SUMMARY:SeqUIaSCOPE is an open-source platform designed for routine clinical oncology diagnostics through case-centric integration and visualization of genomic variants, fusion events, and expression profiles. The platform combines molecular-level validation via embedded genome browsing with systems-level interpretation through dynamic pathway visualization, enabling geneticists to assess how alterations converge across biological networks. Flexible reporting with customizable templates accommodates diverse institutional requirements, while secure cluster-based or local deployment ensures compliance with data protection policies, making advanced multi-omics diagnostics accessible to academic and clinical institutions. AVAILABILITY AND IMPLEMENTATION:SeqUIaSCOPE is freely available on GitHub at https://github.com/BioIT-CEITEC/sequiascope under the MIT license and archived at Zenodo (https://zenodo.org/records/21338445). Due to the sensitive nature of patient data, the repository provides simulated datasets that mimic the structure of real clinical data for testing and exploration. Documentation and a live demo accompany these datasets, allowing users to explore the application without any prior setup. The repository also includes a Helm chart for Kubernetes deployment and Docker containers for local deployment, ensuring compatibility across Linux, macOS, and Windows. No user registration is required, and all data remains on local or institutional infrastructure.

Aims Chemotherapy resistance remains a major challenge in breast cancer (BC) treatment. This study aimed to investigate the role of DNA methylation in this complex process and evaluate the potential of the DNA methyltransferase inhibitor decitabine (DAC) in restoring chemosensitivity. Methods Paclitaxel (PAC)- and doxorubicin (DOX)- resistant BC cell lines were derived from luminal A (T-47D), triple-negative (MDA-MB-231), and HER2-positive (JIMT-1) models and characterized by molecular profiling and functional assays. The therapeutic effects of DAC and DOX were assessed in MDA-MB-231 xenografts, and integrative analyses of DNA methylation and gene expression identified pathways associated with resistance. Follow-up analyses were performed in PAC-resistant MAS98.12 patient-derived xenografts (PDX) and in clinical samples from the NeoAva trial (NCT00773695). Results Resistant cells exhibited a slow-cycling phenotype, reduced tumorigenicity, and widespread genomic alterations. PAC-resistant xenografts showed extensive methylation and transcriptomic reprogramming, partly restored by DAC, which increased Ki-67 expression and enhanced DOX responsiveness. In contrast, PDX tumors displayed less pronounced changes, predominantly hypomethylation, indicating distinct resistance mechanisms. Importantly, xenograft-derived CpG signatures stratified NeoAva patients by treatment response. Conclusions Chemoresistance in BC involves extensive genomic and epigenetic remodeling. Although DAC can modulate methylation and tumor phenotype, rational drug combinations will be required to overcome resistance.

Head and neck squamous cell carcinoma (HNSCC) is a highly heterogeneous malignancy with limited predictive markers to guide personalized treatment, particularly in human papillomavirus (HPV)-negative cases, which exhibit poor outcomes. Identifying reliable biomarkers for prognosis and therapeutic response remains a critical challenge. In a retrospective cohort of 51 patients with primary HPV-negative HNSCC, we investigated the prognostic significance of the Hedgehog (HH) signaling pathway and its association with imaging biomarkers. Genomic and transcriptomic analysis revealed that HH pathway activation correlated with distinct [18F]FDG PET/CT radiomic features, notably the PET-derived “histogram:ih.max”, a surrogate for peak [18F]FDG uptake that was associated with inferior survival outcomes. Functionally, pharmacologic inhibition of HH signaling demonstrated anticancer efficacy across multiple models, including HNSCC cell lines, patient-derived tumoroids, and in vivo xenograft models. Importantly, HH pathway inhibition induced reproducible changes in imaging characteristics in xenografts, including a measurable reduction in [1⁸F]FDG uptake, closely mirroring patterns observed in patient tumors. Together these findings demonstrate that integration of multi-level molecular profiling with functional imaging captures HH-driven tumor biology in HPV-negative HNSCC. Our study underscores the value of [18F]FDG PET/CT multiomics in linking tumor biology with imaging features, providing a framework for biologically-informed patient stratification and hypothesis-driven evaluation of treatment response. These results support further translational validation of HH pathway inhibition in HPV-negative HNSCC within appropriately designed preclinical and clinical studies.

It is well known that Dishevelled (DVL) phosphorylation by casein kinase 1 (CK1) relays Wnt signals from Frizzled (FZD) receptors to downstream effectors, yet any mechanistic aspects of DVL function related to phosphorylation remain unresolved. Here, we uncovered a Wnt-induced DVL phospho-switch that is mutually exclusive with FZD association. CK1 multiphosphorylation changes dramatically the bulk electrostatics to promote DVL intramolecular interaction between the DEP domain and the adjacent disordered region. A panel of DVL3 mutants demonstrated a switch-like behavior at the molecular level when a charge threshold was reached. Charge accumulation proximal to DEP proved to be a key functional event required, but not sufficient, for Wnt/β-catenin signaling. Proximity interactomics revealed FZD receptors as the prominent effectors of the DVL phospho-switch function consistent with the molecular competition at the DEP interface. By integrating findings at different levels, we propose a universal mechanism, in which Wnt-induced DVL conformational phospho-switch attenuates coresidence with FZDs as a means for downstream signaling events.

Colorectal cancer ranks third in global incidence and second in cancer mortality. Patient-derived models are irreplaceable for studying tumor biology. We established a human epithelial cell line from a rectal adenocarcinoma overexpressing cancer stem cell marker ALDH1A1, and we investigated the effect of ALDH1A1 knockout on tumor cell traits. The cell line and its CRISPR-Cas9 ALDH1A1 knockouts were characterized by genomic and cytogenetic methods (CNV, WES, RNAseq, karyotype), in vitro (proliferation, response to chemotherapy, migration, invasion, apoptosis), and in vivo methods. We identified the landscape of somatic mutations and copy number alterations in the original tumor and the derived cell line. Genetic attenuation of ALDH1A1 was characterized by an increase in migratory potential and extensive metastatic ability, accompanied by reduced growth of subcutaneous xenografts and alterations in gene expression associated with inhibited proliferation and promoted invasion and metastasis, ultimately resulting in dysregulation of the Wnt signaling pathway. Increased metastatic potential was also confirmed in HT-29 cells after ALDH1A1 genetic attenuation. CRISPR-Cas9-mediated editing led to functional, cellular, and molecular changes confirming the role of ALDH1A1 in colorectal cancer carcinogenesis.

Plastic-derived materials have become persistent ecological contaminants since their industrial introduction in the mid-20th century. In that context, nanoplastics (NPs) have been discussed as an emerging, ubiquitous plastic-derived pollutant with unique physicochemical properties. Their increased surface-to-volume ratio enhances their adsorption, reactivity, and cellular penetration, driving distinct ecotoxicological behaviours when compared to larger plastic particles. In this study, we identify direct NP-induced DNA mutagenesis in Salmonella enterica. Using a combination of biochemical and biophysical studies, as well as mutagenicity assays, we show that functionalized and non-functionalized NPs induce mutations, depending on the energy state of the bacteria and the NP surface chemistry, by disrupting base-stacking and base-pairing - an intrinsic property of all DNA. Whole-genome analysis revealed that exposure to NPs alters the mutational spectrum and mutation frequency, while circular dichroism spectroscopy demonstrated NP-induced helical flipping from B- to non-B DNA conformations. These motifs preferentially adopt Z-like or A/B-hybrid structures associated with localized mutagenesis through DNA destabilization. Our combined data reveal that NP-mediated mutagenesis is based on surface chemistry and DNA topology, linking surface chemistry on nanoplastics to genomic instability in vivo. The proposed mechanism redefines the current perspective on nanoplastic toxicity shifting it from an indirect stress to direct macromolecular interactions. This mechanism provides a molecular framework for understanding how NPs could impose mutation bias, environmental selection pressure, and potential genomic risk across biological systems.

BACKGROUND:Prostate cancer ranks as the second most frequently diagnosed cancer in men worldwide. Recent research highlights the crucial roles IL6ST-mediated signaling pathways play in the development and progression of various cancers, particularly through hyperactivated STAT3 signaling. However, the molecular programs mediated by IL6ST/STAT3 in prostate cancer are poorly understood. METHODS:To investigate the role of IL6ST signaling, we constitutively activated IL6ST signaling in the prostate epithelium of a Pten-deficient prostate cancer mouse model in vivo and examined IL6ST expression in large cohorts of prostate cancer patients. We complemented these data with in-depth transcriptomic and multiplex histopathological analyses. RESULTS:Genetic cell-autonomous activation of the IL6ST receptor in prostate epithelial cells triggers active STAT3 signaling and significantly reduces tumor growth in vivo. Mechanistically, genetic activation of IL6ST signaling mediates senescence via the STAT3/ARF/p53 axis and recruitment of cytotoxic T-cells, ultimately impeding tumor progression. In prostate cancer patients, high IL6ST mRNA expression levels correlate with better recurrence-free survival, increased senescence signals and a transition from an immune-cold to an immune-hot tumor. CONCLUSIONS:Our findings demonstrate a context-dependent role of IL6ST/STAT3 in carcinogenesis and a tumor-suppressive function in prostate cancer development by inducing senescence and immune cell attraction. We challenge the prevailing concept of blocking IL6ST/STAT3 signaling as a functional prostate cancer treatment and instead propose cell-autonomous IL6ST activation as a novel therapeutic strategy.

Thyroid hormone (TH) signaling plays a major role in the development, energy homeostasis, and metabolism of most tissues. Recent observations have identified THs as drivers of prostate cancer (PCa) tumor development and progression. We reported that the T3-scavenger protein µ-crystallin (CRYM) regulates the development and progression of PCa and that this involved crosstalk with the androgen receptor (AR) signaling. However, the mechanisms remain incompletely understood. Here, we explored the role of thyroid hormone receptor β (TRβ), which is the main effector of TH signaling, in the context of PCa. The use of the TRβ-selective antagonist NH-3 inhibited PCa cell proliferation in vitro and reduced tumor size in PCa xenograft models. Notably, NH-3 was highly effective in the engrafted 22Rv1 cell line, a model for castration-resistant PCa (CRPC). Mechanistic studies revealed that NH-3 downregulates AR and the AR target genes Nkx3.1 and KLK3 ( PSA ). NH-3 was a more effective anticancer agent than enzalutamide and showed synergistic properties in combined use. Evidence from human datasets corroborates our findings whereby elevated TRβ expression and mutations in TH signaling pathways are associated with the onset of PCa. Collectively, these results establish TRβ as a mediator of tumorigenesis in PCa and identify NH-3 as a promising therapeutic agent for targeting AR signaling, particularly in CRPC.

Aims Chemotherapy resistance remains a major challenge in breast cancer (BC) treatment. This study investigated whether resistance development is associated with DNA methylation changes and assessed the potential of the DNA methyltransferase inhibitor decitabine (DAC) to reverse these alterations and enhance chemosensitivity. Methods Molecular profiling and functional assays were used to characterize paclitaxel-(PAC) and doxorubicin-(DOX) resistant BC cell lines derived from luminal A (T-47D), triple-negative (MDA-MB-231), and HER2-positive trastuzumab-resistant (JIMT-1) models. Therapeutic responses to DAC and DOX, alone and in combination, were evaluated in MDA-MB-231 xenografts. DNA methylation–associated gene expression changes were analyzed through integrative approaches. Results Chemoresistant cells exhibited a slow-cycling phenotype, reduced tumorigenicity, and extensive genomic alterations. Upregulation of RELB and downregulation of PPARG were observed across several resistant cell lines, while CDA expression was uniformly elevated in all DOX-resistant models. PAC-resistant xenografts displayed widespread methylation and transcriptomic reprogramming. DAC treatment partially restored aberrant methylation patterns and increased Ki-67 expression, potentially enhancing DOX responsiveness. Conclusions Chemoresistance in BC involves extensive genomic and epigenetic reprogramming. DAC modulates methylation and tumor phenotype but is insufficient to overcome resistance, highlighting the need for rational combination strategies. ![Figure][1] ### Competing Interest Statement The authors have declared no competing interest. Ministry of Education, Science, Research and Sport of the Slovak Republic European Commission, https://ror.org/00k4n6c32 European Union French National Research Agency [1]: pending:yes

Vertebrate ADAR RNA editing enzymes prevent cellular dsRNA from aberrantly activating antiviral dsRNA sensors. ADARs inhibit antiviral sensor activation by deaminating selected adenosines to inosines in dsRNA and by engaging in inhibitory protein interactions with sensors on dsRNA. ADARs interact with Dicers and, in the Drosophila Adar5G1 null mutant Dicer 2 acts as the antiviral dsRNA sensor mediating aberrant innate immune induction. We overexpressed active Adar isoforms or a catalytically-inactive Adar E374A protein from UAS-Adar constructs under the control of a temperature-regulated Act5Cts-GAL4 driver. Overexpression of the edited AdarG isoform or AdarEA cause larval lethality with aberrant innate immune induction. Some escaper pupae are formed with head eversion defects. AdarS overexpression is also lethal with no progeny pupae. Ecdysone signaling gene and innate immune gene expression are aberrantly elevated in the AdarG overexpressing pupae. RNAi knockdown of Ecdysone Receptor A ( EcR A ) or increasing expression of HP1 partially rescue AdarG overexpression defects and normalize gene expression in progeny flies, indicating that aberrant epigenetic silencing is also involved. The structure of an ADAR2 dimer on dsRNA shows the the glycine in AdarG is suitably positioned for Adar contacts with other proteins on dsRNA. ### Competing Interest Statement The authors have declared no competing interest. Czech Science Foundation GAČR, 21-27329X EU Horizon 2020 Research and Innovation Programme, Marie Sklodowska-Curie, 956810 China Scholarship Council, 202106915017

When Wnt ligands bind to Frizzled (FZD) receptors, Dishevelled protein (DVL) gets multiphosphorylated by Casein kinase 1 (CK1). Although, it is well known that DVL phosphorylation relays Wnt signals from receptors to downstream effectors, any mechanistic aspects of DVL function related to phosphorylation remain unresolved. Here, we uncovered a Wnt-induced DVL phospho-switch which is mutually exclusive with FZD engagement. CK1 multiphosphorylation changes dramatically the bulk electrostatics to promote DVL intramolecular coupling between the DEP domain and the adjacent disordered region. A panel of phospho-switch mutants demonstrated a switch-like coupling at the molecular level when a charge threshold is reached. Charge accumulation proximal to DEP proved to be a key functional event required, but not sufficient, for Wnt/β-catenin signaling. Interestingly, the charge-dependent switch-like character of DVL controlled its association with FZD. By integrating findings at different levels, we propose a universal mechanism in which Wnt-induced DVL conformational phospho-switch outcompetes FZD binding and triggers DVL detachment from FZD. ### Competing Interest Statement The authors have declared no competing interest. The Czech Science Foundation (GACR), GA23-06913S, GA22-25365S Ministry of Education Youth and Sports, LUAUS25170, LX22NPO5102

Colorectal cancer (CRC) ranks as the second most prevalent malignancy globally, highlighting the urgent need for more effective diagnostic and therapeutic strategies, as well as a deeper understanding of its molecular basis. Extensive research has demonstrated that cells actively secrete extracellular vesicles (EVs) to mediate intercellular communication at both proximal and distal sites. In this study, we conducted a comprehensive analysis of the RNA content of small extracellular vesicles (sEVs) secreted into the culture media of five frequently utilised CRC cell lines (RKO, HCT116, HCT15, HT29, and DLD1). RNA sequencing data revealed significant insights into the RNA profiles of these sEVs, identifying nine protein-coding genes and fourteen long non-coding RNA (lncRNA) genes that consistently ranked among the top 30 most abundant across all cell lines. Notably, the genes found in sEVs were highly similar among the cell lines, indicating a conserved molecular signature. Several of these genes have been previously documented in the context of cancer biology, while others represent novel discoveries. These findings provide valuable insights into the molecular cargo of sEVs in CRC, potentially unveiling novel biomarkers and therapeutic targets.

Thyroid hormone (TH) signaling plays a major role in the development, energy homeostasis, and metabolism of most tissues. Recent studies have identified THs as drivers of prostate cancer (PCa) development and progression. We reported that the T3-scavenger protein µ-crystallin (CRYM) regulates the development and progression of PCa and that this involved crosstalk with androgen receptor (AR) signaling. However, the mechanisms remain incompletely understood. Here, we explored the role of thyroid hormone receptor β (TRβ), which is the main effector of TH signaling, in the context of PCa. The use of the TRβ-selective antagonist NH-3 inhibited PCa cell proliferation in vitro and reduced tumor size in PCa xenograft models in vivo. Notably, NH-3 was highly effective in the engrafted 22Rv1 cell line, a model for castration-resistant PCa (CRPC). Mechanistic studies revealed that NH-3 downregulates AR and the AR target genes Nkx3.1 and KLK3 (PSA). NH-3 was a more effective anticancer agent than enzalutamide, and their combined use was synergistic. Evidence from human datasets corroborates our findings, whereby elevated TRβ expression and mutations in the TH signaling pathway are associated with the onset of PCa. Collectively, these results establish TRβ as a mediator of tumorigenesis in PCa and identify NH-3 as a promising therapeutic agent for targeting AR signaling, particularly in CRPC.

One of the largest domain-motif interactomes in human involves PSD-95/Discs-large/ZO-1 (PDZ) domains. The framework for understanding the PDZ interactome is well established; however the functional dynamics associated with PDZ-ligand interactions are poorly understood. Here, we report a dual PDZ-binding mode that ascribes unique dynamic features to class III ligand recognition. The crystal structure revealed that the PDZ domain can recognize either of the carboxylate moieties (terminal or internal) present in the class III ligand and laid out the register rules responsible for the dual recognition. Variants of the ligand designed to retain one or the other carboxylate of the native sequence were sufficient for PDZ binding. The conformational dynamics of PDZ probed by NMR relaxation dispersion experiments demonstrated that the class III ligand is shuffling binding modes as it engages with the PDZ domain. Our mechanistic findings reveal yet another aspect of PDZ binding plasticity specific to class III ligands.

Purpose: This study aims to assess whole-mount Gleason grading (GG) in prostate cancer (PCa) accurately using a multiomics machine learning (ML) model and to compare its performance with biopsy-proven GG (bxGG) assessment. Materials and Methods: A total of 146 patients with PCa recruited in a pilot study of a prospective clinical trial (NCT02659527) were retrospectively included in the side study, all of whom underwent 68Ga-PSMA-11 integrated positron emission tomography (PET) / magnetic resonance (MR) before radical prostatectomy (RP) between May 2014 and April 2020. To establish a multiomics ML model, we quantified PET radiomics features, pathway-level genomics features from whole exome sequencing, and pathomics features derived from immunohistochemical staining of 11 biomarkers. Based on the multiomics dataset, five ML models were established and validated using 100-fold Monte Carlo cross-validation. Results: Among five ML models, the random forest (RF) model performed best in terms of the area under the curve (AUC). Compared to bxGG assessment alone, the RF model was superior in terms of AUC (0.87 vs 0.75), specificity (0.72 vs 0.61), positive predictive value (0.79 vs 0.75), and accuracy (0.78 vs 0.77) and showed slightly decreased sensitivity (0.83 vs 0.89) and negative predictive value (0.80 vs 0.81). Among the feature categories, bxGG was identified as the most important feature, followed by pathomics, clinical, radiomics and genomics features. The three important individual features were bxGG, PSA staining and one intensity-related radiomics feature. Conclusion: The findings demonstrate a superior assessment of the developed multiomics-based ML model in whole-mount GG compared to the current clinical baseline of bxGG. This enables personalized patient management by identifying high-risk PCa patients for RP.

Gibel carp (Carassius gibelio) is a cyprinid fish that originated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries) and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling, and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allows the populations of C. gibelio to combine the evolutionary and ecological advantages of the two reproductive strategies. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These findings shed new light on the evolution of this asexual and sexual complex.

Abstract Background Prostate cancer develops through malignant transformation of the prostate epithelium in a stepwise, mutation-driven process. Although activator protein-1 transcription factors such as JUN have been implicated as potential oncogenic drivers, the molecular programs contributing to prostate cancer progression are not fully understood. Methods We analyzed JUN expression in clinical prostate cancer samples across different stages and investigated its functional role in a Pten-deficient mouse model. We performed histopathological examinations, transcriptomic analyses and explored the senescence-associated secretory phenotype in the tumor microenvironment. Results Elevated JUN levels characterized early-stage prostate cancer and predicted improved survival in human and murine samples. Immune-phenotyping of Pten-deficient prostates revealed high accumulation of tumor-infiltrating leukocytes, particularly innate immune cells, neutrophils and macrophages as well as high levels of STAT3 activation and IL-1β production. Jun depletion in a Pten-deficient background prevented immune cell attraction which was accompanied by significant reduction of active STAT3 and IL-1β and accelerated prostate tumor growth. Comparative transcriptome profiling of prostate epithelial cells revealed a senescence-associated gene signature, upregulation of pro-inflammatory processes involved in immune cell attraction and of chemokines such as IL-1β, TNF-α, CCL3 and CCL8 in Pten-deficient prostates. Strikingly, JUN depletion reversed both the senescence-associated secretory phenotype and senescence-associated immune cell infiltration but had no impact on cell cycle arrest. As a result, JUN depletion in Pten-deficient prostates interfered with the senescence-associated immune clearance and accelerated tumor growth. Conclusions Our results suggest that JUN acts as tumor-suppressor and decelerates the progression of prostate cancer by transcriptional regulation of senescence- and inflammation-associated genes. This study opens avenues for novel treatment strategies that could impede disease progression and improve patient outcomes. Graphical Abstract

Despite significant improvement in the survival of pediatric patients with cancer, treatment outcomes for high-risk, relapsed, and refractory cancers remain unsatisfactory. Moreover, prolonged survival is frequently associated with long-term adverse effects due to intensive multimodal treatments. Accelerating the progress of pediatric oncology requires both therapeutic advances and strategies to mitigate the long-term cytotoxic side effects, potentially through targeting specific molecular drivers of pediatric malignancies. In this report, we present the results of integrative genomic and transcriptomic profiling of 230 patients with malignant solid tumors (the "primary cohort") and 18 patients with recurrent or otherwise difficult-to-treat nonmalignant conditions (the "secondary cohort"). The integrative workflow for the primary cohort enabled the identification of clinically significant single nucleotide variants, small insertions/deletions, and fusion genes, which were found in 55% and 28% of patients, respectively. For 38% of patients, molecularly informed treatment recommendations were made. In the secondary cohort, known or potentially driving alteration was detected in 89% of cases, including a suspected novel causal gene for patients with inclusion body infantile digital fibromatosis. Furthermore, 47% of findings also brought therapeutic implications for subsequent management. Across both cohorts, changes or refinements to the original histopathological diagnoses were achieved in 4% of cases. Our study demonstrates the efficacy of integrating advanced genomic and transcriptomic analyses to identify therapeutic targets, refine diagnoses, and optimize treatment strategies for challenging pediatric and young adult malignancies and underscores the need for broad implementation of precision oncology in clinical settings.

Whilst the hybrids of F1 generations usually experience heterosis for fitness-related traits (including the resistance to parasites), post-F1 generations, due to Dobzhansky-Muller genetic incompatibilities, express numerous disadvantageous traits (including susceptibility to parasites). Genetic disruption in hybrids may also result from the broken system of cyto-nuclear coadaptation. Maternal backcrosses (having parents with the same mtDNA) and paternal backcrosses (having parents with different mtDNA) have the same nuclear genetic compositions, but differ in cytoplasmic genetic elements, affecting their viability and survival.Spring viraemia of the carp virus (SVCV), a disease with a serious economic impact in aquacultures, affects almost exclusively cyprinids, primarily common carp (Cyprinus carpio), and causes high mortality, whilst gibel carp (Carassius gibelio) is a less susceptible species. Our study was focused on the transcriptome profile analysis of head kidney to reveal differential gene expression in highly susceptible common carp, weakly susceptible gibel carp, and hybrid lines, hypothetizing that the patterns of differential gene expression will reflect hybrid heterosis in F1 generations and hybrid breakdown in backcrosses and F2 generations. We expected the differences in differential gene expression between maternal and paternal backcrosses to be in line with the hypothesis of broken cyto-nuclear coadaptation.The pattern of differential gene expression revealed from the transcriptomic analysis of head kidney was linked to the resistance or susceptibility to SVCV infections in two pure species, C. gibelio and C. carpio, and their various generations of inter-specific hybrids. We evidenced hybrid heterosis for F1 generations of hybrids, mostly reflected by similarity in the down-regulation of differentially expressed genes classified within the viral infection disease category. High hybrid breakdown was documented throughout the transcriptomic analysis for paternal backcross generations and F2 generation of hybrids, confirming the broken system of cyto-nuclear coadaptation in those post-F1 generations. This evidence may support the role of intrinsic selection acting against inter-specific hybridization in freshwater fish.