Multimodal Liquid-Biopsy Omics Biomarkers of Treatment Response in Breast Cancer

Exploration of Treatment-Response Biomarkers in Breast Cancer Based on Integrated Liquid-Biopsy Multimodal Omics Features

This single-center cohort study integrates humoral immune response profiling (Phage ImmunoPrecipitation Sequencing, PhIP-seq) with circulating cell-free DNA (cfDNA) genomic and epigenomic features, exosome transcriptomics, and plasma metabolomics to discover and validate liquid-biopsy biomarkers of treatment response in breast cancer.

The study comprises four cohorts: (1) a retrospective pan-cancer cohort of approximately 1,000 patients with solid malignant tumor, using archived residual serum/plasma to construct a pan-cancer antigen repertoire and cfDNA mutational/methylation atlas, with priority given to patients who had available Whole Exome Sequencing (WES) data; (2) a prospective cohort of 800 women with non-metastatic (M0) breast cancer receiving standard neoadjuvant chemotherapy (NAC); (3) a prospective cohort of 100 women with metastatic (M1) breast cancer receiving standard systemic therapy; and (4) a control group of 100 individuals, including patients with benign breast disease (breast fibroadenoma) and healthy volunteers.

The primary objective is to identify biomarkers-autoantibody repertoires, cfDNA mutation clearance, methylation reprogramming, exosome transcripts, and metabolic signatures-associated with pathological complete response (pCR) to NAC, and to develop predictive models where feasible.

Study Overview

• Status: Recruiting
• Conditions: Stomach Cancer; Breast Cancer; Hepatocellular Carcinoma; Colorectal Cancer; Lung Cancer Non-small Cell

Detailed Description

Peripheral blood (20 mL) is collected at protocol-defined time points. Serum/Plasma autoantibody repertoires are profiled by PhIP-seq(phage-display immunoprecipitation sequencing); cfDNA methylation is measured by bisulfite-free methylome profiling; exosome RNA is profiled by strand-specific RNA sequencing; and untargeted plasma metabolomics is performed by liquid chromatography-tandem mass spectrometry. The study endpoints include clinical response and pathological complete response after NAC, together with survival follow-up. The study is conducted in accordance with the Declaration of Helsinki and Chinese regulations for investigator-initiated research, and has been approved by the institutional ethics committee.

Ambispective - a retrospective pan-cancer cohort (archived samples, 2020 Jan - 2026. Sep) combined with prospective breast cancer cohorts (enrollment 2026. Oct -2029)

• Study Type: Observational
• Enrollment (Estimated): 2000

Contacts and Locations

• Study Contact: Name: Kai Chen Principal Investigator, MD, PhD; Phone Number: +86 0660-3863000; Email: chenkai23@mail.sysu.edu.cn

Study Locations

• China
  • Guangdong
    • Shanwei, Guangdong, China, 516601
      • Recruiting
      • Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University
      • Contact: Kai Chen Principal Investigator, MD, PhD; Phone Number: +86 0660-3863000; Email: chenkai23@mail.sysu.edu.cn

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years to 80 years (Adult, Older Adult)
• Accepts Healthy Volunteers: Yes
• Genders Eligible for Study: All

• Sampling Method: Non-Probability Sample

Study Population

Study participants will be selected from three main sources: (1) healthy female volunteers recruited for this study; (2) patients receiving clinical treatment at our institution; and (3) patients undergoing relevant diagnostic or clinical examinations at our institution.

Description

Inclusion Criteria:

Retrospective pan-cancer cohort:

1. Aged 18 to 80 years;
2. Both genders
3. Clinically and histopathologically confirmed diagnosis of solid malignant tumors, including but not limited to non-small cell lung cancer, colorectal cancer, gastric cancer, hepatocellular carcinoma, or breast cancer.
4. Complete clinical data available, including definitive TNM stage and established treatment plan;
5. Archived peripheral blood samples (serum/plasma) collected during routine clinical care.

Prospective neoadjuvant chemotherapy (NAC) breast cancer cohort:

1. Female, aged 18 to 80 years (inclusive);
2. Clinically and pathologically confirmed non-metastatic (M0) breast cancer;
3. Planned standard NAC at the study site, with complete pre-treatment ER, PR, and HER2 immunohistochemistry results available;
4. Voluntary participation with signed written informed consent.

Prospective metastatic breast cancer cohort:

1. Female, aged 18 to 80 years (inclusive);
2. Clinically and pathologically confirmed metastatic (M1) breast cancer;
3. Planned standard systemic therapy at the study site, with complete ER, PR, and HER2 immunohistochemistry results available;
4. Voluntary participation with signed written informed consent.

Benign/Healthy control group:

1. Healthy female volunteers, or female patients with breast fibroadenoma undergoing minimally invasive biopsy during the same period;
2. Voluntary participation with signed written informed consent.

Exclusion Criteria:

For prospective breast cancer cohorts:

1. History of mastitis, or systemic rheumatic/autoimmune diseases (e.g., systemic lupus erythematosus, rheumatoid arthritis);
2. Acute or chronic infectious diseases within the past 6 months (e.g., pneumonia, pulmonary tuberculosis, active hepatitis);
3. Long-term use of glucocorticoids, immunosuppressants, biologic agents, or psychotropic medications (short-term or as-needed use excepted);
4. Inability or refusal to provide informed consent.

Study Plan

How is the study designed?

Design Details

• Observational Models: COHORT
• Time Perspectives: OTHER

Number of groups / cohorts

4

Cohorts and Interventions

Group / Cohort
Retrospective Pan-Cancer Cohort; Patients aged 18-80 years with histologically confirmed solid malignant tumors( e.g. non-small cell lung cancer, colorectal cancer, gastric cancer, hepatocellular carcinoma, or breast cancer), diagnosed at the study site between January 2020 and Sep 2026, with complete clinical data (TNM stage and treatment plan) and archived residual serum/plasma samples. Approximately 1,000 cases.
Prospective Neoadjuvant Chemotherapy (NAC) Breast Cancer Cohort; Women aged 18-80 years with clinically and pathologically confirmed non-metastatic (M0) breast cancer who plan to receive standard NAC at the study site, with complete pre-treatment ER, PR, and HER2 immunohistochemistry results. Planned enrollment: 800. Peripheral blood (20 mL) is collected before, during, and after NAC (pre-surgery), in addition to routine clinical data.
Prospective Benign/Control Group (Breast Fibroadenoma or Healthy Volunteers); Patients with breast fibroadenoma undergoing minimally invasive biopsy during the same period, serving as benign controls to calibrate background signals of circulating antigens and liquid-biopsy analytes. Healthy female volunteers will also be enrolled. Planned enrollment: 100.
Prospective Metastatic Breast Cancer Cohort; Women aged 18-80 years with clinically and pathologically confirmed metastatic (M1) breast cancer who plan to receive standard systemic therapy at the study site, with complete ER, PR, and HER2 immunohistochemistry results.Planned enrollment: 100. Serial peripheral blood samples are collected before, during, and after treatment.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Pathological Complete Response (pCR) Rate	Proportion of patients achieving pCR after completion of neoadjuvant chemotherapy, defined as ypT0/is ypN0 (no invasive cancer in the breast and ipsilateral axillary lymph nodes; ductal carcinoma in situ may be present), consistent with RCB-0.	At definitive surgery after completion of NAC (approximately 4-6 months after NAC initiation)

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Residual Cancer Burden (RCB) Class	RCB class (RCB-0, RCB-I, RCB-II, RCB-III) quantifying residual tumor in the breast and lymph nodes after neoadjuvant therapy, calculated using the internationally validated MD Anderson Cancer Center RCB calculator based on standardized pathological assessment of surgical specimens.	At definitive surgery after completion of NAC (approximately 4-6 months after NAC initiation)
Invasive Disease-Free Survival (iDFS)	Time from enrollment to the first occurrence of any of the following: ipsilateral invasive breast cancer recurrence, contralateral invasive breast cancer, distant metastasis, second primary non-breast invasive malignancy, or death from any cause (conservative definition including all deaths), per established consensus definitions. Follow-up includes clinical visits and imaging (breast ultrasound/MRI, chest-abdominal CT, bone scan as risk-stratified) every 6 months.	From enrollment until event or study end, assessed every 6 months (up to approximately 5 years)
Progression-Free Survival (PFS)	Time from enrollment to the first radiographically confirmed disease progression (per RECIST 1.1) or death from any cause. This outcome is only available for M1 patients.	From enrollment until event or study end (up to approximately 5 years)
Overall Survival (OS)	Time from enrollment to death from any cause. Death events are confirmed by death certificates, hospital records, or national vital registration systems. Patients lost to follow-up are censored at the date of last contact.	From enrollment until death or study end (up to approximately 5 years or longer)

Collaborators and Investigators

• Sponsor: Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University
• Collaborators: Shenshan Medical Center of Sun Yat-sen Memorial Hospital

Study record dates

Study Major Dates

• Study Start (Actual): October 12, 2026
• Primary Completion (Estimated): June 30, 2030
• Study Completion (Estimated): December 30, 2034

Study Registration Dates

• First Submitted: October 11, 2026
• First Submitted That Met QC Criteria: October 11, 2026
• First Posted (Actual): October 19, 2026

Study Record Updates

• Last Update Posted (Actual): November 12, 2026
• Last Update Submitted That Met QC Criteria: November 9, 2026
• Last Verified: November 1, 2026

More Information

Terms related to this study

• Keywords: Liquid biopsy; Neoadjuvant chemotherapy; Pathological complete response; cfDNA methylation; PhIP-seq
• Additional Relevant MeSH Terms: Neoplasms by Site; Neoplasms; Intestinal Diseases; Respiratory Tract Diseases; Neoplasms by Histologic Type; Gastrointestinal Neoplasms; Digestive System Neoplasms; Digestive System Diseases; Gastrointestinal Diseases; Stomach Diseases; Intestinal Neoplasms; Rectal Diseases; Lung Diseases; Liver Diseases; Neoplasms, Glandular and Epithelial; Adenocarcinoma; Liver Neoplasms; Respiratory Tract Neoplasms; Thoracic Neoplasms; Colonic Diseases; Lung Neoplasms; Skin Diseases; Breast Diseases; Carcinoma; Carcinoma, Bronchogenic; Bronchial Neoplasms; Skin and Connective Tissue Diseases; Stomach Neoplasms; Carcinoma, Hepatocellular; Colorectal Neoplasms; Breast Neoplasms; Carcinoma, Non-Small-Cell Lung
• Other Study ID Numbers: 2026-SSKY-048; 2026-SSKY-048 (Other Identifier: Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University)

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: UNDECIDED

IPD Plan Description

De-identified individual participant data may be made available upon reasonable request to the corresponding investigator after publication of the primary results, subject to institutional and ethics committee approval.

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No