colorectal cancer (CRC) from fecal metagenomes.
  • CRC colorectal cancer
  • the present inventors performed metagenome-wide association studies on fecal samples from 74 patients with CRC and 54 controls from China, and validated the results in 16 patients and 24 controls from Denmark. The biomarkers were further validated in two published cohorts from France and Austria. Finally, targeted quantitative PCR (qPCR) assays were employed to evaluate diagnostic potential of selected biomarkers in an independent Chinese cohort of 47 patients and 109 controls.
  • qPCR quantitative PCR
  • genes were enriched in early-stage (I-II) patient microbiomes, highlighting the potential for using fecal metagenomic biomarkers for early diagnosis of CRC.
  • the inventors present the first metagenomic profiling study of CRC fecal microbiomes to discover and validate microbial biomarkers in ethnically different cohorts, and to independently validate selected biomarkers using an affordable clinically relevant technology. This study thus provides important indications for developing affordable, reliable, non-invasive early diagnostic biomarkers for CRC from fecal samples.
  • CRC Colorectal cancer
  • Early evidence for gut microbial contribution to CRC pathogenesis came from Apc min/+ mice, a genetic mouse model of CRC, where mice housed in germ-free conditions showed a reduction of tumor formation in the intestine compared with mice housed in specific pathogen-free conditions. 5 Further studies have suggested that several bacteria, including Bacteroides fragilis and a strain of Escherichia coli, may promote colorectal carcinogenesis. 6–11 In humans, bacterial culture-based studies have reported associations between CRC and clinical infections by specific bacteria such as Streptococcus bovis 12 and Clostridium septicum.
  • C1 and C2 were from Hong Kong, China.
  • C1 (see Table S1) comprised 128 individuals: 74 patients with CRC (15 stage I, 21 stage II, 34 stage III and 4 stage IV; median age 67 years; 26 were females) and 54 controls (median age 62 years; 21 were females) .
  • C2 (see Table S16) comprised 156 individuals: 47 patients with CRC (4 stage I, 24 stage II, 15 stage III and 4 stage IV; median age 69 years; 22 were females) and 109 controls (median age 58 years; 69 were females) .
  • Cancer staging in all three cohorts was performed using the tumour, node, metastasis staging system 23 maintained by the American Joint Committee on Cancer and the International Union for Cancer Control. Stool samples were collected by individuals at home, followed by immediate freezing at -20°C. DNA from Chinese samples was extracted using Qiagen QIAamp DNA Stool Mini Kit (Qiagen) according to manufacturer’s instructions. DNA from Danish samples was extracted using previously published method. 24 For comprehensive description of sample collection and DNA extraction as well as ethical committee approval numbers, see methods for Example 1.
  • MLGs metagenomic linkage groups
  • KEGG Kyoto Encyclopedia of Genes and Genomes
  • 25 Species-level molecular operational taxonomic units (mOTUs) were obtained using mOTU profiling software.
  • 26 Reads were mapped to the Integrated Microbial Genome (IMG) reference database27 (v400) to generate IMG species and IMG genus profiles. Genes of MLGs were mapped to the IMG database, and MLGs were annotated to an IMG genome when >50%of genes were mapped. MLG species were constructed by grouping MLGs using this annotation. For comprehensive description of these procedures, see methods for Example 1.
  • PERMANOVA Permutational multivariate analysis of variance
  • Minimum-redundancy maximum-relevancy (mRMR) feature selection method 28 was used to select optimal gene markers, which were then used in constructing a CRC index.
  • Co-occurrence networks were constructed using Spearman’s correlation coefficient (>0.5 or ⁇ -0.5) and visualized in Cytoscape V.3.0.2.
  • Metagenomic sequences from French (F) and Austrian (A) cohorts were downloaded from NCBI Short Read Archive using study identifiers ERP005534 and ERP008729, respectively.
  • FDR French
  • A Austrian
  • ROC receiver operator characteristic
  • Nucleotide sequences of primers and probes are listed in Table S27.
  • qPCR was performed on an ABI7500 Real-Time PCR System using TaqMan Universal PCR Master Mix reagent (Applied Biosystems) .
  • Universal 16S rDNA was used as internal control and abundance of gene markers were expressed as relative levels to 16S rDNA.
  • MWAS metagenome-wide association study
  • 140 455 genes were identified as being associated with disease status (Wilcoxon rank-sum test p ⁇ 0.01 and FDR 11.03%; see Figure 6) .
  • CRC-enriched genes occurred less frequently and at lower abundance compared with control-enriched genes (see Figure 7) , indicating that microbial dysbiosis associated with CRC may not involve dominant species.
  • Such patterns of frequency and occurrence have been observed in two earlier metagenomic case–control studies on type 2 diabetes 25 in Chinese individuals and CRC in Austrian individuals, 31 indicating that this may be a common trend in disease-associated gut microbial dysbiosis.
  • Taxonomic differences between CRC-associated and control microbiomes were examined to identify microbial taxa contributing to the dysbiosis.
  • species profiles derived from three different methods IMG species, species-level mOTUs and MLG species (see section ‘Materials and methods’ ) —were used as supporting evidence from multiple methods would strengthen an association.
  • the analysis identified 28 IMG species, 21 mOTUs and 85 MLG species that were significantly associated with CRC status after adjusting for colonoscopy as a confounding factor (Wilcoxon rank-sum test, q ⁇ 0.05; see Table S8) .
  • Parvimonas micra q ⁇ 7.73 ⁇ 10-6)
  • Solobacterium moorei q ⁇ 0.011
  • F. nucleatum q ⁇ 0.00279
  • Peptostreptococcus stomatis was enriched according to two methods.
  • random forest ensemble learning method 37 was used to identify 17 IMG species, 7 species-level mOTUs and 27 MLG species that were highly predictive of CRC status (see Table S12) , with predictive power of 0.86, 0.89 and 0.96 in ROC analysis, respectively (see Figure 10) .
  • P. micra was identified as a key species from all three methods, while F. nucleatum, P. stomatis and S. moorei were identified from two out of three methods, providing further statistical support for their association with CRC status.
  • the mRMR feature selection method 28 was used to identify potential CRC biomarkers from the 140 455 genes identified by MGWAS. First, to eliminate confounding effects of colonoscopy, blocked independent Wilcoxon rank-sum tests were performed on these genes with colonoscopy as a stratifying factor. This resulted in 102 514 genes at a significance level of p ⁇ 0.01 (FDR ⁇ 13%) and 24 960 genes at a significance level of p ⁇ 0.001 (FDR ⁇ 5.23%) . Then, from the latter, groups of genes were identified that were highly correlated with each other (Kendall’s ⁇ >0.9) and chose the longest gene in each group to generate a statistically non-redundant set of 11 128 significant genes.
  • CRC-enriched gene markers m1704941, butyryl-CoA dehydrogenase from F. nucleatum; m482585, RNA-directed DNA polymerase from an unknown microbe
  • m1704941 butyryl-CoA dehydrogenase from F. nucleatum
  • m482585 RNA-directed DNA polymerase from an unknown microbe
  • Over half (53.6%) of the 1452 CRC-enriched genes were from just three species: P. micra (389 genes) , S. moorei (204 genes) and Clostridium symbiosum (177 genes) (see Table S20) .
  • P. micra was enriched in CRC microbiomes using all three methods, while P. stomatis, Gemella morbillorum and S.
  • the inventors have reported the first successful cross-ethnic validation of metagenomic gene markers for CRC, notably including data from four countries.
  • Two recent studies reported on potential CRC diagnosis using metagenomic sequencing of fecal microbiomes.
  • the first study based on 16S ribosomal RNA gene used five operational taxonomic units to classify CRC from healthy samples in a cohort from the USA. 21 As they did not perform any independent validation, the inventors are unable to compare their validation accuracy with the earlier report.
  • the second study based on shotgun metagenomic sequencing used 21 species discovered in a French cohort to accurately classify patients with CRC in a German cohort.
  • CRC-enriched biomarkers have a higher chance to be shared across populations and have better diagnostic potential than control-enriched biomarkers.
  • biomarkers for being healthy are harder to find than biomarkers for a specific disease, which goes against the Anna Karenina principle applied to gut microbiome that predicts higher number of disease-specific disturbed states than undisturbed states. 42
  • it is mandatory to have further validation for all biomarkers in larger cohorts across different populations these results provide a proof of principle that development of an affordable diagnostic test using fecal microbial gene markers to identify patients with CRC may indeed be possible.
  • micra as a novel bacterial candidate involved in CRC-associated dysbiosis showing stronger associations with CRC across all five cohorts we investigated.
  • Strong co-occurrence pattern between P. micra and the Gram-negative F. nucleatum, 44 and the former’s ability to increase its capacity to induce inflammatory responses by binding to lipopolysaccharides from Gram-negative bacteria, 45 could mean cooperation between the two, both in terms of colonization strategies and in promoting a proinflammatory tumorigenic microenvironment. Enrichment of these species starts as early as in stage II of CRC, suggesting that they may play a role in the progression of CRC. Further work characterizing P. micra could elucidate its role in CRC.
  • the present inventors have demonstrated consistent fecal microbial changes in CRC across four cohorts, identified novel bacterial candidates that may be involved in the development and progression of CRC, validated gene markers in three cohorts from three different countries and reported two bacterial genes that could serve as effective diagnostic biomarkers of CRC. Systematic investigation of key species and gene markers identified here might reveal further candidates. Additional work will be imperative (i) to benchmark these observations against currently used diagnostic approaches, (ii) to identify additional markers with improved predictive value and (iii) to eventually validate them in much larger cohorts. The ultimate goal would be to identify fecal metagenomic markers with strong predictive power to detect early stages of CRC, which would significantly reduce CRC-associated mortality.
  • Cohort D Stool samples were collected from individuals referred to colonoscopy due to symptoms associated with CRC or from patients who had been diagnosed with CRC and referred to large bowel resection for their primary cancer disease (See Table S18) . All individuals were included at their visit to the out-patient clinic either before colonoscopy or before the operation and always before bowel evacuation. The individuals received a stool collection set including a tube without stabilizing buffer and were instructed to collect a stool sample at home one or two days before initiation of large bowel evacuation. Every included individual kept the sample refrigerated at -18°C and contacted a research nurse who collected the sample. At the laboratory stool samples were immediately snap frozen in liquid nitrogen and subsequently stored at -80°Cunder 24/7 electronic surveillance until analysis.
  • Danish samples A frozen aliquot (200 mg) of each fecal sample was suspended in 250 ⁇ l of 4 M guanidine thiocyanate–0.1 M Tris (pH 7.5) and 40 ⁇ l of 10%N-lauroyl sarcosine. Then, DNA extraction was conducted using bead beating method as previously described [24] . The DNA concentration and its molecular size were estimated by nanodrop (Thermo Scientific) and agarose gel electrophoresis.
  • DNA library construction for samples from cohort C1, C2 and D was performed following the manufacturer’s instruction (Illumina) at the same facility.
  • PE paired-end
  • CRC associated marker genes Based on the identified 140, 455 CRC associated marker genes, we constructed the CRC associated MLGs using the method described in our previous study on type 2 diabetes [25] . All the above genes were aligned to the reference genomes of IMG database v400 to get genome level annotation. An MLG was assigned to a genome if >50%constituent genes were annotated to that genome, otherwise it was termed as unclassified. 86 MLGs consisting over 100 genes were selected as CRC associated MLGs. These MLGs were grouped based on the species annotation of these genomes to construct MLG species.
  • KEGG orthologous group (KO) abundance profiles were calculated by summing the abundances of KOs belonging to each functional category.
  • Clean reads were aligned to mOTU reference database (total 79268 sequences) with default parameters [26] .
  • 549 species level mOTUs were identified, including 307 annotated species and 242 mOTU linkage groups (not to be confused with metagenomics linkage groups) without representative genomes.
  • Most of the mOTU linkage groups were putatively Firmicutes or Bacteroidetes.
  • SOAP reference index was constructed for the IMG genome database based on 7 equal size chunks of the original file. Clean reads were aligned to reference using SOAP aligner [47] version 2.22, with parameters “-m 4 -s 32 -r 2 -n 100 -x 600 -v 8 -c 0.9 -p 3” . Then, SOAP coverage software was used to calculate read coverage of each genome, normalized with genome length, and further normalized to relative abundance for each individual sample. The profile was generated based on uniquely mapped reads only.
  • a ij is the relative abundance of marker i in sample j.
  • N is a subset of all CRC-enriched markers in these 20 genes.
  • M is a subset of all control-enriched markers in these 20 genes.
  • are the sizes of these two sets.
  • the ability of the CRC index to distinguish CRC patient microbiomes from non-CRC microbiomes was examined using Wilcoxon rank-sum test. P-values estimated by these tests were adjusted for multiple testing using Benjamini-Hochberg method, when comparing CRC samples in cohort C1 with several other sample sets.
  • MLGs were associated with CRC at a significance level of q ⁇ 0.05 according to Wilcoxon rank-sum tests with Benjamini-Hochberg adjustment. This higher number is expected as the MLGs were constructed with genes that are associated with CRC in the first place. Using the same procedure at the same significance level, 28 IMG species and 21 mOTU species were associated with CRC.
  • Co-occurrence networks were constructed for the 85 MLGs, 28 IMG species and 21 mOTUs associated with CRC (q ⁇ 0.05) using Spearman’s correlation coefficient (>0.5 or ⁇ -0.5) , as described previously [25] .
  • Cytoscape [48] v3.0.2 was used to construct the three networks.
  • Table S6 List of KEGG modules and pathways associated with CRC status at P-value ⁇ 0.01 in cohort C1.
  • Table S10 List of 13 genera associated with CRC status in cohort C1.
  • Example 2 Use of Bacteroides clarus, Roseburia intestinalis, Clostridium hathewayi, M7, and Fusobacterium nucleatum as Fecal Markers for CRC
  • Gut microbiota is an important etiological factor in the development of colorectal cancer (CRC) .
  • CRC colorectal cancer
  • the objective of this study is to evaluate the utility of newly identified fecal bacterial marker candidates by metagenome sequencing for CRC diagnosis.
  • the abundances of five bacteria were quantified in fecal samples of 439 subjects (203 CRC and 236 healthy subjects) from two independent cohorts by duplex quantitative PCR (qPCR) assays.
  • Fn Fusobacterium nucleatum
  • Bc Bacteroides clarus
  • Rh Roseburia intestinalis
  • Ch Clostridium hathewayi
  • m7 undefined species
  • CRC Colorectal cancer
  • Fn is enriched in both the feces and colonic mucosa of CRC patients (3, 5, 8) and plays important roles in colorectal carcinogenesis (9, 10) .
  • Fusobacterium was also found to be enriched in colorectal tumors (11) .
  • bacterial candidates that may serve as non-invasive biomarkers for CRC (12) , including Fn, Bacteroides clarus (Bc) , Roseburia intestinalis (Ri) , Clostridium hathewayi (Ch) , one undefined species (labeled as m7) .
  • Fn Bacteroides clarus
  • Rh Roseburia intestinalis
  • Ch Clostridium hathewayi
  • m7 one undefined species
  • the stool-based bacterial candidate markers were validated in a large cohort of 203 CRC patients and 236 control subjects to identify a panel of markers with good sensitivity and specificity as a novel diagnostic tool for CRC.
  • the inventors established probe-based duplex qPCR assays for the quantification of the bacteria; the technique involved is easy and less costly to perform compared with the currently available tests.
  • Fecal samples were collected from the two independent cohorts, including cohort I-Hong Kong: 370 subjects, consisting of 170 patients with CRC (mean age, 67.2 ⁇ 11.6 years; 100 males and 70 females) and 200 normal controls (59.3 ⁇ 5.8 years; 77 males and 123 females) , at the Prince of Wales Hospital, the Chinese University of Hong Kong between 2009 and 2013 (Table 6) , and cohort II-Shanghai: 69 subjects, consisting of 33 patients with CRC (mean age, 63.4 ⁇ 9.6 years; 17 males and 16 females) and 36 normal controls (53.2 ⁇ 12.2 years; 10 males and 26 females) , at Renji Hospital, Shanghai Jiaotong University between 2014 and 2015 (Table 6) .
  • cohort I-Hong Kong 370 subjects, consisting of 170 patients with CRC (mean age, 67.2 ⁇ 11.6 years; 100 males and 70 females) and 200 normal controls (59.3 ⁇ 5.8 years; 77 males and 123 females
  • Subjects recruited for fecal sample collection included individuals presenting symptoms such as change of bowel habit, rectal bleeding, abdominal pain or anaemia, and asymptomatic individuals aged 50 or above undergoing screening colonoscopy as in our previous metagenomics study (12) . Samples were collected before or one month after colonoscopy, when gut microbiome should have recovered to baseline (13) . The exclusion criteria were: 1) use of antibiotics within the past 3 months; 2) on a vegetarian diet; 3) had an invasive medical intervention within the past 3 months; 4) had a past history of any cancer, or inflammatory disease of the intestine. Subjects were asked to collect stool samples in standardized containers at home, and store the samples in their home -20°C freezer immediately.
  • Frozen samples were then delivered to the hospitals in insulating polystyrene foam containers and stored at -80°Cimmediately until further analysis. Patients were diagnosed by colonoscopic examination and histopathological review of any biopsies taken. Informed consents were obtained from all subjects. The study was approved by the Clinical Research Ethics Committee of the Chinese University of Hong Kong and the Ethics Committee of Renji Hospital, Shanghai Jiaotong University.
  • Primer and probe sequences for the internal control were designed manually on the basis of the conservative fragments in bacterial 16S rRNA genes (14) , and then they were tested using the tool PrimerExpress v3.0 (Applied Biosystems, Foster City, CA) for determination of Tm, GC content and possible secondary structures. Degenerate sites were included in the primers and probes to increase target coverage; Degenerate sites were not close to 3’ ends of primers and 5’ end of the probes. Amplicon target was nt1063-1193 of the corresponding E. coli genome.
  • F. nucleatum F. nucleatum
  • Bc B. clarus
  • R. intestinalis R. intestinalis
  • Ch C.hathewayi
  • m7 undefined species
  • Fn has also been identified to be enriched in CRC patients by others (3, 5, 8) , while the other four have not associated with CRC by other researchers.
  • Primer and probe sequences targeting the nusG gene of Fn were designed using PrimerExpress.
  • the primer-probe sets specifically detect the intended targets and not any other known sequences, as confirmed by Blast search.
  • Each probe carried a 5′reporter dye FAM (6-carboxy fluorescein) or VIC (4, 7, 2’ -trichloro-7’ -phenyl-6-carboxyfluorescein) and a 3′quencher dye TAMRA (6-carboxytetramethyl-rhodamine) .
  • Primers and hydrolysis probes were synthesized by Invitrogen (Carlsbad, CA) . Nucleotide sequences of the primers and probes are listed in Table 8. PCR amplification specificity was confirmed by direct Sanger sequencing of the PCR products or by sequencing randomly picked TA clones.
  • qPCR amplifications were performed in a 20 ⁇ L reaction system of TaqMan Universal Master Mix II (Applied Biosystems) containing 0.3 ⁇ M of each primer and 0.2 ⁇ M of each probe in MicroAmp fast optical 96-well reaction plates (Applied Biosystems) with adhesive sealing.
  • Thermal cycler parameters of an ABI PRISM 7900HT sequence detection system, were 95°C 10 min and (95°C 15 s, 60°C 1 min) ⁇ 45 cycles.
  • a positive/reference control and a negative control H 2 O as template
  • the HemoSure immunogold labeling FIT dipsticks (WHPM Co. Ltd, Beijing, China) , which are certified by the State Food and Drug Administration of China, were used as previously described (15) .
  • ROC curves were then constructed for the logistic regression models. All tests were done by Graphpad Prism 5.0 (Graphpad Software Inc., San Diego, CA) or SPSS software v17.0 (SPSS, Chicago, IL) . P ⁇ 0.05 was taken as statistical significance.
  • the gene marker, butyryl-CoA dehydrogenase from Fn (m1704941; 99.13%identity) , showed an occurrence of only 2.7% (39 out of 74) in CRC patients; whilst at the species level, Fn showed an occurrence of 83.8% (62 out of 74) in CRC patients (Table 9) , inferring that Fn at species level is better than gene marker m1704941 for the diagnosis of CRC. Therefore, the inventors established a duplex-qPCR assay targeting the nusG gene of Fn, which was reported to be transcriptionally more active in colorectal tumors than in matched normal samples, (5) to assess the diagnostic value of Fn for CRC. This qPCR assay showed good correlation with Fn at species level by metagenome sequencing ( Figure 17b) , suggesting qPCR targeting nusG may cover more strains of Fn and could be more sensitive in detecting CRC.
  • Fn is a potential non-invasive fecal biomarker for diagnosing CRC patients
  • Fn showed the best performance in discriminating CRC from healthy controls, giving an area under receiver operating curve (AUROC) of 0.868 (0.831-0.904, 95%confidence interval; P ⁇ 0.0001) ( Figure 18b) .
  • AUROC area under receiver operating curve
  • Figure 18b Fn could discriminate CRC from controls with a sensitivity of 77.7%, specificity of 79.5%, negative predictive value (NPV) of 80.7%, and positive predictive value (PPV) of 76.3%in the first cohort of 170 CRC patients and 200 healthy subjects. This was further verified in a second independent cohort of 33 CRC patients and 36 healthy controls.
  • this panel of four-bacteria could discriminate CRC patients from healthy controls with a sensitivity of 77.7%, specificity of 81.5%, NPV of 81.1%, and PPV of 78.1%, showing a better diagnostic performance than Fn only (Table 4) .
  • the improved performance of four-bacteria was further validated in the second independent cohort.
  • the combination of the four-bacteria also demonstrated an increased AUROC (0.756) as compared to three-bacteria (0.731) , Fn only (0.675) or the logistic regression model (0.746) ( Figure 19c) .
  • FIT is applied to select high-risk patients for colonoscopy (16) .
  • FIT has also been widely used in other regions of the world (17) .
  • the sensitivity of FIT shows limitations for CRC [0.79 (95%CI, 0.69 to 0.86) ] and differed greatly among various studies, according to a recent systematic review and meta-analysis by Lee et. al. (17) .
  • the wide application of FIT makes fecal samples easily obtainable. Detection of molecular biomarkers in fecal samples for the non-invasive diagnosis of CRC may be a more promising alternative than blood/plasma biomarkers to be implemented in present clinical settings.
  • a qPCR platform was established for the quantification in fecal samples.
  • the primer-probe set targeting 16S rRNA genes was designed based on the conserved sequences of all 16S rRNA genes available (14) , guaranteeing sufficient coverage and an amplicon size suitable for qPCR ( ⁇ 150 bp) .
  • This internal control was confirmed to work well to represent the bacterial DNA content in different samples.
  • the probe-based duplex-qPCR assay allows the detection of both internal control and target in the same reaction for each sample, saving both reagents and samples, and producing more reliable data.
  • Target marker abundance is calculated relative to total bacterial content by the ⁇ Cp method.
  • the present inventors defined for the first time that DNA template concentration should be limited ( ⁇ 10 ng/ ⁇ L) to avoid inhibitory effects caused by fecal DNA and >0.1 ng/ ⁇ L to avoid false-negative assessments of the targets using our duplex qPCR assays. A good correlation was further shown in the quantification of bacterial candidates by metagenomics approach and qPCR assays. Therefore, the duplex-qPCR assays are reliable, convenient, and of great clinical application value in the quantitative detection of target bacteria.
  • Fn as a biomarker for the stool-based diagnosis of CRC was further corroborated.
  • the abundance of fecal Fn was significantly higher in CRC patients than in healthy control subjects.
  • Fn had a sensitivity of 77.7%and specificity of 79.5%in the first cohort of 170 CRC patients and 200 healthy control subjects.
  • the significantly increased or decreased fecal abundances of Bc, Ri, Ch and m7 in CRC patients than in control subjects was also shown, as consistent with metagenomics findings.
  • Bc is a gram-negative, obligately anaerobic, non-spore-forming, rod-shaped bacterium species that was isolated from human feces in 2010 (19) .
  • Ch is a strictly anoxic, gram-positive, spore-forming, rod-shaped bacterium that participates in glucose metabolism using carbohydrates as fermentable substrates to produce acetate, ethanol, carbon dioxide and hydrogen (20) .
  • Fn which is known to promote CRC tumorigenesis, whether the altered abundances of Ri, Bc or m7 play a causative role in CRC development or serve as a consequence of CRC development needs further investigation.
  • the quantification of Fn alone can serve as a non-invasive diagnostic method for CRC with a moderate sensitivity and specificity.
  • the combination of four bacterial markers (Fn, Bc, Ch and m7) improved the diagnostic ability of Fn alone for CRC.
  • the combination of the bacterial markers and FIT showed the highest sensitivity and specificity for the diagnosis of CRC, especially for early stage CRC.
  • stool-based detection of bacterial markers can serve as a novel non-invasive diagnostic method for patients with CRC.
  • Table 10 The occurrence rates of bacterial candidates in fecal samples of CRC patients and healthy control subjects
  • Peng H, Long F, Ding C Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 2005; 27: 1226–38.

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Abstract

L'invention concerne une méthode non invasive pour diagnostiquer un cancer colorectal chez un sujet par détection d'un enrichissement ou d'une réduction de certaines espèces bactériennes. L'invention concerne également un kit et un dispositif utiles pour de telles méthodes. De plus, l'invention concerne également une méthode de réduction du risque de cancer du côlon par une régulation des espèces bactériennes pertinentes dans le côlon humain.
PCT/CN2017/098592 2016-08-25 2017-08-23 Marqueurs bactériens fécaux pour le cancer colorectal WO2018036503A1 (fr)

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CN110857450A (zh) * 2018-08-22 2020-03-03 深圳华大生命科学研究院 结直肠癌标志物及其应用
WO2020051559A1 (fr) * 2018-09-06 2020-03-12 Viome, Inc. Systèmes et méthodes d'analyse de microbiome
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WO2020182922A1 (fr) * 2019-03-13 2020-09-17 Goodgut S.L. Procédé amélioré pour le criblage, le diagnostic et/ou la surveillance d'une néoplasie avancée colorectale, d'un adénome avancé et/ou d'un cancer colorectal
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WO2024119614A1 (fr) * 2022-12-07 2024-06-13 臻傲生物科技检测(深圳)有限公司 Nouveau marqueur microbien pour prédire le risque de cancer colorectal

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