DNA in Predicting Response After Systemic Therapy in Women With Metastatic Breast Cancer

• Sponsor: Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins (Other)
• Overall Status: Completed
• CT.gov ID: NCT00899548
• Collaborator: National Cancer Institute (NCI) (NIH)
• Enrollment: 182
• Locations: 4
• Actual Duration (Months): 117
• Patients Per Site: 45.5
• Patients Per Site Per Month: 0.4

Study Details

Study Description

Brief Summary

RATIONALE: Studying samples of blood from patients with cancer and from healthy participants in the laboratory may help doctors learn more about changes that may occur in DNA and identify biomarkers related to cancer. It may also help doctors predict how well patients will respond to systemic therapy.

PURPOSE: This laboratory study is looking at DNA in predicting response after systemic therapy in women with metastatic breast cancer.

Condition or Disease	Intervention/Treatment	Phase
Breast Cancer	Genetic: DNA methylation analysis; Genetic: microarray analysis; Genetic: polymerase chain reaction; Other: laboratory biomarker analysis

Detailed Description

OBJECTIVES:

Primary

• Identify a panel of methylated gene markers in serum from women with metastatic breast cancer that is significantly different from that observed in healthy participants.

• Assess changes in a panel of methylated gene markers from baseline, after 3-4 weeks, and after 9-12 weeks of systemic therapy in patients with metastatic breast cancer.

• Determine the potential effects of common exposures (i.e., alcohol, smoking, medications, and dietary factors) on patterns of serum methylation in patients with metastatic breast cancer and in healthy participants.

• Develop a predictive model using DNA methylation profiles in serum that predicts clinical outcome for an individual patient with metastatic disease.

Secondary

• Correlate circulating tumor cells (CTCs) with clinical outcome in patients with metastatic breast cancer.

• Correlate CTCs with serum methylation in these patients.

• Determine if the addition of CTCs to serum methylation results in an improved predictive model.

OUTLINE: This is a prospective, multicenter study.

Patients and healthy participants fill out health assessment questionnaires at baseline, week 3-4, and week 9-12.

Patients undergo blood collection for methylated marker analysis at baseline, weeks 3-4, and weeks 9-12 and circulating tumor cell levels at baseline and weeks 3-4. Healthy participants undergo blood collection for methylated marker analysis at baseline. An additional cohort of healthy participants undergo follow-up blood collection ≥ 1 week after baseline.

DNA methylation is measured by quantitative multiplex methylation-specific polymerase chain reaction (QM-MSP) assay.

After completion of study procedures, patients are followed every 3-4 months.

PROJECTED ACCRUAL: A total of 150 patients and 150 healthy participants will be accrued for this study.

Study Design

• Study Type: Observational
• Actual Enrollment: 182 participants
• Observational Model: Cohort
• Time Perspective: Prospective
• Official Title: DNA Methylation in Serum as a Predictive Marker of Progression and Survival Following Systemic Therapy in Patients With Metastatic Breast Cancer
• Actual Study Start Date: Jan 1, 2007
• Actual Primary Completion Date: Jun 1, 2010
• Actual Study Completion Date: Oct 1, 2016

Arms and Interventions

Arm	Intervention/Treatment
Metastatic breast cancer patients DNA methylation analysis, microarray analysis, polymerase chain reaction, laboratory biomarker analysis	Genetic: DNA methylation analysis; laboratory analysis; Genetic: microarray analysis; laboratory analysis; Genetic: polymerase chain reaction; laboratory analysis; Other: laboratory biomarker analysis; laboratory analysis

Outcome Measures

Primary Outcome Measures

1. Progression-free Survival in Patients With a High vs. Low Cumulative Methylation Index (CMI) Value [from week 4 to up to 87 months]

2. Changes in Methylated Gene Markers as Measured by Cumulative Methylation Index [baseline, week 4]

   log change in cumulative methylation index (CMI) from baseline to week 4. Individual gene methylation (M) is calculated as a methylation index (MI) where MI = (methylated copies)/(number of methylated genes + gene standard copies) * 100. The MI of each sample was averaged across duplicates. The cumulative methylation index (CMI) is the sum of the MI for all genes. The log change from based line to week 4 could increase or decrease. CMI was evaluated as a continuous marker for change from baseline.

3. Effects of Common Exposures (i.e., Alcohol, Smoking, Medications, and Dietary Factors) on Patterns of Serum Methylation [9-12 weeks]

4. Creation of a Predictive Model of DNA Methylation Profiles [9-12 weeks]

Secondary Outcome Measures

1. Overall Survival in Patients With a High vs. Low CMI Value [from week 4 to up to 3 years]

2. Correlation of CTCs With Serum Methylation [3-4 weeks]

Other Outcome Measures

1. Determination if the Addition of CTCs to Serum Methylation Results in an Improved Predictive Model [3-4 weeks]

Eligibility Criteria

Criteria

• Ages Eligible for Study: 18 Years and Older
• Sexes Eligible for Study: Female
• Accepts Healthy Volunteers: Yes

DISEASE CHARACTERISTICS:

• Meets 1 of the following criteria:

• Histologically and/or cytologically confirmed stage IV adenocarcinoma of the breast (patient)

• No diagnosis of an abnormal breast biopsy (including atypical ductal or lobular hyperplasia), or new diagnosis of breast cancer or breast cancer recurrence within the past five years (healthy participant)

• Evidence of disease progression AND initiating a new systemic treatment regimen with trastuzumab (Herceptin®), chemotherapy, endocrine therapy, or investigational agent(s) (patient)

• Treatment may be given as a single agent or in combination

• Measurable or evaluable disease (patient)

• Measurable disease is defined as ≥ 1 measurable lesion identified by RECIST criteria

• Patients with evaluable disease only must have ≥ 1 tumor marker (e.g., carcinoembryonic antigen, CA 27-29, or CA 15-3) above normal level

• Treated brain metastases (surgery or radiation therapy) allowed provided patient has evidence of disease stability or presence of other site(s) of measurable or evaluable disease (patient)

• No leptomeningeal disease

• Hormone receptor status not specified

PATIENT CHARACTERISTICS:

• Female

• Menopausal status not specified

• ECOG performance status 0-2

• No known cancer within the past 5 years other than basal cell or squamous cell carcinoma of the skin and/or adequately treated cervical cancer (healthy participant)

• Not pregnant or nursing

PRIOR CONCURRENT THERAPY:

• See Disease Characteristics

• Prior therapy in the preoperative, adjuvant, and/or metastatic setting allowed

• Any number of prior regimens in any setting allowed

• No prior radiation therapy to the only site of disease unless there is evidence of post-radiation disease progression

• No selective estrogen receptor modulator or aromatase inhibitor for breast cancer prevention or therapy within the past 12 months (healthy participant)

• Prior or concurrent use of raloxifene for osteopenia or osteoporosis therapy allowed (healthy participant)

• Concurrent participation in another clinical trial, including one involving an investigational agent(s), allowed

Contacts and Locations

Locations

	Site	City	State	Country	Postal Code
1	Indiana University Melvin and Bren Simon Cancer Center	Indianapolis	Indiana	United States	46202-5289
2	Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins	Baltimore	Maryland	United States	21231-2410
3	Mayo Clinic Cancer Center	Rochester	Minnesota	United States	55905
4	Lineberger Comprehensive Cancer Center at University of North Carolina - Chapel Hill	Chapel Hill	North Carolina	United States	27599-7295

Sponsors and Collaborators

• Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins
• National Cancer Institute (NCI)

Investigators

• Principal Investigator: Antonio C. Wolff, MD, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins

Study Documents (Full-Text)

None provided.

More Information

Publications

None provided.

• Responsible Party: Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins
• ClinicalTrials.gov Identifier: NCT00899548
• Other Study ID Numbers: J0524; P30CA006973; JHOC-J0524; JHOC-SKCCC-J0524; CDR0000509417; NA_00000717
• First Posted: May 12, 2009
• Last Update Posted: Jul 26, 2019
• Last Verified: Jul 1, 2019

• Individual Participant Data (IPD) Sharing Statement: Yes
• Plan to Share IPD: Yes
• Keywords provided by Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins: stage IV breast cancer; recurrent breast cancer
• Additional relevant MeSH terms: Breast Neoplasms

Study Results

Participant Flow

Recruitment Details	Participants were recruited at each of the participating institutions at Johns Hopkins and within the Translational Breast Cancer Research Consortium.

Arm/Group Title	Metastatic Breast Cancer Patients
Arm/Group Description	Adult women with metastatic breast cancer.
Period Title: Overall Study
STARTED	182
COMPLETED	179
NOT COMPLETED	3

Baseline Characteristics

Arm/Group Title	Metastatic Breast Cancer Patients
Arm/Group Description	Adult women with metastatic breast cancer.
Overall Participants	182
Age (years) [Median (Full Range) ]
Median (Full Range) [years]	56
Sex: Female, Male (Count of Participants)
Female	182 100%
Male	0 0%
Region of Enrollment (Count of Participants)
United States	182 100%

Outcome Measures

1. Primary Outcome

Title	Progression-free Survival in Patients With a High vs. Low Cumulative Methylation Index (CMI) Value
Time Frame	from week 4 to up to 87 months

Outcome Measure Data

Analysis Population Description

141/179 participants who completed the study were evaluable for this outcome measure. Of these, 8 participants were excluded from analysis for events experienced before week 4, 2 participants had inadequate samples for analysis and data was not collected from 3 participants.

Arm/Group Title	Metastatic Breast Cancer Patients -- CMI High	Metastatic Breast Cancer Patients -- CMI Low
Arm/Group Description	All subjects enrolled to the study with samples analyzed for the primary objective of DNA methylation in metastatic breast cancer patients who had a high CMI.	All subjects enrolled to the study with samples analyzed for the primary objective of DNA methylation in metastatic breast cancer patients who had a low CMI.
Measure Participants	71	57
Median (95% Confidence Interval) [months]	2.1	5.8

Statistical Analysis 1

Statistical Analysis Overview	Comparison Group Selection	Metastatic Breast Cancer Patients -- CMI High, Metastatic Breast Cancer Patients -- CMI Low
	Comments
	Type of Statistical Test	Superiority
	Comments
Statistical Test of Hypothesis	p-Value	.0002
	Comments
	Method	Gehan
	Comments	Distributions compared between using the Gehan test, which gives more weight to early differences.
Method of Estimation	Estimation Parameter	Hazard Ratio (HR)
	Estimated Value	1.76
	Confidence Interval	(2-Sided) 95%; 1.23 to 2.52
	Parameter Dispersion	Type: Value:
	Estimation Comments

2. Primary Outcome

Title	Changes in Methylated Gene Markers as Measured by Cumulative Methylation Index
Description	log change in cumulative methylation index (CMI) from baseline to week 4. Individual gene methylation (M) is calculated as a methylation index (MI) where MI = (methylated copies)/(number of methylated genes + gene standard copies) * 100. The MI of each sample was averaged across duplicates. The cumulative methylation index (CMI) is the sum of the MI for all genes. The log change from based line to week 4 could increase or decrease. CMI was evaluated as a continuous marker for change from baseline.
Time Frame	baseline, week 4

Outcome Measure Data

Analysis Population Description

Data to assess this outcome measure was only collected from 129/182 participants with metastatic breast cancer.

Arm/Group Title	Metastatic Breast Cancer Patients
Arm/Group Description	DNA methylation analysis, microarray analysis, polymerase chain reaction, laboratory biomarker analysis DNA methylation analysis: laboratory analysis microarray analysis: laboratory analysis polymerase chain reaction: laboratory analysis laboratory biomarker analysis: laboratory analysis
Measure Participants	129
Mean (Standard Deviation) [log CMI change]	-1.20 (1.84)

Statistical Analysis 1

Statistical Analysis Overview	Comparison Group Selection	Metastatic Breast Cancer Patients -- CMI High
	Comments	Hazard ratio
	Type of Statistical Test	Other
	Comments
Statistical Test of Hypothesis	p-Value	0.001
	Comments
	Method	Regression, Cox
	Comments
Method of Estimation	Estimation Parameter	Cox Proportional Hazard
	Estimated Value	1.19
	Confidence Interval	(2-Sided) 95%; 1.07 to 1.32
	Parameter Dispersion	Type: Value:
	Estimation Comments

3. Primary Outcome

Title	Effects of Common Exposures (i.e., Alcohol, Smoking, Medications, and Dietary Factors) on Patterns of Serum Methylation
Time Frame	9-12 weeks

Outcome Measure Data

Analysis Population Description

Data was not collected to assess this outcome measure

Arm/Group Title	Metastatic Breast Cancer Patients
Arm/Group Description	DNA methylation analysis, microarray analysis, polymerase chain reaction, laboratory biomarker analysis DNA methylation analysis: laboratory analysis microarray analysis: laboratory analysis polymerase chain reaction: laboratory analysis laboratory biomarker analysis: laboratory analysis
Measure Participants	0

4. Primary Outcome

Title	Creation of a Predictive Model of DNA Methylation Profiles
Time Frame	9-12 weeks

Outcome Measure Data

Analysis Population Description

Data was not collected to assess this outcome measure

Arm/Group Title	Metastatic Breast Cancer Patients
Arm/Group Description	DNA methylation analysis, microarray analysis, polymerase chain reaction, laboratory biomarker analysis DNA methylation analysis: laboratory analysis microarray analysis: laboratory analysis polymerase chain reaction: laboratory analysis laboratory biomarker analysis: laboratory analysis
Measure Participants	0

5. Secondary Outcome

Title	Overall Survival in Patients With a High vs. Low CMI Value
Time Frame	from week 4 to up to 3 years

Outcome Measure Data

Analysis Population Description

141/179 participants who completed the study were evaluable for this outcome measure. Of these, 7 participants were excluded from analysis for events experienced before week 4, 2 participants had inadequate samples for analysis and data was not collected from 3 participants.

Arm/Group Title	Metastatic Breast Cancer Patients -- CMI High	Metastatic Breast Cancer Patients -- CMI Low
Arm/Group Description	All subjects enrolled to the study with samples analyzed for the primary objective of DNA methylation in metastatic breast cancer patients who had a high CMI.	All subjects enrolled to the study with samples analyzed for the primary objective of DNA methylation in metastatic breast cancer patients who had a low CMI.
Measure Participants	62	67
Median (95% Confidence Interval) [months]	12.3	21.7

Statistical Analysis 1

Statistical Analysis Overview	Comparison Group Selection	Metastatic Breast Cancer Patients -- CMI High, Metastatic Breast Cancer Patients -- CMI Low
	Comments
	Type of Statistical Test	Superiority
	Comments
Statistical Test of Hypothesis	p-Value	.001
	Comments
	Method	Gehan
	Comments	Distributions compared between using the Gehan test, which gives more weight to early differences.
Method of Estimation	Estimation Parameter	Hazard Ratio (HR)
	Estimated Value	1.70
	Confidence Interval	(2-Sided) 95%; 1.18 to 2.45
	Parameter Dispersion	Type: Value:
	Estimation Comments

6. Secondary Outcome

Title	Correlation of CTCs With Serum Methylation
Time Frame	3-4 weeks

Outcome Measure Data

Analysis Population Description

Data was not collected for this outcome measure

Arm/Group Title	Metastatic Breast Cancer Patients With Measured CMI and CTC
Arm/Group Description	Subjects who had measured values of both CMI and CTC
Measure Participants	0

7. Other Pre-specified Outcome

Title	Determination if the Addition of CTCs to Serum Methylation Results in an Improved Predictive Model
Time Frame	3-4 weeks

Outcome Measure Data

Analysis Population Description

[Not Specified]

Arm/Group Title

Arm/Group Description

8. Post-Hoc Outcome

Title	Overall Survival in Participants With High CTC vs. Low CTC
Description	overall survival in participants with high or low cumulative tumor cells (CTC). "high CTC" refers to >5 cells/7.5mL and "low CTC" refers to <5 cells/7.5mL.
Time Frame	4 weeks

Outcome Measure Data

Analysis Population Description

Data for this outcome measure was collected from only 96 participants.

Arm/Group Title	Metastatic Breast Cancer Patients With Measured CTC Values
Arm/Group Description	Subjects with metastatic breast cancer who had measured values of CTC
Measure Participants	96
High CTC (>5 cells/7.5 mL)	8.1
Low CTC (<5 cells/7.5 mL)	20.8

Adverse Events

Time Frame	up to 12 weeks from time of consenting to study
Arm/Group Title	Metastatic Breast Cancer Patients
Arm/Group Description	Adult women with metastatic breast cancer.
All Cause Mortality
	Metastatic Breast Cancer Patients
	Affected / at Risk (%)	# Events
Total	3/182 (1.6%)
Serious Adverse Events
	Metastatic Breast Cancer Patients
	Affected / at Risk (%)	# Events
Total	3/182 (1.6%)
Neoplasms benign, malignant and unspecified (incl cysts and polyps)
Death	3/182 (1.6%)	3
Other (Not Including Serious) Adverse Events
	Metastatic Breast Cancer Patients
	Affected / at Risk (%)	# Events
Total	0/182 (0%)

Limitations/Caveats

[Not Specified]

More Information

Certain Agreements

All Principal Investigators ARE employed by the organization sponsoring the study.

There is NOT an agreement between Principal Investigators and the Sponsor (or its agents) that restricts the PI's rights to discuss or publish trial results after the trial is completed.