EP3830300A1 - Traitement et diagnostic du cancer du sein - Google Patents

Traitement et diagnostic du cancer du sein

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Publication number
EP3830300A1
EP3830300A1 EP19773488.2A EP19773488A EP3830300A1 EP 3830300 A1 EP3830300 A1 EP 3830300A1 EP 19773488 A EP19773488 A EP 19773488A EP 3830300 A1 EP3830300 A1 EP 3830300A1
Authority
EP
European Patent Office
Prior art keywords
cadaverine
breast cancer
subject
ldc
level
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP19773488.2A
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German (de)
English (en)
Inventor
Péter BAY
Tünde KOVÁCS
Edit MIKÓ
András VIDA
James J. Goedert
Judit TÓTH
Éva SEB
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Debreceni Egyetem
US National Cancer Institute
Original Assignee
Debreceni Egyetem
US National Cancer Institute
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Application filed by Debreceni Egyetem, US National Cancer Institute filed Critical Debreceni Egyetem
Publication of EP3830300A1 publication Critical patent/EP3830300A1/fr
Pending legal-status Critical Current

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    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification

Definitions

  • the invention relates to the field of diagnosis and treatment of early stage breast cancer. Specifically, a method is provided for determining whether a subject has early stage breast cancer by measuring the abundance of a bacterium species comprising a DNA sequence coding for a lysine decarboxylase. A method for mitigating breast cancer initiation and/or promotion and/or progression in a subject is also provided.
  • Dysbiosis is often reflected as a loss of diversity of the microbiota (e.g.
  • Cadaverine (CAD; pentane- 1,5 -diamine) is produced by the decarboxylation of lysine that is performed by lysine decarboxylase (LDC) enzymes.
  • LDC lysine decarboxylase
  • Human cells code and express LDC and numerous bacterial species of the human microbiome also express LDC either in a constant (LdcC in the LDC operon) or in an inducible (CadA in the Cad operon) fashion [32, 33].
  • Bacteria use diamines, like cadaverine or putrescine, generated by the decarboxylation of lysine or arginine, to buffer the pH of their environment [28]. The effects of cadaverine on cancer cells and its role in carcinogenesis are not yet characterized in detail.
  • WO2013045826A1 describes that a mixture depleted of cadaverine, putrescine, spermidine and spermine and on the other hand containing agmatine at a concentration higher than that supplied by an average food ration is beneficial in the treatment of pathologies associated with cellular hyperproliferation.
  • the invention prvides a method for determining whether a subject has early stage breast cancer or has an in creased probability of having early stage breast cancer by measuring, in a sample derived from said subject, the level of bacterial cadaverine synthesis.
  • the invention provides a method for determining whether a subject has early stage breast cancer or has an increased probability of having early stage breast cancer by measuring the abundance of a bacterium species comprising a DNA sequence coding for a lysine decarboxylase (LDC), the level of a DNA sequence coding for an LDC of a bacterium species, or the level of a gene product of a DNA sequence coding for an LDC produced by a bacterium species, in a sample derived from the subject, wherein the sample comprises microbiota from the subject and wherein the bacterium species is part of the microbiota of the subject.
  • LDC lysine decarboxylase
  • the invention also provides a method for determining whether a subject is at an increased risk of developing breast cancer, by measuring the abundance of a bacterium species comprising a DNA sequence coding for a lysine decarboxylase (LDC), the level of a DNA sequence coding for an LDC of a bacterium species, or the level of a gene product of a DNA sequence coding for an LDC produced by a bacterium species, in a sample derived from the subject, wherein the sample comprises microbiota from the subject and wherein the bacterium species is part of the microbiota of the subject.
  • the invention also provides cadaverine for use in the treatment or prevention of breast cancer in a subject and cadaverine for use in mitigating cancer initiation and/or promo tion and/or progression in a subject. The invention is further detailed in the following paragraphs.
  • ii) has an increased probability of having early stage breast cancer
  • the level of bacterial cadaverine synthesis is assessed by measuring
  • compared to the corresponding reference value indicates that the subject has early stage breast cancer or an increased probability of having early stage breast or is at an increased risk of developing breast cancer.
  • the breast cancer is stage 0 or 1 breast cancer according to the American Joint Committee on Cancer (AJCC) TNM system.
  • the cancer is stage 0 breast cancer and the test sample is compared to a reference value typical of the absence of stage 0 breast cancer.
  • the cancer is breast cancer stage 1 the test sample is compared to a reference value typical of the absence of stage 1 breast cancer.
  • the DNA sequence coding for LDC is ldcC or cadA.
  • test sample is a feces sample.
  • the bacterium species is selected from Escherichia, Enterobacter and Hafnia. More preferably the bacterium species is selected from Escherichia cob, Enterobacter cloacae and Hafnia alvei.
  • stage 0 breast cancer indicates that the subject has stage 0 breast cancer or an increased probability of having stage 0 breast cancer or is at an increased risk of developing breast cancer.
  • stage 0 breast cancer indicates that the subject has stage 0 breast cancer or an increased probability of having stage 0 breast cancer or is at an increased risk of developing breast cancer.
  • the gene product is LDC protein.
  • the subject is a human, preferably a woman, more preferably a postmenopausal woman.
  • cadaverine for use in the treatment or prevention of breast cancer in a sub ject is provided.
  • cadaverine for use in mitigating cancer initiation and/or promotion and/or progression in a subject is provided.
  • the subject has an increased probability of having early stage breast cancer or is at an increased risk of developing breast cancer. More preferably the subject has early stage breast cancer.
  • the level of a DNA sequence coding for an LDC of a bacterium species, or the level of a gene product of a DNA sequence coding for an LDC produced by a bacterium species, is lower in a test sample comprising microbiota from said subject than the corresponding reference value or the level of cadaverine in a test sample from the subject is lower than the corresponding reference value.
  • the test sample is feces.
  • the bacterium species is selected from Escherichia, Enterobacter and Hafiiia. More preferably the bacterium species is selected from Escherichia coli, Enterobacter cloacae and Hafiiia alvei.
  • the DNA sequence coding for an LDC is cadA or ldcC.
  • the gene product is LDC protein.
  • the invention provides a method for mitigating breast cancer initiation and/or promotion and/or progression in a subject, comprising
  • cadaverine administered to the subject to provide or restore physiological serum concentration of cadaverine if
  • the subject has early stage breast cancer.
  • the test sample is feces.
  • the bacterium species is selected from Escherichia, Enterobacter and Hafnia. More preferably the bacte rium species is selected from Escherichia coli, Enterobacter cloacae and Hafnia alvei.
  • the DNA sequence coding for an LDC is cadA or ldcC.
  • the gene product is LDC protein.
  • a pharmaceutical composition comprising cadaverine and at least one pharmaceutically ac ceptable excipient or carrier.
  • the pharmaceutical composition is for use in mitigating breast cancer initiation and/or promotion and/or progression.
  • the pharmaceutical composition is administered to provide or restore physiological serum concentration of cadaverine in a subject having early stage breast cancer or a lower serum cadaverine level compared to the physiological serum cadaverine.
  • Cadaverine treatment reduces breast cancer aggressiveness in vivo.
  • CAD cadaverine
  • VEH vehicle
  • VEH and CAD-treated mice (A) the number and (B) mass of primary tumors were counted and the (C) number and (D) mass of metastases were measured upon autopsy. (E) Upon autopsy, the infiltration rate of the primary tumor was scored.
  • F-I Primary tumors were formalin-fixed and were embedded into paraffin, then sections were hematoxylin-eosin stained and were scored for (F) mitosis, (G) mitosis/hpf, (H) nuclear pleomorphism.
  • FIG. 1 Cadaverine reduces the proliferation and colony forming ability of breast cancer cells.
  • FIG. 3 Cadaverine treatment reverses EMT (epithelial-mesenchymal transition) of breast cancer cells.
  • A- B In control and cadaverine-treated 4T1 cells
  • FIG. 4 Cadaverine treatment attenuates movement, invasion ability, mitochondrial oxidation and sternness of 4T1 cells.
  • B 4T1 cells were treat ed with cadaverine in the concentration indicated for 48 hours and subsequently invasion capacity of the cells was measured using the Corning matrigel invasion chamber. Cells were counted using the Opera HCS system and invasion index was calculated.
  • OCR Oxygen consumption rate
  • ECAR extra cellular acidification rate
  • FIG. 5 TAARs are seemed to be responsible for the effect of cadaverine.
  • A Patient data was accessed at kmplot.com. Kaplan-Meier plots show the correlation between the mRNA expression of human TAARs and survival in breast cancer.
  • FIG. 6 Cadaverine biosynthesis is suppressed in early stages of breast cancer.
  • A Fluman fecal DNA samples were collected from 48 patients with different stages of breast cancer, and from 48 healthy patients. The abundance of DNA coding for CadA and LdC of the indicated bacterial species were determined in the fecal DNA samples by RT-qPCR. Median values are indicated by a line.
  • FIG. 7 Cadaverine reverts EMT in breast cancer cell lines.
  • Bacterial cadaverine biosynthesis has been found to be suppressed in breast cancer. Bacteria of the human microbiota capable of producing cadaverine may be used as an early indicator of the presence or risk of breast cancer.“Bacterial cadaverine synthesis” refers to the potential of the microbiota to produce cadaverine, prefera bly by the enzymatic decarboxylation of lysine. The level of“bacterial cadaverine synthesis” may depend on the number of bacteria capable of producing cadaverine, e.g the number of bacteria comprising a coding sequence for a lysine decarboxylase enzyme or the rate of expression of the enzyme or the level of activity of the enzyme or the level of the enzyme.
  • Bacteria of the gut capable of producing cadaverine are less abundant in the feces of patients with early stage breast cancer.
  • the concentrations or amounts of LDC DNA, mRNA or protein are lower in the feces sample of an individual with stage 0 or 1 breast cancer than in a control feces sample.
  • The“stage” of a cancer in this description is to be understood as a stage determined using the American Joint Committee on Cancer (AJCC) TNM system staging.
  • AJCC American Joint Committee on Cancer
  • TNM system American Joint Committee on Cancer staging system was used according to the 7th edition.
  • the term“early stage” refers to stage 0 and stage 1, preferably to stage 0 or preferably to stage 1.
  • the invention provides a method for diagnosing breast cancer by measuring the abundance of at least one bacterium species which is capable of producing cadaverine under physiological conditions in the human body, in a test sample derived from the subject, wherein the test sample comprises microbiota of said subject.
  • the term“abundance” or“level” in general is meant as a proportion of a given specimen in a given pool relative to certain similar specimens.
  • the term“abundance” or “level” may refer to a concentration or quantity of the specimen.
  • The“abundance” of a bacterium species may refer to the concentration or the number of cells measured in a sample (e.g. a fecal sample).
  • the term“abun dance of the DNA sequence coding for lysine decarboxylase (LDC) relates to the proportion of the special seg ment of bacterial DNA making up the DNA sequence coding for lysine decarboxylase in a DNA pool or isolate (e.g. total DNA in a sample or a pool of samples).
  • the term“abundance (or level) of the DNA sequence coding for lysine decarboxylase” may relate to the amount of the special segment of bacterial DNA making up the DNA sequence coding for lysine decarboxylase in a sample (test sample or reference sample).
  • the abundance or level of an RNA or protein molecule is defined accordingly, i.e. it relates to the amount of the RNA or protein in the sample.
  • “abundance” may refer to relative abundance, e.g. the abundance of E. coli in a sample of a patient may be calculated based on the abundance of E. coli in a reference sample.
  • Cadaverine is produced by direct decarboxylation of L-lysine catalyzed by lysine decarboxylase.
  • a bacterium is capable of producing cadaverine if the genome of said bacterium comprises a DNA sequence coding for a lysine decarboxylase.
  • a bacterium is capable of producing cadaverine if its genome comprises a cad and/or ldc operon, more particularly cadA and/or ldcC.
  • a bacte rium is capable of producing cadaverine if it expresses a lysine decarboxylase.
  • a bacterium that is capable of producing cadaverine produces cadaverine by the decarboxylation of lysine which is catalyzed by LCD.
  • a bacterium that is capable of producing cadaverine under physiological condi tions in the human body is capable of producing cadaverine in the gastrointestinal system.
  • the bacterium whose abundance is to be measured is a bacterium that is part of the healthy human microbiota, preferably the gut microbiota, preferably the fecal microbiota, more preferably the gut and the fecal microbiota.
  • the DNA sequence coding for a lysine decarboxylase may be a constitutive (e.g. ldcC) or an inducible gene (e.g. cadA) and the expression of the protein may be constitutive or inducible.
  • the capability of a bacterial spe cies/strain/genus to convert lysine to cadaverine under physiological conditions may be tested in vitro. In an appropriate in vitro assay bacterial lysates and lysine are mixed and at the end of the assay cadaverine is detect ed by e.g. mass spectrometry and the lysine/cadaverine ratio is calculated. Lysine carboxylase activity may be measured as described in Inoue et al.
  • A“decreased level of bacterial cadaverine synthesis” in a test sample refers to a decrease of bacterial cadaverine synthesis as compared to a reference level.
  • the (corresponding) reference value of abun dance or quantity or level or concentration may be derived from a plurality of samples from individuals not having early stage breast cancer, preferably not having stage 0 or stage 1 breast cancer, preferably not having cancer and most preferably from healthy individuals.
  • the corresponding reference value of the serum cadaverine concentration may be the physiological serum concentration of cadaverine.
  • the corresponding reference value is the value derived from measurements of the level of the DNA sequence coding for the (same) LDC of the (same) bacterium species in the same type of samples from individuals not having early stage breast cancer, preferably from healthy individuals. Accordingly, a level or concentration of an LDC protein in a test sample is compared to the characteristic value derived from measurements of the level or concentration of the LDC protein in the same type of samples from individuals not having early stage breast cancer, preferably from healthy individuals.
  • HPMC Human Pan-Microbe Com munities
  • NIH Human Microbiome Project the NIH Human Microbiome Project
  • Integrated reference catalog of the human gut microbiome are well-known to the skilled person, and may be found in e.g. Turnbaugh et al. [71] The hu man microbiome project: exploring the microbial part of our in a changing world. Nature 2007; 449(7164): 804-810, e.g the KEGG database.
  • human microbiota refers to the microbes capable of living in or on the human body.
  • the terms “(human)”“gut microbiota” and“gut microbiome” refer to species of the (human) microbiota living in the (hu man) gastrointestinal tract and the term“fecal microbiota” refers to microbes found in the feces.
  • the term “microbiome” and“microbiota” as used in the description may refer to both the (human) microbiota and (hu man) microbiome and the gut/fecal microbiota and gut/fecal microbiome, preferably to the gut/fecal microbiota and microbiome.
  • Bacteria capable of producing cadaverine may reside in the gut, on the skin or in other tissues, such as breast tissue and in the feces.
  • the abundance of the DNA coding for LdcC and CadA was assessed in human fecal DNA from the experi mental cohort described in the Examples.
  • the abundance of Escherichia coli CadA and also E. coli, Enterobacter cloacae and Hafnia alvelii LdcC DNA in breast cancer patients was decreased compared to healthy individuals (Fig. 6A).
  • Decreased cadA and ldcC abundance was more pronounced in clinical stage 0 patients as compared to the pool of all patients (Fig. 6A).
  • E. coli LdcC protein levels were markedly lower than the levels in the feces of healthy subjects (Fig. 6B).
  • the GEO database has been assessed to study LDC expression in human breast cancer. There was no differ ence in LDC mRNA expression between control and breast cancer cases [39-42] or in LDC expression of the normal breast epithelium and cancer epithelium in patients [42, 43]. Rather as an exception, LDC expression was lower in basal-like breast cancer as compared to control (normal) breast epithelium of non-diseased indi viduals [43, 44].
  • the kmplot.com database was used to assess how expression of LDC in humans affects the outcome of breast cancer. Differences in LDC expression did affect overall survival of the patients, in grade 1 patients high er expression of LDC was associated with significantly longer survival than lower expression of LDC (Fig. 6C). Interestingly, while LDC expression did not affect survival in ER- PR- patients, higher LDC expression corre lated with better survival in ER+ PR+ patients (Fig. 6D). High expression of human LDC prolongs survival in early stage breast cancer patients, supporting the potential anti-cancer properties of cadaverine.
  • cadaverine administered in a dose corresponding to the physiological serum con centration in humans exerted antitumor effects in mice grafted with either human -derived or mouse-derived breast cancer cells.
  • the physiological concentration in humans refers to a reference range measured in healthy (i.e. not having breast cancer) individuals and is considered to be 100-800 nM/1 (in the serum) [34, 35].
  • the invention provides cadaverine for use in the treatment or prevention of breast cancer in a subject, cadaverine for use in mitigating cancer initiation and/or promotion and/or progression in a subject and cadaverine for use in the treatment or prevention of breast cancer in a subject or in mitigating cancer initiation and/or promotion and/or progression in a subject, wherein in said use physiological serum concentration of cadaverine is provided or restored in said subject.
  • physiological serum concentration refers to the serum concentration (or a range of concentrations) measured in healthy subjects.
  • Cadaverine plays a tumor suppressor role in breast cancer, in concentrations corresponding to the human reference range.
  • cadaverine in the concentrations corresponding to its reference con centration, did not have a cytostatic effect on primary fibroblasts, suggesting that these effects are specific for tumor cells.
  • Cadaverine exerts its effects through inhibiting EMT, cellular movement, chemotaxis and metasta sis. It has been also found that cadaverine treatment reduces the aggressivity of breast cancer, as indicated by the decreased rate of mitosis and heterogeneity of nuclear morphology, reduced number of metastases, lower mass and infiltration of the primary tumor. In human patients, rate of mitosis and heterogeneity of nuclear mor phology are part of the Nottingham grading system. Our results suggest that the effect of cadaverine treatment may be detected by the repeated grading of the tumor. Change in nuclear score due to cadaverine treatment is shown on Fig. 1H.
  • Infiltration rate of the primary tumors has been found to be lower after cadaverine treatment (Fig. IE).
  • “low infiltration” class means that the primeary tumor remained in the mammary fat pads without any attachment to muscle tissues.
  • the tumor mass attached to the muscle tissue but did not penetrate to the abdominal wall it was classified as a“medium infiltration” tumor. If the tumor grew into the muscle tissue and totally penetrated the abdominal wall, it was scored as a“high infiltration” tumor.
  • histopathological evaluation may be used to determine infiltration rate, e.g. sample specimen after surgery or biopsy may be used.
  • Breast cancer is considered systemic when the tumor has infiltrated blood or lymphatic vessels.
  • FDG-PET is also suitable to calculate the number of metastases.
  • the dose of cadaverine used in the experiments with mice corresponds to the physiological concentration in the serum of healthy humans.
  • the human dose of cadaverine to be used may be calculated by known standards, e.g. the Guidance for Industry Estimating the Maximum Safe Starting Dose in Initial Clinical Trials for Thera peutics in Adult Healthy Volunteers from the U.S. Department of Health and Human Services Food and Drug Administration Center for Drug Evaluation and Research (CDER).
  • Cadaverin may be administered in a dose of about 50 nmol/kg bodyweight to 500 miho ⁇ /kg bodyweight, preferably about 50 nmol/kg bodyweight to 250 pmol/kg bodyweight, preferably about 50 nmol/kg bodyweight to 100 pmol/kg bodyweight, preferably about 100 nmol/kg bodyweight to 800 nmol/kg bodyweight, or preferably in a dose providing a serum concentration of 50-2000 nM/1 preferably 100-800 nM/1, more preferably 100-500 nM/1 or 50-500 nM/1.
  • cadaverine is administered in a dose restoring physiological serum concentration of cadaverine.
  • physiological serum concentration of cadaverine refers to a reference serum concen tration measured in healthy subjects. Loser et al found the serum concentration of cadaverine to be 0.32 ( ⁇ SEM:0.07) nmol/ml in healthy volunteers.
  • physiological serum concentration of cadaverine refers to a serum concentration of from about 0.15 nmol/ml to about 0.6 nmol/ml.
  • the“physiological serum concentration of cadaverine” refers to a serum concentration of from about 20 nmol/ml to about 0.5 nmol/ml from about 25 nmol/ml to about 0.4 nmol/ml.
  • biogenic amines putrescine and cadaverine show in vitro cytotoxicity at concentrations that can be found in foods www.nature.com/scientific reports (2019) 9: 120) non-observed adverse effect level (NOAEL) for cadaverine was found to be 2.5 mM (equivalent to 255.45 mg/kg), while the lowest observed adverse effect level (LOAEL) found to be 5 mM (equivalent to 510.89 mg/kg).
  • the IC 50 value for cadaverine was 40.72 ⁇ 1.98 mM. The skilled person may calculate a safe dose for cadaverine from these data.
  • Cadaverine may be administered in the form of a pharmaceutical composition, wherein the pharmaceutical composition comprises cadaverine and at least one pharmaceutically acceptable excipient or carrier.
  • the pharmaceutical composition comprises cadaverine and at least one pharmaceutically acceptable excipient or carrier.
  • Cadaverine is a liquid on room temperature, which fumes and attracts CO2 from the air.
  • Cadaverine is soluble in water and alcohol, however, incompatible with acid chlorides, acids, acid anhydrides, strong oxidizing agents, carbon dioxide. These properties must be considered when manufacturing an appropriate dosage form.
  • the term“miti gating” refers to delaying, inhibiting, decreasing any of the processes leading to and playing a role in cancer development, including the processes in which cells change to grow and divide continously, spread and invade other tissues.
  • primary tumor is used in the generally accepted meaning thereof, indicating the original, or first, tumor(s) in the body. Cancer cells from a primary tumor may spread to other parts of the body and form new, or secondary, tumors.
  • Cadaverine teatment (500 nmol/kg) decreased the invasivity of the primary tumors in mice homotopically grafted with 4T1 breast cancer cells (Fig. IE). Histological examination of the primary tumors revealed that cadaverine teatment decreased the rate of mitosis (Fig. 1F-G), the heterogeneity of nuclear morphology (Fig. 1H) and the pathological grade of the tumors. Cadaverine supplementation did not alter the number of primary tumors that grew from the grafted cells (Fig. 1A), but there was a trend towards tumors with lower mass (Fig. IB). In line with that, the number of metastases decreased (Fig.
  • Fig. ID Cadaverine induced a mesenchymal-to-epithelial (MET) transition and reduced invasion.
  • MET mesenchymal-to-epithelial
  • Fig. 3 A Cadaverine treatment changed the fibroblast-like mor phology of the 4T1 cells to a rather cobblestone -like morphology.
  • 3C-E show the changes found in CAD-treated 4T1 cells, primary tumors and their metastases from treated mice.
  • the effects of CAD were most profound on 4T1 cells but the same trend is evident in vivo: expression of EMT markers MMP2, MMP3, Tgfb3, FgFbpl, Erbb3, Erl, Notchl, IgFbp4, Sppl, Krtl4 and DSC2 are decreased, showing the reversal of the epithelial-mesenchymal transition.
  • cadaverine-treated cells were slower in migrating to open areas in scratch as says (Fig. 4A) and also performed worse in Boyden-chamber transmigration tests (Fig. 4B). These data were further supported by the observation that MMP9 expression was suppressed by cadaverine treatment (Fig 4C). Metabolic changes evoked by cadaverine administration were assessed using the Seahorse flux analyzer. Cadaverine treatment reduced glycolytic flux (Fig. 4D) that is a characteristic of breast cancer stroma cells [36]. The“sternness” of 4T1 cells was assessed using the aldefluor assay and a reduction in cancer cell sternness was found (Fig. 4E).
  • cadaverine administration was also investigated on five different established breast cancer cell lines of which four were of human (MD -MBA-231, SKBR3, ZR-75-1 and MCF7), while one was of murine origin (4T1).
  • the cadaverine concentration used corre sponded to the reference concentration of cadaverine in human serum (100-800 nM) [34, 35, 36].
  • cadaverine did not hinder the proliferation of non-transformed primary human skin fibroblasts (Fig. 2A).
  • Fig. 2A We assessed whether slower proliferation could be due to the toxicity of cadaverine to cells.
  • the proportion of the PI positive cells did not increase upon cadaverine treatment (Fig. 2D), nor did the apoptotic fraction in 4T1 cells (Fig. 2C).
  • Cadaverine exerts its beneficial effects through Trace Amino Acid Receptors (TAARs).
  • the trace amino ac id receptor family serves as receptors for cadaverine [37, 38, 39]. Indeed, higher expression of TAAR1, TAAR2, TAAR4, TAAR5 and TAAR9 provided better survival in breast cancer (Fig 5A).
  • TAAR receptors are G protein-dependent receptors [38] we assessed their involvement by treating 4T1 cells with NF449, a Gsa- subunit-selective G-protein antagonist, a treatment that abolished the anti-EMT effect of cadaverine (Fig. 5B).
  • E. coli FdcC levels in the feces of patients having E-cadherin negative breast cancer are lower than in the feces of patients having E-cadherin positive breast cancer.
  • Fig. 8 E-cadherin ex pression in breast cancer has been linked to disease progression, metastasis, aggressiveness of the tumor and reduced overall survival [76]. This finding further supports the tumor suppressive role of cadaverine.
  • a method for diagnosing early stage breast cancer in a human subject comprising measuring the abundance of at least one bacterium species which is capable of producing cadaverine un der physiological conditions in the human body, in a test sample derived from the subject, wherein the test sam ple comprises human microbiota of said subject, and
  • early stage breast cancer refers to stage 0 and stage 1 breast cancer, preferably to stage 0 breast cancer or preferably to stage 1 breast cancer.
  • the method is for diagnosing breast cancer stage 0 according to the American Joint Com mittee on Cancer (AJCC) TNM system and the test sample is compared to a reference value typical of the ab sence of stage 0 breast cancer.
  • the method is for diagnosing breast cancer stage 1 according to the American Joint Committee on Cancer (AJCC) TNM system and the test sample is compared to a reference value typical of the absence of stage 1 breast cancer.
  • the abundance of the bacterium species to be measured is measured by measuring the abundance of the DNA sequence coding for or a gene product of the DNA sequence coding for lysine decar boxylase (LDC).
  • the DNA sequence coding for LDC is a DNA sequence in the ldc operon and/or in the cad operon or the gene product is a gene product of a gene of the ldc operon and/or of the cad operon. More preferably, the DNA sequence in the ldc operon is ldcC and/or the DNA sequence in the cad operon is cadA or the gene of the ldc operon is ldcC and/or the gene of the cad operon is cadA.
  • the gene product is preferably RNA or protein.
  • the protein is preferably LDC, LdcC protein or CadA protein (lysine decarboxylase).
  • the RNA is preferably mRNA.
  • stage 0 is to be diagnosed, DNA or RNA is used, and when stage 1 is to be disagnosed, protein is used.
  • test sample comprising human microbiota of said subject comprises gut microbiota.
  • the at least one bacterium species is select ed from Escherichia, Enterobacter and Hafnia.
  • the at least one bacterium species is selected from Escherichia coli, Enterobacter cloacae and Hafnia alvei.
  • the bacteria to be measured are Escherichia coli, Enterobacter cloacae and Hafnia alvei.
  • the abundance of a DNA se quence coding for LDC or a gene product of thereof is measured, wherein the DNA sequence codes for LdcC protein;
  • the abundance of a DNA sequence coding for LDC or a gene product of thereof is measured, wherein the DNA sequence codes for LdcC protein and/or CadA protein.
  • the test sample may be serum, plasma, whole blood, breast duct fluid, breast tumor tissue or feces.
  • the sample in which the abundance of bacteria is to be measured is preferably feces.
  • the samples to be compared are corresponding samples, e.g. when the abundance of a bacterium species is measured in a feces sample, the reference value is derived from feces.
  • the reference value is a value calculated from samples of individuals not having breast cancer, preferably early stage breast cancer, more preferably stage 0 breast cancer.
  • the reference value is calculated from samples of healthy individuals.
  • the bacterium species capable of producing cadaverine under physiological conditions in the human body is capable of said production in the human gastrointestinal tract.
  • the invention also provides cadaverine for use in the treatment of breast cancer in a patient.
  • a method for treating breast cancer in a patient, comprising administering an effective dose of cadaverine to the patient, is also provided.
  • the treatment decreases the number of metastases in said patient.
  • said treatment decreases the total mass of the primary tumor(s) and/or the total mass of the metastases.
  • said treatment decreases the infiltration rate of the primary tumor(s) into surrounding tissues. More preferably, infiltration of the primary tumor(s) into surrounding tissues (e.g. blood vessel or lymphatic vessels) is prevented.
  • surrounding tissues e.g. blood vessel or lymphatic vessels
  • said treatment reverses endothelial-mesenchymal transition in the breast can cer cells.
  • endothelial-mesenchymal transition is indicated and measured by the de creased expression of any one of the following genes in primary tumor tissue or metastasis tissue: MMP2, MMP3, Tgfb3, FgFbpl, Erbb3, Erl, Notchl, IgFbp4, Sppl, Krtl4, DSC2 and combinations thereof.
  • MMP3, Erl the expression of any one of the following genes in primary tumor tissue or metastasis tissue is decreased: MMP3, Erl.
  • said patient is a human, more preferably a woman.
  • cadaverine is administered in a dose providing in the patient a serum concen tration corresponding to the reference physiological serum concentration of cadaverine.
  • cadaverine is administered in a dose that provides about 50 nM/1 to 500 mM/l serum concentration in the patient. More preferably, cadaverine is administered in a dose that provides about 100 to 800 nM/1 serum concentration in the patient.
  • cadaverine is administered in a dose of about 50 nmol/kg to 500 mM/kg, preferably about 100 to 800 nM/kg or in a dose of 0.1 - 1000 mg daily.
  • cadaverine is used to treat early stage breast cancer, in particular stage 0 breast cancer.
  • cadaverine is used as an adjuvant therapy, together with a further anti -cancer treatment.
  • Designed primers, cadaverine and putrescine were from Sigma-Aldrich (St. Louis, MI, USA). Antibodies were from Cell Signaling Technology (Beverly, MA, USA), Abeam (Cambridge, UK) or from Thermo Fisher Scientific (Rockford, USA) unless otherwise stated.
  • 4T1 murine breast cancer cells were maintained in RPMI-1640 (Sigma-Aldrich, R5886) medium containing 10 % FBS, 1 % penicillin/streptomycin, 2 mM L-glutamine and 1 % pyruvate at 37 °C with 5 % C02.
  • MDA-MB-231 and SK-BR-3 human breast cancer cells were maintained in DMEM (Sigma- Aldrich, 1000 mg/1 glucose, D5546) containing 10 % FBS, 1 % penicillin/streptomycin, 2 mM L-glutamine and 10 mM HEPES at 37 °C with 5 % C02.
  • ZR-75-1 human breast cancer cells were maintained in RPMI-1640 (Sigma- Aldrich, R5886) medium con taining 10 % FBS, 1 % penicillin/streptomycin, 2 mM L-glutamine at 37 °C with 5 % C0 2 .
  • MCF-7 human breast cancer cells were maintained in MEM (Sigma-Aldrich, M8042) medium containing 10 % FBS, 1 % penicillin/streptomycin, 2 mM L-glutamine and 10 mM HEPES at 37 °C with 5 % C0 2 .
  • Human primary fibroblast cells were maintained in DMEM (Sigma-Aldrich, 1000 mg/1 glucose, D5546) containing 20 % FBS, 1 % penicillin/streptomycin, 2 mM L-glutamine and 10 mM HEPES at 37 °C with 5 % C0 2 .
  • Cells were seeded in 96-well plates (4T1- 1500 cells/well; MDA-MB-231 and ZR-75-1 - 3000 cells/well; SK-BR-3, MCF-7 and human fibroblast - 5000 cells/well) and were let to attach overnight. Cells were treated with different concentration of cadaverine (Sigma Aldrich, C8561) for 48 hours. After 2 days cells were fixed by the addition of 50 % trichloroacetic acid (TCA, final concentration: 10 %) and the plate was incubated for 1 hour at 4 °C. The plate was then washed 5 times with water and was stained with 0.4 % (w/v) sulphorhodamine B solution in 1 % acetic acid. Unbound dye was removed by washing 5 times with 1 % acetic acid. Bound stain was solubilized with 10 mM Tris base and the absorbance was measured at 540 nm.
  • Cells were seeded in 6-well plates (4T1- 750 cells/well; MDA-MB-231, SKBR-3, ZR-75-1 and MCF-7- 1000 cells/well) in complete medium and were treated with the indicated concentrations of cadaverine for 4 days. At the end of the treatment plates were washed in PBS. Colonies were fixed in 4 % PFA for 30 minutes, dried and stained with the solution of May-Griinwald-Giemsa for 30 minutes. Plates were washed with water and the colonies, containing at least 50 cells, were counted using Image J software.
  • PI uptake cells were seeded in 6-well plates (MDA-MB-231, ZR-75-1 and MCF-7 - 100,000 cells/well; SKBR-3 and human fibroblast - 200,000 cells/well). After 2 days of cadaverine treatment cells were stained with 100 pg/rnl propidium iodide for 30 min at 37 °C. Supernatant was collected in FACS tubes, cells were washed with PBS and collected in the same FACS tubes (trypsin: PBS 1:1) then samples were analyzed by flow cytometry (FACSCalibur, BD Biosciences).
  • ECIS Electric Cell-substrate Impedance Sensing
  • ECIS Electro cell-substrate impedance sensing model ZQ, Applied BioPhysics Inc. (Troy, NY, USA) was used to monitor transcellular electric resistance of control and cadaverine treated cells for 20 hours before the treatment, and total impedance values were measured for additional 48 hours upon the indicated cadaverine treatment. Multifrequency measurements were taken at 62.5, 125, 250, 500, 1000, 2000, 4000, 8000, 16000, 32000, 64000 Hz. The reference well was set to a no-cell control with complete medium.
  • 4T1 cells were grown on coverslips, and treated with the indicated concentration of cadaverine for 48 hours.
  • 5mM NF449 Bio-Techne R&D Systems Kft, 627034-85-9
  • G-protein in hibitor was also added to cadaverine-treated cells.
  • Cells were washed with PBS, fixed with 4% PFA for 15 minutes and permeabilized using 1 % Triton X-100 for 5 minutes. After washing twice with PBS, cells were blocked with 1 % BSA for one hour at room temperature.
  • RNA from cells were prepared using TRIzol reagent (Invitrogen, TR118). 2 pg RNA was reverse transcripted using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA, USA, 4368813) according to the manufacturer’s instructions. qPCRBIO SyGreen Lo-ROX Supermix (PCR
  • EMT genes differentially regulated upon cadaverine treatment are listed in Table4. Table 4. List of EMT genes differentially regulated upon cadaverine treatment
  • DH5a Escherichia coli were seeded in liquid LB medium. Cells were incubated at 37°C overnight with gen- tie shaking. E. coli cells were then collected with centrifugation and proteins were isolated using RIPA buffer
  • RIPA buffer 50 mM Tris, 150 mM NaCl, 0.1 % SDS, 1 % TritonX 100, 0.5 % sodium deoxycolate, 1 mM EDTA, 1 mM Na 3 V0 4 , 1 mM NaF, 1 mM PMSF, protease inhibitor coctail
  • Samples were sonicated (Qsonica Q125 Sonicator, Newtown, Connecticut) 3 times for 30 seconds with 50% amplitude.
  • Protein extracts were separated on 8% SDS polyacrylamide gels and transferred onto nitrocellulose mem branes by electroblotting. Then membranes were blocked with 5 % BSA, and incubated with anti-Fysine decar boxylase primary antibody (1: 100, Abeam) for overnight at 4 °C. The membranes were washed with IX TBS- TWEEN and incubated with IgG HRP conjugated secondary antibody (1:2000, Cell Signaling Technology).
  • 4T1 cells were plated in 6-well plates (150,000 cells/well) and were grown overnight. The plates were man ually scratched with sterile 200 m ⁇ pipette tip, followed by washing the cells with complete growth medium. Then cells were treated with 0.1 mM cadaverine in a 37°C thermostat and were monitored every hour for 2 days using JuLi Br Live cell movie analyzer (NanoEnTek Inc., Seoul, Korea).
  • Matrigel invasion assay was carried out on 4T1 cells using Coming BioCoat Matrigel Invasion Chamber (354480). 4T1 cells were seeded in the chambers (50,000 cells/well) in semm free medium, and were grown overnight. Cells were then treated with different concentration of cadaverine (0.1 mM, 0.3 mM, 0.8 mM). The lower chamber contained full 4T1 medium with 100 ng/ml SDFl-alpha (Sigma, SRP4388) as chemoattractant. After 48 hours of cadaverine treatment cells were prepared according to the manufacturer’s instructions and stained with Hematoxylin-Eosin (VWR, 340374T and 341972Q) dye. Cells were then pictured with Opera Phenix High Content Screening System and pictures were analysed using Harmony 4.6 Software. Invasion in dex was calculated from the percentage of invading cells through matrigel membrane and control membrane.
  • 4T1 cells were seeded in 96-well Seahorse assay plates (1500 cells/well) and treated with vehicle and cadaverine for 48 hours. Cells were monitored using XF96 oxymeter (Seahorse Biosciences, North Billerica, MA, USA) to measure the changes in oxygen consumption rate (OCR) and in pH (ECAR) after cadaverine treatment similarly to [27]. Data were normalized to protein content.
  • Lipid peroxidation was measured by detemining the production rate of thiobarbituric acid reactive substrate (TBARS). 4T1 cells were seeded in T75 flasks and allowed to adhere overnight. Cells were exposed to cadaverine for 48 hours, then collected by centrifugation. 8.1 % SDS, 20 % acetic acid, 0.8 % thiobarbituric acid (TBA) and distilled water was added to the pellet and was heated at 96°C for 1 hour in thermoblock. Sam ples were cooled on ice and centrifugated, the absorbance of the supernatant was measured at 540 nm.
  • TBARS thiobarbituric acid reactive substrate
  • the level of the enzyme aldehyde dehydrogenase (ALDH) was determined on 4T1 cells using cadaverine treatment. Cells were seeded on 6 well plates (50000 cells/well) and treated with different concentration of cadaverine (0.1 mM, 0.3 mM, 0.8 mM) for 2 days. Cells were then collected and prepared according to the manu facturer’s instructions. We used SKBR-3 cell line for positive control. Changes in the level of ALDH was measured using flow cytometry and the results were analysed with flowing software 2.5.1.
  • mice Female mice (4 months of age, 20-25g). Animals were bred in the“specific pathogen free” zone of the Animal Facility at the University of Debrecen, and kept in the“minimal disease” zone during the experiments. 4 mice were housed in one cage (standard block shape 365 c 207 c 140 mm, surface 530 cm 2 ; 1284 L Eurostandard Type II. L from Techniplast). Dark/light cycle was 12 h, and temperature was 22 ⁇ 1°C. Mice had ad libitum access to food and water (sterilized tap water). A total of 32 female mice were used in the study, 16 randomly selected control and 16 cadaverine fed mice. The study was performed in two runs at two different occasions, each run comprising of 8 vehicle -treated and 8 cadaverine-treated mice.
  • Tumor was formed in mice by the grafting of 4T1 cells.
  • 4T1 cells were suspended (2xl0 6 /ml) in ice cold PBS-matrigel (1: 1, Sigma- Aldrich) at 1: 1 ratio.
  • 16 female BALB/c mice received 50 pL injections to the ingui nal fat pads below the lower abdominal nipples on both sides (10 5 cells/injection site).
  • Cadaverine stock was prepared in sterilized tap water at lOOx concentration (15 mM) and the stock was stored at -20°C.
  • Cadaverine stock was diluted each day to a working concentration of 150 mM in sterile tap water before the treatment.
  • Animals received a daily oral dose of 100 m1/30 g body weight from cadaverine solution (8 mice) or vehicle (sterilized tap water, 8 mice).
  • researchers administering cadaverine and vehicle solutions were blinded. Treatment was carried out every day during the morning hours between 9am and 11am. Mice were sacrificed on day 14 post grafting.
  • “Low infiltration” class means that primer tumor remained in the mammary fat pads without any attachment to muscle tissues. In case the tumor mass attached to the muscle tissue but did not penetrate the abdominal wall, it classi fied as a“medium infiltration” tumor. If the tumor grew into the muscle tissue and totally penetrated the ab dominal wall, it was scored as a“high infiltration” tumor.
  • Another cohort was used to assess LdcC protein in the feces of healthy volunteers and breast cancer patients.
  • the collection and biobanking of feces was authorized by the Hungarian national authority (ETT).
  • Patients and healthy volunteers meeting the following criteria were excluded from the study according to the corresponding national guideline for fecal transplantation [34]: 1) has previous history of breast cancer or had been operated due to neoplasia, 2) has a disease of unknown origin, 3) has chronic contagious disease, 4) had contagious diar rhea 6 months prior to enrollment, 5) taken antibiotics in the 6 months prior to enrollment, 6) had chemothera py, biological therapy or immunosuppressive therapy 6 months prior to enrollment, 7) used intravenous drugs 12 months prior to enrollment, 8) had piercing, tattooing, acupuncture or other endangering behavior or action 12 months prior to enrollment, 9) exposition to an allergen to which the enrolled individual had been sensitized to, 10) undervent colonoscopy 12 months prior to
  • the kmplot.com database was used to study the link between gene expression levels and breast cancer sur vival in humans.
  • the association of known mutations with breast cancer was retrieved from www.intogen.org/.
  • the sequence of the CadA and LdcC ORFs were retrieved from the KEGG (www.genome.jp/kegg/) database.
  • cacccagcgc atattcaaag aag 23 ⁇ 210> 5
  • NCBI_GEO_Profiles LDC expression in epithelium and stroma of normal breast and invasive breast cancer.
  • NCBI_GEO_Profiles Normal epithelium vs. breast cancer epithelium in patients.
  • CSCs cancer stem cells
  • the Escherichia coli ldcC gene encodes another lysinedecarboxylase, probably a constitutive enzyme. Genes Genet. Syst. (1997) 72, p. 167-172.

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Abstract

L'invention concerne le domaine du diagnostic et du traitement du cancer du sein à un stade précoce. Plus particulièrement, l'invention concerne une méthode permettant de déterminer si un sujet présente un cancer du sein à un stade précoce en mesurant l'abondance d'une espèce de bactérie comprenant une séquence d'ADN codant pour une lysine décarboxylase. L'invention concerne également une méthode d'atténuation de l'initiation et/ou de la promotion et/ou de la progression du cancer du sein chez un sujet.
EP19773488.2A 2018-07-31 2019-07-31 Traitement et diagnostic du cancer du sein Pending EP3830300A1 (fr)

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