Epigenetic Biomarker for Osteosarcoma

NCT ID: NCT03336554

Last Updated: 2017-11-13

Study Results

Results pending

The study team has not published outcome measurements, participant flow, or safety data for this trial yet. Check back later for updates.

Basic Information

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Recruitment Status

UNKNOWN

Total Enrollment

100 participants

Study Classification

OBSERVATIONAL

Study Start Date

2017-09-01

Study Completion Date

2018-12-31

Brief Summary

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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.

Detailed Description

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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.

Conditions

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

Keywords

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osteosarcoma epigenetic biomarker hMe-Seal technique

Study Design

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Observational Model Type

COHORT

Study Time Perspective

PROSPECTIVE

Study Groups

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observation group

One group of participants are under observation. This trial has two phase. Phase I: 40 participants will be enrolled. Only if epigenetic cfDNA library has been built, investigators would move on to Phase II. Another 60 participants will be enrolled for further analysis.

No interventions assigned to this group

Eligibility Criteria

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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.
Minimum Eligible Age

10 Years

Eligible Sex

ALL

Accepts Healthy Volunteers

No

Sponsors

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Peking University

OTHER

Sponsor Role collaborator

Northwestern University

OTHER

Sponsor Role collaborator

University of Chicago

OTHER

Sponsor Role collaborator

Peking University People's Hospital

OTHER

Sponsor Role lead

Responsible Party

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Responsibility Role SPONSOR

Principal Investigators

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Wei Guo, M.D.and Ph.D.

Role: PRINCIPAL_INVESTIGATOR

Musculoskeletal Tumor Center of Peking University People's Hospital

Locations

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Peking University People's Hospital

Beijing, , China

Site Status RECRUITING

Countries

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China

Central Contacts

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Lu Xie, M.D.

Role: CONTACT

Phone: +86-13401044719

Email: [email protected]

Jie Xu, M.D

Role: CONTACT

Phone: +86-15901040835

Email: [email protected]

Facility Contacts

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Tingting Ren, Ph.D.

Role: primary

References

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Reference Type BACKGROUND
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Bielack S, Jurgens H, Jundt G, Kevric M, Kuhne 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.

Reference Type BACKGROUND
PMID: 20213397 (View on PubMed)

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, Jurgens H, Kager L, Kuhne 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.

Reference Type BACKGROUND
PMID: 27569442 (View on PubMed)

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.

Reference Type BACKGROUND
PMID: 26002013 (View on PubMed)

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.

Reference Type BACKGROUND
PMID: 17688817 (View on PubMed)

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. doi: 10.1159/000448705. eCollection 2016 Sep-Dec.

Reference Type BACKGROUND
PMID: 27920692 (View on PubMed)

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.

Reference Type BACKGROUND
PMID: 22371155 (View on PubMed)

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.

Reference Type BACKGROUND
PMID: 24962996 (View on PubMed)

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.

Reference Type BACKGROUND
PMID: 24014053 (View on PubMed)

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.

Reference Type BACKGROUND
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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. doi: 10.1093/nar/gkh739. Print 2004.

Reference Type BACKGROUND
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Chapman CG, Mariani CJ, Wu F, Meckel K, Butun F, Chuang A, Madzo J, Bissonnette 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.

Reference Type BACKGROUND
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Other Identifiers

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CBTRA-02

Identifier Type: -

Identifier Source: org_study_id