Biology subjects

Lam, S.

Publications and source records attributed to Lam, S..

At least 19 recordsLinked to original sources

bioRxiv2026

ASPIRE: the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems

Microbial communities inhabiting the respiratory tract contribute to health status through interactions with host physiology, immune function, and local environmental conditions. Advances in small subunit ribosomal RNA (SSU or 16S rRNA) gene amplicon sequencing enable culture-independent profiling of microbial communities as amplicon sequence variants (ASVs), revealing links between microbial dysbiosis and respiratory diseases, and the use of mass spectrometry to measure volatile organic compounds (VOCs) in exhaled breath shows emerging promise for biomarker discovery. Here we present ASPIRE, the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems, an accessible Nextflow workflow for processing, analyzing, and interpreting linked ASV-VOC data from respiratory microbiome studies. ASPIRE is designed to support scalable comparative analysis across respiratory sample types while preserving intermediate file outputs for inspection and reuse within a standardized file structure.

bioinformatics↗

bioRxiv2026

Quinoa produces an insect molting hormone through a plant biosynthetic gene cluster

The steroid hormone 20-hydroxyecdysone (20E) controls molting and metamorphosis in arthropods, yet it also accumulates in plants, where its biosynthesis has remained unknown. We show that quinoa (Chenopodium quinoa) produces 20E through a seven-gene biosynthetic cluster encoding five cytochrome P450s, a fatty acid hydroxylase-like enzyme (FAH), and a 2-oxoglutarate-dependent dioxygenase (2OGD). Distinct mutant alleles, complementation crosses, and chemical rescue established FAH as essential for pathway entry, whereas natural accessions carrying a large cluster deletion lacked 20E and all detectable intermediates. Heterologous reconstruction in Nicotiana benthamiana demonstrated that the cluster is sufficient to convert lathosterol to 20E through an unusual FAH-catalyzed C6 oxidation and 2OGD-mediated C5 epimerization. Plants and arthropods therefore evolved distinct enzymatic routes to the same molecule. This pathway provides a blueprint for engineering 20E and defining its broader ecological functions.

plant biology↗

bioRxiv2026

Methodological Impacts on Microbiome Structure and Indicator Status in the Human Lower Respiratory Tract

RationaleLung cancer is the leading cause of cancer-related death globally, and rising incidence among traditionally low-risk individuals intensifies the need for improved early-detection methods that the lower-airway microbiome may inform. ObjectivesTo evaluate how respiratory tract sampling method shapes inferred microbiome structure, and whether bronchial brushing recovers a microbial community ecologically distinct from BAL and oral rinse. MethodsProspective cohort of 33 participants (8 lung cancer, 25 non-cancer controls) underwent oral rinse, bilateral bronchoalveolar lavage (BAL), and bronchial brushing. Microbiome structure was characterized by small subunit ribosomal rRNA gene amplicon sequence variant (ASV) profiling, with indicator-species analysis and SPIEC-EASI correlation-network mapping used to identify ASVs associated with sample type or cancer status. Measurements and Main ResultsSampling method was the dominant axis of variation. BAL communities closely resembled oral rinse (65 jointly indicative ASVs; none shared with brushing), whereas bronchial brushing yielded a distinct but low-biomass signal. After excluding host-derived sequences, two brush-specific indicator ASVs affiliated with Sphingomonadaceae and an uncultured Steroidobacteraceae were identified that co-localized within a single co-occurrence module. Cancer-status effects were not detectable in this pilot cohort, consistent with limited statistical power. ConclusionsSampling method is the primary determinant of inferred respiratory microbiome structure. Bronchial brushing recovers a distinct but low-biomass signal that is obscured when BAL is used in isolation. However, overlap between this low-biomass signal with host and contaminant sequences indicates that confidently resolving a discrete lower-airway community will require deeper sequencing and dedicated contamination controls. These methodological findings directly inform the design of future cancer-and disease-association studies.

microbiology↗

bioRxiv2026

Astrocyte diversity and aging in the mouse lemur primate brain

Astrocytes play key roles in maintaining brain homeostasis, metabolism, and neurovascular integrity, yet their diversity and age-related modulation remain insufficiently understood, particularly across primate lineages. While rodent studies have generated extensive knowledge, notable species differences highlight the need for comparative analyses in non-human primates. The gray mouse lemur (Microcebus murinus), a small primate widely used in aging research, offers a valuable but underexplored model for studying astroglial aging. In this study, we characterized astrocyte distribution, morphology, and reactivity in 17 mouse lemurs aged 1.0-11.5 years using GFAP and vimentin immunohistochemistry. We identified marked regional and morphological heterogeneity, with dense astrocytic labeling in white matter, hippocampus, and sparse but diverse cortical populations. Distinct astrocyte subtypes--including fibrous, protoplasmic, projection, pial and subpial interlaminar, radial glia-like cells, tanycytes--were documented. Varicosity-bearing processes were common across multiple astroglial subtypes and may indicate altered physiological states. Quantitative analyses revealed pronounced age-related increases in astrocytic reactivity, particularly in white matter and interlaminar astrocytes. Cortical and hippocampal changes were comparatively modest. These findings indicate region-specific astrocytic vulnerability during aging and support the translational value of the mouse lemur for investigating glial aging in primates. Main PointsO_LIThe mouse lemur is the smallest primate on earth with a key role to understand primate brain characteristics. C_LIO_LIWe characterized seven different astrocyte subtypes: from fibrous to primate-specific astrocyte as interlaminar astrocytes in different brain regions of this primate. C_LIO_LIVaricosities were reported in different astrocyte subtypes found close to brain borders. C_LIO_LIMain age-related changes concerned fibrous astrocytes in the white matter and interlaminar astrocytes at the cortical border. C_LI

neuroscience↗

bioRxiv2025

Thiol Scarcity in Cerebrospinal Fluid Renders Leptomeningeal Acute Lymphoblastic Leukaemia Therapeutically Vulnerable to Ferroptosis

The leptomeninges present a challenging tumour microenvironment with cells receiving low levels of nutrients and oxygen from cerebrospinal fluid (CSF), however these metabolic constraints are yet to be exploited therapeutically. Central nervous system (CNS) relapse in acute lymphoblastic leukaemia (ALL) remains a formidable clinical challenge because the leptomeningeal niche restricts drug penetration and immune surveillance. Current CNS-directed treatments rely on neurotoxic intrathecal chemotherapy, underscoring the urgent need for novel targeted strategies. Here, we uncover a profound niche-specific metabolic vulnerability in CNS-resident ALL cells, characterised by an obligate reliance on LRP8-mediated selenium uptake to sustain selenocysteine biosynthesis and GPX4 activity under profound glutathione limitation. We show that scarcity of thiols and cystine in CSF creates an inherently pro-ferroptotic microenvironment. Interference with selenocysteine biosynthesis under these conditions induces synthetic lethality in both in vitro and in vivo CNS-ALL models. This vulnerability is exploitable both by genetic targeting of the selenocysteine biosynthesis pathway and, notably, through repurposing the FDA-approved agent Auranofin, which disrupts selenium utilisation, induces lipid peroxidation, and demonstrates CNS-specific anti-leukaemic eaicacy with excellent tolerability in vivo. These findings identify a novel mechanistically grounded approach, leveraging features of the unique leptomeningeal microenvironment to selectively kill invading cells, with potential implications for all leptomeningeal-tropic malignancies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/693383v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@2303dforg.highwire.dtl.DTLVardef@d357ceorg.highwire.dtl.DTLVardef@129cb26org.highwire.dtl.DTLVardef@d83183_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO The leptomeningeal tumour microenvironment is intrinsically pro-ferroptotic due to low concentrations of free thiols and cystine in cerebrospinal fluid. ALL cells in this niche exhibit disrupted glutathione metabolism and a novel dependency on LRP8-mediated SELENOP uptake to sustain GPX4 levels and thus protect themselves from spontaneous ferroptotic cell death. Perturbation of selenocysteine biosynthesis via genetic inhibition SEPHS2 or LRP8 leads to synthetic lethality in leukaemic cells exposed to CSF in vitro and in vivo - an effect phenocopied by use of Auranofin. C_FIG

cancer biology↗

bioRxiv2025

Cell-stereotyped DNA repair outcomes are widespread during genome editing

Genome editing outcomes are governed by DNA repair pathways that vary with cell type and state. We developed scOUT-seq (single-cell Outcomes Using Transcript sequencing), a scalable approach that jointly profiles transcriptomes and matched multi-allelic editing outcomes ranging from homology directed repair (HDR) to inter-chromosomal translocations. We mapped editing outcomes in human CD34 hematopoietic stem and progenitor cells (HSPCs), mouse LSK HSPC equivalents, human upper airway organoids, and mouse multi-organ in vivo editing. Profiling 500,000 alleles across 74 cell types, scOUT-seq revealed that outcomes in most cell subtypes differ markedly from the bulk average. Various cell types shifted major repair classes, preferred different molecular sequences, and even enriched large structural variants, with distinctive patterns of allelic co-occurrence. Surprisingly, rare stem subtypes diverged from prevalent progenitors, and inhibitory neuron subtypes efficiently incorporated HDR alleles. These data suggest the potential for tailored therapeutic editing that may have been missed by bulk measurements.

genomics↗

bioRxiv2025

Measuring partner synchrony during salsa dancing and its relationship to changes in psychosocial domains

BackgroundDance is a promising rehabilitation adjunct but understanding the mechanisms through which dance improves physical and psychosocial well-being is necessary for implementation. This study investigated the feasibility of a measure of one possible mechanism: partner synchrony. Secondary objectives were to examine the relationships between partner synchrony, instructor ratings, and changes in psychosocial variables. MethodsParticipants wore an Inertial Measurement Unit (IMU) sensor during a salsa class that was video recorded. Partner synchrony was quantified with correlations of x, y, and z-axis acceleration between dancing pairs. Psychosocial variables were measured pre- and post-class. Salsa instructors rated partner synchrony from video recordings. Feasibility parameters included percentage of participants with data collected and sensor comfort. Pre-post changes were analyzed with Wilcoxon ranked tests and relationships were analyzed with Spearman correlations. ResultsData was collected for 23/24 (96%) participants and 17/24 (81%) reported the sensor was comfortable. All psychosocial variables improved from pre- to post-class. Partner synchrony was significantly associated with instructor ratings and change in positive and negative affect. ConclusionsAn IMU-based measure of dance partner synchrony is feasible, associated with ratings by dance instructors and related to changes in mood. The partner synchrony measure can be used to advance our understanding of dance as a therapeutic tool after its reliability is investigated.

neuroscience↗

bioRxiv2025

Loss of CTLH component MAEA impairs DNA repair and replication and leads to developmental delay

Ubiquitin E3 ligases play crucial roles in the DNA damage response (DDR) by modulating the turnover, localization, activation, and interactions of DDR and DNA replication proteins. To gain further insight into how the ubiquitin system regulates the DDR, we performed a CRISPR-Cas9 knockout screen focused on E3 ligases and related proteins with the DNA topoisomerase I inhibitor, camptothecin. This uncovered the CTLH ubiquitin E3 ligase complex -- and particularly one of its core subunits, MAEA -- as a critical regulator of the cellular response to single-ended DNA double-strand breaks (seDSBs) and replication stress. In tandem, we identified patients with variants in MAEA who present with neurodevelopmental deficits including global developmental delay, dysmorphic facial features, brain abnormalities, intellectual disability, and abnormal movement. Analysis of patient-derived cell lines and mutation modeling reveal an underlying defect in HR-dependent DNA repair and replication fork restart as a likely cause of disease. We propose that MAEA dysfunction hinders DNA repair by reducing the efficiency of RAD51 loading at sites of DNA damage, which compromises genome integrity and cell division during development.

genetics↗

bioRxiv2025

Cell-type-specific plasticity in synaptic, intrinsic, and sound response properties of deep-layer auditory cortical neurons after noise trauma

Peripheral trauma, such as noise-induced hearing loss (NIHL), triggers compensatory plasticity in the auditory cortex (ACtx) to maintain auditory function. While cortical plasticity in superficial cortical layers has been relatively well studied, the plasticity mechanisms governing deep-layer excitatory projection neurons remain less understood. Here, we investigated the plasticity of layer (L)5 extratelencephalic (ETs) and L6 corticothalamic neurons (CTs) following NIHL. Using a combination of in vitro slice electrophysiology, optogenetics, and in vivo two-photon imaging in a mouse model of NIHL, we characterized changes in evoked thalamocortical (TC) synaptic input strength, intrinsic excitability, and sound response properties. We found that TC input was initially equivalent between ETs and CTs, then shifted to CT-dominant one day after noise exposure. This shift renormalized to equivalent seven days after noise exposure and was associated with a transient increase in both the quantal size (q) in TC[->]CT synapses and intrinsic CT suprathreshold excitability. ETs maintained stable intrinsic properties and showed minor changes in their TC input. In vivo imaging revealed that CTs displayed a persistent elevation in sound intensity thresholds, whereas ETs transiently shifted their best frequency representation and reduced their responsiveness to high-frequency tones one day after NIHL, followed by recovery at seven days. Together, our findings highlight cell-type-specific plasticity mechanisms in deep-layer cortical neurons, enhance our understanding of cortical adaptation to peripheral damage, and highlight targets for developing therapeutic strategies to mitigate hearing loss and related disorders such as tinnitus and hyperacusis. Short AbstractPeripheral damage drives auditory cortex (ACtx) plasticity, but the underlying synaptic and cellular mechanisms remain poorly understood. We used a combination of in vitro slice electrophysiology, optogenetics, and in vivo two-photon imaging to investigate layer 5 extratelencephalic (ET) and layer 6 corticothalamic (CT) neuronal plasticity in mice, following noise-induced hearing loss (NIHL). Thalamocortical (TC) input was initially balanced between CTs and ETs but shifted to CT-dominant one day post-NIHL and then normalized by day seven. This transient shift was accompanied by increased quantal size and suprathreshold excitability in CTs, with minimal changes in ETs. In vivo, CTs exhibited persistent elevation in sound intensity thresholds, while ETs showed a transient shift in frequency tuning and reduced high-frequency responsiveness that recovered within a week. These findings reveal distinct, cell-type-specific plasticity mechanisms in deep-layer ACtx neurons following peripheral damage and highlight potential targets for treating hearing loss-related disorders such as tinnitus and hyperacusis.

neuroscience↗

bioRxiv2025

Increased white matter microglial reaction and perivascular macrophages in the aging microcebe primate

As populations age, the incidence of neurodegenerative disorders is rising. Early age-related neuropathological changes are the breeding ground for the development of these disorders. Microglia are the resident macrophages of the central nervous system. They play crucial roles in maintaining brain homeostasis, yet their age-related changes remain not fully understood. While age-related microglia changes have been strongly characterized in rodents, studies in non-human primates are scarce. The microcebe primate (mouse lemur (Microcebus murinus)) is widely used as a model for cerebral aging and to investigate age-related neurodegenerative processes. HLA-DR is a major histocompatibility class II cell surface receptor which presents antigens to cells of the immune response. It is a major marker of microglia reaction. In this study, we explored microglia in the whole brains of middle-aged and old microcebes using HLA-DR immunolabeling. We analyzed microglial morphology and quantified HLA-DR+ cell density and protein expression. A wide range of microglial morphologies was observed in the white matter, including thin processes microglia, "rod-like" elongated and polarized shape, hypertrophic, and amoeboid microglia. Aging was associated with increased HLA-DR+ microglial expression in the white matter while very few HLA-DR+ microglia were observed in the parenchyma of cortical gray matter regions. A second finding was the higher number of HLA-DR+ perivascular macrophages in old animals. This study in a primate outlines that, in the absence of neurodegenerative processes, the most prominent signs of age-related microglia/macrophage changes are region-specific and concern white matter and perivascular regions. This emphasizes the need to target these regions to prevent cerebral aging. Main PointsO_LIHLA-DR+ microglia in Microcebus murinus primate show diverse morphologies and increase with age in white matter. C_LIO_LIHLA-DR+ perivascular macrophage load increase in aged animals. C_LI Table of Contents Image (TOCI) O_FIG O_LINKSMALLFIG WIDTH=167 HEIGHT=200 SRC="FIGDIR/small/645519v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@edb574org.highwire.dtl.DTLVardef@23f606org.highwire.dtl.DTLVardef@ed2e0borg.highwire.dtl.DTLVardef@169f059_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

WEE1 inhibitors synergise with mRNA translation defects via activation of the kinase GCN2

Inhibitors of the protein kinase WEE1 have emerged as promising agents for cancer therapy. In this study, we uncover synergistic interactions between WEE1 small- molecule inhibitors and defects in mRNA translation, mediated by activation of the integrated stress response (ISR) through the kinase GCN2. Using a pooled CRISPRi screen, we identify GSPT1 and ALKBH8 as factors whose depletion confer hypersensitivity to the WEE1 inhibitor, AZD1775. We demonstrate that this synergy depends on ISR activation, which is induced by the off-target activity of WEE1 inhibitors. Furthermore, PROTAC-based WEE1 inhibitors and molecular glues show reduced or no ISR activation, suggesting potential strategies to minimise off-target toxicity. Our findings reveal that certain WEE1 inhibitors elicit dual toxicity via ISR activation and genotoxic stress, with ISR activation being independent of WEE1 itself or cell-cycle status. This dual mechanism highlights opportunities for combination therapies, such as pairing WEE1 inhibitors with agents targeting the mRNA translation machinery. This study also underscores the need for more precise WEE1 targeting strategies to mitigate off-target effects, with implications for optimising the therapeutic potential of WEE1 inhibitors.

cancer biology↗

bioRxiv2025

Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons

Huntingtons Disease (HD) is caused by a CAG repeat expansion in the gene encoding Huntingtin (HTT). While normal HTT function appears impacted by the mutation, the specific pathways unique to CAG repeat expansion versus loss of normal function are unclear. To understand the impact of the CAG repeat expansion, we evaluated biological signatures of HTT knockout (HTT KO) versus those that occur from the CAG repeat expansion by applying multi-omics, live cell imaging, survival analysis and a novel feature-based pipeline to study cortical neurons (eCNs) derived from an isogenic human embryonic stem cell series (RUES2). HTT KO and the CAG repeat expansion influence developmental trajectories of eCNs, with opposing effects on the growth. Network analyses of differentially expressed genes and proteins associated with enriched epigenetic motifs identified subnetworks common to CAG repeat expansion and HTT KO that include neuronal differentiation, cell cycle regulation, and mechanisms related to transcriptional repression and may represent gain-of-function mechanisms that cannot be explained by HTT loss of function alone. A combination of dominant and loss-of-function mechanisms are likely involved in the aberrant neurodevelopmental and neurodegenerative features of HD that can help inform therapeutic strategies.

cell biology↗

bioRxiv2024

Plastid translocon recycling in dinoflagellates demonstrates the portability of complex plastids between hosts

The plastids of photosynthetic organisms on land are predominantly primary plastids derived from an ancient endosymbiosis of a cyanobacterium. Conversely, marine photosynthetic diversity is dominated by plastids gained by subsequent endosymbioses of photosynthetic eukaryotes, so-called complex plastids. The plastids of major eukaryotic lineages including cryptophytes, haptophytes, stramenopiles, dinoflagellates and apicomplexans, were originally all posited to derive from a single secondary endosymbiosis of a red alga--the chromalveloate hypothesis 1. Subsequent phylogenetic resolution of eukaryotes indicated that separate events of plastid acquisition must have occurred to account for this distribution of plastids 2,3. The number of such events, however, and the donor organisms for the new plastid endosymbioses are still not resolved. A perceived bottleneck of endosymbiotic plastid gain is the development of protein targeting from the hosts into new plastids, and this supposition has often driven hypotheses towards minimising the number of plastid-gain events to explain plastid distribution in eukaryotes. But how plastid protein-targeting is established for new endosymbionts is often unclear, which makes it difficult to assess the likelihood of plastid transfers between lineages. Here we show that Kareniaceae dinoflagellates, that possess complex plastids known to be derived from haptophytes, acquired all the necessary protein import machinery from these haptophytes. Furthermore, cryo-electron tomography revealed that no additional membranes were added to the Kareniaceae complex plastid during serial endosymbiosis, suggesting that the haptophyte-derived import processes were sufficient. Our analyses suggests that complex red plastids are preadapted for horizontal transmission, potentially explaining their widespread distribution in aquatic algal diversity.

evolutionary biology↗

bioRxiv2024

Systematic Development of Reprogrammed Modular Integrases Enables Precise Genomic Integration of Large DNA Sequences

Despite recent progress in the ability to manipulate the genomes of eukaryotic cells1-3, there is still no effective and practical method to precisely integrate large synthetic DNA constructs into desired chromosomal sites using a programmable integrase. Serine integrases can perform the necessary molecular steps4, but only if their natural target site is first installed into the recipient genome by other methods. A more elegant approach would be to directly reprogram the serine integrase itself to target a desired genomic site that is different from the natural recognition site of the integrase5. Here, we describe the development of a Modular Integrase (MINT) platform, a versatile protein-guided genome editing tool that can facilitate site-directed targeted integration (TI) of synthetic DNA into chromosomal sites. Through a combination of structural modeling, directed evolution, and screening in human cells we have reprogrammed the specificity of the serine integrase Bxb1. We demonstrate the therapeutic potential of the MINT platform by retargeting Bxb1 to the human AAVS1 and TRAC loci where wild-type Bxb1 has no detectable activity. By combining the MINT platform with known activity-increasing Bxb1 mutants, we achieved 14% TI at the AAVS1 locus, and by additionally fusing zinc finger DNA binding domains to engineered Bxb1 variants, we achieved 35% TI at the TRAC locus in human K562 cells. To further demonstrate clinical potential, we achieved stable 15% TI of a functional donor construct in human T cells.

synthetic biology↗

bioRxiv2024

Genome-aware annotation of CRISPR guides validates targets in variant cell lines and enhances discovery in screens

Pooled CRISPR-Cas9 genetic knockout screens are powerful high-throughput tools for identifying chemo-genetic, synthetic-lethal and synthetic-viability interactions and are used as a key step towards identifying disease-modifying knockout candidates and informing drug design and therapeutic regimens. CRISPR guide libraries are commercially available for purchase and have been widely applied in different cell lines. However, discrepancies between the genomes used to design CRISPR libraries and the genomes of the cells subjected to CRISPR screens lead to loss of signal or introduction of bias towards the most conserved genes. Here, we present an algorithm, EXOme-guided Reannotation of nuCleotIde SEquences (Exorcise), which uses sequence search and CRISPR target annotation to adapt existing CRISPR libraries to user-defined genomes and exomes. Applying Exorcise on 55 commercially available CRISPR-spCas9 knockout libraries for human and mouse, we found that all libraries have mis-annotations, and that design strategy affects off-target effects and targeting accuracy relative to a standard reference sequence. In simulations on synthetic data, we modelled common mis-annotations in CRISPR libraries and found that they adversely affected recovery of the ground truth for all genes except for those with the strongest signals. Finally, we reanalysed DepMap and DDRcs CRISPR screens with Exorcise annotations and found that strong hits were retained, and lower-confidence hits were strengthened. Use of Exorcise on DepMap with exomes inferred from transcriptomic expression data demonstrated that cell-line-aware reannotation is possible without whole-genome sequencing. Taken together, our results show that Exorcise is a powerful reannotation tool that focuses existing CRISPR libraries towards the cell line genome under investigation and allows post-hoc reanalysis of completed CRISPR screens. Exorcise is open-source software licenced under a Creative Commons Zero Universal 1.0 licence and is available at .

bioinformatics↗

bioRxiv2024

PTEN inhibition promotes robust growth of bulbospinal respiratory axons and partial recovery of diaphragm function in a chronic model of cervical contusion spinal cord injury

High spinal cord injury (SCI) leads to persistent and debilitating compromise in respiratory function. Cervical SCI not only causes the death of phrenic motor neurons (PhMNs) that innervate the diaphragm, but also damages descending respiratory pathways originating in the rostral ventral respiratory group (rVRG) located in the brainstem, resulting in denervation and consequent silencing of spared PhMNs located caudal to injury. It is imperative to determine whether interventions targeting rVRG axon growth and respiratory neural circuit reconnection are efficacious in chronic cervical contusion SCI, given that the vast majority of individuals are chronically-injured and most cases of SCI involve contusion-type damage to the cervical region. We therefore employed a clinically-relevant rat model of chronic cervical hemicontusion to test therapeutic manipulations aimed at reconstructing damaged rVRG-PhMN-diaphragm circuitry to achieve recovery of respiratory function. At a chronic time point post-injury, we systemically administered: an antagonist peptide directed against phosphatase and tensin homolog (PTEN), a central inhibitor of neuron-intrinsic axon growth potential; an antagonist peptide directed against receptor-type protein tyrosine phosphatase sigma (PTP{sigma}), another important negative regulator of axon growth capacity; or a combination of these two peptides. PTEN antagonist peptide (PAP4) promoted partial recovery of diaphragm motor activity out to nine months post-injury, while PTP{sigma} peptide did not impact diaphragm function after cervical SCI. Furthermore, PAP4 promoted robust growth of descending bulbospinal rVRG axons caudal to the injury within the denervated portion of the PhMN pool, while PTP{sigma} peptide did not affect rVRG axon growth at this location that is critical to control of diaphragmatic respiratory function. In conclusion, we find that, when PTEN inhibition is targeted at a chronic time point following cervical contusion that is most relevant to the SCI clinical population, our non-invasive PAP4 strategy can successfully promote significant regrowth of damaged respiratory neural circuitry and also partial recovery of diaphragm motor function. HIGHLIGHTSO_LIPTEN antagonist peptide promotes partial diaphragm function recovery in chronic cervical contusion SCI. C_LIO_LIPTP{sigma} inhibitory peptide does not impact diaphragm function recovery in chronic cervical contusion SCI. C_LIO_LIPTEN antagonist peptide promotes growth of bulbospinal rVRG axons in chronic cervical contusion SCI. C_LIO_LIPTP{sigma} peptide does not affect rVRG axon growth in chronic cervical contusion SCI. C_LI

neuroscience↗

bioRxiv2023

A bioinformatics screen reveals Hox and chromatin remodeling factors at the Drosophila histone locus

Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets and 27 factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax, Abdominal-A and Abdominal-B, suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other transcription factors that target the histone gene array: JIL-1, Hr78, the long isoform of fs(1)h as well as the generalized transcription factors TAF-1, TFIIB, and TFIIF. Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.

molecular biology↗

bioRxiv2022

RMeDPower for Biology: guiding design, experimental structure and analyses of repeated measures data for biological studies

Lack of experimental reproducibility has plagued efforts to understand biology at both basic biomedical and preclinical levels. The cause is often improperly powered experiments and the use of inadequate statistical tools. To overcome these problems, we developed RMeDPower2, a complete, user-friendly package of tools in R that will allow scientists that are not deeply familiar with statistical analyses to predict the scope and size of biological data they need when conducting experiments with a repeated measures design. RMeDPower2 is based on Generalized Linear Mixed Effects Models (GLMM), which are better suited to the statistical analysis of these experiments than ANOVA or t-tests. We illustrate the use of RMeDPower2 and compare it to t- test for power calculations, using our own pilot studies of iPSC-derived motor neurons (iMNs) from sporadic ALS (sALS) patients versus healthy controls. We report that sALS iMNs display reduced numbers of soma- emanating processes compared to control iMNs using RMeDPower2. We expect RMeDPower2 to find applications far beyond cell assays, from single-cell RNAseq experiments to brain slice electrophysiology or animal behavior. MotivationThe lack of rigor and reproducibility in biomedical research has caused a crisis that has been highlighted in the popular literature and has become a focus for the National Institutes of Health1-3. It has been estimated that the majority of published empirical observations cannot be reproduced4-9, rendering nearly futile any effort to build on these observations to further our understanding of basic biological mechanisms or design effective therapeutic approaches. Further, the resources and time spent attempting to reproduce findings from low-quality or incorrectly acquired data are estimated to cost the global scientific community about 200 billion dollars per year10. The root cause lies in experimental designs that are not structured or powered adequately for conclusive statistical analyses. Since all biomedical researchers cannot be expected to have a deep knowledge of statistics or easy access to trained statisticians, tools are desperately needed to help them check the design of their experiments and apply adequate statistical power estimation. Not only could this improve our confidence in scientific outcomes, it could help make biological experiments more time-efficient and cost-effective. For example, if a researcher could estimate how many experiments should be performed and how many cell lines, animals or tissue samples should be collected to achieve sufficient statistical power to test their hypothesis, they may adjust their experimental design to fit their time or budgetary constraints without jeopardizing the quality of their findings. Another source of scientific errors comes from technologies such as scRNA-seq, whose advances are leading to a rapid increase in studies involving so-called "pseudo-replication", which treats non-independent measures as if they were independent. For example, carrying out multiple measurements on a single sample instead of using separate, independent samples would represent non-independent replication. The risk of pseudo-replication11 (illustrated further below), can be remedied by the implementation of rigorous statistical methods that apply to all aspects of the data arising from such designs.

cell biology↗