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Biology subjects

Dean, J.

Publications and source records attributed to Dean, J..

15 recordsLinked to original sources
bioRxiv2025

Mechanistic modeling and machine learning identifies optimum radiotherapy schedules to prevent treatment-induced metastasis

Lung cancer patients often experience increased metastasis formation after radiotherapy. However, it is incompletely understood whether radiation affects the migratory behavior of tumor cells and how altered radiotherapy schedules might mitigate this risk. To address these questions, we performed live-cell microscopy experiments to profile changes in cell migration during radiation across 12 cancer cell lines and developed a predictive computational modeling platform describing tumor volume and dissemination during radiotherapy. Using this platform, we identified optimal fractionation schedules and then performed extensive in silico clinical trials, establishing that our optimized schedules substantially reduce metastatic seeding relative to the standard of care schedule. Training transformer models on the in silico clinical trial data enabled us to recover mechanistic parameters with high accuracy, demonstrating that the features determining optimal radiotherapy can be inferred from longitudinal tumor data. Our integrative predictive approach enables the rational design of optimum clinical trials across indications.

bioinformatics↗
bioRxiv2024

Targeted inhibition of Bcl-xL following radiation reduces tumourigenesis in preclinical models of H3K27M-altered diffuse midline glioma

BackgroundDiffuse midline gliomas (DMGs) with histone H3K27M mutations represent a devastating paediatric brain cancer characterized by abysmal prognosis and limited treatment options. The only approved treatment is radiotherapy (RT), but most of the tumours relapse with fatal consequences. In this study, we sought to investigate whether irradiation leads to senescence induction and explore the efficacy of senolytics against DMG. MethodsWe have characterised the senescent phenotype of five genetically heterogeneous H3K27M-altered human DMG cell lines, combining cellular and/or molecular approaches. The sensitivity of senescent cells to Bcl-xL inhibition has been demonstrated in dose/response curves in vitro and in a PDX model of DMG. ResultsHere, we show that ionizing radiation induces senescence and SASP responses in both TP53 mutant and wild-type H3K27M-altered human DMG cell lines. We identify Navitoclax as a potent senolytic agent that selectively targets senescent DMG cells into apoptosis by inhibiting Bcl-xL. Related compounds, such as a proteolysis-targeting chimera (PROTAC)-mediated Bcl-xL degradation and a galacto-conjugated form of Navitoclax also show an effective senolytic activity in senescent cancer cells. Finally, we show that a combination therapy of irradiation and Navitoclax results in reduced tumor burden and increased mouse survival in an orthotopic xenograft DMG model. ConclusionThese results offer a rationale for further clinical development of senolytic therapies as part of multimodal treatment approaches for DMG patients/ Key PointsO_LIIonising irradiation induces senescence in human DMG cells independently of the p53 status. C_LIO_LIBcl-xL inhibition results in apoptosis of human DMG senescent cells in synergy with irradiation. C_LIO_LICombination of irradiation and BcL-xL inhibition reduces tumourigenesis in a PDX model of DMG. C_LI Importance of the StudyH3K27M-altered DMG are devastating paediatric tumours with an abysmal prognosis. The only approved treatment is radiotherapy but this is palliative and tumours almost always relapse with fatal consequences for the patients. In this study, we show that radiotherapy results in senescence induction in five genomically heterogeneous human DMG cell lines. We identify that drugs targeting the anti-apoptotic protein Bcl-xL show a strong senolytic activity in conjunction with radiotherapy both in vitro in DMG cells and in vivo in a PDX model of H3K27M-altered DMG. Treatment with Bcl-xL inhibitor Navitoclax, or related compounds targeting Bcl-xL protein degradation or containing a galactose conjugated form of Navitoclax results in DMG cancer cell apoptosis. As several of these inhibitors are currently being tested in ongoing clinical trials against other diseases, our data support the use of Bcl-xL inhibition mediated senolytics as an adjuvant therapy to radiotherapy to potentially improve outcomes in this challenging disease setting.

cancer biology↗
bioRxiv2023

Winners in good times and bad times: Aerobic anoxygenic phototrophic bacteria profit from photoheterotrophy under carbon-rich and poor conditions

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/572764v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1e52797org.highwire.dtl.DTLVardef@18a568forg.highwire.dtl.DTLVardef@138e2c5org.highwire.dtl.DTLVardef@1b0224c_HPS_FORMAT_FIGEXP M_FIG C_FIG Aerobic Anoxygenic Phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, and by that enhance their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light conditions to elucidate how they profit from photoheterotrophy. We found that it depends on the season. In spring, AAP bacteria induce photoheterotrophic metabolism under carbon limitation but they outperform heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. In autumn photoheterotrophy is less beneficial. In both seasons, AAP bacteria responded negatively to recalcitrant or low-energy carbon sources in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria observed in pelagic environments.

ecology↗
bioRxiv2023

Phenology and ecological role of Aerobic Anoxygenic Phototrophs in fresh waters

Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centres. Despite their substantial contribution to bacterial biomass, microbial food webs and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across three years in a temperate, meso-oligotrophic freshwater lake. AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM gene, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource we demonstrated recurrent and dynamic seasonal succession of the AAP community. The majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. Our results document the indigenous freshwater nature of the AAP community, characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom, contributing significantly to the ecological dynamics of lakes.

microbiology↗
bioRxiv2022

Germ-cell specific eIF4E1B regulates maternal RNA translation to ensure zygotic genome activation

Translation of maternal mRNAs is detected before transcription of zygotic genes and is essential for mammalian embryo development. How certain maternal mRNAs are selected for translation instead of degradation and how this burst of translation affects zygotic genome activation remains unknown. Using gene-edited mice, we document that the eukaryotic translation initiation factor 4E family member 1B (eIF4E1B) is the regulator of maternal mRNA translation that ensures subsequent reprogramming of the zygotic genome. In oocytes, the germ-cell specific eIF4E1B binds to mRNAs encoding chromatin remodeling complexes as well as reprogramming factors to protect them from degradation and promote their translation in zygotes. These protein products establish an open chromatin landscape in one-cell zygotes and enable transcription. Our results define a program for rapid resetting of the zygotic epigenome that is regulated by maternal mRNA translation and provides new insight into the mammalian maternal-to-zygotic transition.

developmental biology↗
bioRxiv2022

RNA exosome ribonuclease DIS3 degrades Pou6f1 to promote mouse pre-implantation cell differentiation

Mammalian development is precisely controlled by cell differentiation. Discovery of new regulators and investigating their crosstalk provide insights into genetic networks defining pre-implantation development. To identify novel developmental repressors, we established a knockout mouse model of Dis3, an RNA exosome associated RNase. Homozygous Dis3 null embryos arrest at the morula-to-blastocyst transition. Using single embryo RNA-seq, we discovered persistence of Pou6f1 mRNA in homozygous null Dis3 embryos and determined that the cognate protein represses transcription of Nanog and Cdx2. The resultant defects in cell differentiation disrupted the morula-to-blastocyst transition and was embryonic lethal. To overcome the paucity of embryos, homozygous Dis3 null mouse embryonic stem cells were derived to identify additional gene targets of POU6F1. While microinjection of the Dis3 cRNA into zygotes rescued the morula-to-blastocyst block, point mutations of Dis3 in individual blastomeres transformed the cell and prevented incorporation into embryos. Our findings uncover a not heretofore reported regulatory pathway of DIS3-POU6F1 in pre-implantation mammalian embryogenesis. In BriefMammalian pre-implantation development is regulated by master transcription factors and their crosstalk. Wu and Dean report that an RNA exosome associated RNase, DIS3, degrades Pou6f1 mRNA to de-repress transcription of Nanog and Cdx2 genes. In the absence of DIS3, POU6F1 protein persists and embryos arrest as morulae unable to become blastocysts due to lack of cell differentiation. HighlightsO_LIDis3 knockout mice have morula arrest due to lack of cell differentiation. C_LIO_LIDIS3 binds and degrades Pou6f1 mRNA before the morula stage. C_LIO_LIPOU6F1 globally occupies promoters to regulate gene transcription. C_LIO_LIDIS3 mutation results in cell transformation in embryonic development. C_LI

developmental biology↗
bioRxiv2022

Persistent pervasive transcription in RNA exosome depleted oocytes results in loss of female fertility

Maturing mammalian oocytes are transcriptionally inactive and attendant RNA degradation determines the maternal transcriptome for embryonic development1. Perturbing oocyte RNA degradation can result in failure of meiosis, fertilization, or zygotic gene activation1-5. We recently reported that conditional depletion of EXOSC10, an RNA exosome associated RNase, blocks oocyte growth-to-maturation transition by interfering with ribosomal RNA processing and meiotic checkpoint genes3. Here we have established oocyte-specific knockout mice of a second RNA exosome associated RNase, Dis3. Mutant females (Dis3cKO) exhibit significantly reduced fertility because oocytes arrest at early maturation. DIS3 depletion allows persistent pervasive transcription, which blocks transcription termination and sequesters RNA polymerase II in intergenic regions. In addition, Dis3cKO oocytes gain H3K27me3 at pre-defined loci6 due to insufficient demethylases KDM6A/B. Oocyte double knockout of Dis3 and Exosc10 causes much earlier growth defects for similar persistence of pervasive transcription, suggesting the RNA exosome complex plays a critical role to ensure transcriptome integrity during oocyte development.

developmental biology↗
bioRxiv2020

Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA

piRNAs are germline-specific, small non-coding RNAs required to maintain genome integrity and preserve RNA homeostasis during male gametogenesis. In murine adult testes, the highest levels of piRNAs are present in the pachytene stage of meiosis, but their mode of action and function remains incompletely understood. We previously reported that BTBD18 binds to 50 pachytene piRNA-producing loci. Here we show that spermatozoa in gene-edited mice lacking a BTBD18 targeted pachytene piRNA cluster on Chr18 have severe sperm head dysmorphology, poor motility, impaired acrosome exocytosis and are sterile. The absence of Chr18 piRNA results in an imbalance of heat shock proteins associated with renaturing proteins and the ubiquitin-proteasome system involved with protein degradation. The mutant phenotype arises from aberrant formation of proacrosomal vesicles, distortion of the trans-Golgi network, and up-regulation of GOLGA2 associated with acrosome dysgenesis. Collectively, our findings reveal central role of pachytene piRNAs in controlling spermiogenesis and male fertility.

developmental biology↗
bioRxiv2020

Oocytes, a single cell and a tissue

Development of single cell sequencing allows detailing the transcriptome of individual oocytes. Here, we compare different RNA-seq datasets from single and pooled mouse oocytes and show higher reproducibility using single oocyte RNA-seq. We further demonstrate that UMI (unique molecular identifiers) based and other deduplication methods are limited in their ability to improve the precision of these datasets. Finally, for normalization of sample differences in cross-stage comparisons, we propose that external spike-in molecules are comparable to using the endogenous genes stably expressed during oocyte maturation. The ability to normalize data among single cells provides insight into the heterogeneity of mouse oocytes.

bioinformatics↗
bioRxiv2019

Variation in protein coding genes identifies information flow as a contributor to animal complexity

Across the metazoans there is a trend towards greater organismal complexity. How complexity is generated, however, is uncertain. Since C.elegans and humans have approximately the same number of genes, the explanation will depend on how genes are used, rather than their absolute number. Functional diversity is a measure that quantifies the isoforms, domains and paralogues of a gene. In this paper we determine functional diversity for each protein-coding gene in the human genome and its orthologues across eight commonly used model organisms. From this we derive the Compx list of genes that correlate positively with their increase in cell-type number. We then select genes common to the Compx list and the ExAC list, whose genes show minimal variation across many human genomes, and identify genes with common functions, notably in chromatin structure, RNA splicing, vesicular transport and ubiquitin-mediated protein degradation. Together these functions reveal that information flow within the cell relates to cell-type number, used as a measure of organismal complexity.

systems biology↗
bioRxiv2019

EXOSC10 mediated RNA degradation sculpts the transcriptome during oocyte growth-to-maturation transition

Growing mammalian oocytes accumulate substantial amounts of RNA, most of which is degraded during subsequent meiotic maturation. The growth-to-maturation transition begins with germinal vesicle or nuclear envelope breakdown (GVBD) and is critical for oocyte quality and early development. The molecular machinery responsible for the oocyte transcriptome transition remains unclear. Here, we report that an exosome-associated RNase, EXOSC10, sculpts the transcriptome to facilitate the growth-to-maturation transition of mouse oocytes. We establish an oocyte-specific conditional knockout of Exosc10 in mice using CRISPR/Cas9 which results in female subfertility due to delayed GVBD. By performing multiple single oocyte RNA-seq, we document dysregulation of several types of RNA, and the mRNAs that encode proteins important for endomembrane trafficking and meiotic cell cycle. As expected, EXOSC10-depleted oocytes have impaired endomembrane components including endosomes, lysosomes, endoplasmic reticulum and Golgi. In addition, CDK1 fails to activate, possibly due to persistent WEE1 activity, which blocks lamina phosphorylation and disassembly. Moreover, we identified rRNA processing defects that cause higher percentage of developmentally incompetent oocytes after EXOSC10 depletion. Collectively, we propose that EXOSC10 promotes normal growth-to-maturation transition in mouse oocytes by sculpting the transcriptome to degrade RNAs encoding growth-phase factors and, thus, support the maturation phase of oogenesis.

developmental biology↗
bioRxiv2018

Differential role of prefrontal and parietal cortices in controlling level of consciousness

There is current controversy regarding the role of prefrontal versus posterior cortices in consciousness. Clinical and correlative data have been used both to support and refute a causal role for prefrontal cortex in the level of consciousness, but a definitive relationship has not been demonstrated. We used anesthetic-induced unconsciousness as a model system to study the effect of cholinergic and noradrenergic stimulation of rat prefrontal and posterior parietal cortices on the level of consciousness. We demonstrate that cholinergic stimulation of prefrontal cortex, but not parietal cortical areas, restored wakefulness in rats despite continuous exposure to sevoflurane anesthesia. Noradrenergic stimulation of the prefrontal or parietal areas did not reverse the anesthetized state. We conclude that cholinergic mechanisms in prefrontal cortex can control the level of consciousness.\n\nOne Sentence SummaryPrefrontal cholinergic stimulation restores consciousness in rats despite continuous exposure to sevoflurane anesthesia

neuroscience↗
bioRxiv2017

Autosomal recessive coding variants explain only a small proportion of undiagnosed developmental disorders in the British Isles

Large exome-sequencing datasets offer an unprecedented opportunity to understand the genetic architecture of rare diseases, informing clinical genetics counseling and optimal study designs for disease gene identification. We analyzed 7,448 exome-sequenced families from the Deciphering Developmental Disorders study, and, for the first time, estimated the causal contribution of recessive coding variation exome-wide. We found that the proportion of cases attributable to recessive coding variants is surprisingly low in patients of European ancestry, at only 3.6%, versus 50% of cases explained by de novo coding mutations. Surprisingly, we found that, even in European probands with affected siblings, recessive coding variants are only likely to explain ~12% of cases. In contrast, they account for 31% of probands with Pakistani ancestry due to elevated autozygosity. We tested every gene for an excess of damaging homozygous or compound heterozygous genotypes and found three genes that passed stringent Bonferroni correction: EIF3F, KDM5B, and THOC6. EIF3F is a novel disease gene, and KDM5B has previously been reported as a dominant disease gene. KDM5B appears to follow a complex mode of inheritance, in which heterozygous loss-of-function variants (LoFs) show incomplete penetrance and biallelic LoFs are fully penetrant. Our results suggest that a large proportion of undiagnosed developmental disorders remain to be explained by other factors, such as noncoding variants and polygenic risk.

genetics↗
bioRxiv2017

A mutation in the LMOD1 actin-binding domain segregating with disease in a large British family with thoracic aortic aneurysms and dissections

We describe a mutation in LMOD1, which predisposes individuals to thoracic aortic aneurysms and dissections in a large multi-generation British family. Exome variant profiles for the proband and two distantly related affected relatives were generated and a rare protein-altering, heterozygous variant was identified, present in all the exome-sequenced affected individuals. The allele c.1784T>C, p.(V595A) in LMOD1 is located in a known actin-binding WH2 domain and is carried by all living affected individuals in the family. LMOD1 was further assessed in a consecutive series of 98 UK TAAD patients and one further mutation was found, yielding an incidence of [~]2% in our study group. Assessment of LMOD1 in international TAAD cohorts discovered nine other missense variants of which three were classed as likely pathogenic.\n\nValidation of LMOD1 was undertaken using a zebrafish animal model. Knock-down of both lmod1a and lmod1b paralogs using morpholino oligonucleotides showed a reproducible abnormal phenotype involving the aortic arches under off-target controls. Injection of the human LMOD1 c.1784T>C, p.(V595A) mutation demonstrated a likely dominant negative effect and illustrated a loss of function cause.\n\nMutations found in the WH2 actin-binding domain of LMOD1 may delay actin polymerization and therefore compromise actin length, dynamics and interaction with myosin in the smooth muscle contraction pathway.

genetics↗