Simultaneous mapping of chromatin states and transcriptomes in rare cell populations is challenging, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers accurately within the same cell. Here we introduce OneCell CUT&Tag, a method that provides matched high-resolution epigenome, full-transcriptome and surface marker quantification from every cell, with input as low as one cell, without relying on computational aggregation into metacells. Using this approach, we uncover epigenomic priming of basal cells in the mammary gland and capture the dynamics of basal-to-luminal transdifferentiation, suggesting that epigenomic and transcriptional remodeling do not occur in complete synchrony during cell-fate conversion. Adaptable to diverse samples and tissues, this method also reveals the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information within individual cells, OneCell CUT&Tag reveals how complementary regulatory layers shape cellular identity and state, enabling the study of rare biological samples in development and disease.

Cervical cancer (CC) is a global public health concern, with frequent relapses and limited therapeutic options for metastatic disease. The RAIDs project, launched by the Curie Institute, aims to improve molecular characterization and risk stratification in CC. High-quality primary frozen tumor samples from 291 (WES), 302 (sWGS), and 270 (RNA-seq) patients enrolled in the Bio-RAIDs European study (NCT02428842) were analyzed alongside clinical data. Frequent alterations included PIK3CA (30%), KMT2D (11%), and KMT2C (11%). Only TERT mutations (13%) were significantly associated with poor progression-free survival (PFS). Targetable mutations in PIK3CA (30%), KRAS (4%), ERBB2 (4%), and FGFR3 fusions (5%), were found in 57% of patients. Transcriptomic analysis identified TERT and the Senescence pathway as significantly linked to PFS and to necrosis. Gene expression deconvolution showed no significant variation across immune populations. Integrative likelihood-based boosting analysis of 234 patients identified GNAQ and THUMPD1 as protective factors for PFS, while necrosis, age >50 years, advanced FIGO stage (III/IV), and HPV-negative status were associated with significantly poorer outcomes. These integrative multi-omics analyses revealed novel prognostic biomarkers in CC and identified over 50 clinically actionable mutations. Transcriptomic profiles were associated with both genetic alterations and histopathological features, suggesting new paths for precision medicine in CC.

Abstract Background: We developed a composite Gene Expression Signature (cGES) comprising 22 protective (P) and 19 adverse (A) genes, agnostic of the tumor type, stratifying IO-treated pts in 3 risk groups: low (L-), intermediate (I-) and high-risk (H-) (abstract#6360 AACR2025). Herein, we validate its predictive value for progression free (PFS) and overall survival (OS) in a prospective cohort and uncover the single-cell and spatial determinants underlying clinical outcomes. Methods: (1) The cGES was computed in 170 pts with LA/M SCCHN from 2 trials (NCT03226756; NCT03412058). (2) Next, we built a scRNAseq SCCHN atlas (scAt) of 219,138 cells from 77 independant pts including 19 and 21 pts classified as H-risk and L-risk respectively, and studied the distribution and functional states of cell populations between the 2 groups of pts. Cell-type-specific enrichments of A & P genes werequantified and intercellular communication networks were inferred to identify ligand-receptor (L-R) interactions. (3) Deconvoluted Visium data from 12 of the 77 SCCHN including 3 H-risk and 3 L-risk pts were used to map the spatial organization of cGES and to localize specific L-R interactions. Results: (1) Multivariate analysis adjusted for ECOG, age, gender, and alcohol/tobacco use showed that I- and L-risk pts had significantly better outcomes. For PFS, hazard ratios were 0.64 (p=0.04) and 0.51 (p=0.005), and for OS 0.81 (p>0.05) and 0.54 (p=0.015), respectively. (2) Analysis of the scAt revealed that A genes from cGES were mainly expressed by epithelial and stromal cells. Conversely, P genes were mainly expressed by immune cells. H-risk tumors exhibited an altered communication landscape marked by strengthened epithelial junctions, developmental signaling, and universally increased EGFR L-R activity, whereas L-risk tumors showed an immune-enriched network dominated by extracellular remodeling, adaptive immune activation and immune cell recruitment. (3) Visium deconvolution identified 5 major cell-composition clusters (C), with epithelial-enriched C2 showing the highest A genes expression, while T cell-enriched C4/C5 displayed the strongest P genes expression. H-risk tumors exhibited prominent EGFR ligand expression, consistent with the results from the scAt data. In contrast, L-risk tumors displayed increased antigen-presentation, T-cell chemotaxis, and complement signaling. Conclusion: cGES reliably stratified prognosis and reflects tumor ecosystem biology. H-risk tumors were dominated by epithelial-driven, EGFR-centered signaling, whereas L-risk tumors showed coordinated inflammatory T-cell-oriented programs. These findings suggest cGES as a prognostic and mechanistic biomarker, and provides a rational for EGFR-IO combination strategies to improve outcomes in LA/M SCCHN. Citation Format: Mehdi Lamkhioued, Thimothee Casini, Elodie Girard, Karène Mahtouk, Sonia Canjura-Rodriguez, Valery Attignon, Bastien Cabarrou, Constance Lamy, Anne Schnitzler, Frederique Penault-Llorca, Caroline Even, Christophe Le Tourneau, Ellen Van Obberghen-Schilling, Nicolas Servant, Fayette Jerome, Nathalie Bendriss-Vermare, Ivan Bièche, Pierre Saintigny. Single cell and spatially resolved determinants of the clinical outcome of patients (pts) treated with locally advanced/metastatic head and neck squamous cell carcinoma (LA/M SCCHN) treated with immunotherapy (IO) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1037.

Abstract Background: IO efficacy in LA/M HNSCC patients is limited. Identifying biomarkers of resistance and response is crucial to better stratify patients. We characterized the genomic and transcriptomic landscape of IO-naive HNSCC patients to identify specific genomic and transcriptomic signatures of response to IO. Methods: We analyzed baseline FFPE samples of 176 LA/M HNSCC patients treated with IO from CHECK’UP (NCT03412058) and TOPNIVO (NCT03226756) trials, for whom baseline RNAseq data were available. A penalized Cox model with Elastic Net procedure was used to identify gene signatures associated with PFS and OS. Using a resampling procedure, a bootstrap selection stability (BSS) index was computed for each gene and only those with a BSS > 30% were included in the final model to determine a score for both PFS and OS. In addition, 149 paired tumor and germline DNA were sequenced using whole exome. For biostatistics analysis using genomic alterations, only variants (SNVs, Indels, CNVs) in oncogenes, tumor suppressor genes with a variant allele frequency (VAF) of at least 10% and altered signaling pathways were considered. Results: The cohort (median age 62.5 yo) included a majority of oropharynx (39.8%) and oral cavity (29.8%) tumors, 77.8% males, 62.3% with alcohol and 81.7% with tobacco use history and 60.0% of them were metastatic. Objective response rate was 17.4%, median PFS and OS were 1.9 months (mo) (95%CI=[1.8-2.5]) and 8.1 mo (95%CI=[6.1-9.7]), respectively (median follow-up of 33.3 mo, 95%CI=[28.7-36.5]). The most frequent genomic alterations affected CCND1, CDKN2A, FAT1, TERT, TP53 genes and a gain of 3q26-q28. In univariable analyses, the presence of TERT or FAT1 alteration were significantly associated with worse PFS. After adjustment for clinical variable, the presence of FAT1 alteration and the upregulation of Hippo signalling pathway remained associated with worse PFS. The presence of TERT mutation was also associated with worse OS whereas the PI3K/AKT/mTOR pathway was associated with improved OS in univariable and multivariable analysis, respectively. Among the 500 most differentially expressed transcripts, 21- and 18-gene expression signatures were selected to assess their association with PFS and OS, respectively. C-Index was 0.72 and 0.71 (0.58 and 0.57 after internal bootstrap validation) for PFS and OS, respectively. Scores were dichotomized using time-dependent ROC Curve (Low vs High) and HR adjusted for clinical factors were 3.62 (95%CI = [2.42; 5.43]) and 3.86 (95%CI = [2.52; 5.91]; p<0.0001) for PFS and OS, respectively. Conclusions: We identified robust transcriptomic signatures and genomic alterations strongly associated with IO resistance, offering potential biomarkers for patient stratification. TERT or FAT1 alteration were associated with worse prognosis. Citation Format: Elodie Girard, Sonia Canjura-Rodriguez, Bastien Cabarrou, Constance Lamy, Anne Schnitzler, Frédérique Penault-Llorca, Emmanuel Bouilhol, Roger Sun, Eric Deutsch, François Legrand, Séverine Tabone-Eglinger, Valery Attignon, Caroline Even, Christophe Le Tourneau, Ellen Van Obberghen-Schilling, Marta Jimenez, Nicolas Servant, Thomas Filleron, Edith Borcoman, Pierre Saintigny, Ivan Bièche. Transcriptomic and genomic signatures associated with response or resistance to immunotherapy(IO) in locally advanced/metastatic (LA/M) head and neck squamous cell carcinoma (HNSCC) patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1034.

Abstract Canonical transcriptomic analysis requires committing from the outset to a reference genome or transcriptome, which imposes a predefined feature set, usually annotated genes or isoforms. Alignment and annotation dilute the signal through feature-level aggregation, discard any sequence absent from the reference, and require reprocessing the entire dataset for each new question (mutations, fusions, transposable elements). Here, we introduce the alignment-last paradigm, in which the read becomes the unit of comparison across samples, and alignment is deferred to annotate only the relevant sequences. Querying the merome , a reference-free cohort k-mer index, with just a handful of reads (about 0.01% of a sample’s) reveals the cohort’s transcriptomic structure in bulk and single-cell data. At single-cell resolution, these reads outperform genes for cell classification and rediscover, without supervision, a transposable-element signature (VL30) of exhausted T cells. Finally, unsupervised read-level differential analysis recovers established lncRNA biomarkers; uncovers new prognostic transposable-element reads in adrenocortical carcinoma and sarcomas; and extracts signals even from reads that fail to align.

Cancer cell fate has been widely ascribed to mutational changes within protein-coding genes associated with tumor suppressors and oncogenes. In contrast, the mechanisms through which the biophysical properties of membrane lipids influence cancer cell survival, dedifferentiation and metastasis have received little scrutiny. Here, we report that cancer cells endowed with high metastatic ability and cancer stem cell-like traits employ ether lipids to maintain low membrane tension and high membrane fluidity. Using genetic approaches and lipid reconstitution assays, we show that these ether lipid-regulated biophysical properties permit non-clathrin-mediated iron endocytosis via CD44, resulting in significant increases in intracellular redox-active iron and enhanced ferroptosis susceptibility. Using a combination of in vitro three-dimensional microvascular network systems and in vivo animal models, we show that loss of ether lipids from plasma membranes also strongly attenuates extravasation, metastatic burden and cancer stemness. These findings illuminate a mechanism whereby ether lipids in carcinoma cells serve as key regulators of malignant progression while conferring a unique vulnerability that can be exploited for therapeutic intervention.

PURPOSE:Rhabdoid tumors (RTs) are highly aggressive pediatric cancers driven by the biallelic inactivation of the SMARCB1 tumor suppressor gene, the sole recurrent genetic alteration. SMARCB1 encodes a core subunit of the SWI/SNF chromatin remodeling complex; its loss disrupts epigenetic gene regulation, supporting the classification of RTs as prototypical epigenetically driven cancers and highlighting the therapeutic potential of targeting epigenetic modifiers. Notably, previous studies have reported the overexpression of DNMT3A and DNMT3B, enzymes responsible for de novo DNA methylation, in RTs. EXPERIMENTAL DESIGN:Using patient samples, cell lines, and an ex vivo brain organoid system, combined with immunohistochemistry and bioinformatics, we investigated the role of DNMT3 enzymes in RT progression. RESULTS:In a composite tumor case, SMARCB1-deficient and -proficient regions displayed distinct methylation profiles. SMARCB1 loss correlated with increased DNA methylation and DNMT3A/B overexpression. To assess their respective roles in RTs, we used CRISPR-Cas9 to knock out DNMT3A/B in a SMARCB1-inducible RT cell line. DNMT3B loss impaired viability more strongly than DNMT3A. DNMT3B knock-out and SMARCB1 re-expression regulated overlapping gene programs related to development and cell adhesion at methylation and transcriptional levels. We next demonstrated that the cytotoxicity of the DNMT inhibitor decitabine, which impairs RT cell growth in human iPS-derived cerebral organoids, is primarily mediated by DNMT3B. CONCLUSIONS:These results show that DNMT3B plays a key role in the cascade of epigenetic effects following SMARCB1 loss and is pivotal in the RT sensitivity to decitabine; our study therefore supports the development of DNMT3B-specific inhibitors for RT.

Abstract Digital Drug Assignment (DDA) is a computational reasoning model that recommends cancer therapies for the complete individual molecular tumor profiles and ranks them by their DDA scores. Prior analysis of the SHIVA01 cohort linked higher DDA scores to improved outcomes (Petak et al., 2021). Here, we evaluated predefined DDA tiers in a broad, real-world cohort from Institut Curie’s Molecular Tumor Board (MTB). We retrospectively analyzed 394 MTB cases (2018-2022, adults w solid tumors) with NGS/WES/WGS data, treatment records, and outcomes. Patients receiving molecularly targeted agents (MTAs; n=134) or chemotherapy (n=177) were included. Administered MTAs (including ICIs) were assigned DDA scores and stratified into low (<0), intermediate, and high (≥1000) tiers. PFS, OS, ORR, DCR, and survival rates were compared across tiers and in relation to chemotherapy. Clinical outcomes improved consistently with higher DDA tiers (see table). Median PFS increased from 3.4 (low) to 6.8 months (high), and median OS from 7.8 to 16.6 months. Intermediate-tier MTAs performed similarly to chemotherapy (mPFS 4.5 vs 4.9 months; mOS 9.0 vs 9.8 months). ORR, DCR, 6-month PFS and 24-month OS all showed positive trends across tiers. DDA-high therapies provided the largest benefit, while DDA-low MTAs underperformed chemotherapy. Cases with no molecular-drug link (n=5) had the poorest outcomes (mPFS and mOS: 2.6 and 6.5 months). In this large, real-world pan-cancer cohort, DDA robustly differentiated therapies by clinical efficacy using each patient’s full molecular profile, independently validating the consistency of treatment-outcome associations across pre-established DDA tiers. These results urge the integration of DDA’s computational reasoning into MTB workflows to ensure consistent, high clinical performance and safety in the implementation of precision oncology. Citation Format: Barbara Vodicska, Eniko Kispeter, Dora Lakatos, Gabor G. Kalmar, Robert Doczi, Dora Gorog-Tihanyi, Anna Dirner, William T. Beck, Ivan Bieche, Edith Borcoman, Nicolas Servant, Kenza Nedara, Sarah Watson, Celia Dupain, Istvan Petak, Christophe Le Tourneau. Clinical efficacy of computational reasoning for personalized treatment planning in a pan-cancer cohort discussed by a French multidisciplinary tumor board: A real-world experience-based analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(8_Suppl):Abstract nr LB129.

e18049 Background: Oral Cavity Squamous Cell Carcinoma (OCSCC) and HPV-negative oropharyngeal SCC (HPV-negative OPSCC) together account for nearly 40% of Head and Neck SCC (HNSCC) and remain an unmet clinical need, with poor prognosis and limited benefit from multimodal therapies, including immune checkpoint inhibitors. The innate immune complement system has emerged as a druggable pathway in cancer, with strategies targeting C3a/C5a signaling or tumor-bound complement regulators to restore membrane attack complex (MAC)–mediated cytotoxicity. GT103, an antibody targeting tumor cell–associated complement regulator Factor H (FH), exemplifies this approach and is currently being evaluated in lung cancer in combination with anti-PD1. However, the role and regulation of complement activation across HNSCC subtypes remain poorly defined. Methods: We established a comprehensive complement atlas of HNSCC using an integrated Complementomics approach combining hyperplex imaging, plasma profiling, and clinical annotation from an institutional longitudinal biobanking cohort: SCANDARE (NCT03017573). Results: We enrolled 159 patients with early-stage HNSCC in the SCANDARE study. Plasma profiling of 17 complement proteins and activation fragments revealed selective alternative pathway activation in OCSCC and OPSCC, with coordinated elevation of Ba and the anaphylatoxins C3a, and C5a. Tumor profiling revealed a dense infiltration of C5aR1-positive macrophage and neutrophil subsets, driven in part by local C5a generation in OCSCC and OPSCC. In situ complement cascade did not reach the terminal step with formation of cytotoxic Membrane Attack Complex (MAC). This could be explained by the binding of FH to tumor cells surface of OCSCC and OPSCC HPV-negative, but not OPSCC HPV-positive. This FH was likely derived from the circulation, as local expression was minimal and it was elutable from our ex vivo preclinical model (Patient Tumor-Derived Fragment), indicating active local inhibition of alternative pathway–mediated cytotoxicity. As autoantibodies against this form of tumor-bound FH tumor neoantigen were protective in lung and renal cancer, we searched them in HNSCC. Positivity was observed in only a small number of patients, primarily in FH-rich OCSCC and HPV-negative OPSCC, suggesting that this potentially protective autoimmunity is rare. Conclusions: OCSCC and OPSCC HPV-negative exhibit a distinctive complement phenotype characterized by systemic anaphylatoxin generation without intratumoral complement-mediated cytotoxicity, mediated by tumor cell-associated FH. Targeting this FH with GT103 may overcome the regulatory barrier, restore immunogenic cell death mediated by the MAC, and enhance responses to immunotherapy, supporting clinical evaluation in these HNSCC subtypes.

Abstract Aberrant activation of the Wnt signaling pathway in triple-negative breast cancer (TNBC) is linked to treatment resistance and recurrence, yet its role in tumoral heterogeneity remains unclear. We developed Wnt reporter cell lines from two mesenchymal TNBC models (MDA-MB-231 and MDA-MB-436) using a Tcf/Lef-eGFP vector and observed intra- and inter-cellular variation in Wnt activity. Paired Wnt-positive and Wnt-negative TNBC cell lines were established and profiled by RNA-Seq. Integrative analyses revealed that Wnt-positive cells consistently upregulate genes involved in epithelial-to-mesenchymal transition, inflammation (e.g., IL6/JAK/STAT3, TNFα via NF-κB), and extracellular matrix remodeling. A 55-gene Wnt signature common to both low and standard serum conditions captured these features. Wnt-related gene sets were also enriched in the mesenchymal-like immune-altered (MLIA) subtype of 699 primary TNBC tumors. These findings highlight the role of basal Wnt activity in driving pro-tumorigenic transcriptional programs in TNBC and provide new insight into its contribution to subtype-specific disease features.

Purpose: We set up a prospective longitudinal biobanking study answering scientific questions within a regulatory framework and patient-centered approach. We aim in this paper to present the opportunities of such a study, as well as the challenges and the limitations. Patients and methods: SCANDARE (NCT03017573) is an institutional first monocentric then multicentric biobanking study. The study enrolled adult patients with newly diagnosed head and neck squamous cell carcinoma, triple negative breast cancer, ovarian and cervical cancer. All patients signed a consent form before any procedure. Tumor tissue and blood samples are collected at several time points during patient's journey, including at diagnosis, post-neoadjuvant chemotherapy in case of neoadjuvant treatment, at surgery, at recurrence and at disease progression following treatment initiated at recurrence. Clinical data are entered into an eCRF, whereas generated data are centralized in a secure database. Results: SCANDARE started in 2017 at Institut Curie and has included 676 patients at date. SCANDARE successfully addressed challenges related to patient consent, regulatory compliance, and logistical integration of sample collection into routine clinical practice. The study facilitated the longitudinal collection and preservation of tumor and blood samples, enabling comprehensive analyses from histopathology to genomics and proteomics needed for the 35 ongoing projects run by academic research groups and industry. The implementation of optimized sampling and data workflows enabled high-quality data. Several other cohorts are planned to open soon. Conclusion: SCANDARE is an institutional, prospective and dynamic biobanking study that successfully enabled the implementation of 35 research projects with clinical and omics data centralized in a secure database available for all collaborators on demand. Looking ahead, SCANDARE aims to expand its scope by including additional cancer types and patient cohorts, further enhancing the potential for translational research and personalized medicine in oncology.

Medulloblastoma, the most common malignant brain tumor of childhood, exhibits significant biological complexity that demands deeper exploration. Here, we present a large multiomics dataset integrating data from 384 primary medulloblastoma patient samples across five omic layers: CpG methylome, transcriptome, proteome, phosphoproteome, and metabolome, paired with associated clinical metadata. Data integration revealed intertumoral heterogeneity of lipid metabolism across proteomic subtypes. Notably, while the MYC-FASN-SCD axis drives lipid biosynthesis, pathway inhibition elicits a compensatory escape mechanism in vivo through exogenous fatty acid uptake. Unexpectedly, we demonstrated that MYC triggers lipid storage, creating a unique dependency on lipid droplet-mitochondria communications to sustain tumor maintenance in vivo. Together, this comprehensive analysis reveals a targetable vulnerability downstream of MYC that constitutes a promising therapeutic approach to treat currently untreatable medulloblastoma subtypes.

[This corrects the article DOI: 10.1016/j.lanepe.2025.101524.].

Single-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers comprehensively within the same cell. Here, we introduce OneCell CUT&Tag a user-friendly method that provides matched high-resolution epigenome, full-transcriptome, and surface marker quantification from every cell, with input as low as one cell. Using this approach, we uncovered epigenomic priming of basal cells in the mammary gland and captured the dynamics of basal-to-luminal transdifferentiation. We identified a transitional cell population with intermediate epigenomic profiles—absent in reference populations—and demonstrated a continuous epigenomic progression from basal to luminal states, while transcriptomes exhibited a binary switch. Adaptable to diverse samples and tissues, this method also revealed the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information at single-cell resolution, OneCell CUT&Tag dissects the complementary roles of each omics layer in shaping cellular identity and function, opening new avenues to study rare and complex biological systems.

Retrotransposons are emerging as novel regulators of embryonic and brain development. We recently demonstrated that the LINE-1-encoded protein ORF1p is abundantly expressed in adult mouse and human neurons, although its function remains unclear. Here, we characterize the ORF1p interactome in differentiated mouse and human neurons using mass spectrometry and identify novel partners implicated in gene regulation and neuron-specific processes. ORF1p localizes not only to neuronal nuclei, where it associates with chromatin under steady-state conditions, but also to neurites, supporting a role in neuronal physiology. To further explore its nuclear functions, we sorted human post-mortem neurons with high or low nuclear ORF1p levels and performed ORF1p knockdown in cultured human neurons, followed by chromatin accessibility assays. Both approaches revealed consistent patterns of differential chromatin accessibility dependent on ORF1p. Loss of ORF1p also led to the down-regulation of long, neuron-specific genes and altered neurite morphology. Together, these findings point to a physiological role of ORF1p in post-mitotic neurons, mediated through converging interactions with proteins and chromatin.

Tumoral BRCA1 promoter methylation occurs frequently in triple-negative breast cancer (TNBC) and contributes to homologous recombination deficiency (HRD). While constitutional BRCA1 methylation has been described, its relationship with tumoral methylation, genomic instability, and prognosis remains unclear. Paired tumor and blood samples from 136 TNBC patients (SCANDARE, NCT03017573) were analyzed for BRCA1 methylation, genomic alterations, HRD and outcomes. Constitutional BRCA1 methylation was detected in 20.6% of patients and tumoral methylation in 31.6%, including 11.5% with somatic-only methylation. In cases with constitutional BRCA1 methylation, tumoral methylation levels increased markedly, with 89% of high-methylation tumors (≥50%) associated with a Loss of Heterozygoty. Tumors with BRCA1 promoter methylation consistently exhibited high HRD (Homologous Recombination Deficiency) scores, comparable to those with pathogenic HRR (Homologous Recombination Repair) gene pathogenic variants (p < 0.001). Conversely, HRD was rare in tumors lacking both BRCA1 methylation and HRR gene alterations. Prognostically, constitutional BRCA1 methylation tended to associate with improved survival, while somatic-only methylation showed a trend toward poorer outcomes (p = 0.06). Constitutional BRCA1 methylation is associated with a high level of tumoral BRCA1 promoter methylation and HRD in TNBC. These findings support integrating constitutional and tumoral BRCA1 methylation into HRD assessment to improve patient stratification and precision treatment in TNBC.

Integrating multi-omics data with Artificial Intelligence offers new opportunities for understanding cancer biology and discovering actionable biomarkers. In this selective review aimed at clinicians and translational researchers, we survey methodological innovations from classical machine learning to deep learning. We synthesize recent innovations, identify persistent technical challenges, and evaluate the landscape of available multi-omics datasets. Ultimately, we propose a strategic roadmap for translating AI-driven integrative models into real-world precision oncology.

INTRODUCTION:Systemic cervical cancer management continues to be challenging. Numerous chemotherapies have been approved, but predicting response is difficult due to the lack of biomarkers. Here, we analyze the genetic and protein profiles of 20 cervical cancer cell lines (CCCLs) and explore their correlation with drug response patterns to commonly used drugs, aiming to identify novel biomarkers of treatment response or resistance. MATERIAL AND METHODS:Twenty cell lines (CLs) were characterized for HPV type, for genetic alterations, and protein expression profiles. Pharmacoprofiling in 10 selected CLs was carried out against 34 drugs used in the clinic, assessing drug concentrations needed to reach half maximal inhibitory concentration (IC50) in nanomolar and micromolar ranges. Subtractive bioinformatics analyses aimed to identify genetic alterations (609 genes of clinical interest), associated with CL drug resistance or on the contrary with synthetic lethality. RESULTS:Despite a small sample size, genetic alteration frequencies and types of CCCLs were in line with those in clinical samples, except for the detection of a higher frequencyin specific genetic alterations such as NBPF1 and STK11 in CLs. Pharmacological screening identified drugs exhibiting therapeutic activity in most CLs while others were highly selective. Bioinformatics analyses suggested, loss-of-function (LoF) alterations in PAPBC3 in CLs sensitive to microtubule interfering agentsin addition to 50 variably present alterations in the microtubule pathway. LoF alterations in CSMD3, OBSCN, ZNF 717, ALPK2, CLDND1, GTF3A, NLRP1, SI, and TRIM66 were associated with Epigenetic acting drug activity and LoF of OSBPL1A with Eprenetapopt (APR-246) activity. Drug synergistic effects were observed with certain drug combinations. CONCLUSION:This paper reports genetic variants in 20 CLs as well as the results of the assessment on whether those variants may help predict response or resistance to certain drug families. With a few exceptions, genetic alteration frequency in CCCLs, conducted in the same analytical batches, compares favorably with published patient data. Results need confirmation in independent larger studies both in CLs and in clinical settings.

Identifying molecular alterations specific to advanced lung adenocarcinomas could provide insights into tumour progression and dissemination mechanisms. We analysed tumour samples, either from locoregional lesions or distant metastases, from patients with advanced lung adenocarcinoma from the SAFIR02-Lung trial by targeted sequencing of 45 cancer genes and comparative genomic hybridisation array and compared them to early tumours samples from The Cancer Genome Atlas. Differences in copy-number alterations frequencies suggest the involvement in tumour progression of LAMB3, TNN/KIAA0040/TNR, KRAS, DAB2, MYC, EPHA3 and VIPR2, and in metastatic dissemination of AREG, ZNF503, PAX8, MMP13, JAM3, and MTURN. Conversely, no meaningful difference was found in pathogenic single-nucleotide variant frequencies, reinforcing the notion that they are early events in tumorigenesis. CDKN2A homozygous deletion was linked to poor clinical outcome in patients with early tumours (overall survival hazard ratio 2.17, 95

Random X-chromosome inactivation is a hallmark of female mammalian somatic cells. This epigenetic mechanism, mediated by the long noncoding RNA Xist, occurs in the early embryo and is stably maintained throughout life, although inactivation is lost during primordial germ cell (PGC) development. Using a combination of single-cell allele-specific RNA sequencing and low-input chromatin profiling on developing mouse PGCs, we provide a detailed map of X-linked gene reactivation. Despite the absence of Xist expression, PGCs still harbor a fully silent X chromosome at embryonic day 9.5 (E9.5). Subsequently, X-linked genes undergo gradual and distinct regional reactivation. At E12.5, a substantial part of the inactive X chromosome resists reactivation, retaining an epigenetic memory of its silencing. Our findings define the orchestration of reactivation of the inactive X chromosome, a key event in female PGC reprogramming with direct implications for reproduction. Here, the authors map X-chromosome activity during female mouse germ cell reprogramming, revealing gradual, region-specific gene reactivation. Some genes resist reactivation, retaining epigenetic memory, offering insights into female germline epigenetics.