Program Official

Principal Investigator

Stephen J
Meltzer
Awardee Organization

Johns Hopkins University
United States

Fiscal Year
2021
Activity Code
UH3
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date

Facile screening for esophageal cancer in LMICs

Esophageal squamous cell carcinoma (ESCC) ranks sixth among all cancers worldwide, with 450,000 new cases diagnosed per year and a very poor prognosis. Low-cost, minimally invasive point-of-care population screening for ESCC is badly needed, particularly in LMICs, where 5-year ESCC survival is less than 10%. Altered methylation occurs frequently in human malignancies, including EC, constituting an early event that can serve as an early cancer detection biomarker. However, for DNA methylation to be used in this manner, we need cost-effective, user-friendly and robust tests that permit clinical translation in LMICs. We propose an early ESCC diagnostic strategy comprising a single-use, swallowable sponge to collect esophageal specimens coupled with a smartphone-manipulated microfluidic chip for automated sample processing and methylation detection. This strategy does not require endoscopy (EGD), can be administered by healthcare workers without medical degrees, and uses an on-phone analytic app. The sponge is cheaper (approximately $30 each), less invasive, and easier to perform than EGD ($1500 total cost, including facility fees); there are no room charges, unlike EGD. The microchip integrates DNA extraction, bisulfite DNA conversion, and methylation analysis into a single device. In addition, the microchip interfaces with a cellphone, for both device control and methylation detection and analysis. The integrated device enables detection of DNA methylation from crude samples in a “sample-to-answer” manner, without the need for sending data back to an analytic center off-site. Thus, the proposed platform promises a cost-effective and user-friendly POC strategy for early ESCC detection that is implementable in LMICs. We have also assembled a talented interdisciplinary, intercontinental team to execute this strategy. Our task will be achieved in 2 phases via the following Aims: UG3 PHASE: Aim 1: To assess a streamlined protocol for sample collection, processing and methylation detection. Aim 2: To implement DNA sample processing and methylation detection into a mobile phonemanipulated microfluidic chip system. Aim 3: To test a prototype ESCC diagnostic strategy integrating the DNA methylation detection system with the swallowable sponge for sample collection. UH3 PHASE: Aim 1: To improve the cost-effectiveness and robustness of the methylation diagnostic system for use in LMICs. Aim 2: To develop a method for ambient chip storage and perform on-chip QC tests to verify assay functionality. Aim 3: To conduct an ESCC diagnostic trial in Uganda using our point-of-care strategy.

Publications

  • Kandimalla R, Xu J, Link A, Matsuyama T, Yamamura K, Parker MI, Uetake H, Balaguer F, Borazanci E, Tsai S, Evans D, Meltzer SJ, Baba H, Brand R, Von Hoff D, Li W, Goel A. EpiPanGI Dx: A Cell-free DNA Methylation Fingerprint for the Early Detection of Gastrointestinal Cancers. Clinical cancer research : an official journal of the American Association for Cancer Research. 2021 Nov 15;27(22):6135-6144. Epub 2021 Aug 31. PMID: 34465601
  • Liu X, Cheng Y, Abraham JM, Wang Z, Wang Z, Ke X, Yan R, Shin EJ, Ngamruengphong S, Khashab MA, Zhang G, McNamara G, Ewald AJ, Lin D, Liu Z, Meltzer SJ. Modeling Wnt signaling by CRISPR-Cas9 genome editing recapitulates neoplasia in human Barrett epithelial organoids. Cancer letters. 2018 Nov 1;436:109-118. Epub 2018 Aug 23. PMID: 30144514
  • Abraham JM, Meltzer SJ. Long Noncoding RNAs in the Pathogenesis of Barrett's Esophagus and Esophageal Carcinoma. Gastroenterology. 2017 Jul;153(1):27-34. Epub 2017 May 18. PMID: 28528706
  • Chen L, Huang M, Plummer J, Pan J, Jiang YY, Yang Q, Silva TC, Gull N, Chen S, Ding LW, An O, Yang H, Cheng Y, Said JW, Doan N, Dinjens WN, Waters KM, Tuli R, Gayther SA, Klempner SJ, Berman BP, Meltzer SJ, Lin DC, Koeffler HP. Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma. Gut. 2020 Apr;69(4):630-640. Epub 2019 Aug 13. PMID: 31409603
  • Hsieh K, Zhao G, Wang TH. Applying biosensor development concepts to improve preamplification-free CRISPR/Cas12a-Dx. The Analyst. 2020 Jul 13;145(14):4880-4888. PMID: 32478351
  • O'Keefe CM, Wang TJ. Fabrication of Multilayer Microfluidic Arrays for Passive, Efficient DNA Trapping and Profiling. Methods in molecular biology (Clifton, N.J.). 2023;2679:315-322. PMID: 37300626
  • O'Keefe CM, Giammanco D, Li S, Pisanic TR, Wang TJ. Multilayer microfluidic array for highly efficient sample loading and digital melt analysis of DNA methylation. Lab on a chip. 2019 Jan 29;19(3):444-451. PMID: 30623957
  • Wang Z, Kambhampati S, Cheng Y, Ma K, Simsek C, Tieu AH, Abraham JM, Liu X, Prasath V, Duncan M, Stark A, Trick A, Tsai HL, Wang H, He Y, Khashab MA, Ngamruengphong S, Shin EJ, Wang TH, Meltzer SJ. Methylation Biomarker Panel Performance in EsophaCap Cytology Samples for Diagnosing Barrett's Esophagus: A Prospective Validation Study. Clinical cancer research : an official journal of the American Association for Cancer Research. 2019 Apr 1;25(7):2127-2135. Epub 2019 Jan 22. PMID: 30670490
  • Wang Z, Ma K, Pitts S, Cheng Y, Liu X, Ke X, Kovaka S, Ashktorab H, Smoot DT, Schatz M, Wang Z, Meltzer SJ. Novel circular RNA circNF1 acts as a molecular sponge, promoting gastric cancer by absorbing miR-16. Endocrine-related cancer. 2019 Mar;26(3):265-277. PMID: 30576282
  • Liu X, Abraham JM, Cheng Y, Wang Z, Wang Z, Zhang G, Ashktorab H, Smoot DT, Cole RN, Boronina TN, DeVine LR, Talbot CC Jr, Liu Z, Meltzer SJ. Synthetic Circular RNA Functions as a miR-21 Sponge to Suppress Gastric Carcinoma Cell Proliferation. Molecular therapy. Nucleic acids. 2018 Dec 7;13:312-321. Epub 2018 Sep 22. PMID: 30326427
  • Stark A, Trick A, Pisanic TR 2nd, Wang TH. Droplet Magnetofluidic Assay Platform for Quantitative Methylation-Specific PCR. Methods in molecular biology (Clifton, N.J.). 2022;2394:199-209. PMID: 35094330
  • Xiong JX, Wang YS, Sheng J, Xiang D, Huang TX, Tan BB, Zeng CM, Li HH, Yang J, Meltzer SJ, Mori Y, Qin YR, Guan XY, Fu L. Epigenetic alterations of a novel antioxidant gene SLC22A3 predispose susceptible individuals to increased risk of esophageal cancer. International journal of biological sciences. 2018 Sep 7;14(12):1658-1668. doi: 10.7150/ijbs.28482. eCollection 2018. PMID: 30416380
  • Shao F, Hsieh K, Zhang P, Kaushik AM, Wang TH. Facile and scalable tubing-free sample loading for droplet microfluidics. Scientific reports. 2022 Aug 3;12(1):13340. PMID: 35922529
  • Wang Z, Cheng Y, Abraham JM, Yan R, Liu X, Chen W, Ibrahim S, Schroth GP, Ke X, He Y, Meltzer SJ. RNA sequencing of esophageal adenocarcinomas identifies novel fusion transcripts, including NPC1-MELK, arising from a complex chromosomal rearrangement. Cancer. 2017 Oct 15;123(20):3916-3924. Epub 2017 Jun 22. PMID: 28640357
  • Ke X, Yan R, Sun Z, Cheng Y, Meltzer A, Lu N, Shu X, Wang Z, Huang B, Liu X, Wang Z, Song JH, Ng CK, Ibrahim S, Abraham JM, Shin EJ, He S, Meltzer SJ. Esophageal Adenocarcinoma-Derived Extracellular Vesicle MicroRNAs Induce a Neoplastic Phenotype in Gastric Organoids. Neoplasia (New York, N.Y.). 2017 Nov;19(11):941-949. Epub 2017 Sep 29. PMID: 28968550
  • Liu X, Meltzer SJ. Gastric Cancer in the Era of Precision Medicine. Cellular and molecular gastroenterology and hepatology. 2017 Feb 20;3(3):348-358. doi: 10.1016/j.jcmgh.2017.02.003. eCollection 2017 May. PMID: 28462377
  • Song Y, Kilburn D, Song JH, Cheng Y, Saeui CT, Cheung DG, Croce CM, Yarema KJ, Meltzer SJ, Liu KJ, Wang TH. Determination of absolute expression profiles using multiplexed miRNA analysis. PloS one. 2017 Jul 13;12(7):e0180988. doi: 10.1371/journal.pone.0180988. eCollection 2017. PMID: 28704432
  • Park JS, Pisanic T, Zhang Y, Wang TH. Ligation-Enabled Fluorescence-Coding PCR for High-Dimensional Fluorescence-Based Nucleic Acid Detection. Analytical chemistry. 2021 Feb 2;93(4):2351-2358. Epub 2021 Jan 11. PMID: 33427441
  • Ma K, Kalra A, Tsai HL, Okello S, Cheng Y, Meltzer SJ, Esophageal Squamous Cell Carcinoma Consortium, Lumori BAE, Opio CK, Jit S, Danilova L, Wang Z, Simsek C, Ngamruengphong S, Shin EJ, Khashab MA, Singh VK, Tieu AH, Nolet C, Gong D, Chang KH, Prasath V, Bollinger RC, Wang TH, Feliciano J, Lam VK, Battafarano R, Turner M, Lang P, Marrone KA, Wang H. Accurate Nonendoscopic Detection of Esophageal Squamous Cell Carcinoma Using Methylated DNA Biomarkers. Gastroenterology. 2022 Aug;163(2):507-509.e2. Epub 2022 Apr 26. PMID: 35483446
  • Buckle GC, Mrema A, Mwachiro M, Ringo Y, Selekwa M, Mulima G, Some FF, Mmbaga BT, Mody GN, Zhang L, Paciorek A, Akoko L, Ayuo P, Burgert S, Bukusi E, Charles A, Chepkemoi W, Chesumbai G, Kaimila B, Kenseko A, Kibwana KS, Koech D, Macharia C, Moirana EN, Mushi BP, Mremi A, Mwaiselage J, Mwanga A, Ndumbalo J, Nvakunga G, Ngoma M, Oduor M, Oloo M, Opakas J, Parker R, Seno S, Salima A, Servent F, Wandera A, Westmoreland KD, White RE, Williams B, Mmbaga EJ, Van Loon K, of the African Esophageal Cancer Consortium (AfrECC). Treatment outcomes of esophageal cancer in Eastern Africa: protocol of a multi-center, prospective, observational, open cohort study. BMC cancer. 2022 Jan 19;22(1):82. PMID: 35045815
  • Ng CK, Ma K, Cheng Y, Miyashita T, Harmon JW, Meltzer SJ. Krüppel-like Factor 5 Promotes Sonic Hedgehog Signaling and Neoplasia in Barrett's Esophagus and Esophageal Adenocarcinoma. Translational oncology. 2019 Nov;12(11):1432-1441. Epub 2019 Aug 8. PMID: 31401336
  • Stark A, Shin DJ, Wang TH. A sample-to-answer droplet magnetofluidic assay platform for quantitative methylation-specific PCR. Biomedical microdevices. 2018 Mar 28;20(2):31. PMID: 29594810
  • Shao F, Park JS, Zhao G, Hsieh K, Wang TH. Elucidating the Role of CRISPR/Cas in Single-Step Isothermal Nucleic Acid Amplification Testing Assays. Analytical chemistry. 2023 Feb 21;95(7):3873-3882. Epub 2023 Feb 6. PMID: 36745596
  • Zhao H, Cheng Y, Kalra A, Ma K, Zheng Y, Ziman B, Tressler C, Glunde K, Shin EJ, Ngamruengphong S, Khashab M, Singh V, Anders RA, Jit S, Wyhs N, Chen W, Li X, Lin DC, Meltzer SJ. Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model. Science translational medicine. 2022 Nov 30;14(673):eabq6146. Epub 2022 Nov 30. PMID: 36449602

Clinical Trials

Study Name Clinical Trial ID
Novel Strategy for Early Detection of Esophageal Squamous Cell Carcinoma NCT05028725