Biology subjects

Floyd, T.

Publications and source records attributed to Floyd, T..

6 recordsLinked to original sources

bioRxiv2026

Patient-derived organoid xenografts reveal the multifaceted role of the lncRNA MALAT1 in breast cancer progression

Long non-coding RNAs (lncRNAs) have emerged as key regulators of tumor biology, however, thus far none have translated to cancer therapies. The lncRNA MALAT1 is overexpressed in more than 20 cancers, including breast cancer and has been shown to function via various mechanisms in a context-dependent manner, in 2D cell lines and mouse models. However, its functional role and therapeutic potential have not been evaluated in clinically relevant patient-derived models. We investigated the therapeutic potential of MALAT1-targeting antisense oligonucleotides (ASOs) for breast cancer, using clinically relevant 3D human patient-derived organoids (PDOs) and PDO-xenograft (PDO-X) models. We systematically evaluated the efficiency of MALAT1-targeting ASOs using a biobank of 28 PDO models. Across three independent PDO-X models of triple negative breast cancer (TNBC), MALAT1 depletion reproducibly drove widespread alternative splicing changes across all event types, with an enrichment of intron retention. Differentially spliced transcripts were enriched for targets of shared cancer-associated transcription factors, and MALAT1 knockdown specifically altered the relative abundance of previously unannotated splicing isoforms. Beyond tumor-intrinsic effects, tumor-specific MALAT1 depletion induced a consistent reduction in macrophage-associated gene signatures and reduced lung metastatic burden. Our data defines MALAT1s multifaceted role in TNBC, coordinating alternative splicing, tumor-stroma crosstalk, and metastatic progression. Our study provides strong preclinical evidence supporting MALAT1-targeted ASO therapy and establishes PDO-X models as a clinically relevant platform for functional interrogation of TNBC therapies. SignificanceUsing clinically relevant human PDO-X models, we show that MALAT1 influences alternative splicing, metastatic potential and the tumor microenvironment. These data support the potential of oncogenic lncRNA MALAT1 as a therapeutic target.

cancer biology↗

bioRxiv2022

Glutamatergic Supramammillary Nucleus Neurons Promote Active Coping to Stress

Threat-response neural circuits are conserved across species and play roles in normal behavior and psychiatric diseases. Maladaptive changes in these neural circuits contribute to stress, mood, and anxiety disorders. Active coping in response to stressors is a psychosocial factor associated with resilience against stress-induced mood and anxiety disorders. The neural circuitry underlying active coping is poorly understood, but the functioning of these circuits could be key for overcoming anxiety and related disorders. The supramammillary nucleus (SuM) has been suggested to be engaged by threat. SuM has many projections and contains a poorly understood diversity of populations. We identified a unique population of glutamatergic SuM neurons (SuMVGLUT2+::POA) based on projection to the preoptic area of the hypothalamus (POA) and found SuMVGLUT2+::POA neurons have extensive arborizations. SuMVGLUT2+::POA neurons project to brain areas that mediate various features of the stress and threat responses including the paraventricular nucleus thalamus (PVT), periaqueductal gray (PAG), and the habenula (Hb). Thus, SuMVGLUT2+::POA neurons are positioned as a hub, connecting to areas implicated in regulating stress responses. Here we report SuMVGLUT2+::POA neurons are recruited by diverse threatening stressors, and recruitment of SuMVGLUT2+::POA neurons correlated with active coping behaviors. We found that selective photoactivation of the SuMVGLUT2+::POA population drove aversion but not anxiety like behaviors. Activation of SuMVGLUT2+::POA neurons in the absence of acute stressors evoked active coping like behaviors and drove instrumental behavior (selective port activations) (Figure 6). Also, activation of SuMVGLUT2+::POA neurons was sufficient to convert passive coping strategies to active behaviors during acute stress. In contrast, we found activation of GABAergic (VGAT+) SuM neurons (SuMVGAT+) neurons did not alter drive aversion or active coping, but termination of photostimulation was followed by increased mobility in the forced swim test. These findings establish a new node in stress response circuitry that has projections to many brain areas, evokes flexible active coping behaviors, and offers new opportunities for furthering our neurobiological understanding of stress. O_FIG O_LINKSMALLFIG WIDTH=134 HEIGHT=200 SRC="FIGDIR/small/507167v4_fig6.gif" ALT="Figure 6"> View larger version (30K): org.highwire.dtl.DTLVardef@717f84org.highwire.dtl.DTLVardef@16ad323org.highwire.dtl.DTLVardef@4ba5b6org.highwire.dtl.DTLVardef@6c811e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 6.C_FLOATNO SuMVGLUT2+::POA neurons can drive instrumental action-outcome operant behavior (A) Schematic of injection and implant in VGLUT2+ Cre mice and paradigm of testing in 10-minute trials with four days before a progressive ratio (PR) trial on day five. (B) Illustration of the testing paradigm and set up. 10 Hz photostimulation was applied during the trials. Activation of the active port triggered the house light and paused stimulation for 10 seconds. Also shown is the progressive ratio used with number of required port activations per reward on vertical axis and reward number on the horizontal. (C) Cre+ mice (n=11) activated the active port triggering significantly (****p<0.0001) more pauses in stimulation than Cre- mice (n=11) mice on all four days of testing. (D) Cre+ mice activated the port significantly (****p<0.0001, ***p<0.001) more than the Cre- mice on all four trials. (E) The time to first activation of the active port was significantly (*p=0.046) different during the first trial, and Cre+ mice activated the active port significantly (**p<0.01, **p<0.01, **p=0.034) faster on subsequent trials. (F) On the fifth day after four 10-minute trials, mice were tested for 30 minutes using a progressive ratio. Cre+ performed significantly (****p<0.001) more active port activations than Cre- mice and activated the inactive port significantly more (**p=0.001) times. Cre+ mice also triggered significantly (****p<0.001) more pauses in photostimulation than Cre- mice. (G) Individual data for a representative (n=7) cohort of Cre+ mice showing cumulative active port activations as a function of time during the progressive ratio test show on-going engagement of the active port throughout the 30-minute trial. (H) The cumulative pauses in photostimulation (rewards) earned as a function of time during the progressive ratio trial are shown for individual Cre+ mice. Mice earned between 7 and 11 pause rewards during the trial. All data plotted as means {+/-}SEM. C_FIG

neuroscience↗

bioRxiv2022

Age, experience, social goals, and engagement with research scientists may promote innovation in ecological restoration

Innovation in ecological restoration is necessary in order to achieve the ambitious targets established in United Nations conventions and other global restoration initiatives. Innovation is also crucial for navigating uncertainties in repairing and restoring ecosystems, and thus practitioners often develop innovations at project design and implementation stages. However, innovation in ecological restoration can be hindered by many factors (e.g., time and budget constraints, project complexity, and others). Theory and research on innovation has been formally applied in many fields, yet explicit study of innovation in ecological restoration remains nascent. In order to assess the use of innovation in restoration projects, including its drivers and inhibitors, we conducted a social survey of restoration practitioners in the United States. Specifically, we assessed relationships between project-based innovation and traits of: the individual practitioner (including, for example, age, gender, experience); company (including, for example, company size and companys inclusion of social goals); project (including, for example, complexity and uncertainty); and project outcomes (such as completing the project on time/on budget and personal satisfaction with the work). We found positive relationships between project-based innovation and practitioner traits (age, gender, experience, engagement with research scientists), one company trait (companys inclusion of social goals in their portfolio), and project traits (project complexity and length). In contrast, two practitioner traits, risk aversion and the use of industry-specific information, were negatively related to project-based innovation. Satisfaction with work outcomes was positively correlated with project-based innovation. Collectively, the results provide insights into the drivers and inhibitors of innovation in restoration and suggest opportunities for research and application.

ecology↗

bioRxiv2021

Systemic infection with highly pathogenic H5N8 of avian origin produces encephalitis and mortality in wild mammals at a UK rehabilitation centre

Europe has experienced extensive outbreaks of highly pathogenic avian influenza (HPAI) during the autumn/winter 2020/21 season. These avian influenza A viruses are highly transmissible and have infected over 1000 commercial and backyard poultry premises in Europe in this period causing high mortality. The impact on wild bird populations has also been significant, with over 400 detections in at least 47 different species reported across Europe as being positive with the H5N8 virus. Although different H5Nx combinations within the H5 clade 2.3.4.4b have been detected, the H5N8 subtype has predominated both in wild birds and domestic poultry outbreaks. In the UK there have been 22 outbreaks of H5N8 in domestic poultry and captive birds and more than 300 wild bird detections involving H5N8 over the autumn/winter 2020/21 period to April 2021. Here we detail the series of events surrounding the detection of an H5N8 influenza A virus of avian origin in five swans, a fox and three seals in a wildlife rehabilitation centre.

microbiology↗

bioRxiv2020

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

The novel betacoronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after initially emerging in Wuhan, China. Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. To our knowledge, this is the first meta-analysis to predict host factors that play a specific role in SARS-CoV-2 pathogenesis, distinct from other respiratory viruses. We identified differentially expressed genes, isoforms and transposable element families specifically altered in SARS-CoV-2 infected cells. Well-known immunoregulators including CSF2, IL-32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were overexpressed. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1, PABPC1 and eIF4b, which may play important roles in the viral life cycle. We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19. The host factors we identified likely represent important mechanisms in the disease profile of this pathogen, and could be targeted by prophylactics and/or therapeutics against SARS-CoV-2. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/225581v3_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@15ca5a6org.highwire.dtl.DTLVardef@17f455forg.highwire.dtl.DTLVardef@a39f50org.highwire.dtl.DTLVardef@306ec1_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2018

Single-cell isoform RNA sequencing (ScISOr-Seq) across thousands of cells reveals isoforms of cerebellar cell types.

Full-length isoform sequencing has advanced our knowledge of isoform biology1-11. However, apart from applying full-length isoform sequencing to very few single cells12,13, isoform sequencing has been limited to bulk tissue, cell lines, or sorted cells. Single splicing events have been described for <=200 single cells with great statistical success14,15, but these methods do not describe full-length mRNAs. Single cell short-read 3 sequencing has allowed identification of many cell sub-types16-23, but full-length isoforms for these cell types have not been profiled. Using our new method of single-cell-isoform-RNA-sequencing (ScISOr-Seq) we determine isoform-expression in thousands of individual cells from a heterogeneous bulk tissue (cerebellum), without specific antibody-fluorescence activated cell sorting. We elucidate isoform usage in high-level cell types such as neurons, astrocytes and microglia and finer sub-types, such as Purkinje cells and Granule cells, including the combination patterns of distant splice sites6-9,24,25, which for individual molecules requires long reads. We produce an enhanced genome annotation revealing cell-type specific expression of known and 16,872 novel (with respect to mouse Gencode version 10) isoforms (see isoformatlas.com).\n\nScISOr-Seq describes isoforms from >1,000 single cells from bulk tissue without cell sorting by leveraging two technologies in three steps: In step one, we employ microfluidics to produce amplified full-length cDNAs barcoded for their cell of origin. This cDNA is split into two pools: one pool for 3 sequencing to measure gene expression (step 2) and another pool for long-read sequencing and isoform expression (step 3). In step two, short-read 3-sequencing provides molecular counts for each gene and cell, which allows clustering cells and assigning a cell type using cell-type specific markers. In step three, an aliquot of the same cDNAs (each barcoded for the individual cell of origin) is sequenced using Pacific Biosciences (\"PacBio\")1,2,4,5,26 or Oxford Nanopore3. Since these long reads carry the single-cell barcodes identified in step two, one can determine the individual cell from which each long read originates. Since most single cells are assigned to a named cluster, we can also assign the cells cluster name (e.g. \"Purkinje cell\" or \"astrocyte\") to the long read in question (Fig 1A) - without losing the cell of origin of each long read.\n\nO_FIG O_LINKSMALLFIG WIDTH=180 HEIGHT=200 SRC=\"FIGDIR/small/364950_fig1.gif\" ALT=\"Figure 1\">\nView larger version (66K):\norg.highwire.dtl.DTLVardef@4df0cdorg.highwire.dtl.DTLVardef@fc4beborg.highwire.dtl.DTLVardef@1dc485forg.highwire.dtl.DTLVardef@1138a3e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO (A) Outline of our ScISOr-Seq approach. (B) TSNE-plot depicting cell clusters, marker genes and names given to clusters, including: Bergman glia (BG), External granule cell layer neurons (EGL), Internal granule cell layer and other neurons in the interior of the cerebellum (IGL), two clusters of Purkinje cell layer neurons (PCL), oligodendrocyte progenitor cells (OPCs), Atoh1+ neuronal progenitors, Ptf1a+ neuronal progenitors and other neuronal progenitors (NPCs) (C) In-situ hybridization images from the Allen Brain Atlas depicting expression of marker genes in specific layers. (D) Expression patterns of selected marker genes across cell types.\n\nC_FIG

molecular biology↗