Methods and compositions for detecting esophageal neoplasias and/or metaplasias in the esophagus
Inventors
Markowitz, Sanford D. • Moinova, Helen • Chak, Amitabh • Willis, Joseph • LaFramboise, Thomas
Assignees
Case Western Reserve University
Publication Number
US-12227810-B2
Publication Date
2025-02-18
Expiration Date
2037-07-05
Interested in licensing this patent?
MTEC can help explore whether this patent might be available for licensing for your application.
Abstract
The disclosure provides methods for identifying genomic loci (e.g., vimentin and/or SqBE18) that are differentially methylated in metaplasias (e.g., Barrett's esophagus) and/or neoplastic cancers (e.g., esophageal cancers). Identification of methylated genomic loci has numerous uses, including for example, to characterize disease risk, to predict responsiveness to therapy, to non-invasively diagnose subjects and to treat subjects determined to have gastrointestinal metaplasias and/or neoplasias.
Core Innovation
The disclosed invention provides methods for detecting methylated genomic loci, particularly vimentin and/or SqBE18, that are differentially methylated in esophageal metaplasias and neoplasias. By obtaining an esophageal sample, treating it with bisulfite, and sequencing targeted nucleic acid sequences, the method quantitatively assesses the methylation status of CpG dinucleotides. Classification of a sample as methylated is based on the percentage of reads with methylation above a specified threshold.
This approach solves the problem of current diagnostic methods for esophageal cancers, which are invasive, uncomfortable, costly, or lack sensitivity and specificity. Existing techniques such as endoscopy, imaging, and cytological isolation have multiple drawbacks, including patient discomfort, high cost, and suboptimal accuracy, leading to the need for improved, non-invasive, and accurate diagnostic modalities.
By measuring methylation levels in these specific loci, the methods allow for the detection and classification of esophageal neoplasias and metaplasias in a non-invasive or minimally invasive manner. This technology enables quantitative assessment from samples obtained through brushing or balloon collection, providing a more precise classification of disease status based on molecular biomarkers, thus aiding diagnosis and potential treatment guidance.
Claims Coverage
The patent claims one independent inventive feature pertaining to the identification, amplification, measurement, and classification of methylated bisulfite-converted SqBE18 sequences from esophageal samples.
Classifying esophageal samples by quantifying methylation of bisulfite-converted SqBE18 sequences
The method includes: 1. Providing an esophageal sample from a human subject and treating it with bisulfite to create bisulfite-converted SqBE18 nucleic acid sequences. 2. Amplifying these sequences to generate amplicons, where each amplicon (read) comprises a nucleotide sequence at least 90% identical to SEQ ID NOs: 8318, 8360, 8332, or 8374, or a fragment that is at least 50 nucleotides long. 3. Measuring the number of methylated cytosines of the CpG dinucleotides in each amplicon, classifying a read as methylated if at least 70% of its CpG cytosines are methylated. 4. Calculating the percentage of total reads that are methylated, wherein classification as a methylated sample occurs if at least 0.1% of total reads are methylated.
Overall, the claim coverage centers on the inventive application of bisulfite conversion, amplification, and quantitative analysis of methylation in specific SqBE18 sequences to classify esophageal samples as methylated.
Stated Advantages
The methods enable non-invasive or minimally invasive diagnosis of esophageal neoplasia and metaplasia by molecular biomarker detection instead of relying on traditional, more invasive approaches.
They offer improved sensitivity and specificity in detecting esophageal neoplasias compared to previous methods such as endoscopy, imaging, and cytology.
The technology facilitates more accurate disease classification that can inform clinical management, monitoring for disease progression or regression, and aid in therapeutic decision making.
Documented Applications
Non-invasively or minimally invasively diagnosing esophageal neoplasias and metaplasias (including Barrett's esophagus and esophageal adenocarcinoma) using methylation status of genomic loci.
Monitoring disease progression, recurrence, or therapeutic response in subjects with esophageal neoplasia by longitudinal assessment of methylated loci.
Selecting or stratifying subjects for appropriate therapy or surveillance based on methylation profiles in esophageal samples.
Interested in licensing this patent?