WO2022013880A1

WO2022013880A1 - Blood based biomarkers for early diagnosis and follow up of breast cancer

Info

Publication number: WO2022013880A1
Application number: PCT/IN2020/050942
Authority: WO
Inventors: Thangarajan Rajkumar; Amritha S; Gopisetty Gopal; Sridevi V; Sabitha K
Original assignee: Cancer Institute {Wia}
Priority date: 2020-07-14
Filing date: 2020-11-09
Publication date: 2022-01-20

Abstract

The present invention discloses an accurate and reliable method for early detection and follow-up of breast cancer in a subject, with remarkable sensitivity and specificity along with minimal false results. The present invention also discloses a multianalyte biomarker panel for accurate and reliable method of early detection and follow-up of breast cancer in a subject with remarkable sensitivity and specificity along with minimal false results. The biomarker panel encompasses characterized three methylation biomarkers of genes comprising of SOSTDC1, WIF1, DACT2

Description

TITLE: BLOOD BASED BIOMARKERS FOR EARLY DIAGNOSIS AND

FOLLOW UP OF BREAST CANCER

FIELD OF THE INVENTION:

The present invention relates to diagnosis of breast cancer. More particularly the present invention relates to a diagnostic method for early detection and follow-up of breast cancer and multianalyte biomarkers panel thereof.

BACKGROUND OF THE INVENTION:

Breast cancer is the most common malignancy among females and accounts for 11.6% of global cancer burden (Globocan 2018). Clinical breast examination along with mammography and ultrasonography are commonly used for detection of breast abnormalities. The sensitivity of these imaging modalities is moderate and results in false negatives particularly in women with dense breast tissue. So, the definitive diagnosis of breast cancer requires fine needle aspiration of breast epithelial cells or core needle biopsy which is currently the gold standard.

Blood based biomarkers offer a minimally invasive and cost-effective means for screening and diagnosis of breast cancer. Carcinoembryonic antigen (CEA), human epidermal growth factor receptor-2 (HER2), circulating cytokeratin fragments (tissue polypeptide antigen (TPA) and tissue polypeptide specific antigen (TPS) have been recommended as diagnostic markers, but they were deficient in sensitivity and specificity for early breast cancer detection (Table 1).

Table 1: The sensitivity and specificity of candidate blood-based biomarkers for breast cancer diagnosis. Overall represents a random mixed population of breast cancer patients. Patients in all categories but one had their sample taken prior to treatment.

While the pre-existing single biomarkers lacked desired reliability as diagnostic markers, further studies proved that a combination of biomarkers can provide greater predictive value of a particular status than single biomarkers alone.

US2015024960A1 provides a multiple biomarker set capable of detecting the onset breast cancer in blood. The differential levels of the 5 proteins namely, apolipoprotein Cl, apolipoprotein (a), neural cell adhesion molecule LI -like protein, carbonic anhydrase 1 and fibronectin in 80 breast cancer patients and 80 controls measured by ELISA (customized antibody for each protein) demonstrated an AUC of 0.86 with sensitivity of 75% and specificity of 80%. Additionally, the panel showed a sensitivity of 92% and specificity of 80% in 80 controls and 37 stage I breast cancer patients making it effective for detecting early stage breast cancer. US2009035801A1 discloses 12 protein biomarkers in blood serum of individuals that can be used in diagnosis, determination of disease severity, and monitoring of therapeutic response of patients with breast cancer. The method is based on the use of two-dimensional (2D) gel electrophoresis to separate the complex mixture of proteins found in blood serum, the quantitation of 12 identified protein spots, and statistical analysis, to distinguish patients with breast cancer from patients with benign breast disease or abnormalities, and from normal women.

US10436787B2 yields a panel consisting of Olfactomedin-4, neudesin and desmoplakin as blood biomarkers for breast cancer diagnosis. These markers are ideal because, the expression level of Olfactomedin-4 and Neudes in are higher in breast cancer patients throughout progression of the disease, while the expression level of Desmoplakin is lower at an early stage and higher in the case of recurrence, by comparison to healthy subject.

W02005083440 suggests a method for diagnosing ovarian cancer, breast cancer and colorectal cancer based on the simultaneous identification of multiple biomarkers, which are dysregulated in cancer patients. The biomarkers include leptin, prolactin, chymotrypsin enzymes, kallikreins, tumor markers CA125, CA15-3, CA19-9, MUC1, OVX1, CEA, M-CSF, OPN and IGF-II, prostatin, CA54-61, CA72, HMFG2, IF-interleukins 6, IF-10, FSA, M-CSF, NB70K, PFAP, TAG72 and factors TNF, TPA, UGTF, VEGF, CFDN3, NOTCH3, E2F. The final diagnostic breast cancer panel contains leptin, prolactin, OPN and IGF-I.

WO2019189990A1 relates to a diagnostic method which makes use of recombinant proteins or fragments to detect level autoantibodies of TXNL2 and CAST in blood samples of breast cancer and non-cancer population. The subject was considered positive for breast cancer if the test level of the test subject (cancer) is higher than the test level of the normal test subject. The sensitivity of TXNL2 and CAST combined was 94% and specificity 65%.

US2018284120A1 have deciphered a 49-plex tissue biomarker signature which can diagnose and differentiate three histological grades of breast cancer with high sensitivity and specificity. Apart from this, studies using multiplex immunoassays to evaluate breast cancer biomarkers in pre-diagnostic serum samples have also been performed, but they were found unsuitable as diagnostic markers because the results were inconsistent and the markers did not show association with any histological parameters.

The prior arts discussed above reveal some of the multi-marker panels devised for diagnosis of breast cancer. However, there are certain drawbacks associated with these inventions such as, lack of desired sensitivity and specificity for detecting non-malignant breast abnormalities and early stage breast cancer, cumbersome experimental procedures, low reproducibility, panels with excess number of markers, high cost, demand for trained pathologists and high-end proteomics facilities. Hence, despite the considerable research efforts being put into the discovery of a definitive single biomarker/multi-marker panel for breast cancer early diagnosis, the need exists for a diagnostic kit which is devoid of the above disadvantages.

OBJECT OF THE INVENTION:

The main object of the present invention is to develop an accurate and reliable method for early detection and follow-up of breast cancer in a subject, with remarkable sensitivity and specificity along with minimal false results.

Another object of the present invention is to formulate a multianalyte biomarker panel for accurate and reliable method of early detection and follow-up of breast cancer in a subject with remarkable sensitivity and specificity along with minimal false results.

Yet another object of the present invention is to formulate a multianalyte biomarker panel encompasses characterized three methylation biomarkers of genes comprising of WIFI, SOSTDC1, DACT2.

Yet another object of the present invention is to assess the differential methylation status of markers SOSTDC1, DACT2 and WIFI in circulating cell free DNA.

Further object of the present invention is to provide a minimally invasive and robust diagnostic test with minimal false results for accurate diagnosis and monitoring of human breast cancer. BRIEF DESCRIPTION OF DRAWINGS:

Figure 1 depicts the Methylation Specific PCR Analysis of cell free circulating DNA from blood. 1A and ID represent methylation specific PCR products of SOSTDC1 amplified in cases and controls, respectively; IB and IE represent methylation specific PCR products of WIFI amplified in cases and controls respectively; 1C and IF represent methylation specific PCR products of DACT2 amplified in cases and controls respectively. Methylated allele is denoted as M and unmethylated allele denoted as U. Invasive breast cancer samples are designated with the prefix Έ and healthy controls with ‘C\

Figure 2 depicts the Methylation Specific PCR Analysis. 2A and 2D represent methylation specific PCR products of SOSTDC1 in DCIS and benign cases respectively; 2B and 2E represent methylation specific PCR products of DACT2in DCIS and benign cases respectively; 2C and 2F represent methylation specific PCR products of WIFI in DCIS and benign cases respectively. Methylated allele is denoted as M and unmethylated allele is denoted as U. DCIS samples are designated with the prefix ‘D’ and benign samples with Έ’.

SUMMARY OF THE INVENTION:

The present invention discloses an accurate and reliable method for early detection and follow up of breast cancer in a subject, with remarkable sensitivity and specificity along with minimal false results. The method of the present invention comprises of a. collecting a peripheral blood sample from a subject b. determining methylation status of characterized gene biomarkers comprises of following steps i. isolating circulating cell free DNA (cfDNA) from the peripheral blood samples of step (a); ii. treating the cfDNA with bisulfite to detect methylation of CpG sites; iii. amplifying 3 target genes comprising of WIFI, SOSTDC1, DACT2 in bisulfite treated cfDNA samples using PCR primers for methylated and unmethylated gene sequence; iv. quantifying relative intensity of amplicons and determining ratio of complete/partial methylated and unmethylated alleles of the target genes by image analysis software to evaluate the methylation intensity c. statistical analysis of the methylation intensity of the 3 target genes from step b(iv) in which i. if the ratio of complete/partial methylated to unmethylated band intensity is equal to or above 1, a positive score of 1 is given and for ratio is below 1, a score of 0 is given; ii. if sum of the scores for the 3 genes is above 1, it indicates cancer [invasive and non-invasive breast cancer] and if the sum is 0, indicates normal subject or a subject with benign disease of breast.

The present invention also discloses a multianalyte biomarker panel for accurate and reliable method of early detection and follow-up of breast cancer in a subject with remarkable sensitivity and specificity along with minimal false results. The biomarker panel encompasses characterized three methylation biomarkers of genes comprising of SOSTDC1, WIFI, DACT2.

DETAILED DESCRIPTION OF THE INVENTION:

The present invention discloses a diagnostic method for early detection and follow-up of breast cancer and multianalyte biomarkers panel thereof.

The present work seeks to provide a multianalyte panel which is more sensitive (few false negatives) and specific (less false positives) than the existing biomarkers. This panel might act as an efficient adjunct to current diagnostic methods and may help in monitoring the disease.

The invention involves a method for assessing the methylation status of 3 circulating DNA markers ( SOSTDC1 , DACT2, WIFI ) in subjects using methylation and unmethylated specific PCR. The detection of complete or partial methylation of these markers were indicative of presence of breast cancer in the said subject.

Epigenetic alterations in genome such as DNA methylation, histone modifications and nucleosome modelling are instrumental in genesis of cancer. DNA methylation is a covalent addition of a methylgroup to DNA, usually to a cytosine located 5' to guanosine (CpG dinucleotide). CpG dinucleotides frequently appear as clusters, known as CpG islands, located in or near the promoter of genes. In breast cancer, promoter methylation of tumor suppressor genes leading to their transcriptional inactivation is a key contributor to tumorigenesis. Hence, identification and validation of epigenetically silenced cancer -related genes may be critical in establishment of early diagnostic biomarkers because gene-specific epigenetic changes for breast cancer are likely to occur early in carcinogenesis.

The microarray gene expression studies showed that SOSTDC1, DACT2, WIFI were among the genes which were down-regulated in breast cancers and ductal carcinoma in-situ non-invasive breast cancer. We identified that the down regulation of SOSTDC1, DACT2, WIFI is due to promoter methylation of the genes in breast cancer cell lines and breast cancer tissues. The normal breast tissues and benign breast tissues did not show any promoter methylation and were unmethylated.

In view of this, epigenetic regulation of 3 genes were checked in circulating DNA of patient and healthy controls to explore their potential as breast cancer biomarkers. The epigenetic panel included WIFI along with Disheveled binding antagonist of b-catenin 2 ( DACT2 ) and Sclerostin domain-containing protein 1 ( SOSTDC1 ). DACT2 is also a Wntsignalling pathway antagonist which is downregulated and frequently methylated in human breast cancer. SOSTDC1 is a bone morphogenetic protein (BMP) antagonist involved in cellular proliferation, differentiation and apoptosis. Decreased expression of SOSTDC1 in breast tumor tissues and cell lines correlate with its promoter hypermethyl ation at CpG sites.

For validation of epigenetic biomarkers, the methylation status of WIFI, DACT2 and SOSTDC1 was evaluated in 202 breast cancer patients and 203 age matched healthy controls. Additionally, 16 patients with DCIS and 37 patients with benign breast disease were included in the study. The samples used for this study, were aliquots of the blood samples collected for the case-control study.

The method involves, isolation of circulating nucleic acid from 1ml of cell-free plasma in cases and controls using, QIAamp circulating nucleic acid kit(Qiagen)according to manufacturer’s instructions. Protocol

1. Sample Lysis

• IOOmI of Proteinase K, 1ml of plasma and 0.8 ml of Buffer ACL (lysis buffer) containing 1.0 pg carrier RNAare added to a 50ml centrifuge tube by pulse- vortexed for 30 secs

• The mixture is incubated at 60 for 30 mins

• 1.8 ml buffer ACB is added to the lysate in the tube and pulse -vortexed for 15-30 secs

• The lysate-Buffer ACB (binding buffer) mixture is incubated in the tube for 5 mins on ice

2. Adsorption to the QIAamp Mini membrane

• QIAampMinicolumn with vacuum manifold (QIAvac24Plus system) is set up

• The lysate-buffer mixture is applied to the column and circulating nucleic acids are adsorbed onto the small silica membrane as the lysate is drawn through by vacuum pressure

3. Removal of impurities

• 600 pi of ACW 1 (wash buffer 1 ) is applied to the column and vacuum pump is switched on to draw the entire content through column

• 750 mΐ of ACW2 (wash buffer 2) is applied to the column and vacuum pump is switched on to draw the entire content through column

• 750 mΐ of ethanol (96-100%) is applied to the column and once the ethanol is drawn, the spin column is placed in a 2ml collection tube and is dried at 56°C for 10 min

4. Elution

• The column is placed in a clean 1.5ml centrifuge tube and 15-20m1 of AVE (elution buffer)is added to the center of the column and incubated at room temperature for 3 min

• The column is centrifuged at 14,000 rpm for 1 min to elute the cell free DNA (cf DNA)

5. Quantification The cfDNA was quantitated using Qubit™ dsDNA HS Assay Kit(Invitrogen).

BISULFITE CONVERSION OF CELL FREE DNA

This technique involves treating cfDNA with bisulfite, which converts unmethylated cytosines into uracil. Methylated cytosines remain unchanged during the treatment. Once converted, the methylation profile of the DNA can be determined by PCR amplification followed by DNA sequencing. Bisulfite conversion was performed using EZ-96 DNA Methylation-Gold™ Kit (Zymo Research Corp).

Protocol

L 130 mΐ of the CT Conversion Reagent is added to 20 mΐ of each DNA sample in a tube. If the volume of the DNA sample is less than 20 mΐ, the difference is made up with water. Samples are mixed by pipetting up and down.

2. The tubes are closed and transferred to a thermal cycler with the set conditions 98°C for 10 mins, 64°C for 2.5 hours, 4°C for 30 mins

3. 600 mΐ of M-Binding Buffer is added to the product and pipette mixed

4. The mixture is applied to the binding column and centrifuged at 13,000 rpm for 30 seconds. The flow-through is discarded.

5. 400 mΐ of M-Wash buffer is added to each column and centrifuged at 13,000 rpm for 30s.Theflow-through is discarded.

6. 200 mΐ of M-Desulphonation buffer is added to column and incubated at room temperature for 15-20 mins.

7. Post incubation, column is centrifuged for 30 s. Flow-through is discarded.

8. 400 mΐ of M-Wash Buffer is added to each well of the plate column and centrifuged at 13,000 rpm for 30 s. Flow-through is discarded.

9. The wash step is repeated and the column is centrifuged at 13,000 rpm for 1 min.

10. The column is transferred to a fresh 1.5 ml microcentrifuge tube and 15 mΐ of M-Elution buffer is added to the centre of the column.

11. The set up is incubated for 5 mins and centrifuged at 13,000 rpm for 1 min to elute the DNA. 12. The bisulfite modified DNA is quantitated using NanoDrop ™ ND1000 (NanoDrop Technologies) spectrophotometer. The DNA is stored at or below -20°C for later use.

METHYLATION SPECIFIC PCR (MS PCR)

The DACT2, WIFI and SOSTDC1 promoter methylation status was assessed using MS PCR.The method involves PCR amplification of bisulfite modified DNA with primers specific for detecting methylated and unmethylated alleles of a gene (table 2). The promoter sequences for all three genes were retrieved from Ensembl database. CpG island prediction and MS PCR primers specific for each gene was extracted using MethPrimer database. The bisulfite modified genomic DNA was amplified using HotStarTaq Master Mix Kit (Qiagen) according to manufacturer’s instructions. The PCR conditions were: Initial Activation 95 15 mins with

Denaturation 94 1 min,Aimealing55- 60 50 Secs, Extension 72 1 min for 30 cycles and

Final extension 72 for 7 min. Amplification products were visualized on 2.5% agarose gel using Gel Doc™ (BioRad Laboratories)(Fig 1, table 3).The relative band intensity of each product was quantified using Image Lab™ (BioRad Laboratories). lOObp DNA ladder (Promega) was used asreference to calculate relative intensity. Specificity of the MSP primers in detecting the promoter methylation status was demonstrated by the use of universal human methylated and unmethylated DNA (Zymo Research) as template.

Table 2: Primer sequences of the genes used for Methylation Specific PCR

The ratio of the relative intensity of the methylated allele and unmethylated allele (M/U) for each sample was calculated for all 3 target genes. In, non-invasive and invasive breast cancer cases, if M/U value is greater than 1 , a score of ‘ 1 ’ was assigned and if M/U value is lesser than 1 , a score of O’ was assigned. In benign cases and controls, if M/U value is greater than 1, a score of ‘-U was assigned and if M/U value is lesser than 1, a score of O’ was assigned. Combined diagnostic test evaluation for the 3 genes was performed using MEDCALC® (https://www.medcalc.org/calc/diaonostic test.php).

Table 3: Methylation patterns across groups

Table 4: SUMMARY STATISTICS

From Table 3 and 4, it is inferred that the use of the 3 gene methylation status in cell-free DNA, can help in early diagnosis and in follow-up of breast cancer.

In one of the preferred embodiment, the present invention shall disclose an accurate and reliable method for early detection and follow-up of breast cancer in a subject, with remarkable sensitivity and specificity along with minimal false results. The method of the present invention comprises of a. collecting peripheral blood sample from a subject b. determining methylation status of characterized gene biomarkers comprises of following steps i. isolating circulating cell free DNA (cfDNA) from the peripheral blood samples of step (a); ii. treating the cfDNA with bisulfite to detect methylation of CpG sites; iii. amplifying 3 target genes comprising of WIFI, SOSTDC1, DACT2 in bisulfite treated cfDNA samples using PCR primers for methylated and unmethylated gene sequence; iv. quantifying relative intensity of amplicons and determining ratio of complete/partial methylated and unmethylated alleles of the target genes by image analysis software to evaluate the methylation intensity c. statistical analysis of the methylation intensity of the 3 target genes from step b(iv) in which i. if the ratio of complete/partial methylated to unmethylated band intensity is equal to or above 1 , a positive score of 1 is given and for below 1 , a score of 0 is given; ii. if sum of the scores for the 3 genes is above 1 , indicates cancer [invasive and non-invasive breast cancer] and if the sum is 0, indicates normal subject or a subject with benign disease of breast.

As per the invention, in the method described above in step(b), the Methylation PCR conditions were Initial Activation 95 15 minutes, with Denaturation 94 1 minute,

Annealing 55- 60 50 Seconds, Extension 72 1 minute for 30 cycles and Final extension

72 for 7 minutes in which Amplification products were visualized on 2.5% agarose gel using Gel Doc and intensity of bands quantitated using Image analysis software.

In accordance with the invention, in the method described above in step(b),the amplification of 3 target genes comprising of WIFI, SOSTDC1, DACT2 in bisulfite treated cfDNA samples for detection of methylated and unmethylated gene sequence can be alternately performed by Methylation-specific PCR or variations of PCR or Hybridization Techniques or Biosensor Based Detection Or any other technique.

According to the invention, in the method described above in step(c), the complete/partial methylation of WIFI, SOSTDC1, DACT2 indicates detection of breast cancer in individuals with non-invasive and invasive forms of breast cancer in comparison with patients with benign breast condition and a healthy subject control group. In accordance with the invention, in the method described above in step(c), the absence of methylation or very low methylation of WIFI, SOSTDC1, DACT2] indicates no breast abnormalities or benign breast conditions from subjects with non-invasive and invasive forms of breast cancer

In another preferred embodiment, the present invention shall disclose a multianalyte biomarker panel for accurate and reliable method of early detection and follow-up of breast cancer in a subject with remarkable sensitivity and specificity along with minimal false results. The biomarker panel encompasses characterized three methylation biomarkers of genes comprising of WIFI, SOSTDC1, DACT2.

As per the invention, the subjects include patients having histo-pathologically invasive breast cancer and patients having histo-pathologically confirmed non-invasive breast cancer [DCIS], patients having a biopsy confirmed benign breast abnormality or disease, or healthy subjects having no evidence of breast disease or breast abnormality which ensures both early detection and follow-up of breast cancer.

Although the invention has now been described in terms of certain preferred embodiments and exemplified with respect thereto, one skilled in art can readily appreciate that various modifications, changes, omissions and substitutions may be made without departing from the spirit thereof. It is intended therefore that the present invention be limited solely by the scope of the following claims

Claims

WE CLAIM

1. An accurate and reliable method for early detection and follow-up of breast cancer patients, with remarkable sensitivity and specificity along with minimal false results, the claimed method comprises of a. collecting a peripheral blood sample from a subject b. determining methylation status of characterized gene biomarkers comprises of following steps i. isolating circulating cell free DNA (cfDNA) from the said peripheral blood samples of step (a); ii. treating the said cfDNA with bisulfite to detect methylation of CpG sites; iii. amplifying 3 target genes comprising of WIFI, SOSTDC1, DACT2 in bisulfite treated cfDNA samples using PCR primers for methylated and unmethylated gene sequence; iv. quantifying relative intensity of amplicons and determining ratio of complete/partial methylated and unmethylated alleles of the said target genes by image analysis software to evaluate the methylation intensity c. statistical analysis of the said methylation intensity of the said 3 target genes from step b(iv) wherein i. if the said ratio of complete/partial methylated to unmethylated band intensity is equal to or above 1 , a positive score of 1 is given and for below 1 , a score of 0 is given; ii. if sum of the said scores for the said 3 genes is above 1, indicates cancer [invasive and non-invasive breast cancer] and if the said sum is 0, indicates normal subject or a subject with benign disease of breast.

2. The method as claimed in claim 1 step(b) wherein the said Methylation PCR conditions were Initial Activation 95 15 minutes, with Denaturation 94 1 minute, Annealing 55-

60 50 Seconds, Extension 72 1 minute for 30 cycles and Final extension 72 for 7 minutes wherein Amplification products were visualized on 2.5% agarose gel using Gel Doc and intensity of bands quantitated using Image analysis software.

3. The method as claimed in claim 1 step(b) wherein the said amplification of 3 target genes comprising of WIFI, SOSTDC1, DACT2 in bisulfite treated cfDNA samples for detection of methylated and unmethylated gene sequence can be alternately performed by Methylation-specific PCR or variations of PCR or Hybridization Techniques or Biosensor Based Detection Or any other technique.

4. The method as claimed in claim 1 step(c) wherein the ratio of intensity of amplicons of complete/partial methylated and unmethylated alleles of WIFI, SOSTDC1, DACT2indicates the presence of either invasive or non-invasive breast cancer in patients in comparison to patients with benign breast condition and a healthy subject control group.

5. The method as claimed in claim 1 step(c) wherein absence of methylation or very low methylation of WIFI, SOSTDC1, DACT2 indicates no breast abnormalities or benign breast conditions and helps distinguish from subjects with non-invasive and invasive forms of breast cancer.

6. A multianalyte biomarker panel for accurate and reliable method of early detection and follow-up of breast cancer in a subject with remarkable sensitivity and specificity along with minimal false results, the claimed biomarker panel encompasses characterized three methylation biomarkers of genes comprising of WIFI, SOSTDC1, DACT2.

7. The said subject in any of the preceding claims, includes patients having histopathologically confirmed breast cancer, patients having histopathologically confirmed non-invasive breast cancer [DCIS], patients having a biopsy confirmed benign breast abnormality or disease, or subjects having no evidence of breast disease or breast abnormality [healthy subjects] which ensures both early detection and follow-up of breast cancer.