CANCER

Abstract

The invention relates to biomarkers, and to novel biological markers for diagnosing cancer. In particular, the invention relates to the use of these compounds as diagnostic and prognostic markers in assays for detecting cancer, such as oesophagogastric cancer, and corresponding methods of detection. The invention also relates to methods of determining the efficacy of treating these diseases with a therapeutic agent. The assays are qualitative and/or quantitative, and are adaptable to large-scale screening and clinical trials.

Claims

1. A method for diagnosing a subject suffering from cancer, or a pre-disposition thereto, or for providing a prognosis of the subject's condition, the method comprising analysing the level of at least one signature compound in a bodily sample from a test subject and comparing this level with a reference level, wherein the reference level is the level of the at least one signature compound in an individual, or the average level for a group of individuals, wherein the individual or group of individuals do not suffer from cancer, wherein (i) an increase in the level of at least one signature compound selected from the group consisting of methyl 2,3,5,6-tetra-O-methyl-α-D-galactofuranoside; 1-tetradecanol; N-butyl-benzenesulfonamide; hexadecanoic acid; tetradec-5-yl ester 3,5,5-trimethyl-hexanoic acid; tetradecyl ester undec-10-ynoic acid; 1-dotriacontanol; 1-chloro-tetradecane; 4-methyloctan-1-ol; carbon monoxide; nickel; 2-ethyl-cyclohexylamine; 3-ethyl-1-octene; ethyl lactate; tetramethyl succinimide; 6-methyl-2-heptanone; (E)-ethen-2-d-ol; 4-anilino-4-keto-2-phenyl-butyric acid; diisobutyl (oxybis(ethane-2,1-diyl)) dicarbonate; nickel tetracarbonyl; (E)-2-ethylene-4-methylene-5-hexenal; 3-methyl-1-butyne; (R)-5-methyl-2-(1-methylethylidene)-cyclohexanone; α-propyl-benzeneethanol; 4-methyl-1-pentene; 1,3,3-trimethyl-2-oxabicyclo[2.2.2]oct-5-ene; 2,2′-(ethene-1,2-diylbis(sulfanediyl))diethanol; 3-methyl-thiophene; butanal; tert-butyl alcohol; and 2-methoxysuccinonitrile, or an analogue or derivative thereof, in the bodily sample from the test subject, compared to the reference, and/or (ii) a decrease in the level of at least one signature compound selected from the group consisting of 4-hydroximino-2,2,6,6-tetramethyl-1-piperidinyl ester 4-amino-benzoic acid; 4,4-dimethyl-octane; benzyl 3-deuterio-α-diazopropionate; and 1-methylethyl ester formic acid, or an analogue or derivative thereof, in the bodily sample from the test subject, compared to the reference, suggests that the subject is suffering from cancer, or has a pre-disposition thereto, or provides a negative prognosis of the subject's condition.

2. A method for determining the efficacy of a treatment a subject suffering from cancer, the method comprising analysing the level of at least one signature compound in a bodily sample from a test subject and comparing this level with a reference level, wherein the reference level is the level of the at least one signature compound in a sample taken from the subject previously, wherein (i) a decrease in the level of at least one signature compound selected from the group consisting of methyl 2,3,5,6-tetra-O-methyl-α-D-galactofuranoside; 1-tetradecanol; N-butyl-benzenesulfonamide; hexadecanoic acid; tetradec-5-yl ester 3,5,5-trimethyl-hexanoic acid; tetradecyl ester undec-10-ynoic acid; 1-dotriacontanol; 1-chloro-tetradecane; 4-methyloctan-1-ol; carbon monoxide; nickel; 2-ethyl-cyclohexylamine; 3-ethyl-1-octene; ethyl lactate; tetramethyl succinimide; 6-methyl-2-heptanone; (E)-ethen-2-d-ol; 4-anilino-4-keto-2-phenyl-butyric acid; diisobutyl (oxybis(ethane-2,1-diyl)) dicarbonate; nickel tetracarbonyl; (E)-2-ethylene-4-methylene-5-hexenal; 3-methyl-1-butyne; (R)-5-methyl-2-(1-methylethylidene)-cyclohexanone; α-propyl-benzeneethanol; 4-methyl-1-pentene; 1,3,3-trimethyl-2-oxabicyclo[2.2.2]oct-5-ene; 2,2′-(ethene-1,2-diylbis(sulfanediyl))diethanol; 3-methyl-thiophene; butanal; tert-butyl alcohol; and 2-methoxysuccinonitrile, or an analogue or derivative thereof, in the bodily sample from the test subject, compared to the reference, or (ii) an increase in the level of at least one signature compound selected from the group consisting of 4-hydroximino-2,2,6,6-tetramethyl-1-piperidinyl ester 4-amino-benzoic acid; 4,4-dimethyl-octane; benzyl 3-deuterio-α-diazopropionate; and 1-methylethyl ester formic acid, or an analogue or derivative thereof, in the bodily sample from the test subject, compared to the reference, suggests that the treatment is effective, or wherein (i) an increase in the level of at least one signature compound selected from the group consisting of methyl 2,3,5,6-tetra-O-methyl-α-D-galactofuranoside; 1-tetradecanol; N-butyl-benzenesulfonamide; hexadecanoic acid; tetradec-5-yl ester 3,5,5-trimethyl-hexanoic acid; tetradecyl ester undec-10-ynoic acid; 1-dotriacontanol; 1-chloro-tetradecane; 4-methyl octan-1-ol; carbon monoxide; nickel; 2-ethyl-cyclohexylamine; 3-ethyl-1-octene; ethyl lactate; tetramethyl succinimide; 6-methyl-2-heptanone; (E)-ethen-2-d-ol; 4-anilino-4-keto-2-phenyl-butyric acid; diisobutyl (oxybis(ethane-2,1-diyl)) dicarbonate; nickel tetracarbonyl; (E)-2-ethylene-4-methylene-5-hexenal; 3-methyl-1-butyne; (R)-5-methyl-2-(1-methylethylidene)-cyclohexanone; α-propyl-benzeneethanol; 4-methyl-1-pentene; 1,3,3-trimethyl-2-oxabicyclo[2.2.2]oct-5-ene; 2,2′-(ethene-1,2-diylbis(sulfanediyl))diethanol; 3-methyl-thiophene; butanal; tert-butyl alcohol; and 2-methoxysuccinonitrile, or an analogue or derivative thereof, in the bodily sample from the test subject, compared to the reference, or (ii) a decrease in the level of at least one signature compound selected from the group consisting of 4-hydroximino-2,2,6,6-tetramethyl-1-piperidinyl ester 4-amino-benzoic acid; 4,4-dimethyl-octane; benzyl 3-deuterio-α-diazopropionate; and 1-methylethyl ester formic acid, or an analogue or derivative thereof, in the bodily sample from the test subject, compared to the reference, suggests that the is ineffective.

3. The method of claim 2, wherein the subject is being treated with a therapeutic agent and/or radiotherapy, is on a specialised diet and and/or has been treated with surgery.

4. A method of treating an individual suffering from cancer, said method comprising the steps of: a) determining the level of at least one signature compound in a bodily sample from a test subject and comparing this level with a reference level, wherein the reference level is the at least one signature compound in an individual, or the average level for a group of individuals, wherein the individual or group of individuals do not suffer from cancer, wherein (i) an increase in at least one signature compound selected from the group consisting of methyl 2,3,5,6-tetra-O-methyl-α-D-galactofuranoside; 1-tetradecanol; N-butyl-benzenesulfonamide; hexadecanoic acid; tetradec-5-yl ester 3,5,5-trimethyl-hexanoic acid; tetradecyl ester undec-10-ynoic acid; 1-dotriacontanol; 1-chloro-tetradecane; 4-methyloctan-1-ol; carbon monoxide; nickel; 2-ethyl-cyclohexylamine; 3-ethyl-1-octene; ethyl lactate; tetramethyl succinimide; 6-methyl-2-heptanone; (E)-ethen-2-d-ol; 4-anilino-4-keto-2-phenyl-butyric acid; diisobutyl (oxybis(ethane-2,1-diyl)) dicarbonate; nickel tetracarbonyl; (E)-2-ethylene-4-methylene-5-hexenal; 3-methyl-1-butyne; (R)-5-methyl-2-(1-methylethylidene)-cyclohexanone; α-propyl-benzeneethanol; 4-methyl-1-pentene; 1,3,3-trimethyl-2-oxabicyclo[2.2.2]oct-5-ene; 2,2′-(ethene-1,2-diylbis(sulfanediyl))diethanol; 3-methyl-thiophene; butanal; tert-butyl alcohol; and 2-methoxysuccinonitrile, compared to the reference, or an analogue or derivative thereof, in the bodily sample from the test subject, or (ii) a decrease in the level of at least one signature compound selected from the group consisting of 4-hydroximino-2,2,6,6-tetramethyl-1-piperidinyl ester 4-amino-benzoic acid; 4,4-dimethyl-octane; benzyl 3-deuterio-α-diazopropionate; and 1-methylethyl ester formic acid, or an analogue or derivative thereof, in the bodily sample from the test subject, compared to the reference, suggests that the subject is suffering from cancer, or has a pre-disposition thereto, or has a negative prognosis; and b) treating the test subject, wherein the treatment reduces or delays progression of cancer and/or treats cancer.

5. The method of claim 4, wherein treating the subject comprises administering, or having administered to the subject, a therapeutic agent and/or radiotherapy, putting the subject on a specialised diet and and/or treating the subject with surgery.

6. A method according to claim 4, wherein the cancer is an oesophagogastric cancer.

7. A method according to claim 4, wherein the at least one signature compound is selected from the group consisting of methyl 2,3,5,6-tetra-O-methyl-α-D-galactofuranoside; 4-hydroximino-2,2,6,6-tetramethyl-1-piperidinyl ester 4-amino-benzoic acid; 1-tetradecanol; N-butyl-benzenesulfonamide; hexadecanoic acid; tetradec-5-yl ester 3,5,5-trimethyl-hexanoic acid; 4,4-dimethyl-octane; tetradecyl ester undec-10-ynoic acid; 1-dotriacontanol; benzyl 3-deuterio-α-diazopropionate; 1-methylethyl ester formic acid; 1-chloro-tetradecane; 4-methyloctan-1-ol; carbon monoxide; nickel; and 2-ethyl-cyclohexylamine, or an analogue or derivative thereof.

8. A method according to claim 7, wherein the at least one signature compound is selected from the group consisting of methyl 2,3,5,6-tetra-O-methyl-α-D-galactofuranoside; 4-hydroximino-2,2,6,6-tetramethyl-1-piperidinyl ester 4-amino-benzoic acid; 1-tetradecanol; N-butyl-benzenesulfonamide; hexadecanoic acid; tetradec-5-yl ester 3,5,5-trimethyl-hexanoic acid; 4,4-dimethyl-octane; tetradecyl ester undec-10-ynoic acid; 1-dotriacontanol; and benzyl 3-deuterio-α-diazopropionate, or an analogue or derivative thereof.

9. A method according to claim 8, wherein the at least one signature compound is selected from the group consisting of methyl 2,3,5,6-tetra-O-methyl-α-D-galactofuranoside; 4-hydroximino-2,2,6,6-tetramethyl-1-piperidinyl ester 4-amino-benzoic acid; 1-tetradecanol; N-butyl-benzenesulfonamide; and hexadecanoic acid, or an analogue or derivative thereof.

10. A method according to claim 4, wherein the at least one signature compound is selected from the group consisting of 3-ethyl-1-octene; ethyl lactate; tetramethyl succinimide; 6-methyl-2-heptanone; (E)-ethen-2-d-ol; 4-anilino-4-keto-2-phenyl-butyric acid; diisobutyl (oxybis(ethane-2,1-diyl)) dicarbonate; nickel tetracarbonyl; (E)-2-ethylene-4-methylene-5-hexenal; 3-methyl-1-butyne; (R)-5-methyl-2-(1-methylethylidene)-cyclohexanone; α-propyl-benzeneethanol; 4-methyl-1-pentene; 1,3,3-trimethyl oxabicyclo[2.2.2]oct-5-ene; 2,2′-(ethene-1,2-diylbis(sulfanediyl))diethanol; 3-methyl-thiophene; butanal; tert-butyl alcohol; and 2-methoxysuccinonitrile, or an analogue or derivative thereof.

11. A method according to claim 10, wherein the at least one signature compound is selected from the group consisting of 3-ethyl-1-octene; ethyl lactate; tetramethyl succinimide; 6-methyl-2-heptanone; (E)-ethen-2-d-ol; 4-anilino-4-keto-2-phenyl-butyric acid; diisobutyl (oxybis(ethane-2,1-diyl)) dicarbonate; nickel tetracarbonyl; (E)-2-ethylene-4-methylene-5-hexenal; 3-methyl-1-butyne; (R)-5-methyl-2-(1-methylethylidene)-cyclohexanone; α-propyl-benzeneethanol; 4-methyl-1-pentene; and 1,3,3-trimethyl-2-oxabicyclo[2.2.2]oct-5-ene, or an analogue or derivative thereof.

12. A method according to claim 11, wherein the at least one signature compound is selected from the group consisting of 3-ethyl-1-octene; ethyl lactate; tetramethyl succinimide; 6-methyl-2-heptanone; (E)-ethen-2-d-ol; 4-anilino-4-keto-2-phenyl-butyric acid; diisobutyl (oxybis(ethane-2,1-diyl)) dicarbonate; and nickel tetracarbonyl, or an analogue or derivative thereof.

13. A method according to claim 12, wherein the at least one signature compound is selected from the group consisting of 3-ethyl-1-octene; and ethyl lactate, or an analogue or derivative thereof.

14. A method according to claim 4, wherein the at least one signature compound is detected from a gas or vapour.

15. A method according to claim 4, wherein the bodily sample is a breath sample from the test subject.

16. A method according to claim 4, wherein the at least one signature compound is detected using gas chromatography, mass spectrometry, GCMS and/or TOF.

17. (canceled)

Description

[0042] For a better understanding of the invention, and to show how embodiments of the same may be carried into effect, reference will now be made, by way of example, to the accompanying drawings, in which:

[0043] FIG. 1 shows Receiver Operating Characteristic (ROC) curves constructed using VOCs found to be significantly altered in breath from cancer patients in study 1 (blue) and study 2 (red).

EXAMPLE 1

[0044] The inventors conducted two studies (Study 1: n=631 samples and Study 2: n=219 samples, respectively) on breath analysis associated with oesophageal and gastric cancers.

[0045] Methods

[0046] Participant Recruitment

[0047] Ethical approval was obtained (REC 14/LO/1136) and all participants provided written informed consent. Participants for this study were recruited from Imperial College Healthcare NHS Trust. Participants were recruited into two possible groups—either those with known oesophago-gastric cancer (OGC) or a non-cancer control group. The participants who entered into the non-cancer control group were recruited from the endoscopy suite at Imperial College Healthcare NHS Trust and were undergoing an upper gastrointestinal endoscopy on the day of providing an exhaled breath sample (and were found not to have oesophageal or gastric cancer). If patients were also undergoing a colonoscopy at the same time (and had received bowel preparation medications) they were not eligible to participate in the study. The participants who entered into the OGC group were patients who had a biopsy proven invasive gastric or oesophageal adenocarcinoma. These patients were recruited from three possible locations—either on the day of undergoing a diagnostic upper gastrointestinal endoscopy, on the day of having a staging laparoscopy and upper gastrointestinal endoscopy under general anaesthetic (part of the routine staging investigations for OGC), or on the day of review in the outpatient clinic. Patients who had already received surgical or oncological (chemotherapy or radiotherapy) treatment for the oesophageal or gastric cancer were not eligible to participate in the study. Participants were between the ages of 18 and 90, and were excluded if they were known to have liver disease (including oesophageal varices and known portal hypertension), an acute infection, another type of cancer presently or within the past 5 years, or known inflammatory conditions of the small or large bowel.

[0048] Breath Sample Collection

[0049] Exhaled breath samples were collected using a standardised breath-sampling device, ‘Respiration Collector for In Vitro Analysis’ (ReCIVA™) (Owlstone Medical, Cambridge, UK) in combination with a dedicated clean air supply ‘Clean Air Supply Pump for ReCIVA’ (CASPER) (Owlstone Medical, Cambridge, UK). All participants were fasted for a minimum of four hours and rested for 20 minutes prior to exhaled breath sample collection.

[0050] Two studies were performed. For study one, four sampling thermal desorption (TD) tubes (Tenax/Carbograph-5TD, Markes International Ltd, Llantrisant, UK) were used per participant. For study two, one sampling TD tube (Tenax/Carbograph-5TD, Markes International Ltd, Llantrisant, UK) was used per participant. Prior to sample collection all TD tubes were conditioned for 40 minutes at 330° C. using a TC-20 tube conditioner (Markes International Ltd, Llantrisant, UK). The TD tubes were stored in an airtight polypropylene container at room temperature and used for sample collection within 24 hours of conditioning.

[0051] Exhaled breath collection was performed using a standardised protocol with the participant performing normal tidal respiration whilst seated. For study one exhaled breath sample collection with the ReCIVA device was performed using a sample volume 250 ml per TD tube, and a sample flow rate of 400 ml/min. For study two exhaled breath sample collection with the ReCIVA device was performed using a sample volume 500 ml per TD tube, and a sample flow rate of 200 ml/min. Prior to analysis TD tubes were stored in an airtight polypropylene container at room temperature and all TD tubes were analysed within 12 hours of breath sample collection. TD tubes that had been conditioned in preparation for exhaled breath sample collection and subsequently not used (due to a lower than expected number of participants being recruited were) analysed concurrently with the exhaled breath samples as ‘blank’ TD tubes.

[0052] Analysis with TD-GC-MS

[0053] The exhaled breath and blank TD tubes samples were analysed using TD-GC-MS. The TD tubes were desorbed using a Markes TD-100 thermal desorption unit (Markes International Ltd, Llantrisant, UK) using a two stage desorption programme, applying a constant flow of helium at 50 ml/min. In the primary desorption stage, TD tubes were dry-purged for 3 min and heated at 280° C. for 10 min. In the secondary desorption stage, the cold trap (U-T12ME-2S, Markes International Ltd, Llantrisant, UK) was rapidly (99° C./min) heated to from 10° C. to 290° C. VOCs were transferred from the TD unit to the GC by means of a capillary line heated at 140° C. GC-MS analysis was performed using an Agilent 7890 B GC with 5977A MSD (Agilent Technologies Ltd, Santa Clara, USA) equipped with a ZB-642 capillary column (60 m×0.25 mm ID×1.40 um df; Phenomenex Inc, Torrance, USA) with helium used as the carrier gas (1.0 ml/min flow rate). The GC column temperature programme was set as follows: 4 min at 40° C., ramp to 100° C. at 5° C./min with a 1 min hold, ramp to 110° C. at 5° C./min with a 1 min hold, ramp to 200° C. at 5° C./min with a 1 min hold and finally ramp to 240° C. at 10° C./min with a 4 min hold. The MS transfer line temperature was 240° C. and EI source conditions were 70 eV at 230° C. Mass acquisition was carried out in the range 20-250 m/z with a rate of approximately 6 scans/s-1.

[0054] Results

[0055] In breath, biological signatures are usually obscured by intra- and inter-subject variability, experimental conditions, e.g. ambient air quality, etc. Most of the time biologically relevant compounds are present in very low abundances. To mitigate this, large number of samples were collected, as outlined above. It was possible to predict OGC with high accuracy in both studies and identify the corresponding metabolomic “fingerprint”. The results are shown in tables 1 and 2 below.

TABLE-US-00001 TABLE 1 Biomarkers identified that were found to be significantly altered in breath from cancer patients and corresponding p values in study 1 Logarithm fold p-values VOC changes 0.00019 methyl 2,3,5,6-tetra-O-methyl-α-D- −0.56777 galactofuranoside 0.00019 4-hydroximino-2,2,6,6-tetramethyl-1- 0.60436 piperidinyl ester 4-amino-benzoic acid 0.00018 1-tetradecanol −1.2674 0.00016 N-butyl-benzenesulfonamide −0.71766 0.00015 hexadecanoic acid −0.87638 8.95E−05 tetradec-5-yl ester 3,5,5-trimethyl- −0.91395 hexanoic acid 4.81E−05 4,4-dimethyl-octane 0.31272 4.45E−05 tetradecyl ester undec-10-ynoic acid −0.5371 4.14E−05 1-dotriacontanol −1.3416 2.86E−05 Benzyl 3-deuterio-α-diazopropionate 0.8055 9.40E−06 1-methylethyl ester formic acid 1.0375 5.31E−06 1-chloro-tetradecane −0.85828 5.10E−06 4-methyloctan-1-ol −0.4607 4.27E−06 carbon monoxide; nickel −0.5693 5.66E−07 2-ethyl-cyclohexylamine −0.81605

TABLE-US-00002 TABLE 2 Biomarkers identified that were found to be significantly altered in breath from cancer patients and corresponding p values in study 2 Logarithm fold p-values VOC changes 3.41E−08 3-ethyl-1-octene −1.3811 3.31E−08 ethyl lactate −1.6347 2.32E−08 tetramethyl succinimide −0.75236 9.05E−09 6-methyl-2-heptanone −2.8561 8.62E−09 (E)-ethen-2-d-ol −2.5854 5.58E−09 4-anilino-4-keto-2-phenyl-butyric acid −1.889 1.94E−09 Diisobutyl (oxybis(ethane-2,1- −1.9607 diyl))dicarbonate 1.50E−09 nickel tetracarbonyl −1.5801 9.98E−10 (E)-2-ethylene-4-methylene-5-hexenal −1.5124 7.39E−10 3-methyl-1-butyne −1.7809 2.84E−10 (R)-5-methyl-2-(1-methylethylidene)- −1.8082 cyclohexanone 1.27E−10 α-propyl-benzeneethanol −3.4456 1.06E−10 4-methyl-1-pentene −3.1494 4.87E−11 1,3,3-trimethyl-2-oxabicyclo[2.2.2]oct-5-ene −1.68 2.52E−11 2,2′-(ethene-1,2- −2.0075 diylbis(sulfanediyl))diethanol 2.24E−11 3-methyl-thiophene −2.4387 3.50E−12 butanal −3.1176 1.57E−12 Tert-butyl alcohol −4.5814 5.93E−14 2-Methoxysuccinonitrile −5.4045

[0056] A negative value for the log fold change indicates that the VOC increases in a sample from a patient with cancer. Conversely, a positive value for the log fold change indicates that the VOC decreases in a sample from a patient with cancer.

[0057] ROC plots (see FIG. 1) were constructed using the VOCs for studies 1 and 2, respectively. The ROC plot for study 1 biomarkers produced an AUC of 0.902 for distinguishing Cancer vs. Non-Cancer and for study 2 biomarkers the AUC was 0.740.