Genome-wide association studies (GWAS) have identified germline genetic variants for follicular lymphoma (FL) susceptibility. We conducted a GWAS of prognosis in FL patients to identify genetic predictors of event-free survival (EFS) as well as failure within the first 24 months after treatment initiation (EFS24) using patients treated with rituximab-based immunochemotherapy from three clinical trials and one prospective observational study (N = 1054). Statistical approaches consisted of a pooled GWAS of the four cohorts and a leave-one-cohort-out (LOCO) strategy to identify robust findings that replicated across the four cohorts. The top SNPs for EFS and EFS24 were marked by rs72625024 at 3q27.3 near FETUB and HRG (P = 9.37 × 10−8) and rs114695031 at 14q32.13 near TCL6 (P = 1.93 × 10−8), respectively. These two loci, which were discovered and validated in all 4 LOCO rounds, map near long-non-coding RNAs with putative tumor suppressor functions. Our results pinpoint potential novel biology and the contribution of host genetics to prognosis in FL.

Protein synthesis plays a central role in cancer development and progression. eukaryotic initiation factor 5 A (eIF5A), a translation factor activated by hypusination, is implicated in tumorigenesis, however, its mode of action is still unclear. We find that hypusinated eIF5A (eIF5Ahyp) promotes metastasis and tumor growth in prostate cancer (PCa) by supporting mitochondrial metabolism and translation. eIF5Ahyp controls the subcellular localization of Mitochondrial Ribonuclease P Protein 3 (MRPP3) mRNA encoding a protein essential for mitochondrial tRNA (mt-tRNA) maturation. We show that eIF5Ahyp regulates the nuclear export of MRPP3 mRNA, its expression, thereby promoting mt-tRNA maturation. Our findings establish that MRPP3 enhances mitochondrial metabolism and supports PCa metastasis. Importantly, its expression restores mitochondrial translation and tumor growth inhibited by the downregulation of eIF5Ahyp. Together, we uncover a critical role for eIF5Ahyp in mitochondrial protein synthesis and highlight its broader implications in coordinating the expression of nuclear and mitochondrial genomes, linking hypusination to cancer progression.

Rice yellow mottle virus (RYMV) is one of the most devastating viral pathogens affecting rice cultivation in Africa. The eukaryotic translation initiation factor 4G isoform eIFiso4G1 plays a pivotal role in rice susceptibility to the virus. Naturally occuring resistance alleles impair infection but are predominantly found in the African cultivated species Oryza glaberrima, whose use in breeding programs is limited by interspecific sterility barriers with the widely grown O. sativa. Here, we used CRISPR-Cas9 to generate knockout (KO) mutations in eIFiso4G1 as well as insertion-deletion (Indel) variants within the region involved in interaction with the viral protein VPg. KO mutations conferred high resistance to RYMV. No resistance-breaking events were observed, suggesting that this resistance may be more durable than that conferred by naturally occuring alleles. However, complete gene KO slightly affected plant growth. Lines carrying Indel mutations in the VPg-interacting region displayed variable resistance levels, with some variants conferring high resistance without compromising plant development. Structural modeling of the eIFiso4G1 variants and their complexes with VPg provided mechanistic insights into how specific Indels modulate the resistance phenotype. ### Competing Interest Statement The authors have declared no competing interest. CGIAR, Research Program on rice agri-food systems (RICE, 2017–2022) IRD

The epithelial-mesenchymal transition (EMT) is a dynamic transdifferentiation of epithelial cells into mesenchymal cells. EMT programs exhibit great diversity, based primarily on the distinct impact of molecular activities of the EMT transcription factors. Using a panel of cancer cell lines and a series of 71 triple-negative primary breast tumors, we report that the EMT transcription factor ZEB1 modulates site-specific chemical modifications of ribosomal RNA (rRNA). Overexpression of ZEB1 and ZEB2, but not TWIST1, decreased the level of 2 '-O-ribose methylation (2 ' Ome) of 28S rRNA at position Um2402. ZEB1 overexpression specifically reduced the expression of the corresponding C/D box small nucleolar RNAs (snoRNAs) SNORD143/144, which guide the rRNA 2 ' Ome complex at the 28S_Um2402 site. During ZEB1-induced EMT induction/reversion, the levels of both 2 ' Ome at 28S_Um2402 and SNORD143/144 were dynamically comodulated. Taken together, these data demonstrate that 2 ' Ome rRNA epitranscriptomics is a novel marker of ZEB1-induced EMT.

The epithelial-mesenchymal transition (EMT) is a dynamic transdifferentiation of epithelial cells into mesenchymal cells. EMT programs exhibit great diversity, based primarily on the distinct impact of molecular activities of the EMT transcription factors. Using a panel of cancer cell lines and a series of 71 triple-negative primary breast tumors, we report that the EMT transcription factor ZEB1 modulates site-specific chemical modifications of ribosomal RNA (rRNA). Overexpression of ZEB1 and ZEB2, but not TWIST1, decreased the level of 2'-O-ribose methylation (2'Ome) of 28S rRNA at position Um2402. ZEB1 overexpression specifically reduced the expression of the corresponding C/D box small nucleolar RNAs (snoRNAs) SNORD143/144, which guide the rRNA 2'Ome complex at the 28S_Um2402 site. During ZEB1-induced EMT induction/reversion, the levels of both 2'Ome at 28S_Um2402 and SNORD143/144 were dynamically comodulated. Taken together, these data demonstrate that 2'Ome rRNA epitranscriptomics is a novel marker of ZEB1-induced EMT.

Apolipoprotein Ɛ4 genotype (APOE4) has been associated with cancer-related cognitive impairment, but its interaction with treatments remains unclear. This longitudinal study aims to evaluate the association between APOE4 and cognitive impairment in women with breast cancer (BC) undergoing chemotherapy (CT) or endocrine therapy (ET). Patients with stage I–III breast cancer completed cognitive tests at diagnosis (before surgery), then at year-1, year-2, and year-4 post-diagnosis. APOE4 status (APOE4+ [carriers] vs. APOE4− [non-carriers]) was genotyped from blood sample. Cognitive outcomes included episodic memory, working memory, attention, processing speed, and executive functions. Patients were defined as having overall cognitive impairment if ≥ 2 domains were impaired. We fitted logistic and linear mixed models to assess associations of APOE4 status with cognitive impairment over time and interactions of APOE4 with CT and ET. Among 334 patients, 64 (19

Background: More than half of patients with early BC on aromatase inhibitors (AI) experience AIMT. Inflammatory traits linked with treatment-related estrogen depletion have been associated with AIMT. A potential role for germline variants in genes regulating inflammation, bone turnover, estrogen metabolism and AI pharmacokinetics has also been suggested (Reinbolt 2018, Stearns 2024, Lintermans 2016, Wang 2016, Hertz 2017). Yet study were relatively small and results inconsistent or not validated. Therefore, the understanding of the biological and potential genetic underpinnings of AIMT is still limited. We aimed to comprehensively explore the association of genetic variants with AIMT in order to identify targets for impactful interventions. Methods: We included postmenopausal patients with stage I-III BC treated with adjuvant AI from the longitudinal CANTO cohort (NCT01993498). AIMT was evaluated at month 3-6, year (Y) 1, Y3 and Y5 of AI treatment and defined as presence of any grade [G] articular or muscular pain by CTCAE v4.0. All germline variants were assessed on blood samples obtained at BC diagnosis. We performed a GWAS between 1,894,475 single nucleotide polymorphisms (SNPs) (Illumina InfiniumExome24 / Illumina GSA24) and AIMT, using multivariable logistic regressions. Each model was adjusted on pre-specified clinical and behavioral factors, including age, socio-economic status, comorbidities, tumor and treatment-related variables (including type of AI), and patient-reported health outcomes, all assessed at BC diagnosis. Missing data was handled by multiple imputation with a set of 15 complete datasets. The study had approximately 80% power to detect associations with AIMT at Y3 at suggestive GWAS significance alpha level of 10-6 targeting variant with minor allele frequency (MAF) of 0.25 and odds ratio (OR) of 1.5. Therefore, our primary outcome of interest was AIMT at Y3. Given the exploratory nature of these analyses, we report relevant associations at an alpha threshold of 10-4. Genes harboring significant top SNPs were annotated to identify potential explicatory biological pathways. Results: Overall 4854 patients treated with AI were included. Of these, 3847 had available genetic data. Mean age was 63.9 years (SD 7.2), mean BMI was 27.0 (5.6). 63% patients reported history of articular disease, 41% received chemotherapy. 55% received letrozole, 40% anastrozole and 5% exemestane as first AI. 65% of patients reported AIMT at Y3 (of whom G3 9%), while 86% patients reported AIMT overall (at any time point; of whom G3 18%). Patients with AIMT at Y3 were generally younger, with higher BMI, had previous history of articular or muscular disease, and reported more frequently anxiety or depression at diagnosis. The GWAS identified 9 SNPs as associated with AIMT at Y3: rs4096589 (MAF 0.39; OR 1.36 [95% CI 1.21-1.53]), rs983495 (MAF 0.46; OR 0.76 [0.68-0.85]), rs12964962 (MAF 0.25; OR 0.73 [0.64-0.84]), rs348780 (MAF 0.42; OR 0.77 [0.69-0.86), rs72485589 (MAF 0.13; OR 0.67 [0.56-0.81]), rs2559854 (MAF 0.42; OR 0.78 [0.69-0.87]), rs895876 (MAF 0.16; OR 0.72 [0.61-0.83]), rs2926866 (MAF 0.17; OR 1.40 [1.20-1.66]), rs2240027 (MAF 0.08; OR 1.58 [1.28-1.96]). rs2926866 was also associated with AIMT at Y1 (1.22 [1.05-1.41]), Y5 (1.36 [1.12-1.66]), and overall (1.48 [1.24-1.76]). Relevant molecular functions that were associated with the identified SNPs included protein homodimerization activity (rs4096589), identical protein binding (rs895876), actin- and actin-filament binding (rs2240027). Conclusions: This was an exploratory study aimed to assess associations between genetic variants and AIMT in postmenopausal patients with early BC. Results of this relatively large prospective cohort identified several SNPs that might be involved in AIMT. Further analyses are warranted for model validation and to better elucidate the mechanistic role of the described genetic variants from a functional perspective. Citation Format: Pietro Lapidari, Youenn Drouet, Emilie Thomas, Jérémie Jacquemin, Maria Alice Franzoi, Martina Pagliuca, Sophie Laurent, Chayma Bousrih, Maryam Lustberg, Olivier Tredan, Anne-laure Martin, Catherine Gaudin, Christelle Jouannaud, Marion Fournier, William Jacot, Marina Rousseau, Jean Francois Deleuze, Alain Viari, Ines Vaz-Luis, Antonio Di Meglio. Genome-wide association study (GWAS) of aromatase inhibitor musculoskeletal toxicity (AIMT) among early-stage breast cancer (BC) survivors [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr PS15-02.

IntroductionRice (Oryza sativa) is a staple food worldwide, but its production is under constant pressure from both abiotic and biotic stresses, resulting in high use of agrochemicals. The plant microbiome harbours microorganisms that can benefit plant health and provide alternatives to the use of agrochemicals. The composition of plant microbiomes depends on many factors (soil composition, age, and health) and is considered a primary driver of future plant health. To identify plant microbiomes that protect against disease, we hypothesised that asymptomatic rice plants in fields under high pathogen pressure (i.e., healthy islands of plants among predominantly diseased plants) might harbour a microbiota that protects them from disease.Material and MethodsWe sampled healthy and leaf-diseased plants in rice fields with high disease incidence in Cambodia and profiled their microbiota at leaf, root, and rhizosphere levels using 16S V3V4 and 18S V4 amplicon barcoding sequencing.ResultsComparison of amplicon sequence variants (ASV) of the microbiota of healthy and diseased samples revealed both disease and healthy signatures (significant enrichment or depletion at ASV/species/genus level) in both fields. The genera Methylobacterium and Methylorubrum were identified health taxa signatures with several species significantly enriched in healthy leaf samples (Methylobacterium indicum, Methylobacterium komagatae, Methylobacterium aerolatum, and Methylorubrum rhodinum). A cultivation approach on rice samples led to the isolation of bacterial strains of these two genera, which were further tested as bioinoculants on rice leaves under controlled conditions, showing for some of them a significant reduction (up to 77%) in symptoms induced by Xanthomonas oryzae pv. oryzae infection.DiscussionWe validated the hypothesis that healthy plants in fields under high disease occurrence can host specific microbiota with biocontrol capacities. This strategy could help identify new microbes with biocontrol potential for sustainable rice production.

Background Fatigue, cognitive impairment, anxiety, depression, and sleep disturbance are cancer-related behavioral symptoms that may persist years after early-stage breast cancer, affecting quality of life. We aimed to generate a predictive model of long-term cancer-related behavioral symptoms clusters among breast cancer survivors 4 years after diagnosis.Methods Patients with early-stage breast cancer were included from the CANcer TOxicity trial (ClinicalTrials.gov identifier NCT01993498). Our outcome was the proportion of patients reporting cancer-related behavioral symptoms clusters 4 years after diagnosis (>= 3 severe symptoms). Predictors, including clinical, behavioral, and treatment-related characteristics; Behavioral Symptoms Score (BSS; 1 point per severe cancer-related behavioral symptom at diagnosis); and a proinflammatory cytokine (interleukin 1b; interleukin 6; tumor necrosis factor alpha) genetic risk score were tested using multivariable logistic regression, implementing bootstrapped augmented backwards elimination. A 2-sided P less than .05 defined statistical significance.Results In the development cohort (n = 3555), 642 patients (19.1%) reported a cluster of cancer-related behavioral symptoms at diagnosis, and 755 (21.2%) did so 4 years after diagnosis. Younger age (adjusted odds ratio for 1-year decrement = 1.012, 95% confidence interval [CI] = 1.003 to 1.020), previous psychiatric disorders (adjusted odds ratio vs no = 1.27, 95% CI = 1.01 to 1.60), and BSS (adjusted odds ratio ranged from 2.17 [95% CI = 1.66 to 2.85] for BSS = 1 vs 0 to 12.3 [95% CI = 7.33 to 20.87] for BSS = 5 vs 0) were predictors of reporting a cluster of cancer-related behavioral symptoms (area under the curve = 0.73, 95% CI = 0.71 to 0.75). Genetic risk score was not predictive of these symptoms. Results were confirmed in the validation cohort (n = 1533).Conclusion Younger patients with previous psychiatric disorders and higher baseline symptom burden have greater risk of long-term clusters of cancer-related behavioral symptoms. Our model might be implemented in clinical pathways to improve management and test the effectiveness of risk-mitigation interventions among breast cancer survivors.

Abstract BACKGROUND: Previous studies suggested that bio-behavioral models explain part of the variability of cancer-related fatigue, and pro-inflammatory and age-related processes emerged as contributors to persistent fatigue. However, the biological underpinnings of this complex symptom, including its relevant genomic correlates, are still poorly understood. We aimed to comprehensively explore the association of genetic variants with long-term cancer-related fatigue. METHODS: We used the prospective, multicenter, longitudinal CANcer TOxicity cohort, enrolling patients at diagnosis of stage I-III BC (NCT01993498). Outcomes included severe (≥40/100) global (EORTC QLQ-C30) as well as physical, emotional, and cognitive (FA12) fatigue at year (Y)1, Y2, and Y4 after BC diagnosis. Applying a hypothesis-driven approach, we investigated (i) germline genetic variants in a pre-specified Genetic Risk Index (GRI) assaying expression-regulating single nucleotide polymorphisms (SNPs) in the promoter regions of 3 pro-inflammatory cytokine genes (IL1B [rs16944], IL6 [rs1800795], and TNF [rs1800629]; Bower J, JCO 2013; N=9035), and (ii) age-related expansions of hematopoietic clones carrying recurrent acquired mutations, commonly defined as clonal hematopoiesis of indeterminate potential (CHIP; NGS with unique molecular identifiers for 17 genes [including DNMT3A, TET2, ASXL1, PPM1D, ATM, JAK2, and TP53]; N=1219). The contribution of GRI and CHIP to fatigue was assessed by multivariable logistic regression models. Taking an agnostic approach, we then performed a genome-wide association study (GWAS) of fatigue and 1,894,511 germline SNPs (Illumina InfiniumExome24/Illumina GSA24; N=9056). All genetic variants were assessed at BC diagnosis. Tested associations were adjusted by validated clinical predictors (Di Meglio A, JCO 2022). RESULTS: In the overall cohort (N=9056) mean age was 56.5 years (SD 11.2), 51.0% had stage II or III BC, 52.6% received chemotherapy, and 82.1% endocrine therapy. The prevalence of severe fatigue was 26.1% at diagnosis and increased to 36.5%, 34.3%, and 32.6% at Y1, Y2, and Y4 after diagnosis, respectively. Most patients (77.4%) had 3-6 high-frequency alleles across the 3 SNPs in the pro-inflammatory GRI. Among patients with available CHIP data, 15.2% and 3.7% had a Variant Allele Frequency (VAF) >2% and >10%, respectively. The pro-inflammatory GRI was not associated with fatigue outcomes. We found significant associations between CHIP and severe long-term global fatigue at Y4 (adjusted OR [95%CI]: VAF ≥2% vs < 2%, 1.64 [1.08-2.51], p=0.021; VAF ≥10% vs < 10%, 2.22 [1.00-4.94], p=0.050). The GWAS identified several regions (each including ≥2 SNPs) as associated with severe fatigue outcomes (suggestive p-value cut-off < 5 × 10−5; see Table for number of identified regions by outcome and respective nearby genes). Overlap in biological pathways was observed in some of the gene regions associated with global and physical fatigue, but not for emotional or cognitive fatigue. Common biological processes that were associated (FDR < 0.05) with such genes included synaptic transmission, hemoglobin-oxygen binding, and response to stress. CONCLUSIONS: This study provides suggestive association data between gene variants and long-term cancer-related fatigue. While previously reported associations with pro-inflammatory GRI were not confirmed, some biological processes that may inform the mechanistic understanding of this symptom emerged, including associations with aging and response to stress that warrant further exploration. ///: marks different regions. All association analyses were adjusted by age, body mass index, smoke behavior, pre-treatment fatigue, pain, insomnia, and anxiety, and by the first ten axes of principal component analysis of the genetic data to control for population stratification. There was no overlap in biological pathways for the gene regions associated with emotional or cognitive fatigue (gene regions not shown). Table. Genes in proximity of regions associated with severe fatigue outcomes Citation Format: Antonio Di Meglio, Emilie Thomas, Youenn Drouet, Jean-Baptiste Micol, Davide Soldato, Maria Alice Franzoi, Martina Pagliuca, Julie Havas, Anne-Laure Martin, Sibille Everhard, Celine Besse, Anne Boland, Christophe Marzac, Nathalie Droin, Sandrine Boyault, Marina Rousseau, Olivier Trédan, Paul Cottu, Christelle Jouannaud, Marion Fournier, Laurence Vanlemmens, Charles Coutant, Asma Dhaini Merimeche, Baptiste Sauterey, Florence Joly, Mario Campone, Florence Lerebours, Marie-Ange Mouret-Reynier, Olivier Rigal, Thierry Petit, Sophie Guillermet, Antoine Arnaud, Mahmoud Ibrahim, Sylvie Giacchetti, Florence Dalenc, Johanna Wassermann, Olivier Arsène, Ariane Darut-Jouve, Aurélie Bertaut, Fabrice André, Jean-Francois Deleuze, Alain Viari, Ines Vaz Luis. Germline and acquired genetic variants and long-term cancer-related fatigue among survivors of early-stage breast cancer (BC) [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-14-05.

Abstract Background Peripheral neuropathy (PN) is a debilitating adverse event in patients with early breast cancer (BC) receiving (neo)adjuvant chemotherapy (CT). We harnessed the CANTO cohort study to detail clinical trajectories and explore clinical and genetic predictors of PN. Methods CANTO (CANcer TOxicities - NCT01993498) prospectively enrolled invasive stage I-III BC patients (pts) of 26 French comprehensive cancer centers. Pts were assessed at diagnosis, 3-6 (M6), 12 (M12), 36 (M36), and 60 (M60) months after treatment, defined as completion of surgery, CT or radiotherapy, whichever comes last. At each time point, PN events including paresthesia, sensory and motor neuropathy were collected according to NCI-CTC v4.0 criteria. A genome-wide association study (GWAS) was conducted to identify genetic predictors of PN, using Illumina GSA BeadChips. Minimac4/1000G was used to impute additional single nucleotide polymorphisms (SNPs). After stringent quality control measures, 1,894,475 SNPs with a minor allele frequency (MAF) >0.05 were evaluated. Longitudinal trajectories of PN events were descriptively examined. Statistical associations between each SNP and PN events measured at different time points, and between SNPs and trajectories, were performed with logistic regression assuming a log-additive genetic model. All analyses were adjusted for key clinical parameters and the first ten axes of principal component analysis of the genetic data to control for population stratification. Results Of 12,012 included pts (data lock Aug. 2022), 11,014 (91.7%) were analyzed. Age was < 50 and >65 in 3407 and 2759 pts (31% and 25%, respectively). Overweight/obesity and diabetes were recorded in 5328 (48%) and 458 pts (4%). A neurologic history was observed in 1360 pts (13%). Stage 0-I and II-III were observed in 5356 (49%) and 5512 pts (51%), and 4011 pts had an axillary dissection (37%). CT was administered in 5790 pts (53%), including a taxane (tax) in 5542 pts (96%). Shortly, all grade and grade 2+ PN was observed in 29% and 12%; 27% and 10%; 20% and 10%; 13% and 10% of pts at M6, M12, M36 and M60, respectively. We derived 5 trajectories of overall PN, deemed “never”, “always”, “appears”, “transient” and “disappears”, in respectively 54%, 10%, 9%, 7% and 19% of the pts. Similar trajectories were built for the 3 categories of PN events. We built 9 predictive nomograms including key clinical parameters and time of analysis. E.g., grade 2+ PN at M6 was independently predicted by a medical history of carpal tunnel syndrome, past neurologic history and exposure to tax. Grade 2+ PN at M36 was predicted by past neurologic history and exposure to tax, and largely by previous PN at M6 or M12. The GWAS analysis included 7633 pts (84%). Four independent SNPs adding predictive value to the clinical nomograms were identified at a suggestive level of association (p < 1e-6), including one SNP in the NCAM1 gene (involved in neurogenesis) for M6 PN (OR=1.40, 95%CI 1.23-1.60, p=4.8e-7, see table) and one SNP in the CLDN11 gene (regulates oligodendrocytes) for M12 sensory PN (OR=1.32; 95%CI 1.17-1.49, p=7.5e-6). For rare ( < 5%) toxicities, 10 independent suggestive SNPs were identified, including one SNP in the NELL1 gene (neural cell growth regulation and differentiation) for the “always” trajectory (OR=1.61, 95%CI 1.31-1.99, p=7.6e-6) and one SNP in the KCNIP1 gene (neuronal sensor) for M36 motor PN (OR=1.5, 95%CI 1.7-3.5, p=3.1e-07). Conclusions Risk of early peripheral neuropathy is associated with previous neurological history and taxane exposure. Patients with PN at M6 or M12 are highly exposed to long-term PN. Some key SNPs may add independent predictive value for specific PN endpoints. Exploratory results of interest were produced for rarer toxicities and typical clinical trajectories. Detailed results will be presented at the meeting. All PN, M6 Multivariate analyses of the risk of peripheral neuropathy, all grades, at M6, without and with GWAS input. Citation Format: Youenn Drouet, Emilie Thomas, Florence Lerebours, Barbara Pistilli, Olivier Trédan, Christelle Jouannaud, Marion Fournier, Philippe Rouanet, Laurence Vanlemmens, CHARLES COUTANT, Asma Dhaini Merimeche, Baptiste Sauterey, Christelle Levy, Mario Campone, Carole Tarpin, Marie-Ange Mouret-Reynier, Olivier Rigal, Thierry Petit, Sophie Guillermet, Antoine Arnaud, Mahmoud Ibrahim, Sylvie Giacchetti, Florence Dalenc, Johanna Wassermann, Olivier Arsène, Ariane Darut-Jouve, Sibille Everhard, Ines Vaz Luis, Anne-Laure Martin, Fabrice André, Jean-François Deleuze, Alain Viari, Matthieu Carton, Paul Cottu. Trajectories and predictors of peripheral neuropathy after neoadjuvant chemotherapy in a prospective cohort of 11,014 patients with early breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS02-05.

AbstractPD-1/PD-L1 blockade has so far shown limited survival benefit for high-grade ovarian carcinomas. By using paired samples from the NeoPembrOv randomized phase II trial (NCT03275506), for which primary outcomes are published, and by combining RNA-seq and multiplexed immunofluorescence staining, we explore the impact of NeoAdjuvant ChemoTherapy (NACT) ± Pembrolizumab (P) on the tumor environment, and identify parameters that correlated with response to immunotherapy as a pre-planned exploratory analysis. Indeed, i) combination therapy results in a significant increase in intraepithelial CD8+PD-1+ T cells, ii) combining endothelial and monocyte gene signatures with the CD8B/FOXP3 expression ratio is predictive of response to NACT + P with an area under the curve of 0.93 (95% CI 0.85-1.00) and iii) high CD8B/FOXP3 and high CD8B/ENTPD1 ratios are significantly associated with positive response to NACT + P, while KDR and VEGFR2 expression are associated with resistance. These results indicate that targeting regulatory T cells and endothelial cells, especially VEGFR2+ endothelial cells, could overcome immune resistance of ovarian cancers.

Heterogeneity of genomic rearrangements in carcinosarcoma.

Background High-grade adult-type diffuse gliomas (HGGs) constitute a heterogeneous group of aggressive tumors that are mostly incurable. Recent advances highlighting the contribution of ribosomes to cancer development have offered new clinical perspectives. Here, we uncovered that isocitrate dehydrogenase (IDH)wt and IDHmut HGGs display distinct alterations of ribosome biology, in terms of rRNA epitranscriptomics and ribosome biogenesis, which could constitute novel hallmarks that can be exploited for the management of these pathologies. Methods We analyzed (1) the ribosomal RNA 2’O-ribose methylation (rRNA 2’Ome) using RiboMethSeq and in-house developed bioinformatics tools (https://github.com/RibosomeCRCL/ribomethseq-nfandrRMSAnalyzer) on 3 independent cohorts compiling 71 HGGs (IDHwt n = 30, IDHmut n = 41) and 9 non-neoplastic samples, (2) the expression of ribosome biogenesis factors using medium throughput RT-qPCR as a readout of ribosome biogenesis, and (3) the sensitivity of 5 HGG cell lines to RNA Pol I inhibitors (CX5461, BMH-21). Results Unsupervised analysis demonstrated that HGGs could be distinguished based on their rRNA 2’Ome epitranscriptomic profile, with IDHwt glioblastomas displaying the most significant alterations of rRNA 2’Ome at specific sites. In contrast, IDHmut HGGs are largely characterized by an overexpression of ribosome biogenesis factors compared to non-neoplastic tissues or IDHwt glioblastomas. Finally, IDHmut HGG-derived spheroids display higher cytotoxicity to CX5461 than IDHwt glioblastoma, while all HGG spheroids display a similar cytotoxicity to BMH-21. Conclusions In HGGs, IDH mutational status is associated with specific alterations of the ribosome biology and with distinct sensitivities to RNA Pol I inhibitors.

Supplementary Figure S2 shows in A the percentage of indicated cells positive for CD10 staining by flow-cytometry and in B the mean fluorescence intensity of CD10-positive cells after infection with a vector expressing a control or anti-CD10 shRNA. In C the percentage of indicated cells positive for CD10 staining by flow-cytometry and in D the mean fluorescence intensity of CD10-positive cells after infection with a vector expressing the CD10 cDNA or an empty control vector are shown. In E the frequency of soft-agar colony forming cells is shown in the indicated cell lines after infection with a vector expressing the CD10 cDNA or an empty control vector. In F the frequency of soft-agar colony forming cells is shown in the indicated cell lines after infection with a vector expressing a control or anti-CD10 shRNA.

The ENI10 molecular signature is enriched in genes involved in chromosome segregation during mitosis. A, GO analysis on the CD10 signature genes using the “Biological Process” terms. The most downstream terms in the hierarchy with an FDR less than 0.01 are shown. B, Ratio of the percentage of CD10+ over CD10-negative cells in each phase of the cell cycle determined by flow-cytometry analysis of MCF10A-Fucci-CA cells stained with an anti-CD10 antibody. C, GSEA using RNA-seq experiments comparing MCF10A cells expressing a scramble (shCTRL) or CD10 specific shRNA (shCD10), the gene sets used are the ENI10 genes (top), ENI10 genes belonging to all enriched GO terms shown in A (middle) and ENI10 genes belonging to the “mitotic spindle assembly checkpoint signaling” GO term (bottom). D, ssGSEA quantification of the indicated gene sets in normal healthy breast tissue (H) or in DCIS (D) from GSE21422 series. E, Quantification of E-CFC from CD10+ MC26 or M1B26 cells infected with lentiviruses carrying a scramble (sh ctl) or sh CD10 vector. F, Quantification of spheres forming cells from CD10+ MC26 or M1B26 cells infected with lentiviruses carrying a scramble (sh ctl) or sh CD10 vector. G, Quantification of soft-agar clones from M1B26 CD10+ cells infected with lentiviruses carrying a scramble (sh ctl) or sh CD10 vector.

Clustering of somatic copy number alterations profiles.