Epigenetic Biomarker for Osteosarcoma

Histologic Response (Tumor Necrosis Rate) Clinical Trial

Official title:

Indentifying Epigenetic Biomarkers From Peripheral Blood of Osteosarcoma Patients Based on hMe-Seal Technique

Clinical Trial Details — Status: Recruiting

Administrative data

• NCT number: NCT03336554
• Other study ID #: CBTRA-02
• Status: Recruiting
• Phase: N/A
• First received: November 6, 2017
• Last updated: November 8, 2017
• Start date: September 1, 2017
• Est. completion date: December 31, 2018

Study information

• Verified date: November 2017
• Source: Peking University People's Hospital
• Contact: Lu Xie, M.D.
• Phone: +86-13401044719
• Email: sweetdoctor[@]163.com
• Is FDA regulated: No
• Study type: Observational [Patient Registry]

Clinical Trial Summary

hMe-Seal is a low-input whole-genome cell-free 5hmC sequencing method based on selective chemical labeling. It uses β-glucosyltransferase (βGT) to selectively label 5hmC with a biotin via an azide-modified glucose for pull-down of 5hmC-containing DNA fragments for sequencing. After selectively constructing 5hmC library, highthroughput-sequencing will be performed on an Illumina Nextseq-500 instrument. By ways of Rawdata processing, differential loci between Osteosarcoma group and control group will be detected to indentify specific epigenetic biomarkers of Osteosarcoma.

Description:

The investigator want to enroll 100 osteosarcoma participants initially treated in Musculoskeletal Tumor Center of Peking University People's Hospital(PKUPH). All those participants will follow the chemo-protocol for osteosarcoma in PKUPH.8 ml of peripheral blood would be drawed before each cycle of chemotherapy for further analysis. After definitive surgery, participants will need to take 8ml of peripheral blood every 2 months for 6 months. A total of 6 times of blood drawing will need to be done.

In hMe-Seal approach, peripheral blood is collected into EDTA-coated Vacutainers. Plasma is collected from the blood samples after centrifugation at 1 600× g for 10 min at 4 °C and 16 000× g at 10 min at 4 °C. CfDNA is extracted using the Circulating Nucleic Acid Kit(QIAGEN). After that, cfDNA (1-10 ng) is end repaired, 3'-adenylated and ligated to DNA Barcodes using KAPA Hyper Prep Kit (Kapa Biosystems). Ligated DNA is incubated in a solution containing HEPES buffer, UDP-6-N3-Glc and βGT . After that, DBCO-PEG4-biotin is directly added to the reaction mixture. Next, DNA is purified by Micro Bio-Spin 30 Column (Bio-Rad). The purified DNA is incubated with M270 Streptavidin beads (Life Technologies) in specific buffer. The beads are subsequently undergone three 5-min washes each with four kinds of different buffers. All binding and washing are done at room temperature with gentle rotation. Beads are then resuspended in water and amplified with 16 cycles of PCR amplification. The PCR products are purified using AMPure XP beads. Pair-end 38bp sequencing is performed on the NextSeq-500 instrument.

Recruitment information / eligibility

• Status: Recruiting
• Enrollment: 100
• Est. completion date: December 31, 2018
• Est. primary completion date: October 30, 2018
• Accepts healthy volunteers: No
• Gender: All
• Age group: 10 Years and older

Eligibility

Inclusion Criteria:

• 1) histologically confirmed high-grade osteosarcoma;

• 2) older than 10 yrs;

• 3) initially treated in Musculoskeletal Tumor Center of Peking University People's Hospital;

• 4) Serum samples are available;

• 5) completed neo-adjuvant chemotherapy and at least 8 cycles of adjuvant chemotherapy;

• 6) expected to live longer than 3 months with Eastern Cooperative Oncology Group performance status of 0 or 1;

• 7) acceptable hematologic, hepatic, and renal function.

Exclusion Criteria:

• 1) Serum samples are not qualified;

• 2) Patients who could not complete neo-adjuvant chemotherapy or at least 4-month adjuvant chemotherapy;

• 3) lost to follow-up.

Related Conditions & MeSH terms

• Disease Progression
• Histologic Response (Tumor Necrosis Rate)
• Necrosis
• Objective Response Rate for Neoadjuvant Chemotherapy, ORR
• Osteosarcoma
• Overall Survival, OS
• Progression-free Survival, PFS

Locations

Country	Name	City	State
China	Peking University People's Hospital	Beijing

Sponsors (4)

Lead Sponsor	Collaborator
Peking University People's Hospital	Northwestern University, Peking University, University of Chicago

Country where clinical trial is conducted

China, 

References & Publications (12)

Bachman M, Uribe-Lewis S, Yang X, Williams M, Murrell A, Balasubramanian S. 5-Hydroxymethylcytosine is a predominantly stable DNA modification. Nat Chem. 2014 Dec;6(12):1049-55. doi: 10.1038/nchem.2064. Epub 2014 Sep 21. — View Citation

Bernthal NM, Federman N, Eilber FR, Nelson SD, Eckardt JJ, Eilber FC, Tap WD. Long-term results (>25 years) of a randomized, prospective clinical trial evaluating chemotherapy in patients with high-grade, operable osteosarcoma. Cancer. 2012 Dec 1;118(23):5888-93. doi: 10.1002/cncr.27651. Epub 2012 May 30. — View Citation

Bielack S, Jürgens H, Jundt G, Kevric M, Kühne T, Reichardt P, Zoubek A, Werner M, Winkelmann W, Kotz R. Osteosarcoma: the COSS experience. Cancer Treat Res. 2009;152:289-308. doi: 10.1007/978-1-4419-0284-9_15. Review. — View Citation

Chapman CG, Mariani CJ, Wu F, Meckel K, Butun F, Chuang A, Madzo J, Bissonette MB, Kwon JH, Godley LA. TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer. Sci Rep. 2015 Dec 3;5:17568. doi: 10.1038/srep17568. Erratum in: Sci Rep. 2016 Apr 28;6:24963. — View Citation

Duchman KR, Gao Y, Miller BJ. Prognostic factors for survival in patients with high-grade osteosarcoma using the Surveillance, Epidemiology, and End Results (SEER) Program database. Cancer Epidemiol. 2015 Aug;39(4):593-9. doi: 10.1016/j.canep.2015.05.001. Epub 2015 May 20. — View Citation

Fei D, Li Y, Zhao D, Zhao K, Dai L, Gao Z. Serum miR-9 as a prognostic biomarker in patients with osteosarcoma. J Int Med Res. 2014 Aug;42(4):932-7. doi: 10.1177/0300060514534643. Epub 2014 Jun 24. — View Citation

Fu HL, Shao L, Wang Q, Jia T, Li M, Yang DP. A systematic review of p53 as a biomarker of survival in patients with osteosarcoma. Tumour Biol. 2013 Dec;34(6):3817-21. doi: 10.1007/s13277-013-0966-x. Epub 2013 Sep 7. Review. — View Citation

Guo W, Sun X, Ji T, Tang X. Outcome of surgical treatment of pelvic osteosarcoma. J Surg Oncol. 2012 Sep 15;106(4):406-10. doi: 10.1002/jso.23076. Epub 2012 Feb 27. — View Citation

Marina NM, Smeland S, Bielack SS, Bernstein M, Jovic G, Krailo MD, Hook JM, Arndt C, van den Berg H, Brennan B, Brichard B, Brown KLB, Butterfass-Bahloul T, Calaminus G, Daldrup-Link HE, Eriksson M, Gebhardt MC, Gelderblom H, Gerss J, Goldsby R, Goorin A, Gorlick R, Grier HE, Hale JP, Hall KS, Hardes J, Hawkins DS, Helmke K, Hogendoorn PCW, Isakoff MS, Janeway KA, Jürgens H, Kager L, Kühne T, Lau CC, Leavey PJ, Lessnick SL, Mascarenhas L, Meyers PA, Mottl H, Nathrath M, Papai Z, Randall RL, Reichardt P, Renard M, Safwat AA, Schwartz CL, Stevens MCG, Strauss SJ, Teot L, Werner M, Sydes MR, Whelan JS. Comparison of MAPIE versus MAP in patients with a poor response to preoperative chemotherapy for newly diagnosed high-grade osteosarcoma (EURAMOS-1): an open-label, international, randomised controlled trial. Lancet Oncol. 2016 Oct;17(10):1396-1408. doi: 10.1016/S1470-2045(16)30214-5. Epub 2016 Aug 25. — View Citation

Tang XD, Guo W, Yang RL, Yang Y, Ji T. [Limb salvage surgery for osteosarcoma around the knee in children and adolescent patients]. Zhonghua Wai Ke Za Zhi. 2007 May 15;45(10):669-72. Chinese. — View Citation

Valinluck V, Tsai HH, Rogstad DK, Burdzy A, Bird A, Sowers LC. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res. 2004 Aug 9;32(14):4100-8. Print 2004. — View Citation

Xie L, Guo W, Tang X, Yang Y, Xu J. Effects of Arsenic Trioxide on Minor Progressive High-Grade Osteosarcoma of the Extremities Metastatic to the Lung: Results of 39 Patients Treated in a Single Institution. Case Rep Oncol. 2016 Oct 17;9(3):610-628. eCollection 2016 Sep-Dec. — View Citation

* Note: There are 12 references in all — Click here to view all references

Outcome

Type	Measure	Description	Time frame	Safety issue
Primary	Histologic response	For osteosarcoma, tumor necrosis rate will be done for every participant. On pathologic examination, the surgical specimens were carefully studied and sectioned. This evaluation included establishing the gross extent of the tumor[26, 27] and noting its soft tissue component and lines of surgical resection[27]. An average of 10-20 histologic specimens were examined in each of the en bloc resections to delineate the extension of osteosarcoma up and down the marrow cavity and to study the effects of chemotherapy on the tumor (viable, partially, largely, or totally necrotic), which were then calculated as tumor necrosis rate as paper described.	2 months
Secondary	Objective Response Rate	According to RECIST 1.1, participants who meet the criteria of complete response and partial response.	2 months
Secondary	Progression-free survival	Progression-free survival (PFS) will be calculated from the start of chemotherapy to first progression.	2 years
Secondary	Overall survival	Overall survival (OS) will be calculated from the start of chemotherapy to death.	5 years