SEARCH · Search bioRxiv

Results for “Cancer Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37Linked to original sources

bioRxiv2024

Receptor tyrosine kinase inhibition leads to regression of acral melanoma by targeting the tumor microenvironment

Acral melanoma (AM) is an aggressive melanoma variant that arises from palmar, plantar, and nail unit melanocytes. Compared to non-acral cutaneous melanoma (CM), AM is biologically distinct, has an equal incidence across genetic ancestries, typically presents in advanced stage disease, is less responsive to therapy, and has an overall worse prognosis. Independent analysis of published genomic and transcriptomic sequencing identified that receptor tyrosine kinase (RTK) ligands and adapter proteins are frequently amplified, translocated, and/or overexpressed in AM. To target these unique genetic changes, a zebrafish acral melanoma model was exposed to a panel of narrow and broad spectrum multi-RTK inhibitors, revealing that dual FGFR/VEGFR inhibitors decrease acral-analogous melanocyte proliferation and migration. The potent pan-FGFR/VEGFR inhibitor, Lenvatinib, uniformly induces tumor regression in AM patient-derived xenograft (PDX) tumors but only slows tumor growth in CM models. Unlike other multi-RTK inhibitors, Lenvatinib is not directly cytotoxic to dissociated AM PDX tumor cells and instead disrupts tumor architecture and vascular networks. Considering the great difficulty in establishing AM cell culture lines, these findings suggest that AM may be more sensitive to microenvironment perturbations than CM. In conclusion, dual FGFR/VEGFR inhibition may be a viable therapeutic strategy that targets the unique biology of AM.

cancer biology↗

bioRxiv2026

Single cell Correlation Analysis (SCA): Identifying self-renewing subpopulation of human acute myeloid leukemia stem cells using single cell RNA sequencing analysis

Leukemia stem cells (LSCs), a rare and self-renewing subpopulation, drive Acute myeloid leukemia (AML) relapse and therapy resistance. While single-cell gene expression profiling (scGEP) offers high-resolution insights into LSC biology, existing computational tools rely on relative and arbitrary similarity metrics. This limits their ability to definitively identify true biological cell identities or compare rare cell populations across independent datasets. To overcome these limitations, we developed Single cell Correlation Analysis (SCA), a novel computational method that utilizes a permutation-based false discovery rate (FDR) framework and common background datasets to establish standardized, statistically rigorous thresholds of similarity. We applied SCA to query human AML scRNA-seq datasets using an experimentally validated murine scGEP of LSC self-renewal as our reference. SCA demonstrated superior specificity and precision, maintaining low false positive rates compared to existing reference-based annotation tools. Using SCA, we successfully identified cells expressing a conserved self-renewal program (scaLSC-SR) in both adult and pediatric human AML samples. These scaLSC-SR cells share classical LSC immunophenotypic markers (e.g., CD34, CD96, CD200) and exhibit transcriptomic hallmarks of LSC biology, including evasion of apoptosis and immune responses. Furthermore, this self-renewal program is significantly enriched in poor-risk genetic subtypes, specifically TP53 and NRAS mutated AML. Finally, we derived a 28-gene signature (LSC-SR28) from human AML patients that accurately captures LSC stemness and is highly prognostic across multiple independent clinical cohorts. SCA provides a robust, statistically principled framework for identifying rare and biologically meaningful cell populations across heterogeneous single-cell datasets. By successfully identifying a functional self-renewal profile to human AML, SCA reveals conserved, clinically relevant LSC populations that drive relapse and therapy resistance across different age groups.

cancer biology↗

bioRxiv2022

Interplay between Polycomb PCGF protein interactomes revealed by screening under endogenous conditions

The six PCGF proteins (PCGF1-6) define the biochemical identity of Polycomb Repressor Complex 1 (PRC1) subcomplexes. While structural and functional studies of PRC1 subcomplexes have revealed specialized roles in distinct aspects of epigenetic regulation, our understanding of variation in protein interaction networks between the PCGF subunits is incomplete. We carried out an affinity purification mass spectrometry (AP-MS) screen of subunits PCGF1 (NSPC1), PCGF2 (MEL18), and PCGF4 (BMI1), using an immunoprecipitation approach that replicated endogenous cellular conditions in a cell line capable of differentiation programs. Over 200 interactions were found, including 83 that had not been described previously. Bioinformatic analysis found that these interacting proteins covered a range of functional pathways, often focused on cell biology and chromatin regulation. We found evidence of mutual regulation (at mRNA and protein level) between distinct PCGF subunits. Furthermore, we confirmed that disruption of each subunit using shRNA results in reduced proliferation ability. Overall, our work adds to understanding of the role of PCGF proteins within the wider cellular network.

cancer biology↗

bioRxiv2025

ShapeUpLMD: An Automated Pipeline for Spatially Optimized Laser Microdissection in Multi-omic Tissue Profiling

Laser microdissection (LMD) enables enrichment of defined cellular populations from heterogeneous tissues, providing histologically-resolved molecular profiles with spatial resolution. However, the absence of standardized methods for generating optimized regions of interest (ROIs) limits reproducibility and scalability for spatial multi-omic workflows. To address this gap, we developed ShapeUpLMD, an open-source software tool and integrated workflow that automates the optimization of spatially defined ROIs for LMD, directly from digital pathology annotations. Fresh-frozen uterine serous carcinoma (USC) tumors (n = 11) were sectioned onto polyethylene naphthalate slides, scanned and subsequently annotated by an expert pathologist. Tumor and non-tumor ROIs were used to train tumor-specific classifiers in HALO (Indica Labs). Classified tumor or unbiased whole tissue ROIs were refined and optimized by ShapeUpLMD prior to automated collection on a Leica LMD7 microscope. Across the cohort, predicted tumor ROIs increased effective tumor purity by 86 {+/-} 6% relative to whole tissue while maintaining high spatial concordance between predicted and collected ROIs (accuracy = 0.9 {+/-} 0.05). Data-independent acquisition mass spectrometry quantified upwards of [~]6,500 proteins across spatially resolved ROIs, revealing regionally coherent clustering of adjacent tumor regions and abundance patterns consistent with tumor and non-tumor cell admixture in an unbiased spatial proteomic application. ShapeUpLMD provides an automated, reproducible, and scalable framework that bridges digital pathology with LMD enabling high-fidelity spatial enrichment for multi-omic analyses. This workflow increases throughput, reduces inter-operator variability, and supports standardized, regionally resolved tissue collection for spatial systems biology applications. The software is available at https://github.com/GYNCOE/ShapeUpLMD.

cancer biology↗

bioRxiv2024

Selective targeting of TBXT with DARPins identifies regulatory networks and therapeutic vulnerabilities in chordoma

Aberrant expression of the embryonal transcription factor TBXT (also known as brachyury) drives chordoma, a rare spinal neoplasm with no effective drug therapies. The gene network regulated by TBXT is poorly understood, and strategies to disrupt its abnormal activity for therapeutic purposes are lacking. Here, we developed TBXT-targeted designed ankyrin repeat proteins (T-DARPins) that selectively bind TBXT, inhibiting its binding to DNA and expression. In chordoma cells, T-DARPins reduced cell cycle progression, spheroid formation, and tumor growth in mice and induced morphologic changes indicative of senescence and differentiation. Combining T-DARPin-mediated TBXT inhibition with transcriptomic and proteomic analyses, we determined the TBXT regulome in chordoma cells, which comprises in particular networks involved in cell cycle regulation, DNA replication and repair, embryonal cell identity, metabolic processes, and interferon response. The analysis of selected TBXT regulome components provided new insights into chordoma biology, such as the strong upregulation of IGFBP3 upon TBXT inhibition to fine-tune part of TBXTs downstream effectors. Finally, we assigned each TBXT regulome member a druggability status to create a resource for future translational studies and found high interferon response signaling in chordoma cell lines and patient tumors, which was promoted by TBXT and associated with strong sensitivity to clinically approved JAK2 inhibitors. These findings demonstrate the potential of DARPins to investigate the function of nuclear proteins to understand the regulatory networks of cancers driven by aberrant transcription factor activity, including novel entry points for targeted therapies that warrant testing in patients.

cancer biology↗

bioRxiv2021

Metabolic and transcriptomic profiles of glioblastoma invasion revealed by comparisons between patients and corresponding orthotopic xenografts in mice

The invasive behavior of glioblastoma, the most aggressive primary brain tumor, is considered highly relevant for tumor recurrence. However, the invasion zone is difficult to visualize by Magnetic Resonance Imaging (MRI) and is protected by the blood brain barrier, posing a particular challenge for treatment. We report biological features of invasive growth accompanying tumor progression and invasion based on associated metabolic and transcriptomic changes observed in patient derived orthotopic xenografts (PDOX) in the mouse and the corresponding patients tumors. The evolution of metabolic changes, followed in vivo longitudinally by 1H-Magnetic Resonance Spectroscopy (MRS) at ultra-high field, reflected growth and the invasive properties of the human glioblastoma transplanted into the brains of mice (PDOX). Comparison of MRS derived metabolite signatures, reflecting temporal changes of tumor development and invasion in PDOX, revealed high similarity to spatial metabolite signatures of combined multi-voxel MRS analyses sampled across different areas of the patients tumors. Pathway analyses of the transcriptome associated with the metabolite profiles of the PDOX, identified molecular signatures of invasion, comprising extracellular matrix degradation and reorganization, growth factor binding, and vascular remodeling. Specific analysis of expression signatures from the invaded mouse brain, revealed extent of invasion dependent induction of immune response, recapitulating respective signatures observed in glioblastoma. Integrating metabolic profiles and gene expression of highly invasive PDOX provided insights into progression and invasion associated mechanisms of extracellular matrix remodeling that is essential for cell-cell communication and regulation of cellular processes. Structural changes and biochemical properties of the extracellular matrix are of importance for the biological behavior of tumors and may be druggable. Ultra-high field MRS reveals to be suitable for in vivo monitoring of progression in the non-enhancing infiltration zone of glioblastoma.

cancer biology↗

bioRxiv2022

CNTNAP4 signaling regulates osteosarcoma disease progression

Improved treatment strategies for sarcoma rely on clarification of the molecular mediators of disease progression. Recently, we reported that the secreted glycoprotein NELL-1 modulates osteosarcoma (OS) disease progression in part via altering the sarcomatous extracellular matrix (ECM) and cell-ECM interactions. Of known NELL-1 interactor proteins, Contactin-associated protein-like 4 (Cntnap4) encodes a member of the neurexin superfamily of transmembrane molecules best known for its presynaptic functions in the central nervous system. Here, CRISPR/Cas9 gene deletion of CNTNAP4 reduced OS tumor growth, sarcoma-associated angiogenesis, and pulmonary metastases. CNTNAP4 knockout (KO) in OS tumor cells largely phenocopied the effects of NELL-1 KO, including reductions in sarcoma cell attachment, migration, and invasion. Further, CNTNAP4 KO cells were found to be unresponsive to the effects of NELL-1 treatment. Transcriptomic analysis combined with protein phospho-array demonstrated notable reductions in the MAPK/ERK signaling cascade with CNTNAP4 deletion, and the ERK1/2 agonist isoproterenol restored cell functions among CNTNAP4 KO tumor cells. Finally, human primary cells and tissues in combination with sequencing datasets confirmed the significance of CNTNAP4 signaling in human sarcomas. In summary, our findings demonstrate the biological importance of NELL-1/CNTNAP4 signaling axis in disease progression of human sarcomas and suggest that targeting the NELL-1/CNTNAP4 signaling pathway represents a strategy with potential therapeutic benefit in sarcoma patients.

cancer biology↗

bioRxiv2026

Reverse molecular pharmacology identifies the non-canonical axis of IRAK as a chemoresistance factor in neuroblastoma

Owing to chemoresistance, the prognosis of relapsed neuroblastoma is dismal with less than 10% of patients surviving after 5 years. We developed a reverse molecular pharmacology approach that is based on high-throughput drug screening coupled with chemo-informatic and transcriptomic analyses. This led to the identification of IRAK1 as a key chemoresistance factor in neuroblastoma. By performing functional and pharmacological drug combination screens targeting IRAK1, we revealed a synergy between IRAK1 inhibition/silencing and BET, EGFR and mTOR inhibitors as well as microtubule-targeting agents. The synergistic combination of microtubule-targeting agent, vincristine and IRAK inhibitors was then confirmed in tumor spheroids, patient-derived tumoroids and a syngeneic orthotopic mouse model. Mechanistically, IRAK inhibition potentiated the pro-apoptotic and cell cycle arrest properties of vincristine via a pathway involving the PIDDosome complex rather than its canonical MyDDosome axis. Altogether, this study represents a proof-of-concept of our reverse molecular pharmacology approach to quickly develop biology-guided drug combinations, that could be applied to any other human diseases.

cancer biology↗

bioRxiv2026

An Isoform-Centric, Structure-Aware Framework for Protein Function Prediction and Evaluation, Instantiated in 3DisoDeepPF

Understanding and accurately predicting function across protein isoforms has been a long-standing challenge with profound implications for both biological and translational research. However, most functional annotations and benchmarks remain tied to genes or reference protein sequences, leaving limited support for distinguishing protein isoforms from the same gene whose sequence, structure and domain composition may lead to different functions. To address this gap, we developed an isoform-centric framework for protein function and domain annotation that integrates a dense graph of sequence and structure similarity with protein features. We implemented this framework as 3DisoDeepPF, a graph-based multimodal model, and applied it to a breast cancer isoform atlas. Across canonical benchmarks and evaluations at isoform resolution, 3DisoDeepPF showed strong performance in predicting GO terms and Pfam domains and remained robust in tests with homology control. It further captured changes in Pfam domain composition among isoforms from the same gene, including reference-relative domain gain and loss. An evidence tracing module links predicted labels to supporting proteins in the graph, as illustrated by the calcium and integrin binding protein 1 (CIB1). Together, this study provides a framework informed by protein structure for function and domain annotation at isoform resolution, converting human protein isoform diversity into traceable functional evidence for cancer atlas interpretation.

cancer biology↗

bioRxiv2021

INPP4B promotes leukemia by restricting leukemic stem cell differentiation through regulation of lysosomal functions

Signaling pathways that control vital features of leukemic stem cells including multipotency, self-renewal, clonal expansion and quiescence remain unclear. Emerging studies illustrate critical roles for lysosomes in hematopoietic and leukemic stem cell fate. By investigating consequences of INPP4B alterations in AML, we have discovered its role in driving leukemic stemness. We observed that INPP4B is highly expressed leukemic stem cell populations and Inpp4b-deficeint leukemias demonstrate increased disease latency, reduced leukemia initiating potential which is associated with a differentiated leukemic phenotype. Molecular analyses show that Inpp4b-deficient leukemias have compromised lysosomal gene expression, lysosomal content, and lysosomal activity. Our discovery of a novel pathway linking INPP4B, lysosomal biogenesis and leukemic stemness, provides a mechanism to explain the association of high INPP4B expression with poor AML prognosis, and highlights novel patient stratification strategies and LSC-specific leukemic therapies. Key PointsOur findings highlight a novel pathway linking INPP4B, lysosomal function and leukemic stemness that explains the prognostic role of INPP4B in AML. Our data reveal the utility of INPP4B as a biomarker of aggressive AML and provide a rationale to explore INPP4B and its associated function in lysosome biology as novel strategies to target LSC and AML

cancer biology↗

bioRxiv2022

A cellular hierarchy framework for understanding heterogeneity and predicting drug response in AML

The treatment landscape of AML is evolving with promising therapies entering clinical translation, yet patient responses remain heterogeneous and biomarkers for tailoring treatment are lacking. To understand how disease heterogeneity links with therapy response, we determined the leukemia cell hierarchy make-up from bulk transcriptomes of over 1000 patients through deconvolution using single-cell reference profiles of leukemia stem, progenitor, and mature cell types. Leukemia hierarchy composition was associated with functional, genomic, and clinical properties and converged into four overall classes, spanning Primitive, Mature, GMP, and Intermediate. Critically, variation in hierarchy composition along the Primitive vs GMP or Primitive vs Mature axes were associated with response to chemotherapy or drug sensitivity profiles of targeted therapies, respectively. A 7-gene biomarker derived from the Primitive vs Mature axis was predictive of patient response to 105 investigational drugs. Thus, hierarchy composition constitutes a novel framework for understanding disease biology and advancing precision medicine in AML.

cancer biology↗

bioRxiv2023

Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

Emerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with pathological features, and are thus particularly well-suited for applications in formalin fixed paraffin embedded (FFPE) tissues. Here, we benchmarked the performance of three commercial iST platforms on serial sections from tissue microarrays (TMAs) containing 23 tumor and normal tissue types for both relative technical and biological performance. On matched genes, we found that 10x Xenium shows higher transcript counts per gene without sacrificing specificity, but that all three platforms concord to orthogonal RNA-seq datasets and can perform spatially resolved cell typing, albeit with different false discovery rates, cell segmentation error frequencies, and with varying degrees of sub-clustering for downstream biological analyses. Taken together, our analyses provide a comprehensive benchmark to guide the choice of iST method as researchers design studies with precious samples in this rapidly evolving field.

cancer biology↗

bioRxiv2026

The RNA helicase DDX21 cooperates with ETS1 and FLI1 in cell cycle, immune evasion, and snoRNA processing in activated B-cell-like diffuse large B-cell lymphoma cells

Diffuse large B-cell lymphoma (DLBCL) is a clinically and biologically heterogeneous disease, with the activated B-cell-like (ABC) subtype showing inferior outcomes. The ETS transcription factors ETS1 and FLI1 are recurrently gained and functionally relevant in DLBCL, yet their pathogenetic function is still to be fully elucidated. Here, we describe their cooperation with the RNA regulatory machinery, demonstrating that the RNA helicase DDX21 is a central effector of the ETS1/FLI1 transcriptional network in ABC-DLBCL. Our proteomic analyses revealed that ETS1 physically interacted with DDX21 and other RNA processing factors. As ETS1, DDX21 was preferentially expressed in ABC-DLBCL, particularly in the MCD/C5 genetic subtype, and it was associated with adverse clinical outcomes in this lymphoma subtype. Genetic and pharmacological studies demonstrated that DDX21 was essential for ABC-DLBCL cell proliferation. DDX21 also coordinated various transcriptional programs, which were revealed by integrated RNA-Seq, small RNA-Seq, ChIP-Seq, and Capture Hi-C analyses. DDX21-dependent transcription was relevant for ribosome biogenesis, MYC signaling, cell cycle progression, and immune evasion, but also regulated non-coding RNA networks, including microRNAs and small nucleolar RNAs, in particular SNORA37. Collectively, our data establish DDX21 as a nucleolar hub linking ETS transcription factors to coding and non-coding RNA programs that sustain aggressive lymphoma biology. These findings suggest DDX21 and ETS-RNA helicase complexes as promising therapeutic vulnerabilities in ABC-DLBCL.

cancer biology↗

bioRxiv2023

Analytical Comparability to Evaluate Impact of Manufacturing Changes of ARX788, an Anti-HER2 ADC in Late-Stage Clinical Development

ARX788 is an anti-HER2 antibody drug conjugate (ADC) developed using Ambrx proprietary Engineered Precision Biologics technology. The manufacturing process of ARX788 has been optimized during the course of early to late-phase clinical development. A comprehensive evaluation of side-by-side comparability between pre- and post-change process for ARX788 drug substance and drug product from a quality perspective was conducted based on ICH Q5E guidelines consisting of batch release assays, physicochemical and biophysical characterization, biological characterization, and forced degradation studies. All results have demonstrated a high degree of similarity between the pre- and post-change ARX788 drug substance batches and drug product lots, demonstrating that the process manufacturing changes did not impact product quality.

cancer biology↗

bioRxiv2024

The Dual Roles of the CXCL10-CXCR3 Axis and Its Therapeutic Potential in Osteosarcoma

The CXCL10-CXCR3 axis is recognized for its dual role in tumor biology, promoting tumor growth and metastasis via autocrine signaling while also eliciting anti-tumor responses through paracrine signaling. However, its specific functions in osteosarcoma (OS), the most prevalent malignant bone tumor in children, remain poorly understood. Our previous research has demonstrated that elevated circulating CXCL10 levels correlate with poor prognosis in OS patients. Analysis of the TARGET OS RNAseq dataset revealed that high expression levels of CXCL10 or its receptor CXCR3 are associated with improved prognosis. Given the known role of CXCL10 in recruiting CXCR3+ immune cells to combat cancer, we further analyzed single-cell RNAseq data and found that CXCR3 is predominantly expressed in CD3+ T cell populations. These findings suggest that CXCL10 may also play a protective role in OS by recruiting anti-tumor immune cells. To elucidate the causal role of the CXCL10-CXCR3 axis in OS, we conducted in vitro phenotypic assays on three OS cell lines with and without CXCL10. The chemokine was found to enhance tumor cell migration and AKT phosphorylation. Utilizing a CRISPR-mediated CXCR3 deletion mutant, we demonstrated that the absence of CXCR3 significantly inhibited OS tumor growth and pulmonary metastasis in an orthotopic xenograft mouse model. Transfection with the CXCR3A isoform, but not the CXCR3B isoform, restored the migratory phenotype of the CXCR3 deletion mutant to levels comparable to the parental cell line. Additionally, pharmacological inhibition of CXCR3 with AMG487 markedly reduced OS cell migration in vitro and metastasis development in the orthotopic xenograft mouse model. Our research highlights the complex interplay of the CXCL10-CXCR3 axis in both tumor and immune cells. We propose a working model for the roles of the CXCL10-CXCR3 axis in OS, suggesting that targeting CXCR3 may be an effective strategy to inhibit OS metastasis, particularly in immune-cold OS subtypes.

cancer biology↗

bioRxiv2024

Adult-type diffuse gliomas share recurring cell states driven by a common astrocyte-like glioma stem cell population

Adult-type diffuse gliomas are a family of aggressive brain tumours with few effective treatments. Their complex cellular makeup adds to the challenge of finding successful therapies. This intratumoural heterogeneity is fuelled by a subpopulation of glioma stem-like cells (GSCs) that drive tumour growth and resistance to standard treatments. Previous research focused on the three glioma types (astrocytoma, oligodendroglioma, glioblastoma) individually revealed malignant cells mimic the transcriptional profiles of normal brain cell types. Whether these diverse cellular states stem from a shared biological origin is unknown. Here, we show through single-cell RNA sequencing of 40 glioma tumours that all gliomas are described by seven recurring cell states. We also identify a shared astrocyte-like GSC population. Our unique method of identifying GSCs, based on reconstructed tumour phylogenies, repositions astrocyte-like cells at the apex of a differentiation hierarchy in glioma. Our findings indicate the transcriptional heterogeneity observed in gliomas stems from a GSC population recapitulating lineages of healthy adult neural stem cells. These results suggest a shared lineage drives the intratumoural heterogeneity observed in adult-type diffuse gliomas. We anticipate that a deeper understanding of the molecular mechanisms maintaining the GSC state will provide a new framework for future therapeutic development and research into glioma cell biology. HighlightsO_LIRecurring cell states are shared across adult-type diffuse gliomas C_LIO_LIReconstructed tumour phylogenies identify an astrocyte-like glioma stem cell population C_LIO_LITumour subclones are segregated non-randomly across cell states C_LI

cancer biology↗

bioRxiv2024

Epigenetic investigation of multifocal small intestinal neuroendocrine tumours reveals accelerated ageing of tumours and epigenetic alteration of metabolic genes

BackgroundSmall intestinal neuroendocrine tumours (SI-NETs) are the most common malignancy of the small intestine and around 50% of patients present in clinic with multifocal disease. Recent investigations into the genomic architecture of multifocal SI-NETs have found evidence that these synchronous primary tumours evolve independently of each other. They also have extremely low mutational burden and few known driver genes, suggesting that epigenetic dysregulation may be driving tumorigenesis. Very little is known about epigenetic gene regulation, metabolism and ageing in these tumours, and how these traits differ across multiple tumours within individual patients. MethodsIn this study, we performed the first investigation of genome-wide DNA methylation in multifocal SI-NETs, assessing multiple primary tumours within each patient (n=79 primary tumours from 14 patients) alongside matched metastatic tumours (n=12) and normal intestinal epithelial tissue (n=9). We assessed multifocal SI-NET differential methylation using a novel method, comparing primary tumours with matched normal epithelial tissue and an enterochromaffin-enriched cell line to enrich for tumour-specific effects. This method reduced the identification of false positive methylation differences driven by cell composition differences between tumour and normal epithelial tissue. We also assessed tumour ageing using epigenetic clocks and applied metabolic predictors in the dataset to assess methylation variation across key metabolic genes. ResultsWe have identified 12,392 tumour-specific differentially methylated positions (Bonferroni corrected p<0.05) which were enriched for neural pathways. The expression levels of the genes associated with top sites were also found to be significantly altered in SI-NETs. Age acceleration was observed across SI-NETs and a variability in epigenetic age of tumours within each patient, which we believe is reflecting the order in which tumours have developed. This is supported by the correlation of age acceleration with somatic mutational count in the tumours. We have identified SI-NET associated alterations to the methylation patterns in key metabolic genes compared to matched normal tissue, which is more pronounced in metastatic tumours and tumours harbouring chromosome 18 loss of heterozygosity, indicating metabolic differences in these tumour subtypes. ConclusionsWe have identified accelerated ageing and changes to regulation of metabolic genes, alongside an epigenetic signature of multifocal SI-NETs. These findings add to our understanding of multifocal SI-NET biology and their molecular differences which may be instrumental in the development of these elusive tumours.

cancer biology↗

bioRxiv2018

The functional genomic circuitry of human glioblastoma stem cells

SummarySuccessful glioblastoma (GBM) therapies have remained elusive due to limitations in understanding mechanisms of growth and survival of the tumorigenic population. Using CRISPR-Cas9 approaches in patient-derived GBM stem cells to interrogate function of the coding genome, we identify diverse actionable pathways responsible for growth that reveal the gene-essential circuitry of GBM stemness. In particular, we describe the Sox developmental transcription factor family; H3K79 methylation by DOT1L; and ufmylation stress responsiveness programs as essential for GBM stemness. Additionally, we find mechanisms of temozolomide resistance and sensitivity that could lead to combination strategies with this standard of care treatment. By reaching beyond static genome analysis of bulk tumors, with a genome wide functional approach, we dive deep into a broad range of biological processes to provide new understanding of GBM growth and treatment resistance.\n\nSignificanceGlioblastoma (GBM) remains an incurable disease despite an increasingly thorough depth of knowledge of the genomic and epigenomic alterations of bulk tumors. Evidence from multiple approaches support that GBM reflects an aberrant developmental hierarchy, with GBM stem cells (GSCs), fueling tumor growth and invasion. The properties of this tumor subpopulation may also in part explain treatment resistance and disease recurrence. Unfortunately, we still have a limited knowledge of the molecular circuitry of these cells and progress has been slow as we have not been able, until recently, to interrogate function at the genome-wide scale. Here, using parallel genome-wide CRISPR-Cas9 screens, we identify the essential genes for GSC growth. Further, by screening in the presence of low and high dose temozolomide, we identify mechanisms of drug resistance and sensitivity. These functional screens in patient derived cells reveal new aspects of GBM biology and identify a diversity of actionable targets such as genes governing stem cell traits, epigenome regulation and the response to stress stimuli.

cancer biology↗