LBPO.CL02 · 临床研究 · Late-Breaking
ctDNA false negativity in colorectal cancer reflects CMS3 phenotype and DNASE1L3 positive macrophages, identifying recurrence prone subgroup
作者与单位
摘要 Abstract
Circulating tumor DNA (ctDNA) assays are increasingly used for minimal residual disease (MRD) detection in colorectal cancer (CRC), yet false-negative results remain a critical limitation. We aimed to identify biological determinants of ctDNA false-negativity and evaluate their prognostic significance.
From a nationwide prospective registry (CIRCULATE-JAPAN), we first analyzed 1,727 stage II-III CRC patients with preoperative ctDNA results; 82 (4.7%) were ctDNA-negative at baseline. We sequenced 1,290 tumors with available tissue and subdivided them into a discovery cohort (n=737; 48 ctDNA-negative) and a validation cohort (n=553; 36 ctDNA-negative) using stratified sampling. Multi-omics integration included whole-exome sequencing, bulk RNA-seq, and ctDNA assay data. Single-cell RNA sequence was performed on ctDNA-negative tumors. Disease-free survival (DFS) was assessed in 920 evaluable patients.
Preoperative ctDNA-negative tumors were enriched in right-sided CRC and exhibited a low-proliferation phenotype with negative enrichment of G2/M checkpoint and MYC signaling pathways. Transcriptomic classification revealed predominant Consensus Molecular Subtype (CMS) 3. Mutation analysis showed RAS/RAF pathway alterations ( KRAS / BRAF ) were significantly more frequent in ctDNA-negative tumors. ctDNA‑negative tumors showed significantly higher DNASE1L3 expression-a macrophage‑secreted nuclease-localized to resident/C1QC‑type macrophages and mutually exclusive with pro‑tumor, SPP1‑positive tumor associated macrophage that co‑vary with CAF abundance; this pattern supports enhanced extracellular DNA digestion in the tumor microenvironment (TME) as a contributor to reduced ctDNA detectability. Clinically, ctDNA negativity trended toward improved DFS versus ctDNA positivity (HR 2.01, P=0.087). However, within ctDNA-negative patients, high DNASE1L3 expression identified a subgroup with significantly higher recurrence risk (P=0.03). Among relapse cases, DNASE1L3 expression was higher in patients with false-negative ctDNA at recurrence.
ctDNA detectability reflects both tumor cell state and TME-mediated DNA clearance. DNASE1L3 emerges as a biological contributor to ctDNA false-negativity and a prognostic marker that uncovers a recurrence-prone subgroup among ctDNA-negative CRC patients. These findings highlight the need for DNASE1L3-informed MRD interpretation and tailored surveillance strategies.
利益披露 Disclosure
H. Ebi,
AMGEN Independent Contractor.
Chugai Pharmaceutical Independent Contractor.
AstraZeneca Independent Contractor.
Guardant Independent Contractor.
Konica Minolta Independent Contractor.
Riken Genesis Independent Contractor.
Amoy Diagnostics Independent Contractor, ).
Astellas Pharmaceutical Independent Contractor, ).
Incyte Independent Contractor.
Ono Pharmaceutical Independent Contractor.
Merck Biopharma Independent Contractor.
Boehringer Ingelheim Independent Contractor.
Otsuka Pharmaceutical Independent Contractor.
Bristol-Myers Squibb Independent Contractor.
Cyberomix Independent Contractor.
R. Yamaguchi, None.
Y. Nakamura,
Becton, Dickinson and Company, CareNet, Inc., Chugai Pharmaceutical Co., Ltd., Daiichi Sankyo Co., Ltd., Eisai Co., Ltd., Exact Sciences Corporation, Genomedia Inc., Gilead Sciences, Inc. Independent Contractor.
Hisamitsu Pharmaceutical Co., Inc., Merck Biopharma Co., Ltd., Miyarisan Pharmaceutical Co., Ltd., MSD K.K., Natera, Inc., Premo Partners, Inc., Roche Diagnostics K.K., Roche Ltd., Seagen, Inc. Independent Contractor.
Taiho Pharmaceutical Co., Ltd., Takeda Pharmaceutical Co., Ltd., Tempus Labs, Inc., Zeria Pharmaceutical Co., Ltd. Independent Contractor.
Tempus Labs, Inc., Roche Diagnostics K.K., Genomedia Inc., ).
Daiichi Sankyo Co., Ltd, Chugai Pharmaceutical Co., Ltd., Guardant Health Independent Contractor, ).
S. Kisoda, None.
J. Watanabe,
Johnson and Johnson, Medtronic, Eli Lilly, Takeda Pharmaceuticals Independent Contractor.
Medtronic, AMCO, TERUMO, Stryker Japan ).
O. Muto, None..
H. Yukami, None.
S. Mishima,
Taiho Pharmaceutical Co., Ltd., Chugai Pharmaceutical Co., Ltd., Eli Lilly CO, Ltd. Independent Contractor.
H. Bando,
Ono Pharmaceutical Independent Contractor, ).
Eli Lilly Japan, and Taiho Pharmaceutical. Independent Contractor.
H. Taniguchi,
MSD K.K, Merck Biopharma, Taiho, Lilly Japan, Bristol-Myers Squibb Japan, Chugai Pharmaceutical, Ono Yakuhin, Amgen Independent Contractor.
Takeda Phamaceutical Independent Contractor, ).
Daiichi Sankyo ).
I. Takemasa,
Johnson &Johnson, Intuitive, Medicaroid, Eli Lilly Independent Contractor.
Medtronic Independent Contractor, ).
Sysmex ).
T. Kato, None.
A. Aleshin,
Natera, Inc. Stock.
D. Kotani,
Takeda, Chugai, Lilly, Seagen, Guardant Health, Eisai, Taiho, Bristol Myers Squibb, Daiichi-Sankyo, Pfizer, Merck biopharma, and Sysmex Independent Contractor.
Novartis, Servier, Janssen, IQVIA, Syneoshealth, CIMIC, Cimicshiftzero ).
Ono, MSD, Independent Contractor, ).
I. Imoto, None.
E. Oki,
Guardant Health, Inc.; ).
Chugai Pharmaceutical, Bristol Meyers, Ono Pharmaceutical., Eli Lilly, Takeda Pharmaceutical, Glaxosmithkline plc Independent Contractor.
M. Aoki, None.
T. Yoshino,
Chugai Pharmaceutical, Ono Pharmaceutical, Takeda Pharmaceutical Independent Contractor, ).
Merck Biopharma, Bayer Yakuhin, and MSD K.K, Sumitomo Corp Independent Contractor.
Amgen, Bristol-Myers Squibb, Daiichi Sankyo, Eisai, FALCO biosystems, Genomedia, Medical & Biological Laboratories, Merus N.V., Molecular Health GmbH, MSD, Nippon Boehringer Ingelheim, Pfizer Japan ).
Roche Diagnostics, Sanofi, Sysmex, Taiho Pharmaceutical ).