Biology subjects

Maniati, E.

Publications and source records attributed to Maniati, E..

13 recordsLinked to original sources

bioRxiv2026

An RNA-centric atlas of human cell cycle regulation

Cell cycle progression is orchestrated by protein networks coordinating cell growth and division, yet the role of RNA-mediated mechanisms remains underexplored. Here, we define an RNA-centric landscape of human cell cycle control using palbociclib-synchronised normal diploid cells, profiling long non-coding RNAs (lncRNAs), transposable elements (TEs), alternative splicing (AS), and RNA-binding proteins (RBPs). We identify 104 cell cycle-regulated lncRNAs and validate lncRNA ENSG00000230615, whose perturbation alters cell cycle progression and downregulates neighbouring KLF17. Across the transcriptome, 297 TE loci exhibit differential expression dynamics during the cell cycle, with Alu elements upregulated during the G1-to-S transition. Cell-cycle-dependent AS changes affect 598 genes, with alternative 5' splice sites showing the largest shift in usage at the G1-to-S transition. Furthermore, we show that cytokinesis proteins act as non-canonical RBPs with RNA-dependent stability. This study provides a comprehensive resource on RNA-based cell cycle control and highlights an underappreciated layer of regulation mediated by RNA mechanisms.

cell biology↗

bioRxiv2026

Mural β3-integrin signposts Stroma6, a gene signature predicting early relapse in low-risk and chemoresistant breast cancer

The Oncotype DX (ODX) assay guides adjuvant chemotherapy in ER+/HER2- breast cancer but overlooks drivers from the tumour stroma, leaving some low-risk and chemotherapy-spared patients vulnerable to rapid relapse. Here, we show that perivascular mural {beta}3-integrin protein expression predicts early (3-year) relapse in ODX low-risk patients (HR = 15.80, P = 0.010), from which we derived a translatable 6-gene stromal signature, termed Stroma6. High Stroma6 expression predicted early recurrence in the ODX low-risk discovery cohort, with zero early relapses in the low-expression group. External validation in the METABRIC dataset confirmed that Stroma6 independently predicts rapid recurrence in ODX low-risk patients (HR = 11.68, P = 0.002). Furthermore, Stroma6 utility extends to clinical chemoresistance, independently predicting early events in a pan-subtype cohort with residual disease following neoadjuvant chemotherapy (HR = 2.29, P = 0.003). Ultimately, Stroma6 is a robust prognostic signature identifying patients at high risk of early recurrence across diverse clinical contexts.

cancer biology↗

bioRxiv2026

Reconstruction of epithelial transcriptional trajectories reveals heterogeneous progression and early therapy-resistance programs in high-grade serous carcinomaprecursors

BackgroundSerous-tubal intraepithelial-carcinoma (STIC) is considered the principal precursor of tubo-ovarian high-grade serous-carcinoma (HGSC), yet its biological uniformity, progression risk and potential response to poly(ADP-ribose) polymerase-inhibitors (PARPi) remain poorly defined. MethodsWe performed trajectory-based transcriptomic reconstruction of Fallopian-tube epithelial regions spanning normal epithelium, precursor lesions, STIC, and invasive carcinoma using pseudotime inference and publicly available spatial transcriptomic data. Gene expression and pathway dynamics were defined along pseudotime, and interpatient heterogeneity examined at both lesion and patient levels. Transcriptional signatures associated with PARPi-resistance were quantified across STICs, BRCA-mutant and BRCA-wild type subtypes. ResultsTrajectory inference captured a continuous transcriptional progression from normal epithelium to HGSC, with STICs occupying heterogeneous evolutionary positions rather than a single precursor state. Incidental isolated STICs(STICi) spanned early to later pseudotime states and frequently aligned with loss-of-cilium organisation and less advanced epithelial phenotypes. STICs associated with concurrent cancer(STICc) exhibited more advanced malignant progression signatures, including cell-cycle activation, epithelial-to-mesenchymal transition (EMT), interferon signaling, and DNA-repair. Histologically similar lesions occupied divergent pseudotime positions with marked interpatient heterogeneity. PARPi resistance-associated signatures were variably enriched across precursor and precancer-stage lesions, with persistence into invasive disease. ConclusionsSTICs are heterogeneous and occupy distinct evolutionary positions along a continuum, highlighting potentially different progression risks from normal epithelium to HGSC. STICi differ from STICc which harbour signatures of more advanced malignant progression. Heterogeneity in PARPi resistance-associated programs in STICs cautions against uniform (non-stratified) use of PARPi-based primary prevention strategies. Future research should explore evolutionary-trajectory informed biomarkers for risk stratification and early interception strategies. Translational relevanceSerous tubal intraepithelial-carcinoma (STIC) represents a precursor of tubo-ovarian high-grade serous carcinoma (HGSC), offering unique translational opportunities for early detection, risk stratification, and prevention. However, its phenotypic uniformity, progression risk and therapeutic drug response are not fully understood. Our study shows that STICs are not a uniform precursor state, but instead occupy a range of evolutionary positions along a continuum from normal epithelium to invasive HGSC. This heterogeneity reflects continuous transcriptional variation rather than discrete precursor categories. We report gene expression dynamics and molecular signature changes across the malignant transformation timeline. We further illustrate that precursor lesions exhibit phenotypic variability that impacts therapeutic drug resistance-associated programs. Our data highlight potential disease biomarkers defined by evolutionary trajectory inference and transcriptional processes associated with drug resistance operating in precursor lesions. These findings may help improve our ability to distinguish clinically significant lesions and inform targeted interception strategies.

cancer biology↗

bioRxiv2025

Pancreatic cancer metastasis is regulated by an eleven amino-acid sequence

Pancreatic ductal adenocarcinoma (PDAC) has a very poor prognosis with a 5-year survival rate less than 5% because of its ability to metastasise, its late detection and the lack of effective therapies. The Integrin v{beta}6 is highly overexpressed in PDAC and correlates with poor prognosis. The integrin {beta}6 subunit contains a unique C-terminal tail of 11 amino acids (aa) that regulates downstream signals, although the mechanism remains unclear. Here, using integrin {beta}6-deficient cells lines, we have developed two PDAC mouse models overexpressing the full-length {beta}6 and a mutant {beta}6 lacking the C-terminal 11aa (v{Delta}{beta}6). In vitro, v{beta}6 overexpression increased cell proliferation, migration and invasion in a 3D spheroid model. The elimination of the C-terminal 11aa decreased proliferation and totally impaired cell migration and invasion. v{Delta}{beta}6 cells also expressed reduced MMPs in vitro. In vivo, orthotopic implantation of v{beta}6 overexpressing cells showed decreased overall survival and more spontaneous metastasis compared to v{Delta}{beta}6 and v{beta}6-null cells. Therefore, the C-terminal 11aa of the integrin {beta}6 subunit regulates PDAC progression and metastasis.

cancer biology↗

bioRxiv2025

An AGO2 adaptor expands the functional and evolutionary reach of microRNA targeting

Current models of microRNA (miRNA) silencing posit that RNA-sequence rules are sufficient for canonical targeting of mRNAs by Argonaute 2 (AGO2), the central protein of the miRNA-induced silencing complex (miRISC). Using chimeric eCLIP in CRISPR-edited LIMD1+/+, LIMD1+/-, and LIMD1-/- human small airway epithelial cells (hSAECs), we reveal a transcriptome-wide dependency on LIMD1, an AGO2 adaptor, for effective miRNA targeting and repression. In LIMD1-deficient cells, miRNA loading is uncoupled from productive targeting: despite increased AGO2-miRNA interactions, complexes engage fewer transcripts and sites, reducing occupancy and more than halving both the breadth and depth of targeting. We also observe altered AGO2 positional footprints across targets in LIMD1-deficient cells. LIMD1 dependence is most pronounced at defined RNA contexts: weak (GC-poor) seed pairings, interactions involving evolutionarily young miRNAs or sites that nonetheless form thermodynamically stable duplexes, with these losses particularly enriched in coding sequences of rapidly evolving C2H2-zinc-finger genes. Even within canonical seed repertoires of individual AGO2-miRNAs, LIMD1 is most critical at poorly conserved sites, indicating that LIMD1 broadens miRNA regulation beyond ancient, deeply conserved targets. In culture, LIMD1 deficiency de-represses oncogenic proteins that, in vivo, inversely correlate with LIMD1 levels in normal lung and adenocarcinoma, where LIMD1 is characteristically reduced, and whose dysregulation predicts poor survival. Thus, LIMD1 emerges as a key determinant of miRISC architecture, targeting, and potency, challenging RNA-centric models of miRNA function and exemplifying how adaptor proteins diversify post-transcriptional regulation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=180 HEIGHT=200 SRC="FIGDIR/small/680889v2_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@e0f4f5org.highwire.dtl.DTLVardef@f23fd9org.highwire.dtl.DTLVardef@3de3f2org.highwire.dtl.DTLVardef@1404af2_HPS_FORMAT_FIGEXP M_FIG LIMD1 defines the scope of miRNA-mediated targeting and repression O_LIAGO2-chimeric eCLIP in CRISPR-edited human small airway epithelial cells (hSAECs) shows LIMD1 is required for productive AGO2-miRNA engagement transcriptome-wide. C_LIO_LILIMD1 deficiency reduces the AGO2-miRNA:targetome. Each AGO2-miRNA binds fewer targets, with lower occupancy per site and per transcript and fewer global silencing events. C_LIO_LILIMD1 dependence is strongest for GC-poor seed-sites, less conserved miRNAs and sites, and thermodynamically stronger duplexes. C_LIO_LIDosage-dependent effects of LIMD1 deficiency are broadly observed. C_LIO_LITarget-mRNA decay and translational repression are reduced in LIMD1-deficient hSAECs, increasing protein output. C_LIO_LIIn vivo, LIMD1 LOH-associated deficiency is prevalent and typically clonal in NSCLC. LIMD1 expression inversely correlates with oncogene levels in normal lung and adenocarcinoma, and target dysregulation predicts poor survival. C_LI C_FIG

molecular biology↗

bioRxiv2025

Matrix structure and microenvironment dynamics correlate with chemotherapy response in ovarian cancer

Elevated extracellular matrix (ECM) in the tumor microenvironment (TME) is associated with chemoresistance and poor prognosis. We hypothesized that modifying the ECM may enhance response to chemotherapy. We measured chemotherapy-induced changes in the TME of two mouse models of high-grade serous ovarian cancer (HGSOC) that differed in chemotherapy response. Treatment of the chemo-sensitive tumors triggered dynamic transcriptional ECM and immune changes and structural modifications of ECM proteins. These changes, observed over twenty-days post-chemotherapy, had relevance to HGSOC patient responses to chemotherapy. Integrating transcriptomics with ECM structure metrics, we identified ECM targets, including lysyl oxidase (LOX), that might enhance chemotherapy in less responsive mouse tumors. Given alone or in combination with chemotherapy, a pan-LOX inhibitor (PXS-5505) modulated fibroblast and immune cell distribution and reduced tumor stiffness in HGSOC chemo-resistant mouse tumors. Moreover, pre-treatment with PXS-5505 improved response to chemotherapy. We conclude that pretreatment with ECM targeting agents may improve response to chemotherapy, by altering ECM structure and immune responses.

cancer biology↗

bioRxiv2025

The RNA-binding protein RSRC2 promotes mitotic fidelity by interacting with the lncRNA C1QTNF1-AS1

Mitotic fidelity depends on proper chromosome alignment at the spindle equator, a process known as chromosome congression, driven by well-established protein networks. Whereas RNA-binding proteins and noncoding RNAs have been implicated in cell division, their interplay during this process remains unknown. Here, we discover that RSRC2, an arginine/serine-rich RNA-binding protein, plays an essential role in cell division by interacting with the long non-coding RNA C1QTNF1-AS1. The loss of either RSRC2 or C1QTNF1-AS1 results in defects in chromosome congression and mitotic progression. We show that RSRC2 interacts with distinct sets of proteins involved in splicing and centrosome biogenesis, contributing to the fidelity of cell division through two different mechanisms: one linked to the splicing of mitotic regulators and the other by localising to mitotic centrosomes for which the interaction with the C1QTNF1-AS1 RNA is required. Our study uncovers RSRC2 as a new regulator of cell division and illustrates how RNA-protein complexes promote error-free mitosis.

cell biology↗

bioRxiv2024

The DNA Mismatch repair protein, MSH6 is a novel regulator of PD-L1 expression

Immune checkpoint inhibitors (ICIs) are extremely effective in a subgroup of mismatch repair-deficient (MMRd) cancers, but [~]50% remain resistant to treatment. We have shown for the first time that this may be due to the differential regulation of factors linked to response to ICIs upon loss of the different MMR genes. Here, we show that increased PD-L1 expression is observed upon loss of the MMR genes MLH1, MSH2 and PMS2. However, this is not true upon loss of MSH6. Here, we show that this is due to a novel role for MSH6 as a direct regulator of PD-L1 transcription, dependent on recruitment by the histone trimethyltransferase SETD2. Next-generation sequencing of MLH1 and MSH6 knockout (KO) cells revealed that MSH6 KO cells have significantly lower microsatellite instability in comparison to MLH1 KO cells, despite MSH6 KO cells having a higher mutational burden. These findings emphasise the need for gene-specific stratification in the MMRd cohort.

cancer biology↗

bioRxiv2023

Non-coding mutations at enhancer clusters contribute to pancreatic ductal adenocarcinoma

Non-coding mutations (NCMs) that perturb the function of cis-regulatory elements (CRE, enhancers) contribute to cancer. Due to the vast search space, mutation abundance and indirect activity of non-coding sequences, it is challenging to identify which somatic NCMs are contributing to tumour development and progression. Here, we focus our investigation on the somatic NCMs that are enriched at enhancers from 659 pancreatic ductal adenocarcinoma (PDAC) tumours. We identify cis-regulatory NCMs within PDAC-specific enhancers derived from high and low-grade PDAC cell lines and patient derived organoids using two independent computational approaches. Five such CREs enriched for PDAC associated NCMs are also frequently mutated in other common solid tumours. Functional validation using STARR-seq reporter assays enables the prioritisation of 43 NCMs (7.3%) from a pool of 587 NCMs with 6,082 oligos, that significantly alter reporter enhancer activity compared to wild-type sequences. CRISPRi perturbation of an enhancer cluster harbouring NCMs over long non-coding RNA gene MIR100HG, which hosts a microRNA cluster (mir100-let7a-2-125b-1), leads to the downregulation of MIR100HG accompanied by a significant reduction in the TGF-{beta} pathway (known to induce MIR100HG) and other PDAC critical pathways, including KRAS, p53, MTOR and TNF signalling. Collectively, we have reported here cis-regulatory NCMs in PDAC proximal to many cancer-relevant genes, and our integrated approach paves way to explore CRE-associated NCMs in other human cancer genomes.

genomics↗

bioRxiv2022

Extracellular matrix educates a tumor macrophage phenotype found in ovarian cancer metastasis

Recent studies have shown the tumor extracellular matrix (ECM) associates with immunosuppression, and that targeting the ECM can improve immune infiltration and immunotherapy response. A question that remains is whether the ECM is directly educating the immune phenotypes seen in cancer. We identified a tumor-associated macrophage (TAM) population correlated with poor prognosis, interruption of the cancer immunity cycle, and tumor ECM composition. To investigate whether ECM was capable of generating the TAM phenotype seen, we developed a decellularized tissue model that retains the native ECM architecture and composition. Macrophages cultured on decellularized ovarian metastasis shared transcriptional profiles with the TAMs found in human tissues. ECM educated macrophages have a tissue remodeling and immunoregulatory phenotype, inducing altered T cell function. We conclude that the tumor ECM is directly educating this macrophage population found in cancer tissues. Therefore, current and emerging cancer therapies that target the tumor ECM may be tailored to improve macrophage phenotype and their downstream regulation of immunity.

cancer biology↗

bioRxiv2021

Modelling TGFβR and Hh pathway regulation of prognostic matrisome molecules in ovarian cancer

In a multi-level deconstruction of omental metastases, we previously identified a prognostic matrisome gene expression signature in high-grade serous ovarian cancer (HGSOC) and twelve other malignancies. Here, our aim was to understand how six of these extracellular matrix, ECM, molecules, COL11A1, COMP, FN1, VCAN, CTSB and COL1A1, are up-regulated in cancer. Using biopsies, we identified significant associations between TGF{beta}R activity, Hedgehog signalling and these ECM molecules and then studied the associations in mono-, co- and tri-culture. Activated omental fibroblasts produced more matrix than malignant cells, directed by TGF{beta}R and Hedgehog signalling crosstalk. We reconstructed omental metastases in tri-culture of HGSOC cells, omental fibroblasts and adipocytes. This combination was sufficient to generate all six ECM proteins and the matrisome expression signature. TGF{beta}R and Hedgehog inhibitor combinations attenuated fibroblast activation, gel remodelling and ECM remodelling in these models. The tri-culture model reproduces key features of omental metastases and allows study of diseased-associated ECM.

cancer biology↗

bioRxiv2020

Platinum resistance induces diverse evolutionary trajectories in high grade serous ovarian cancer

Resistance to therapy is an enduring challenge in cancer care. Here we interrogate this critical unmet need using high grade serous ovarian cancer (HGSC) as a disease model. We have generated a unique panel of platinum-resistant HGSC models and shown that they share multiple transcriptomic features with relapsed human HGSC. Moreover, they evolve diverse in vivo phenotypes reflecting the human disease. We previously characterised copy number signatures in HGSC that correlate with patient survival and now provide the first evidence that these signatures undergo recurrent alterations during platinum therapy. Furthermore, specific, resistance-associated signature change is associated with functionally relevant gene expression differences. For example, reduced signature 3 (BRCA1/2-related homologous recombination deficiency) is associated with increased expression of homologous recombination repair genes (Rad51C, Rad51D, BRCA1) and DNA recombination pathway enrichment. Our mechanistic examination therefore provides new and clinically relevant insights into the genomic evolution of platinum-resistant cancers.

cancer biology↗

bioRxiv2019

Replication Stress Generates Multiple Distinct Classes of Copy Number Alterations

BackgroundWe previously showed that a major driver of cancer chromosomal instability (CIN) is replication stress, the slowing or stalling of DNA replication. However, the precise drivers of replication stress in cancer and the mechanisms by which these cause CIN and influence tumour evolution remain unclear. Common fragile sites are well-known genomic locations of breakage after aphidicolin-induced replication stress, but their precise causes of fragility are debated, and additional genomic consequences of replication stress are not fully explored. ResultsUsing single cell sequencing we detected DNA copy number alterations (CNAs) caused by one cell cycle under replication stress in diploid non-transformed cells. Aphidicolin-induced replication stress caused multiple types of CNAs associated with different genomic regions and features. Coupling cell type-specific analysis of CNAs to gene expression and single cell replication timing analyses allowed us to pinpoint the causative large genes of the most recurrent chromosome-scale CNAs. In RPE1 cells these were largely confined to three sites on chromosomes 1, 2 and 7 and generated acentric lagging chromatin and micronuclei containing these chromosomes. Different replicative stresses generated distinct profiles of CNAs providing the potential to interpret specific replication stress mechanisms from cancer cells. ConclusionsChromosomal instability driven by replication stress occurs via focal CNAs and chromosome arm-scale changes, with the latter confined to a very small subset of chromosome regions, potentially heavily skewing cancer genome evolution trajectories. Single cell CNA analysis thus reveals new insights into the impact of replication stress on the genome and provides a platform to further dissect molecular mechanisms involved in the replication stress response and to gain insights into how replication stress fuels chromosomal instability in cancer.

molecular biology↗