bims-tumhet 2025-06-08 papers

bims-tumhet

Biomed News

on Tumor heterogeneity

Issue of 2025–06–08
twenty-one papers selected by
Sergio Marchini, Humanitas Research

Tumor-stroma proportion on primary tumor as a prognostic biomarker in advanced ovarian cancer patients receiving chemo-immunotherapy as first-line therapy: analyses from the NeoPembrOV/GINECO phase II randomized trial.
cfDNAFE: Comprehensively extracting multi-omics features of cell-free DNA for noninvasive diagnosis.
Tertiary lymphoid structures: exploring opportunities to improve immunotherapy in ovarian cancer.
Plasma cfDNA multi-omic biomarkers profiling for detection and stratification of gastric carcinoma.
Relacorilant and nab-paclitaxel in patients with platinum-resistant ovarian cancer (ROSELLA): an open-label, randomised, controlled, phase 3 trial.
Circulating cell-free DNA methylation as biomarker for lung cancer detection: a systematic review and meta-analysis of diagnostic studies.
Before They Were Malignant.
Chromosomal instability by low-coverage whole-genome sequencing assay predicts prognosis in bladder cancer patients underwent radical cystectomy.
The pivotal role of tertiary lymphoid structures in the tumor immune microenvironment.
Methyl-CODEC enables simultaneous methylation and duplex sequencing.
Comparison of enzymatic and bisulfite conversion of circulating cell-free tumor DNA for DNA methylation analyses.
Elevated ctDNA Tumor Fraction Is Associated with Improved Mutation Detection but Worse Overall Survival in Advanced Non-Small Cell Lung Cancer: a Lung-MAP Study.
Dostarlimab and niraparib in primary advanced ovarian cancer.
cfTools: an R/Bioconductor package for deconvolving cell-free DNA via methylation analysis.
Longitudinal and multisite sampling reveals mutational and copy number evolution in tumors during metastatic dissemination.
Comprehensive tumor-agnostic evaluation of genomic and epigenomic-based approaches for the identification of circulating tumor DNA in early-stage breast cancer.
Spatial omics technology potentially promotes the progress of tumor immunotherapy.
Peri-operative atezolizumab in early-stage triple-negative breast cancer: final results and ctDNA analyses from the randomized phase 3 IMpassion031 trial.
Determination of the position of DNA Methylation and Base Modifications Using a Biological Nanopore.
Evaluation of automatic cell free DNA extraction metrics using different blood collection tubes.
Cancer more deadly when tumours lack Y chromosomes - and the loss could be contagious.

ESMO Open. 2025 Jun 04. pii: S2059-7029(25)00973-1. [Epub ahead of print]10(6): 105104

Tumor-stroma proportion on primary tumor as a prognostic biomarker in advanced ovarian cancer patients receiving chemo-immunotherapy as first-line therapy: analyses from the NeoPembrOV/GINECO phase II randomized trial.

L Collet, J-C Noël, X Catteau, M Ardin, J Berthet, S Ghamry-Barrin, I Treilleux, L Bengrine Lefevre, M Martinez, F Rothé, C Sotiriou, C Caux, B Dubois, I Ray-Coquard, O Le Saux.

   BACKGROUND: The efficacy of immune checkpoint inhibitors is limited in patients with high-grade serous ovarian cancer (HGSC). The predictive and prognostic value of tumor-stroma proportion (TSP) was assessed in patients with HGSC treated with platinum-based chemotherapy and pembrolizumab in the NeoPembrOV trial.
MATERIALS AND METHODS: TSP was quantified as the relative proportion of stromal tissue to tumor cells (low if <30% or high if ≥30%). RNA sequencing and multiplex immunofluorescence were conducted.
RESULTS: TSP was assessed on 85 pre-treatment samples. Patients with a low TSP had a prolonged progression-free survival (PFS) compared with those with a high TSP (median PFS 23.4 versus 18.3 months, respectively, hazard ratio 0.51, 95% confidence interval 0.31-0.83, P = 0.010). The prognostic impact was higher when TSP was assessed on tubo-ovarian primary tumors (P = 0.01) and remained significant in the pembrolizumab arm (P = 0.01). Tumors with a low TSP were enriched in intratumoral CD8+PD1+ T cells and stromal proliferative CD8+Ki67+ T cells, while tumors with a high TSP exhibited an enrichment in M2 macrophages. A significant increase in intratumoral CD8+ T cells following pembrolizumab was observed only in low-TSP tumors (P = 0.02).
CONCLUSIONS: We confirmed the prognostic value of TSP in HGSC and demonstrated its significance in patients treated with chemo-immunotherapy. TSP is associated with an immunosuppressive tumor microenvironment and influences CD8+ T-cell enrichment with immunotherapy.

Keywords:  high-grade serous ovarian cancer; immunotherapy; platinum-based chemotherapy; tumor microenvironment; tumor–stroma proportion

DOI:  https://doi.org/10.1016/j.esmoop.2025.105104
Methods. 2025 Jun 03. pii: S1046-2023(25)00134-3. [Epub ahead of print]

cfDNAFE: Comprehensively extracting multi-omics features of cell-free DNA for noninvasive diagnosis.

Wanxin Cui, Junjie You, Wenlong Jie, Zihao Li, Xiaoqing Peng.

  The tissues-of-origin of circulating cell-free DNA (cfDNA) holds great promise for non-invasive diagnosing cancers, monitoring allograft rejection, and prenatal testing. Many features for inferring the tissues-of-origin of cfDNAs are being revealed from different angles, including genetics, epigenetics, and fragmentomics, with whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data of cfDNA. However, it lacks integrative toolkits for automatically extracting the revealed features from the WGS and WGBS data of cfDNA samples. Here, we propose cfDNAFE, a comprehensive and easy-to-use python package for extracting multi-omics features from the aligned cfDNA sequencing data. It covers three aspects: cfDNA genetic features, cfDNA methylation features, and cfDNA fragmentation features, including 13 types of feature profiles. The genetic features include substitution mutations, mutation signatures and copy number variations. The methylation features are the proportions of methylated fragments, unmethylated fragments, and mixed methylated fragments on cell-type-specific markers. The fragmentation features related to the fragment sizes, end/breakpoint motifs, and nucleosome positions are also integrated. To verify the functions of cfDNAFE, we perform analysis on the WGS/WGBS data of cfDNA samples based on the feature profiles extracted by cfDNAFE. The comparison between the cfDNA samples of hepatocellular carcinoma (HCC) patients and normal controls suggests HCC cfDNA samples exhibit significant difference in fragment size related features and breakpoint/end motif patterns, and obtain significant higher OCF values in the liver-specific open regions than the health controls. Conclusively, cfDNAFE is a most comprehensive toolkit which covers the most features for inferring the tissues-of-origin of cfDNAs in existing studies up to date. It will facilitate researchers to build machine learning models for auxiliary diagnosis based on these features. Availability and implementation: https://github.com/Cuiwanxin1998/cfDNAFE.

Keywords:  cell-free DNA; fragmentation; methylation; mutations; noninvasive diagnosis

DOI:  https://doi.org/10.1016/j.ymeth.2025.05.013
Front Immunol. 2025 ;16 1473969

Tertiary lymphoid structures: exploring opportunities to improve immunotherapy in ovarian cancer.

Aaron Varghese, Suzanne M Hess, Shanmuga Chilakapati, Jose R Conejo-Garcia, A J Robert McGray, Emese Zsiros.

  Tertiary lymphoid structures (TLS) are organized ectopic lymphoid clusters of immune cells that develop in non-lymphoid tissue to promote antigen presentation, drive cytotoxic immune responses, and enhance humoral immunity via B cell clonal expansion. Their presence within the tumor microenvironment (TME) correlates with increased patient survival and an improved response to immune checkpoint inhibitors (ICIs), positioning TLS as potential predictive and prognostic biomarkers. Despite the widespread use of ICIs across various cancers, their effectiveness remains limited in gynecological malignancies, including ovarian cancer (OC), a notably challenging disease characterized by poor responses to both single and combination ICI therapies. Interestingly, the infiltration of T cells into the OC TME is linked to enhanced progression-free survival (PFS) and overall survival (OS), yet an immunosuppressive TME frequently impedes therapeutic efficacy, suggesting cell activity within localized immune niches can impact antitumor immunity. This review explores the roles of TLS, their maturity, functionality, identification, and related gene signatures; specific immune cells and cytokines that play a role in TLS formation and antitumor response; and other modifiable elements, including gut microbiota, that may drive improving OC survival by leveraging a TLS-driven antitumor response to bolster immunotherapy outcomes.

Keywords:  biomarkers; gut microbiome; immunotherapy; ovarian cancer; tertiary lymphoid structures; tumor microenvironment

DOI:  https://doi.org/10.3389/fimmu.2025.1473969
BMC Cancer. 2025 Jun 05. 25(1): 1003

Plasma cfDNA multi-omic biomarkers profiling for detection and stratification of gastric carcinoma.

Shiyi Song, Xiuli Zhang, Pin Cui, Weihuang He, Jiyuan Zhou, Shubing Wang, Yong Xiong, Shu Xu, Xiaohui Lin, Guozeng Huang, Xiaohua Tan, Qinglong Xu, Yongling Liu, Qingqun Li, Kehua Yuan, Mingji Feng, Hanming Lai, Hui Yang, Shaorong Zhang.

  Despite being the third in death rate among all cancers globally, gastric carcinoma (GC) is far from being detected accurately and timely, which could benefit the prognosis. To achieve this, we performed whole-genome sequencing (WGS) to plasma cfDNA of 733 participants, including healthy individuals, patients with benign gastric diseases and GC patients. The multi-omic biomarkers in this study, including fragmentation profile, end motif and genome-wide Copy Number Variations (CNV) of plasma cfDNA, are recently developed means for cancer detection and monitoring. And these biomarkers were extracted from WGS data to build machine learning algorithm based classifiers, prediction models, to discriminate GC patients from healthy individuals, achieving extremely high precision of sensitivity at 94.87% and specificity at 99.35%. Therefore, these cfDNA multi-omic biomarkers may serve as means to detect GC accurately, affordably and timely.

Keywords:  Cell-free DNA(cfDNA); Epigenetic modification; Gastric carcinoma(GC); Machine learning; Transcription factor binding site(TFBS); Whole genome sequencing (WGS)

DOI:  https://doi.org/10.1186/s12885-025-14409-0
Lancet. 2025 Jun 02. pii: S0140-6736(25)01040-2. [Epub ahead of print]

Relacorilant and nab-paclitaxel in patients with platinum-resistant ovarian cancer (ROSELLA): an open-label, randomised, controlled, phase 3 trial.

Alexander B Olawaiye, Laurence Gladieff, David M O'Malley, Jae-Weon Kim, Gabriel Garbaos, Vanda Salutari, Lucy Gilbert, Linda Mileshkin, Alix Devaux, Elizabeth Hopp, Yong Jae Lee, Ana Oaknin, Mariana Scaranti, Byoung-Gie Kim, Nicoletta Colombo, Michael E McCollum, Connie Diakos, Andrew Clamp, Aliza L Leiser, Boglárka Balázs, Bradley J Monk, Giuseppa Scandurra, Emily McClung, Emilie Kaczmarek, Brian Slomovitz, Helena De La Cueva, Aknar Freire de Carvalho Calabrich, Chiara Cassani, Benoit You, Toon Van Gorp, Cristina Churruca, Giuseppe Caruso, Shibani Nicum, Andrea Bagaméri, Grazia Artioli, Lubomir Bodnar, Sokbom Kang, Ignace Vergote, Amanda Kesner-Hays, Hristina I Pashova, Sachin G Pai, Iulia Cristina Tudor, Adrian M Jubb, Domenica Lorusso.

BACKGROUND: Relacorilant, a first-in-class selective glucocorticoid receptor antagonist, increases a tumour's sensitivity to chemotherapy by reducing cortisol signalling. This study aimed to show whether the addition of relacorilant to nab-paclitaxel improves progression-free and overall survival in females with platinum-resistant ovarian cancer.
METHODS: This randomised, controlled, open-label phase 3 trial (ROSELLA [GOG-3073/ENGOT-ov72]) was done at 117 hospitals and community oncology treatment centres in 14 countries across Australia, Europe, Latin America, North America, and South Korea. Patients had to be aged 18 years or older and had to have a confirmed diagnosis of platinum-resistant, epithelial (ie, high-grade serous, endometrioid, or carcinosarcoma with a ≥30% epithelial component) ovarian, primary peritoneal, or fallopian tube cancer; up to three previous lines of anticancer therapy and previous bevacizumab and disease progression or intolerance to the most recent therapy; measurable disease according to the Response Evaluation Criteria in Solid Tumours (RECIST; version 1.1); an Eastern Cooperative Oncology Group performance status of 0 or 1; and adequate organ function. Patients were assigned (1:1) to relacorilant (150 mg orally the day before, of, and after nab-paclitaxel infusion) plus nab-paclitaxel (80 mg/m2 intravenously on days 1, 8, and 15 of each 28-day cycle) or nab-paclitaxel monotherapy (100 mg/m2 intravenously on the aforementioned schedule). The dual primary endpoints were progression-free survival assessed by blinded independent central review per Response Evaluation Criteria in Solid Tumours (version 1.1) and overall survival, and were assessed in all randomly assigned patients by intention to treat. The safety population included all randomly assigned patients who received at least one dose of the assigned treatment. This trial was registered at ClinicalTrials.gov, NCT05257408, and is ongoing.
FINDINGS: Between Jan 5, 2023, and April 8, 2024, 381 patients were randomly assigned to the combination group (n=188) or to the nab-paclitaxel monotherapy group (n=193). Patients receiving relacorilant plus nab-paclitaxel had a statistically significant improvement in progression-free survival assessed by blinded independent central review compared with those receiving nab-paclitaxel monotherapy (hazard ratio 0·70 [95% CI 0·54-0·91]; median 6·54 months [95% CI 5·55-7·43] vs 5·52 months [3·94-5·88]; stratified log-rank p=0·0076). At the planned interim analysis, there was a clinically meaningful difference in overall survival with the addition of relacorilant to nab-paclitaxel (0·69 [95% CI 0·52-0·92]; 15·97 months [95% CI 13·47-not reached] vs 11·50 months [10·02-13·57]; log-rank p=0·0121). Adverse events were similar across study groups when adjusted for nab-paclitaxel exposure; no new safety signals were observed.
INTERPRETATION: The addition of relacorilant to nab-paclitaxel prolonged progression-free survival and interim results also showed an improvement in overall survival. Together, the results position the combination of relacorilant and nab-paclitaxel as a potential new standard treatment for patients with platinum-resistant ovarian cancer.
FUNDING: Corcept Therapeutics.

DOI: https://doi.org/10.1016/S0140-6736(25)01040-2
Syst Rev. 2025 Jun 02. 14(1): 120

Circulating cell-free DNA methylation as biomarker for lung cancer detection: a systematic review and meta-analysis of diagnostic studies.

Diana Inês Machado, Tiago Brito-Rocha, Sofia Salta, Teresa Monjardino, Rui Henrique, Carmen Jerónimo.

  Lung cancer (LC) is the most incident malignancy and a leading cause of cancer-related fatalities. The lack of dissemination of effective screening tools hinders early detection, resulting in late-stage diagnosis, mostly associated with high mortality. Gene-specific methylation alterations detected in plasma or serum circulation cell-free DNA (ccfDNA) have been investigated as a possible screening tool. Thus, the main aim of this systematic review and meta-analysis was to critically assess published data on the use of ccfDNA methylation-based biomarkers for detection of LC. PubMed, including MEDLINE and Scopus databases, were systematically searched for eligible articles evaluating the diagnostic performance of ccfDNA methylation alterations in that setting. A bivariate random-effect model was employed to calculate pool estimated sensitivity and specificity. Accuracy subgroup analyses, according to histological subtype, stage, and smoker status were carried out. A total of 1961 articles were retrieved, of which 44 met inclusion criteria. The meta-analysis generated a pooled sensitivity of 54% (CI 95% 48-60%) and a pooled specificity of 86% (CI 95% 83-87%) for LC detection. The most frequently tested host-genome methylation markers were RASSF1 A, APC, SHOX2, SOX17, and HOXA9. Overall, methylation analysis of ccfDNA detects LC with high specificity but modest sensitivity. Further research is required to improve diagnostic performance, establish methodological standards and determine whether this might complement existing screening strategies to increase effectiveness. Systematic review registration PROSPERO CRD42023408964.

Keywords:  Biomarkers; DNA methylation; Early detection; Liquid biopsies; Lung cancer; Screening

DOI:  https://doi.org/10.1186/s13643-025-02860-w
Cancer Discov. 2025 Jun 03. 15(6): 1093-1095

Before They Were Malignant.

Maria Sol Recouvreux, Sandra Orsulic.

A lack of understanding of how ovarian cancer originates in fallopian tube cells has hindered early detection and prevention, often resulting in diagnosis at advanced stages when treatment options are limited. In this issue of Cancer Discovery, two studies uncover critical microenvironmental changes that drive tumor initiation and progression, offering potential targets for earlier intervention. See related article by Kader et al., p. 1180 See related article by Garcia et al., p. 1203.

DOI: https://doi.org/10.1158/2159-8290.CD-25-0429
BMC Med Genomics. 2025 Jun 05. 18(1): 103

Chromosomal instability by low-coverage whole-genome sequencing assay predicts prognosis in bladder cancer patients underwent radical cystectomy.

Qi Ding, Hailiang Zhu, Bo Fan, Lisheng Wang, Xiaohua Jin, Cheng Cao, Ying Shi, Zhijiang Fan, Wenjian Tu, Feng Li.

   PURPOSE: To investigate chromosomal instability (CIN) in tumor tissue from radical bladder resection and to evaluate whether it can be used as a biomarker for the molecular typing of (BC).
METHODS: DNA was extracted from formalin-fixed paraffin-embedded samples of 50 BC patients who were followed up to March 23 2023 using the Qiagen nucleic acid kits. We analyzed CIN in tumor of bladder by low-coverage whole genome sequencing (LC-WGS). Kaplan-Meier log-rank test was used to perform survival analysis. The association between variables and overall and progression-free survival was analyzed using the Cox proportional hazards model.
RESULTS: There were 44 genome segments with statistically significant changes in copy number. CIN was significantly correlated with tumor stage, lymph node metastasis, relapse and survival status. Patients with high CIN were found to have a worse survival, with a median overall survival (OS) of 15 months. In addition, patients with high CIN were more likely to relapse, with a median progression-free survival (PFS) of 7 months. Patients with low CIN showed better OS and PFS. However, there was no significant difference in OS and PFS between T2 and T3-T4 patients. Multivariate cox regression analysis showed that high CIN was an independent predictor of OS, and high CIN and muscle invasion were independent predictors of PFS. Furthermore, patients with abnormal copy number of a single chromosome also had a poor prognosis, with a median survival of 14-30 months for OS and 5-10 months for PFS, while negative patients had a better prognosis.
CONCLUSION: CIN was significantly correlated with tumor stage, lymph node metastasis, relapse and survival status of BC. Patients with high CIN or abnormal copy numbers of a single chromosome have a poor prognosis. CIN might be better than T stage in predicting the prognosis of patients with BC. Molecular typing of CIN can be used as an independent prognostic factor for BC.

Keywords:  Biomarker; Bladder cancer; Chromosomal instability; Low-coverage whole genome sequencing; Prognosis

DOI:  https://doi.org/10.1186/s12920-025-02172-x
Front Oncol. 2025 ;15 1616904

The pivotal role of tertiary lymphoid structures in the tumor immune microenvironment.

Chengsen Liu, Jiandong Cao.

  Tertiary lymphoid structures (TLS) are ectopic lymphoid structures that form in non-lymphoid tissues in response to chronic inflammatory stimulation. Structurally and functionally resembling lymph nodes, TLS are primarily composed of B cells, T cells, dendritic cells, and other immune cell populations. Critically, TLS serve as direct sites for initiating anti-tumor immune responses. Within tumors, TLS facilitate the accumulation of immune cells-particularly effector subsets such as cytotoxic T cells and antibody-producing B cells-in the tumor microenvironment, thereby establishing a localized hub for both cellular and humoral immunity. This localized immune activation correlates with improved patient prognosis and enhanced responses to immunotherapy. In this review, we summarize the organization, formation drivers, detection markers, and the interplay between TLS and tumor-associated genes. Furthermore, we discuss the potential of TLS as biomarkers for immunotherapy efficacy and their translational clinical applications.

Keywords:  TLS; TME; immunotherapy; tertiary lymphoid structure; tumor immune microenvironment

DOI:  https://doi.org/10.3389/fonc.2025.1616904
Nucleic Acids Res. 2025 May 22. pii: gkaf482. [Epub ahead of print]53(10):

Methyl-CODEC enables simultaneous methylation and duplex sequencing.

Ruolin Liu, Farzaneh Darbeheshti, Laurel Walsh, Rachel Li, Jin H Bae, Hayet Radia Zeggar, Azeet Narayan, Kan Xiong, G Mike Makrigiorgos, Viktor A Adalsteinsson.

DNA mutations and methylation often contribute to disease development in a synergistic manner. While duplex sequencing is the most accurate method for detecting DNA mutations, it typically lacks the ability to simultaneously assess methylation or requires many reads. Here, we developed Methyl-CODEC to enable simultaneous methylation sequencing and duplex sequencing using single read pairs. To achieve this, Methyl-CODEC links an enzymatically deaminated sense strand to the reverse complement of the antisense strand, which is protected from conversion by using conversion-resistant dCTPs in the strand linking step. Methyl-CODEC shows high concordance with standard enzymatic or bisulfite-based whole genome methylation sequencing, while also uniquely preserving the original DNA sequence. We show that hydroxy-methyl-dCTP is superior in this regard relative to other conversion-resistant dCTPs. Methyl-CODEC improves genetic sequencing accuracy, enables better read alignment for next-generation sequencing, and distinguishes C > T mutations from unmethylated Cs. It also identifies rare mutations including those producing methylated Cs, which are enriched in CpG contexts. Methyl-CODEC opens new horizons for enhanced detection of biomarkers in cancer and molecular medicine.

DOI: https://doi.org/10.1093/nar/gkaf482
Clin Epigenetics. 2025 Jun 04. 17(1): 93

Comparison of enzymatic and bisulfite conversion of circulating cell-free tumor DNA for DNA methylation analyses.

Stine H Kresse, Evy Marie Thorkildsen, Sara Brandt-Winge, Heidi Pharo, Hege Marie Vedeld, Guro E Lind.

   BACKGROUND: Detection of DNA methylation biomarkers in circulating cell-free DNA (cfDNA) has great clinical potential for cancer management, but there is a high need for method optimization and standardization. Bisulfite conversion of DNA is the gold-standard pre-treatment method for DNA methylation analyses, but causes also DNA fragmentation and loss. Enzymatic conversion of DNA represents a promising alternative due to the more gentle treatment minimizing damage to DNA. The aim of this study was to evaluate and compare enzymatic and bisulfite conversion to identify the best pre-treatment method for detecting DNA methylation biomarkers in cfDNA from plasma using droplet digital PCR (ddPCR).
RESULTS: The performance of the NEBNext Enzymatic Methyl-seq Kit (both the full kit intended for sequencing and the sub-component NEBNext Enzymatic Methyl-seq Conversion Module) and the EpiTect Plus DNA Bisulfite Kit was evaluated and compared using normal cfDNA and tumor cfDNA samples from colorectal cancer patients. The cytosine conversion efficiency was 99-100% for both enzymatic and bisulfite conversion. Enzymatic conversion resulted in longer DNA fragments with higher peak fragment sizes compared to bisulfite conversion, but the DNA recovery was considerably lower after enzymatic conversion (34-47%) compared to bisulfite conversion (61-81%). For enzymatic conversion, the full kit gave slightly better DNA recovery than the conversion module. A comparison of five magnetic bead brands, as well as several different magnetic bead-to-sample ratios revealed no major improvements in DNA recovery for the enzymatic conversion. DNA methylation of the biomarker BCAT1 was detected at similar rates in parallel tumor cfDNA samples pre-treated with either enzymatic or bisulfite conversion. However, enzymatic conversion resulted in lower number of positive droplets for both target and control ddPCR assays, in line with the lower DNA recovery after conversion.
CONCLUSIONS: Based on a thorough evaluation of enzymatic and bisulfite conversion of cfDNA using ddPCR, bisulfite conversion emerges as the best pre-treatment method due to higher DNA recovery after conversion and higher number of positive droplets in the ddPCR reactions.

Keywords:  Bisulfite conversion; Circulating cell-free tumor DNA; Colorectal cancer; DNA methylation; Enzymatic Methyl-seq; Enzymatic conversion; Liquid biopsy; Magnetic beads; Plasma; cfDNA; ctDNA; ddPCR

DOI:  https://doi.org/10.1186/s13148-025-01901-4
Clin Cancer Res. 2025 Jun 04.

Elevated ctDNA Tumor Fraction Is Associated with Improved Mutation Detection but Worse Overall Survival in Advanced Non-Small Cell Lung Cancer: a Lung-MAP Study.

Philip C Mack, Mary W Redman, Hanna Tukachinsky, David E Kozono, Katherine Minichiello, Konstantin H Dragnev, Khaled A Tolba, Joel W Neal, Russell W Madison, Saiama N Waqar, Charu Aggarwal, Fred R Hirsch, Jyoti D Patel, Roy S Herbst, Anne C Chiang, Karen L Reckamp, Karen Kelly, Hossein Borghaei, Jhanelle E Gray, David R Gandara.

PURPOSE: Circulating tumor DNA (ctDNA) is a powerful diagnostic companion to tissue profiling. Tumor fraction (TF) is a global assessment of an individual's ctDNA burden. We evaluated the impact of plasma TF on mutation detection and clinical outcomes in patients with previously treated, advanced NSCLC on Lung-MAP.
EXPERIMENTAL DESIGN: Paired tumor tissue and plasma were collected prospectively from Lung-MAP patients. Plasma was collected within 30 days of a new biopsy with no intervening therapies. Tissue and ctDNA genomic profiling and ctDNA TF levels were assessed by Foundation Medicine. TF was primarily calculated from tumor aneuploidy, defaulting to fragmentomics and maximum somatic allele frequencies when aneuploidy was not detectable. The effect of TF on tissue-plasma mutation concordance, overall survival, and its relation to variant allele frequencies was assessed using linear regression, Lin's coefficient, and Cox modeling/log-rank testing.
RESULTS: 194 patients were eligible for analysis. TF≥1% was significantly associated with improved positive percent agreement (PPA) between ctDNA and tissue across multiple alteration types with the exception of copy number gains. For short variants, PPA improved from 51% when TF<1% to 95% when TF≥1%. TF showed a significant robust correlation with VAF for KRAS, STK11 and TP53 - the three most common mutations. TF<1% were significantly associated with improved patient overall survival compared to TF≥1% or TF≥10%.
CONCLUSIONS: TF provides an accurate, clinically useful assessment of ctDNA plasma levels from patients with refractory, advanced NSCLC. TF levels ≥ 1% are associated with significantly worse overall survival, but improved mutation detection in liquid biopsies.

DOI: https://doi.org/10.1158/1078-0432.CCR-24-3658
Ann Oncol. 2025 May 30. pii: S0923-7534(25)00201-7. [Epub ahead of print]

Dostarlimab and niraparib in primary advanced ovarian cancer.

A-C Hardy-Bessard, E Pujade-Lauraine, R G Moore, F Montestruc, A Redondo, M R Mirza, D Cibula, T-E Ciuleanu, L Gilbert, R Eitan, F Zagouri, S Pignata, R Glasspool, J Pfisterer, R Phaëton, C K Anderson, M Rodrigues, L Gaba, E Bakirtzi, J M Fauci, E Kalbacher, F B Musa, S Gorman, L R Duska, L Gladieff, P Braly, F Joly, J Thomes Pepin, I Ray-Coquard, K N Moore.

   BACKGROUND: The combination of immunotherapies and poly (ADP-ribose) polymerase inhibitors (PARPis) has been hypothesized to improve outcomes in advanced ovarian cancer (aOC). The FIRST/ENGOT-OV44 trial evaluated adding dostarlimab to first-line platinum-based chemotherapy (PBCT) and niraparib maintenance ± bevacizumab in patients with aOC.
PATIENTS AND METHODS: In this randomized, double-blind, phase III trial, patients with newly diagnosed stage III-IV epithelial OC were randomized (1:2) to arm 2 (PBCT-placebo with niraparib maintenance) or arm 3 (PBCT-dostarlimab with dostarlimab-niraparib maintenance); arm 1 (PBCT-placebo with placebo maintenance) enrollment terminated following PARPi approvals. Efficacy was assessed in arms 2 and 3 (intention-to-treat population). The primary endpoint was investigator-assessed progression-free survival (PFS) as per RECIST v1.1. The key secondary endpoint was overall survival (OS). Safety was assessed in patients who received one or more doses of study treatment (arms 1-3; analyzed as per treatment received).
RESULTS: From 14 November 2018 to 5 January 2021, 1138 patients were randomized to arms 2 (n = 385) and 3 (n = 753) and included in efficacy analyses. Median follow-up was 53.1 (interquartile range 47.5-59.7) months. There was a statistically significant difference in PFS in arm 3 versus arm 2 (median 20.6 versus 19.2 months; hazard ratio [HR] 0.85, 95% confidence interval [CI] 0.73-0.99, P = 0.0351). OS had reached 57% maturity and was not statistically significant (median 44.4 versus 45.4 months; HR 1.01, 95% CI 0.86-1.19, P = 0.9060). Toxicities observed were consistent with known safety profiles of the agents used in the study.
CONCLUSIONS: In the first-line treatment of patients with aOC, the addition of dostarlimab to PBCT and niraparib maintenance was associated with a statistically significant, but clinically modest, PFS improvement, with no difference in OS.

Keywords:  PD-(L)1 inhibition; advanced ovarian cancer; dostarlimab; first line; immunotherapy; niraparib

DOI:  https://doi.org/10.1016/j.annonc.2025.05.009
Bioinform Adv. 2025 ;5(1): vbaf108

cfTools: an R/Bioconductor package for deconvolving cell-free DNA via methylation analysis.

Ran Hu, Shuo Li, Mary L Stackpole, Qingjiao Li, Xianghong Jasmine Zhou, Wenyuan Li.

Motivation: Cell-free DNA (cfDNA) released by dying cells from damaged or diseased tissues can lead to elevated tissue-specific DNA, which is traceable and quantifiable through unique DNA methylation patterns. Therefore, tracing cfDNA origins by analyzing its methylation profiles holds great potential for detecting and monitoring a range of diseases, including cancers. However, deconvolving tissue-specific cfDNA remains challenging for broader applications and research due to the scarcity of specialized, user-friendly bioinformatics tools.
Results: To address this, we developed cfTools, an R package that streamlines cfDNA tissue-of-origin analysis for disease detection and monitoring. Integrating advanced cfDNA tissue deconvolution algorithms with R/Bioconductor compatibility, cfTools offers data preparation and analysis functions with flexible parameters for user-friendliness. By identifying abnormal cfDNA compositions, cfTools can infer the presence of underlying pathological conditions, including but not limited to cancer. It simplifies bioinformatics tasks and enables users without advanced expertise to easily derive biologically interpretable insights from standard preprocessed sequencing data, thus increasing its accessibility and broadening its application in cfDNA-based disease studies.
Availability and implementation: cfTools and its supplementary package cfToolsData are freely available at Bioconductor: https://bioconductor.org/packages/release/bioc/html/cfTools.html and https://bioconductor.org/packages/release/data/experiment/html/cfToolsData.html. The development version of cfTools is maintained on GitHub: https://github.com/jasminezhoulab/cfTools.

DOI: https://doi.org/10.1093/bioadv/vbaf108
Nat Genet. 2025 Jun 02.

Longitudinal and multisite sampling reveals mutational and copy number evolution in tumors during metastatic dissemination.

Karena Zhao, Joris Vos, Stanley Lam, Lillian A Boe, Daniel Muldoon, Catherine Y Han, Cristina Valero, Mark Lee, Conall Fitzgerald, Andrew S Lee, Manu Prasad, Swati Jain, Xinzhu Deng, Timothy A Chan, Michael F Berger, Chaitanya Bandlamudi, Xi Kathy Zhou, Luc G T Morris.

To understand genetic evolution in cancer during metastasis, we analyzed genomic profiles of 3,732 cancer patients in whom several tumor sites were longitudinally biopsied. During distant metastasis, tumors were observed to accumulate copy number alterations (CNAs) to a much greater degree than mutations. In particular, the development of whole genome duplication was a common event during metastasis, emerging de novo in 28% of patients. Loss of 9p (including CDKN2A) developed during metastasis in 11% of patients. To a lesser degree, mutations and allelic loss in human leukocyte antigen class I and other genes associated with antigen presentation also emerged. Increasing CNA, but not increasing mutational load, was associated with immune evasion in patients treated with immunotherapy. Taken together, these data suggest that CNA, rather than mutational accumulation, is enriched during cancer metastasis, perhaps due to a more favorable balance of enhanced cellular fitness versus immunogenicity.

DOI: https://doi.org/10.1038/s41588-025-02204-3
ESMO Open. 2025 Jun 04. pii: S2059-7029(25)01155-X. [Epub ahead of print]10(6): 105286

Comprehensive tumor-agnostic evaluation of genomic and epigenomic-based approaches for the identification of circulating tumor DNA in early-stage breast cancer.

M J Elliott, J Kim, A Dou, J Fuentes Antrás, E Amir, M B Nadler, E Van de Laar, C Yu, R Cheikh, A Silvestro, L L Siu, P L Bedard, H K Berman, D W Cescon.

   BACKGROUND: The detection of circulating tumor DNA (ctDNA) after curative-intent therapy, referred to as molecular/minimal residual disease (MRD), is prognostic of disease recurrence in early-stage breast cancer (EBC). Tumor-agnostic approaches that rely on mutation-based assessment in fixed panels of common cancer driver genes have shown limited utility for detecting MRD in EBC. Methylation-based MRD (mMRD) may overcome the limitations of genomic-based MRD (gMRD), though limited clinical validation is available.
MATERIALS AND METHODS: To investigate this, we analyzed 290 longitudinally banked plasma samples from 95 participants diagnosed with early-stage estrogen receptor (ER)-positive/human epidermal growth factor receptor 2-negative (ER-positive) and triple-negative breast cancer (TNBC) undergoing neoadjuvant chemotherapy using a high-sensitivity genomic and epigenomic-based, tumor-agnostic ctDNA platform.
RESULTS: The baseline (pre-chemotherapy) ctDNA detection (mMRD) rate was 72.5% (66/91) across all participants (ER-positive: 33/48, 69%; TNBC: 33/43, 77%). Baseline ctDNA detection (mMRD) was associated with a higher risk of recurrence [hazard ratio (HR) 9.4, 95% confidence interval (CI) 1.3-70.3, P = 0.03]. Detection of ctDNA (mMRD) in the post-operative and follow-up periods were prognostic of worse event-free survival (EFS) (HR 17.0, 95% CI 6.0-48.0, P < 0.0001) with 62.5% sensitivity and 100% specificity for recurrence (positive predictive value 100%). The median lead time from mMRD detection to clinical recurrence was 152 days (range 15-748 days). gMRD, derived from plasma-only panel-based next-generation sequencing, was evaluated in all matched time points; the prognostic value was limited by clonal hematopoiesis of indeterminate potential, including pathogenic mutations in common cancer driver genes. Despite refinements in gMRD analysis, it remained inferior to mMRD. A combination of mMRD and gMRD did not outperform mMRD alone.
CONCLUSION: These results support further development of tumor-agnostic mMRD assays for the detection of ctDNA and assessment of these assays to develop clinical utility in this setting.

Keywords:  DNA methylation; breast cancer; circulating tumor DNA; molecular residual disease

DOI:  https://doi.org/10.1016/j.esmoop.2025.105286
Br J Cancer. 2025 Jun 02.

Spatial omics technology potentially promotes the progress of tumor immunotherapy.

Zhen Lan, Yuanyuan Yang, Lingling Li, Chaoguan Wang, Zhenqiang Sun, Qiming Wang, Yang Liu.

Immunotherapy has become an indispensable modality in the treatment of cancer, yet challenges such as resistance and substantial variability in therapeutic responses among patients remain significant obstacles. Key technologies, including spatial omics, have emerged as critical methods for exploring the complex tumor microenvironment. Increasing evidence suggests that, compared to single-cell sequencing, spatial omics technologies offer the advantage of preserving spatial context and integrating multimodal analyses, thereby advancing our understanding of complex interactions within biological tissues. In this perspective article, we present a comprehensive overview of the origins, classifications, and characteristics of various modalities of spatial omics analyses. Furthermore, we discuss the heterogeneity of the TME in the spatial context, such as the phenotypic differences between B cells and T cells near normal versus tumorous tissues-where they predominantly express immune-suppressive receptors in proximity to the tumor. Additionally, we summarize the applications of spatial omics in different cancer therapies, recent advancements in exploring cellular interactions and tertiary lymphoid structures, and the challenges faced in clinical translation. In light of these findings, we advocate for a broader application of spatial omics, combined with other technologies, as this will unveil overlooked therapeutic targets and could potentially realize precision immunotherapy for cancer.

DOI: https://doi.org/10.1038/s41416-025-03075-5
Nat Med. 2025 Jun 04.

Peri-operative atezolizumab in early-stage triple-negative breast cancer: final results and ctDNA analyses from the randomized phase 3 IMpassion031 trial.

Elizabeth A Mittendorf, Zoe June Assaf, Nadia Harbeck, Hong Zhang, Shigehira Saji, Kyung Hae Jung, Roberto Hegg, Andreas Koehler, Joohyuk Sohn, Hiroji Iwata, Melinda L Telli, Cristiano Ferrario, Kevin Punie, Aditi Qamra, Max Dieterich, Yun Xu, Mario Liste-Hermoso, Esther Shearer-Kang, Luciana Molinero, Stephen Y Chui, Carlos H Barrios.

Previously published results demonstrated that the randomized phase 3 IMpassion031 trial met its primary objective: adding atezolizumab to neoadjuvant chemotherapy significantly improved pathologic complete response (pCR) rate in patients with stage II/III triple-negative breast cancer (TNBC). Here we report the prespecified final analysis of the secondary endpoints with 3 years' follow-up, together with exploratory analyses of circulating tumor (ct)DNA. Patients with previously untreated stage II/III TNBC enrolled in 75 academic and community sites in 13 countries were randomized 1:1 to receive neoadjuvant chemotherapy with either peri-operative atezolizumab (n = 165) or preoperative placebo (n = 168). Descriptive secondary endpoints included event-free, disease-free and overall survival. Long-term outcomes favored the atezolizumab group (event-free survival hazard ratio (HR), 0.76; 95% confidence interval (CI), 0.47-1.21; disease-free survival HR, 0.76; 95% CI, 0.44-1.30; overall survival HR, 0.56; 95% CI, 0.30-1.04). Among patients without pCR, 14 of 70 (20%) atezolizumab-treated and 33 of 99 (33%) placebo-treated patients received additional adjuvant therapy, frequently capecitabine. In exploratory biomarker analyses, patients with baseline ctDNA-negative status (6%) had excellent long-term outcomes. Most patients (87%) had cleared ctDNA at surgery. ctDNA-positive status at surgery identified a subset of non-pCR patients with poorest prognosis. Long-term safety was consistent with primary results. These data show that adding atezolizumab to chemotherapy for stage II/III TNBC is associated with favorable long-term outcomes, and ctDNA dynamics provide prognostic value beyond pCR. ClinicalTrials.gov identifier: NCT03197935 .

DOI: https://doi.org/10.1038/s41591-025-03725-4
Small Methods. 2025 Jun 04. e2401760

Determination of the position of DNA Methylation and Base Modifications Using a Biological Nanopore.

Ping Liu, Masayuki Honda, Ryuji Kawano.

  A method for detecting DNA methylation and modifications is developed using biological nanopores. By exploiting the interaction between bases and acidic amino acids within the entrance and neck region of the α-hemolysin nanopore, we determined the position and frequency of 5-methylcytosine in oligonucleotides. Furthermore, the detection of demethylation intermediates is optimized by examining various ion species and concentrations in the electrolyte. Efforts are also made to employ commercial nanopore devices for high-throughput detection. This approach offers the potential for direct detection of DNA methylation and modifications using biological nanopores.

Keywords:  DNA methylation; nanopore

DOI:  https://doi.org/10.1002/smtd.202401760
Sci Rep. 2025 Jun 03. 15(1): 19364

Evaluation of automatic cell free DNA extraction metrics using different blood collection tubes.

Daniel Andersson, Helena Kristiansson, Manuel Luna Santamaría, Huma Zafar, Ivan Mijakovic, Åsa Torinsson Naluai, Anders Ståhlberg.

  Liquid biopsies and cell-free DNA (cfDNA) analysis are used in numerous clinical applications. The amount of cfDNA is generally limited and many approaches require assessment of individual molecules. Optimized pre-analytical steps are therefore fundamental for accurate interpretation. Here, we established an automated extraction approach providing cfDNA of high yield and quality. We analyzed 649 blood plasma samples collected from 23 healthy individuals and assessed the performance of four different blood collection tubes, time between sampling and plasma isolation and number of centrifugation steps. CfDNA was quantified by fluorometric analysis and quantitative polymerase chain reaction, while contaminating cellular DNA was assessed by quantitative polymerase chain reaction and parallel capillary electrophoresis. Data showed that cfDNA yield depends on both choice of blood collection tube and time between sampling and plasma isolation. Plasma isolated directly after sampling in K2EDTA tubes and plasma isolated within one week from preservative Streck tubes provided high cfDNA yield. We demonstrate that contaminating cellular DNA may be challenging to detect and that quantitative polymerase chain reaction and parallel capillary electrophoresis provide complementary information. In summary, reliable cfDNA analysis requires optimized experimental workflows, where the effects of pre-analytical factors should be considered in study designs and in clinical implementations.

Keywords:  Automated extraction; Blood plasma; Cell-free DNA; Liquid biopsy; Pre-analytics

DOI:  https://doi.org/10.1038/s41598-025-03508-4
Nature. 2025 Jun 04.

Cancer more deadly when tumours lack Y chromosomes - and the loss could be contagious.

Liam Drew.



Keywords:  Cancer; Genetics; Medical research

DOI:  https://doi.org/10.1038/d41586-025-01656-1