Biology subjects

Oppermann, U.

Publications and source records attributed to Oppermann, U..

At least 19 recordsLinked to original sources

bioRxiv2026

A platform for deep topographic multiomic mapping of the bone marrow environment in multiple myeloma

Multiple myeloma is a genetically complex plasma cell malignancy in which profound intratumoral heterogeneity shapes disease progression and therapeutic resistance. Genomic subclones dynamically emerge and evolve under treatment pressure, yet their spatial organization within intact bone marrow remains poorly defined. We hypothesized that genetically distinct myeloma subclones occupy spatially discrete ecological niches associated with unique molecular and microenvironmental states. To test this, we here demonstrate a proof-of-concept spatial tri-omics workflow combining laser capture microdissection-based genomics and deep LC-MS/MS proteomics with single-cell spatial transcriptomics, integrated by digital co-registration of adjacent tissue sections. Applied to a myeloma bone marrow trephine, this approach enabled coordinated profiling of matched anatomical regions demonstrating that genomic, transcriptomic and proteomic profiles converged to define clone-specific microenvironmental programmes. We show that genetically distinct myeloma subclones occupy mutually exclusive regions of the same bone marrow biopsy. Remarkably, an aggressive del(17p) clone and a gain(12q) clone occupied defined anatomical territories within the same trephine-biopsied section, each clone exhibiting distinct genomic, transcriptomic, proteomic and cellular ecosystems. The del(17p) clone localized to a fibrotic, osteolytic and angiogenic niche enriched for activated stromal cells, osteoblasts, osteoclasts and immunoregulatory myeloid populations, whereas the gain(12q) clone occupied a comparatively quiescent marrow niche with limited stromal remodelling. Together, these findings demonstrate that genetically distinct myeloma subclones establish spatially and biologically discrete ecological niches through coordinated remodelling of stromal, immune and bone compartments, providing a framework for understanding clonal evolution within the bone marrow microenvironment.

cancer biology↗

bioRxiv2026

BRD9 inhibition induces selective radiosensitivity in glioblastoma through MYC pathway modulation

Radiotherapy (RT) is a cornerstone of glioblastoma (GBM) treatment, yet therapeutic resistance remains nearly universal due to the rapid activation of stress-adaptive survival programs. Identifying molecular regulators that sustain these adaptive responses may reveal context-dependent vulnerabilities that can be therapeutically exploited. Here, we performed an epigenetic drug screen under low-dose irradiation to identify modifiers of radiotherapy response in glioblastoma. We identify BRD9 inhibition as a priming strategy that selectively enhances irradiation-induced lethality without inducing substantial cytotoxicity under baseline conditions. Mechanistically, BRD9 perturbation delays the resolution of irradiation-induced DNA damage, leading to increased apoptosis following irradiation. This effect is selective for malignant glioblastoma cell lines and patient-derived primary cells, while sparing non-malignant human astrocytes. Transcriptomic profiling reveals that BRD9 inhibition or genetic depletion produces a coordinated, MYC-centered suppression of translational programs, including ribosome biogenesis, rRNA processing, tRNA aminoacylation, and translational initiation. Ectopic MYC expression attenuates BRD9-dependent radiosensitization, functionally linking MYC suppression to the enhanced radiation response. Importantly, analysis of independent glioblastoma patient cohorts reveals a consistent positive association between BRD9 and MYC expression, alongside elevated BRD9 expression in recurrent compared with primary tumors. Together, these findings identify BRD9 as a regulator of MYC-associated translational programs and support its therapeutic targeting as a strategy to enhance radiotherapy efficacy in glioblastoma.

cancer biology↗

bioRxiv2026

Targeting CBP/p300 Overcomes Acquired Vincristine Resistance in Medulloblastoma

BackgroundMedulloblastoma is the most common malignant pediatric brain tumor. Although advances in conventional therapies have improved survival over the years, acquired drug resistance remains a major barrier to durable cure. As dysregulation of epigenetic mechanisms is increasingly recognized as a driver of medulloblastoma pathogenesis and therapeutic adaptation, targeting epigenetic vulnerabilities represents a promising strategy to overcome treatment resistance. MethodsWe generated vincristine-resistant medulloblastoma cell line models and performed chemical screening to identify therapeutically targetable vulnerabilities. Candidate hits were validated using transcriptomic analyses, chromatin immunoprecipitation, and CRISPR-mediated genetic ablation to define the molecular mechanisms underlying drug sensitivity. ResultsChemical screening identified multiple active epigenetic compound classes capable of resensitizing vincristine-resistant medulloblastoma cells, including histone methyltransferase inhibitors, histone deacetylase inhibitors, and bromodomain inhibitors. Among these, the CBP/p300 bromodomain inhibitor SGC-CBP30 emerged as the most potent sensitizer to vincristine. Transcriptomic profiling revealed that, while ABCB1 was among the most highly upregulated genes in resistant cells, SGC-CBP30 treatment selectively downregulated ABCC3 and ABCA4, an effect not observed in parental cells. Mechanistically, chromatin immunoprecipitation demonstrated enrichment of p300 and H3K27ac at the ABCC3 and ABCA4 promoters in resistant cells, which was markedly reduced following SGC-CBP30 treatment. Consistent with these findings, genetic ablation of CREBBP or EP300 phenocopied the effects of pharmacological inhibition. Analysis of patient datasets further demonstrated elevated CREBBP, EP300, and ABCC3 expression in SHH MB, with positive correlations between ABCC3 and both CREBBP and EP300, supporting the clinical relevance of this regulatory axis. ConclusionsTogether, our findings demonstrate that CBP/p300 activity contributes to acquired vincristine-resistance in medulloblastoma. Targeting this axis represents a promising strategy to overcome drug resistance and enhance the efficacy of vincristine-based chemotherapy particularly in the context of relapsed or refractory disease. PLAIN ENGLISH SUMMARYMedulloblastoma is the most common cancerous brain tumor in children. Although many children respond well to the treatment, some tumors become resistant to chemotherapy, making them much harder to treat. Understanding why this resistance develops could lead to better treatment options for children whose cancer returns or no longer respond to therapy. In this study, we created laboratory models of medulloblastoma that had become resistant to the chemotherapy drug vincristine. We then tested a collection of drugs to identify compounds, which would restore the cancer cells sensitivity to treatment. We have discovered that several drugs were effective, with one compound, called SGC-CBP30, showing particularly strong activity. We investigated how SGC-CBP30 works and found that it decreases the activity of genes that are linked to chemotherapy resistance. Using multiple complementary experimental approaches, we confirmed that this gene-regulating pathway plays an important role in helping medulloblastoma cells survive treatment. Our findings suggest that targeting this pathway could restore the effectiveness of chemotherapy in drug-resistant tumors. Although further research is needed before this approach can be used in patients, these results provide a promising foundation for developing new treatments for children with relapsed or treatment-resistant medulloblastoma.

cancer biology↗

bioRxiv2026

Sequential acquisition of 1p31.1-p12 LOH and 1q Gain is a common double-hit event in relapsed/refractory myeloma

Therapy-driven genomic changes in multiple myeloma (MM) remain poorly defined. We analyzed whole-genome sequencing (WGS) data from relapsed/refractory MM (rrMM, N=386) and identified regional 1p31.1-p12 (hereafter 1pCEN, a region proximal to the centromere) loss-of-heterozygosity (LOH) as the only enriched aberration showing strong therapy-associated clonal selection (clonal timing rank fold-change = 3.7, P<2.2x10-16). This event showed enriched co-occurrence with 1qGain (OR = 2.3 (1.5-3.8), P=2x10-4) forming a recurrent "double-hit" in rrMM. To validate the clonal selection process, we examined three longitudinal cohorts (180 patients, 390 samples) and confirmed clonal expansion of 1pCEN and consistent prevalence of the 1pCEN+1q double-hit (20-24%). Survival analyses demonstrated significantly reduced progression-free survival in rrMM patients with this double-hit compared with those without. Comparison with a large newly diagnosed MM (ndMM) cohort confirmed previously-described 1p32 LOH is the prognostic locus at baseline, whereas 1pCEN is therapy-selected and largely independent of the 1p32 locus. Thus, 1pCEN+1q represents a recurrent double-hit event that clonally emerges in rrMM, conferring selective advantage under drug exposure and is distinct from the ndMM high-risk markers defined by current consensus guidelines. These findings nominate 1pCEN as a new genomic biomarker in rrMM and 1pCEN+1q may help patient stratification for therapeutic monitoring. Key PointsA therapy-driven common genomic double-hit (1p31.1-p12 LOH with 1q gain) clonally emerges in relapsed/refractory myeloma.

cancer biology↗

bioRxiv2026

Early plasma proteomic alterations precede amyloidosis diagnosis, reflecting cardiac and immune dysregulation

Systemic amyloidosis is typically diagnosed only after irreversible organ damage has occurred, limiting the effectiveness of available therapies. Whether the disease is preceded by detectable molecular changes long before clinical presentation has remained unclear. Here, we leveraged population-scale plasma proteomics and longitudinal follow-up from the UK Biobank to investigate early circulating protein signatures associated with future diagnosis of amyloidosis. Among approximately 53,000 participants with proteomic profiling, we identified 61 individuals who developed amyloidosis up to 14 years after protein assessment. Differential expression and correlation analyses identified a seven-protein panel, including MYL3, MYBPC1, NT-proBNP, NPPB, FCRLB, IGFBP1, and FABP1, consistent with early cardiac stress and immune dysregulation. Time-to-event modelling demonstrated robust stratification of amyloidosis risk and timing. Importantly, a parsimonious subset of these proteins retained strong predictive performance, indicating that a reduced set of biologically informative markers is sufficient for risk stratification. Furthermore, these proteomic signals were not explained by pre-existing cardiac disease, clonal haematopoiesis, or related plasma cell disorders, indicating that they capture disease-specific biological processes preceding clinical diagnosis. Together, these findings show that amyloidosis is preceded by persistent plasma proteomic alterations, providing a framework for early risk stratification and insight into the preclinical biology of this under-recognised disease.

bioinformatics↗

bioRxiv2026

Chemical screens identify HDAC6 as an epigenetic vulnerability in acquired Temozolomide-resistant models of glioblastoma

Glioblastoma (GBM) is an aggressive primary brain tumor associated with a median survival of approximately 15 months following diagnosis. Current standard-of-care treatment includes surgical resection followed by radiotherapy and chemotherapy with the DNA-alkylating agent temozolomide (TMZ). However, tumor recurrence in a therapy-resistant state remains a major driver of poor patient outcomes. To investigate the molecular mechanisms underlying TMZ resistance, we generated in vitro models of acquired resistance by exposing initially TMZ-sensitive GBM cells to escalating doses of TMZ. Transcriptomic and chromatin accessibility profiling revealed extensive remodeling of DNA damage response (DDR) and DNA repair pathways that favored protection against TMZ-induced genotoxic stress. Although upregulation of O-6-methylguanine-DNA methyltransferase (MGMT) emerged as a dominant determinant of resistance in our models, the data suggested that additional adaptive resistance mechanisms contribute to the resistant phenotype. To identify targetable epigenetic dependencies associated with TMZ resistance, we performed a chemical screen using an epigenetic probe library. This screen identified multiple histone deacetylase (HDAC) inhibitors that selectively impaired the viability of TMZ-resistant cells, either as monotherapy or in combination with TMZ. Among these, HDAC6-selective inhibitors, including Ricolinostat, were particularly effective at inducing cell death in TMZ-resistant GBM models. Mechanistically, HDAC6 inhibition reduced the expression of key DDR-associated genes, while MGMT responses varied depending on cellular context and treatment duration. Furthermore, pharmacological inhibition and loss-of-function studies demonstrated that targeting HDAC6 could restore TMZ sensitivity by altering the balance of DNA repair pathway activity, potentially acting as a compensatory mechanism for MGMT-mediated resistance. Collectively, our findings identify HDAC6 as an epigenetic vulnerability in acquired TMZ-resistant GBM and support the therapeutic potential of HDAC6 inhibition as a strategy to overcome TMZ resistance in glioblastoma patients.

cancer biology↗

bioRxiv2025

Distinct 5' and 3' Coverage Biases Shape Transcriptome Interpretation in Nanopore Direct RNA versus PCR-cDNA Sequencing

Long-read RNA sequencing enables isoform-resolved transcriptomics, but library preparation introduces systematic biases that shape biological interpretation. We benchmarked Oxford Nanopores two protocols--PCR-cDNA and direct RNA--using SKMM2 myeloma cells stimulated with interleukin-6 (IL-6) and ERCC synthetic spike-ins. Direct RNA produced longer, higher-quality reads and more high-confidence isoforms, but showed pronounced 5' coverage loss. PCR-cDNA yielded shorter fragments with 3' underrepresentation, detecting more low-abundance transcripts at reduced confidence. Protocol-specific biases had major consequences: differential expression analysis revealed limited overlap in IL-6-responsive genes, and pathway enrichment was broader in direct RNA. At the isoform level, differential transcript usage was almost entirely protocol-specific, with case studies (e.g. RPL22L1, GRB2, RNF220) illustrating concordance and divergence. ERCC controls confirmed these biases as technical rather than biological. Together, our results show that while both methods provide accurate gene-level quantification, transcript-level conclusions depend critically on protocol choice, highlighting the need for careful selection in long-read transcriptomics.

cell biology↗

bioRxiv2025

Biomolecular tracking by FIRESCAPE reveals distinct modes of clearance, damage induction and cellular uptake for extracellular histone H3

In attempting to observe the behaviour of a protein of interest in vivo, akin to other observer effects, current techniques require modifications or interventions that inherently alter the protein or its host, leaving one uncertain as to whether natural behaviour remains unperturbed. The study of chromatin has mostly been restricted to defining its function in the nucleus, where histone proteins fulfil vital roles in packaging genomic DNA and regulating transcription. However, chromatin components can be released into the extracellular space, either intentionally via cellular secretion or during disease-induced cell death. These extracellular chromatin components, depending on the context, can consist of: free histones, free DNA, intact nucleosomes (histone octamers wrapped by DNA), or heterogeneous, higher order structures such as neutrophil extracellular traps (NETs). They have been associated with diverse pathologies such as inflammation, cancer, and sepsis, and distinct toxic effects. However, there is a widely acknowledged lack of methods that distinguish between them and between their unique functions. Here, we now address protein observer effects to explore the fate and function of extracellular free histones by utilizing FIRESCAPE ([18F]-Fluorine Isotopic Radiolabeling Enabling Scanning of Clearance After Proteolytic Events), a novel radiolabeling concept that leverages the unique, high-sensitivity properties of the radioisotope fluorine-18, 18F, and residue-specific protein editing chemistry. By installing close and then true 18F-containing protein sidechain mimics site-specifically, FIRESCAPE enables the hierarchical in vivo scanning of the half-lives, proteolytic susceptibility and clearance of single residues in a protein of interest, and at microdoses far below toxic levels (low nanomole). These radioequivalent proteins bearing near-zero-size, zero-background labels now precisely reveal the strikingly distinct distribution, half-lives, damage-inducing abilities and accumulation of free extracellular histones in cellulo and in vivo compared to intact nucleosomes. Free extracellular histone H3 is rapidly cleared from circulation, mediated first by proteolysis of the histone tail. By contrast, direct injection of free histones vs nucleosomes into tissue that is unprotected by such proteolysis (brain), provokes a starkly different response; free histones exhibited limited diffusion and swiftly promoted damage both in cell culture and in vivo, whilst intact nucleosomes were essentially passive and benign. Remarkably, synthetic extracellular histone H3 was observed to enter cells and integrate into chromatin, indistinguishable from native H3 in both localization and post-translational modification (PTM) accumulation, yet paired with cellular and tissue damage. The exploratory studies described here now provide much needed clarity to the distinct fates and effects of extracellular histones vs nucleosomes, in particular the strongly damaging effects of free histones, their rapid uptake into cells, and an associated histone-specific proteolysis pathway via the removal of the histone tail.

biochemistry↗

bioRxiv2025

ATF4-Mediated Metabolic Stress Response as a Therapeutic Vulnerability in Chordoma

Chordoma, a rare primary bone malignancy, currently lacks effective targeted therapies. Despite surgical resection and adjuvant radiotherapy, prognosis remains poor. Recent preclinical studies have highlighted potential therapeutic targets, including the transcription factor TBXT. However, clinical outcomes associated with therapies targeting TBXT remain underexplored or have been modest, warranting further investigation. In this study, we investigated the therapeutic potential of tRNA synthetase inhibitors in chordoma treatment. Focused compound screening identified distinct chemotypes targeting human glutamyl-prolyl-tRNA synthetase (EPRS) as effective in reducing cell viability in chordoma cell lines through an ATF4-mediated stress response rather than through TBXT regulation. Mechanistically significant upregulation of ATF4 and associated stress response genes was identified with consecutive pro-apoptotic DDIT3-mediated cell death. The prototypic EPRS inhibitor halofuginone demonstrated significant tumour growth inhibition in an in vivo patient-derived xenograft model. These results suggest that targeting metabolic stress pathways via ATF4 activation presents a novel therapeutic approach for chordoma, warranting further clinical investigation.

cancer biology↗

bioRxiv2025

comBO: A combined human bone and lympho-myeloid bone marrow organoid for pre-clinical modelling of haematopoietic disorders

The bone marrow supports lifelong blood and immune cell production. Current human bone marrow organoid models do not include both lymphoid and myeloid elements and lack the complexity of stromal cell types present in native haematopoietic tissues, precluding the accurate ex vivo modelling of human pathologies. Here we introduce "comBOs" (combined bone and lympho-myeloid bone marrow organoids) that include osteolineage, vascular, lymphoid and myeloid cells. comBOs are generated by the differentiation of induced pluripotent stem cells guided by physiologically-relevant oxygen and cytokine exposures within an innovative granular microgel scaffold to increase scalability and reproducibility. We demonstrate that comBOs can be used to generate "chimeroids" - incorporating healthy or aberrant cells from adult donors - and recapitulate features of diseased microenvironments. ComBOs are one of the most physiologically-relevant human organoid systems to date, and this study showcases the potential of 3D in vitro disease models for discovery science and translational studies.

cancer biology↗

bioRxiv2024

The KDM6 histone demethylase inhibitor GSK-J4 induces metal and stress responses in multiple myeloma cells

Thioneins are cysteine-rich apoproteins that regulate divalent metal homeostasis by virtue of their metal-chelation properties resulting in the ligand-bound metallothionein state. Previous studies show transient upregulation of the metallothionein (MT) gene cluster as part of a complex transcriptional response to a class of histone demethylase tool compounds targeting human Fe2+ dependent ketoglutarate oxygenases KDM6A (UTX) and KDM6B (JmjD3). The prototypic bioactive KDM6 inhibitor GSK-J4 induces apoptotic cell death in multiple myeloma cells and corresponding transcriptomic profiles are dominated by metal and metabolic stress response signatures, also observed in primary human myeloma cells. Here we investigate the hypothesis that metal-chelation by GSK-J4 provides the means for transport and intracellular release of Zn2+ leading to a metallothionein transcriptomic response signature. Live cell imaging of myeloma cells shows transient increases in intracellular free Zn2+ concentrations when exposed to GSK-J4, consistent with a model of inhibitor-mediated metal transport. Comparisons of GSK-J4 and ZnSO4 treatments in the presence or absence of metal chelators show that both treatment conditions induce different transcription factor repertoires with an overlapping MTF1 transcriptional regulation responsible for metallothionein and metal ion transport regulation. The data provide a possible explanation for the observed metal response upon GSK-J4 inhibition however the relationship with the pro-apoptotic mechanism in myeloma cells requires further investigation.

cell biology↗

bioRxiv2024

Chromatin-focused genetic and chemical screens identify BRPF1 as a targetable vulnerability in Taxol-resistant triple-negative breast cancer

Triple-negative breast cancer (TNBC) stands out as a particularly aggressive and frequently recurring form of breast cancer. Due to the absence of hormone receptors, the available treatment avenues are constrained, making chemotherapy the primary approach. Unfortunately, the development of resistance to chemotherapy poses a significant challenge, further restricting the already limited therapeutic alternatives for recurrent cases. Understanding the molecular basis of chemotherapy resistance in TNBC is pivotal for improving treatment outcomes. Here, we generated two different Taxol-resistant TNBC cell lines with a dose-escalation method to mimic chemotherapy resistance in vitro. These cells exhibited hallmark features of resistance, including reduced cell growth, altered morphology, and evasion of apoptosis. Transcriptome analysis uncovered elevated ABCB1 expression and multidrug-resistant phenotype in the resistant cells. To comprehensively investigate the key epigenetic regulators of Taxol resistance, we conducted chromatin-focused genetic and chemical screens and pinpointed Bromodomain and PHD Finger Containing 1 (BRPF1) as a novel regulator of Taxol resistance in TNBC cells. Knockout of BRPF1, the reader protein in the MOZ/MORF histone acetyl-transferase complex, but not the other complex members, sensitized resistant cells to Taxol. Additionally, BRPF1 inhibitors, PFI-4 and OF-1, in combination with Taxol significantly reduced cell viability. Transcriptome analysis upon BRPF1 loss or inhibition revealed a negative impact on ribosome biogenesis-related gene sets, resulting in a global decrease in protein translation in Taxol-resistant cells. Our ChIP-qPCR analysis demonstrated that active BRPF1 directly interacts with the ABCB1 promoter, enhancing its expression towards inducing a multidrug-resistant phenotype. Conversely, knockout or inhibition of BRPF1 leads to decreased ABCB1 expression. This dual mechanism critically sensitizes Taxol-resistant TNBC cells to chemotherapy. Our findings uncover a comprehensive molecular framework, highlighting the pivotal role of epigenetic reader protein BRPF1 in Taxol resistance and providing potential avenues for therapeutic intervention in TNBC.

cancer biology↗

bioRxiv2024

Anchor-Enhanced Bead Design for Reduced Oligonucleotide Synthesis Errors in Single-cell sequencing

Single-cell transcriptomics, reliant on the incorporation of barcodes and unique molecular identifiers (UMIs) into captured polyA+ mRNA, faces a significant challenge due to synthesis errors in oligonucleotide capture sequences. These inaccuracies, which are especially problematic in long-read sequencing, impair the precise identification of sequences and result in inaccuracies in UMI deduplication. To mitigate this issue, we have modified the oligonucleotide capture design, which integrates an interposed anchor between the barcode and UMI, and a V base anchor adjacent to the polyA capture region. This configuration is devised to ensure compatibility with both short and long-read sequencing technologies, facilitating improved UMI recovery and enhanced feature detection, thereby improving the efficacy of droplet-based sequencing methods.

molecular biology↗

bioRxiv2024

High-dimensional mass cytometry reveals stemness state heterogeneity in pancreatic ductal adenocarcinoma

Stem-like cancer cells harbour high self-renewal capacity, exhibit enhanced tumourigenicity and have been associated with therapy resistance, metastasis and tumour relapse. Therefore, understanding the molecular features of stem-like cells is critical for targeting them effectively and improving treatment outcomes for cancer patients. Several markers have been used to isolate and study the putative stem-like cells of pancreatic ductal adenocarcinoma (PDAC), but the patterns of marker co-expression and overlap between identified individual subpopulations are yet to be comprehensively studied. Here we developed a mass cytometry antibody panel for simultaneous analysis of 33 stemness-associated markers at single-cell resolution. High-dimensional mass cytometry analysis of PDAC cell lines revealed molecularly heterogeneous stemness states and highlighted the role of genotype in determining the cell line-specific stemness signature. Stemness marker expression lie along a continuum in PDAC cell lines and patient samples indicative of stepwise phenotypic transitions. We also identified a subset of PDAC cells co-expressing high levels of Musashi-2, DCLK1 and CXCR4, and harbouring basal-like and EMT transcriptional programmes associated with highly plastic phenotype. This multiplexed analysis uncovers nuance and complexities of the stemness state in the PDAC.

cancer biology↗

bioRxiv2024

A systems-based approach to uterine fibroids identifies differential splicing associated with abnormal uterine bleeding

Uterine fibroids (UFs), benign tumours prevalent in up to 80% of women of reproductive age, are associated with significant morbidity, including abnormal uterine bleeding, pain and infertility. Despite identification of key genomic alterations in MED12 and HMGA2, the pathogenic mechanisms underlying UFs and heavy menstrual bleeding (HMB) remain poorly understood. To correlate systematically genetic, transcriptional and proteomic phenotypes, our study involved an integrative analysis of fibroid, myometrium and endometrium tissues from 137 patients, utilising genome-wide SNP arrays, targeted sequencing, RNA sequencing and proteomics. Our findings reveal 39.7% of UFs possess MED12 mutations, alongside novel variants in genes such as COL4A5 and COL4A6. Multi-omics factor analysis of integrated protein and mRNA highlighted differential regulation related to extracellular matrix remodelling, proteolysis and homeostasis in fibroid versus myometrium tissues, and distinct gene sets associated with RNA splicing in the endometrium of patients with HMB, particularly in MED12-mutated fibroids. Our study proposes a model, which is supported by in vivo evidence, where altered signalling of MED12-mutated fibroids influences RNA transcript isoform expression in endometrium, potentially leading to abnormal uterine bleeding. This integrative approach unravels complex molecular pathways in UF pathogenesis and HMB, offering novel insights for targeted therapeutic development.

systems biology↗

bioRxiv2023

Correcting PCR amplification errors in unique molecular identifiers to generate absolute numbers of sequencing molecules.

Unique Molecular Identifiers (UMIs) are random oligonucleotide sequences that remove PCR amplification biases. However, the impact that PCR associated sequencing errors have on the accuracy of generating absolute counts of RNA molecules is underappreciated. We show that PCR errors are the main source of inaccuracy in both bulk and single-cell sequencing data, and synthesizing UMIs using homotrimeric nucleotide blocks provides an error correcting solution, that allows absolute counting of sequenced molecules.

genomics↗

bioRxiv2023

BRD9-SMAD2/3 orchestrates stemness and tumorigenesis in pancreatic ductal adenocarcinoma

The dismal prognosis of pancreatic ductal adenocarcinoma (PDAC) is linked to the presence of pancreatic cancer stem-like cells (CSCs) that respond poorly to current chemotherapy regimens. By small molecule compound screening targeting 142 epigenetic enzymes, we identified that bromodomain-containing protein BRD9, a component of the BAF histone remodelling complex, is a key chromatin regulator to orchestrate the stemness of pancreatic CSCs via cooperating with the TGF{beta}/Activin-SMAD2/3 signalling pathway. Inhibition and genetic ablation of BDR9 block the self-renewal, cell cycle entry into G0 phase and invasiveness of CSCs, and improve the sensitivity of CSCs to gemcitabine treatment. In addition, pharmacological inhibition of BRD9 significantly reduced the tumorigenesis in patient-derived xenografts mouse models and eliminated CSCs in tumours from pancreatic cancer patients. Mechanistically, inhibition of BRD9 disrupts enhancer-promoter looping and transcription of stemness genes in CSCs. Collectively, the data suggest BRD9 as a novel therapeutic target for PDAC treatment via modulation of CSC stemness.

cancer biology↗

bioRxiv2022

HSD3B1 is an Oxysterol 3β-Hydroxysteroid Dehydrogenase in Human Placenta

Most biologically active oxysterols have a 3{beta}-hydroxy-5-ene function in the ring system with an additional site of oxidation at C-7 or on the side-chain. In blood plasma oxysterols with a 7-hydroxy group are also observed with the alternative 3-oxo-4-ene function in the ring system formed by ubiquitously expressed 3{beta}-hydroxy-{Delta}5-C27-steroid oxidoreductase {Delta}5-isomerase, HSD3B7. However, oxysterols without a 7-hydroxy group are not substrates for HSD3B7 and are not usually observed with the 3-oxo-4-ene function. Here we report the unexpected identification of oxysterols in plasma derived from umbilical cord blood and blood from pregnant women taken before delivery at 37+ weeks of gestation, of side-chain oxysterols with a 3-oxo-4-ene function but no 7-hydroxy group. These 3-oxo-4-ene oxysterols were also identified in placenta, leading to the hypothesis that they may be formed by a previously unrecognised 3{beta}-hydroxy-{Delta}5-C27-steroid oxidoreductase {Delta}5-isomerase activity of HSD3B1, an enzyme which is highly expressed in placenta. Proof of principle experiments confirmed that HSD3B1 has this activity. We speculate that HSD3B1 in placenta is the source of the unexpected 3-oxo-4-ene oxysterols in cord and pregnant womens plasma and may have a role in controlling the abundance of biologically active oxysterols delivered to the fetus.

biochemistry↗