Biology subjects

Feng, Y.

Publications and source records attributed to Feng, Y..

At least 217 records · Page 12Linked to original sources

bioRxiv2023

Human basal-like breast cancer is represented by one of the two mammary tumor subtypes in dogs

BackgroundAbout 20% of breast cancers in humans are basal-like, a subtype that is often triple negative and difficult to treat. An effective translational model for basal-like breast cancer (BLBC) is currently lacking and urgently needed. To determine if spontaneous mammary tumors in pet dogs could meet this need, we subtyped canine mammary tumors and evaluated the dog-human molecular homology at the subtype level. MethodsWe subtyped 236 canine mammary tumors from 3 studies by applying various subtyping strategies on their RNA-seq data. We then performed PAM50 classification with canine tumors alone, as well as with canine tumors combined with human breast tumors. We investigated differential gene expression, signature gene set enrichment, expression association, mutational landscape, and other features for dog-human subtype comparison. ResultsOur independent genome-wide subtyping consistently identified two molecularly distinct subtypes among the canine tumors. One subtype is mostly basal-like and clusters with human BLBC in cross-species PAM50 classification, while the other subtype does not cluster with any human breast cancer subtype. Furthermore, the canine basal-like subtype recaptures key molecular features (e.g., cell cycle gene upregulation, TP53 mutation) and gene expression patterns that characterize human BLBC. It is enriched histological subtypes that match human breast cancer, unlike the other canine subtype. However, about 33% of canine basal-like tumors are estrogen receptor negative (ER-) and progesterone receptor positive (PR+), which is rare in human breast cancer. Further analysis reveals that these ER-PR+ canine tumors harbor additional basal-like features, including upregulation of genes of interferon-{gamma} response and of the Wnt-pluripotency pathway. Interestingly, we observed an association of PGR expression with gene silencing in all canine tumors, and with the expression of T cell exhaustion markers (e.g., PDCD1) in ER-PR+ canine tumors. ConclusionsWe identify a canine mammary tumor subtype that molecularly resembles human BLBC overall, and thus could serve as a vital spontaneous animal model of this devastating breast cancer subtype. Our study also sheds light on the dog-human difference in the mammary tumor histology and the hormonal cycle.

cancer biology↗

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↗

bioRxiv2023

Variational Autoencoders for Generating Synthetic Tractography-Based Bundle Templates in a Low-Data Setting

White matter tracts generated from whole brain tractography are often processed using automatic segmentation methods with standard atlases. Atlases are generated from hundreds of subjects, which becomes time-consuming to create and difficult to apply to all populations. In this study, we extended our prior work on using a deep generative model a Convolutional Variational Autoencoder - to map complex and data-intensive streamlines to a low-dimensional latent space given a limited sample size of 50 subjects from the ADNI3 dataset, to generate synthetic population-specific bundle templates using Kernel Density Estimation (KDE) on streamline embeddings. We conducted a quantitative shape analysis by calculating bundle shape metrics, and found that our bundle templates better capture the shape distribution of the bundles than the atlas data used in the original segmentation derived from young healthy adults. We further demonstrated the use of our framework for direct bundle segmentation from whole-brain tractograms.

neuroscience↗

bioRxiv2023

Dissociable contributions of the amygdala and ventral hippocampus to stress-induced changes in defensive behavior

BackgroundSevere stress can produce multiple persistent changes in defensive behavior relevant to psychiatric illness. While much is known about the circuits supporting stress-induced associative fear, how stress-induced circuit plasticity supports non-associative changes in defensive behavior remains unclear. MethodsMice were exposed to an acute severe stressor, and subsequently, both associative and non-associative defensive behavioral responses were assessed. A mixture of local protein synthesis inhibition, pan-neuronal chemogenetic inhibition, and projection-specific chemogenetic inhibition were utilized to isolate the roles of the basolateral amygdala (BLA) and ventral hippocampus (vHC) to the induction and expression of associative and non-associative defensive behavioral changes. ResultsStress-induced protein synthesis in the BLA was necessary for enhancements in stress sensitivity but not enhancements in anxiety-related behaviors, whereas protein synthesis in the vHC was necessary for enhancements in anxiety-related behavior but not enhancements in stress sensitivity. Like protein synthesis, neuronal activity of the BLA and vHC were found to differentially support the expression of these same defensive behaviors. Additionally, projection-specific inhibition of BLA-vHC connections failed to alter these behaviors, indicating that these defensive behaviors are regulated by distinct BLA and vHC circuits. Lastly, contributions of the BLA and vHC to stress sensitivity and anxiety-related behavior were independent of their contributions to associative fear. ConclusionsStress-induced plasticity in the BLA and vHC were found to support dissociable non-associative behavioral changes, with BLA supporting enhancements in stress sensitivity and vHC supporting increased anxiety-related behavior. These findings demonstrate that independent BLA and vHC circuits are critical for stress-induced defensive behaviors, and that differential targeting of BLA and vHC circuits may be needed in disease treatment.

neuroscience↗

bioRxiv2023

Manipulating single-unit theta phase-locking with PhaSER: An open-source tool for real-time phase estimation and manipulation

The precise timing of neuronal spiking relative to the brains endogenous oscillations (i.e., phase-locking or spike-phase coupling) has long been hypothesized to coordinate cognitive processes and maintain excitatory-inhibitory homeostasis. Indeed, disruptions in theta phase-locking have been described in models of neurological diseases with associated cognitive deficits and seizures, such as Alzheimers disease, temporal lobe epilepsy, and autism spectrum disorders. However, due to technical limitations, determining if phase-locking causally contributes to these disease phenotypes has not been possible until recently. To fill this gap and allow for the flexible manipulation of single-unit phase-locking to on-going endogenous oscillations, we developed PhaSER, an open-source tool that allows for phase-specific manipulations. PhaSER can deliver optogenetic stimulation at defined phases of theta in order to shift the preferred firing phase of neurons relative to theta in real-time. Here, we describe and validate this tool in a subpopulation of inhibitory neurons that express somatostatin (SOM) in the CA1 and dentate gyrus (DG) regions of the dorsal hippocampus. We show that PhaSER is able to accurately deliver a photo-manipulation that activates opsin+ SOM neurons at specified phases of theta in real-time in awake, behaving mice. Further, we show that this manipulation is sufficient to alter the preferred firing phase of opsin+ SOM neurons without altering the referenced theta power or phase. All software and hardware requirements to implement real-time phase manipulations during behavior are available online (https://github.com/ShumanLab/PhaSER).

neuroscience↗

bioRxiv2023

High-throughput screening of functional neo-antigens and their specific TCRs via the Jurkat reporter system combine with droplet microfluidics

T-cell receptor (TCR)-engineered T cells can precisely recognize a broad repertoire of targets derived from both intracellular and surface proteins of tumor cells. TCR-T adoptive cell therapy has shown safety and promising efficacy in solid tumor immunotherapy. However, antigen-specific functional TCR screening is time-consuming and expensive, which limits its application clinically. Here, we developed a novel integrated antigen-TCR screening platform based on droplet microfluidics technology, enabling high-throughput peptide-major histocompatibility complex (pMHC) library-to-TCR library screening with high sensitivity and low background signal. We introduced DNA barcoding technology to label peptide antigen candidate-loaded antigen-presenting cells (APCs) and Jurkat reporter cells to check the specificity of pMHC-TCR candidates. Coupled with the next-generation sequencing pipeline, interpretation of the DNA barcodes and the gene expression level of the Jurkat T-cell activation pathway provided a clear peptide-MHC-TCR recognition relationship. Our proof-of-principle study demonstrates that the platform could achieve unbiased pMHC-TCR library-on-library screening, which is expected to be used in the cross-reactivity and off-target testing of candidate pMHC-TCR libraries in clinical applications.

bioengineering↗

bioRxiv2023

Cell-free multi-omics analysis reveals tumor status-informative signatures in gastrointestinal cancer patients' plasma

During cancer development, hosts tumorigenesis and immune signals are released to and informed by circulating molecules, like cell-free DNA (cfDNA) and RNA (cfRNA) in blood. However, these two kinds of molecules are still not systematically compared in gastrointestinal cancer. Here, we profiled 4 types of cell-free omics data from colorectal and stomach cancer patients, and assayed 15 types of genomic, epi-genomic, and transcriptomic variations. First, we demonstrated that the multi-omics data were more capable of detecting cancer genes than the single-omics data, where cfRNAs were more sensitive and informative than cfDNAs in terms of detection ratio, variation type, altered number, and enriched functional pathway. Moreover, we revealed several peripheral immune signatures that were suppressed in cancer patients and originated from specific circulating and tumor-microenvironment cells. Particularly, we defined a {gamma}{delta}-T-cell score and a cancer-associated-fibroblast (CAF) score using the cfRNA-seq data of 143 cancer patients. They were informative of clinical status like cancer stage, tumor size, and survival. In summary, our work reveals the cell-free multi-molecular landscape of colorectal and stomach cancer, and provides a potential monitoring utility in blood for the personalized cancer treatment.

systems biology↗

bioRxiv2023

Senescence of cortical neurons following persistent DNA double-strand breaks induces cerebrovascular lesions

DNA double strand breaks (DSBs), neuroinflammation, and vascular alterations in the brain are all associated with neurodegenerative disorders. However, the interconnections between these neuropathological changes and how they act synergistically to promote irreversible neurodegeneration remain unclear. Here we show that abrogating the BRCA1-associated protein Brap in cerebral cortical neurons, as opposed to vascular endothelium cells, causes cerebrovascular defects. This non-cell autonomous effect is mediated by cellular senescence resulting from persistent neuronal DSBs. We show that in the state of senescence, there is a massive upregulation of genes involved in cell secretion, inflammatory responses, and vascular changes, which coincides with cerebral microclots and microbleeds. The vascular lesions intertwine with neuroinflammation and exacerbate neuronal DSBs, culminating in oxidative stress, metabolic alteration, and downregulation of genes essential for neuronal function. By demonstrating the cerebrovascular impact of cortical neuronal DSBs, our data suggest that senescence-associated secretory phenotype can initiate brain-wide neurodegeneration.

neuroscience↗

bioRxiv2023

Global analysis of aging-related protein structural changes uncovers enzyme polymerization-based control of longevity

Aging is associated with progressive phenotypic changes over time. Virtually all cellular phenotypes are produced by proteins and structural alterations in proteins can lead to age-related diseases. Nonetheless, comprehensive knowledge of proteins undergoing structural-functional changes during cellular aging and their contribution to age-related phenotypes is lacking. Here, we conducted proteome-wide analysis of early age-related protein structural changes in budding yeast using limited proteolysis-mass spectrometry. The results, compiled in online ProtAge-catalog, unravelled age-related functional changes in regulators of translation, protein folding and amino acid metabolism. Mechanistically, we found that folded glutamate synthase Glt1 polymerizes into supramolecular self-assemblies during aging causing breakdown of cellular amino acid homeostasis. Inhibiting Glt1 polymerization by mutating the polymerization interface restored amino acid levels in aged cells, attenuated mitochondrial dysfunction and led to life span extension. Altogether, this comprehensive map of protein structural changes enables identifying novel mechanisms of age-related phenotypes and offers opportunities for their reversal.

cell biology↗

bioRxiv2023

Extremely potent pan-sarbecovirus neutralizing antibodies generated by immunization of macaques with an AS03-adjuvanted monovalent subunit vaccine against SARS-CoV-2

The rapid emergence of SARS-CoV-2 variants that evade immunity to vaccination has placed a global health imperative on the development of therapeutic countermeasures that provide broad protection against SARS-CoV-2 and related sarbecoviruses. Here, we identified extremely potent pan-sarbecovirus antibodies from non-human primates vaccinated with an AS03 adjuvanted subunit vaccine against SARS-CoV-2 that recognize conserved epitopes in the receptor binding domain (RBD) with femtomolar affinities. Longitudinal analysis revealed progressive accumulation of somatic mutation in the immunoglobulin genes of antigen-specific memory B cells for at least one year following primary vaccination. 514 monoclonal antibodies (mAbs) were generated from antigen-specific memory B cells. Antibodies isolated at 5 to 12 months following vaccination displayed greater potency and breadth, relative to those identified at 1.4 months. Notably, 15 out of 338 ([~]4.4%) antibodies isolated at 1.4[~]6 months after the primary vaccination showed extraordinary neutralization potency against SARS-CoV-2 omicron BA.1, despite the absence of BA.1 neutralization in serum. Two of them, 25F9 and 20A7, neutralized authentic clade Ia sarbecoviruses (SARS-CoV, WIV-1, SHC014) and clade Ib sarbecoviruses (SARS-CoV-2 D614G, SARS-CoV-2 BA.1, Pangolin-GD) with half-maximal inhibition concentrations of (0.85 ng/ml, 3 ng/ml, 6 ng/ml, 6 ng/ml, 42 ng/ml, 6 ng/ml) and (13 ng/ml, 2 ng/ml, 18 ng/ml, 9 ng/ml, 6 ng/ml, 345 ng/ml), respectively. Furthermore, 20A7 and 27A12 showed potent neutralization against all SARS-CoV-2 variants of concern and multiple Omicron sublineages, including BA.1, BA.2, BA.3, BA.4/5, BQ.1, BQ.1.1 and XBB variants. X-ray crystallography studies revealed the molecular basis of broad and potent neutralization through targeting conserved RBD sites. In vivo prophylactic protection of 25F9, 20A7 and 27A12 was confirmed in aged Balb/c mice. Notably, administration of 25F9 provided complete protection against SARS-CoV-2, SARS-CoV-2 BA.1, SARS-CoV, and SHC014 challenge, underscoring that these mAbs are promising pan-sarbecovirus therapeutic antibodies. One Sentence SummaryExtremely potent pan-sarbecovirus neutralizing antibodies

immunology↗

bioRxiv2023

Preneoplastic cells switch to Warburg metabolism from their inception exposing multiple vulnerabilities for targeted elimination

Otto Warburg first described tumour cells as displaying enhanced aerobic glycolysis whilst maintaining defective oxidative phosphorylation (OXPHOS) for energy production almost 100 years ago 1,2. Since then, the Warburg effect has been widely accepted as a key feature of rapidly proliferating cancer cells3,4. Targeting cancer metabolism is now being considered as a promising precision oncology therapeutic approach5. What is not clear is how early "Warburg metabolism" initiates during cancer progression and whether changes in energy metabolism might influence tumour progression ab initio. We set out to investigate energy metabolism in HRASG12V driven preneoplastic cell (PNC) at inception, in a zebrafish skin PNC model; and to test how the impact of manipulating energy metabolism in the whole animal may impact PNC initiation. We find that, within 24 hours of HRASG12V induction, PNCs upregulate "Warburg metabolism", and that this is required for their expansion. We show that blocking glycolysis reduces PNC proliferation, whilst increasing available glucose both enhances PNC proliferation and also reduces apoptosis. Impaired OXPHOS of PNCs might be exploited therapeutically since a mild complex I inhibitor, metformin, selectively induces apoptosis and suppresses proliferation of PNCs. In addition, we find mitochondrial fragmentation in PNCs occur prior to metabolic alteration and this is important for their survival since exposure to Drp1/Dnml1 inhibitor, mdivi, which blocks mitochondrial fragmentation leads to enhanced PNC apoptosis. Our data indicate that altered energy metabolism is one of the earliest events upon oncogene activation in somatic cells, which provide a targeted and effective tumour prevention therapy. Key findingsO_LIGlycolysis is upregulated in HRASG12V expressing preneoplastic cells (PNCs) in zebrafish skin, and is required for PNC proliferation C_LIO_LIOXPHOS respiration is impaired in PNCs and metformin complex I inhibition specifically eliminates PNCs C_LIO_LIPNC undergo mitochondrial fragmentation and exhibit reduced membrane potential C_LIO_LIMdivi reverses mitochondrial fragmentation in PNCs and triggers apoptosis C_LI

cancer biology↗

bioRxiv2023

Structural insights into transcription activation mechanism of the global regulator GlnR from actinobacteria

GlnR, an OmpR/PhoB subfamily protein, is an orphan response regulator that globally coordinates the expression of genes responsible for nitrogen, carbon and phosphate metabolism in actinobacteria. Although much efforts at biochemical and genetic analyses have been made on the mechanism of GlnR-dependent transcription activation, it still remains unclear owing to lacking the structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a crystal structure of a binary complex including a C terminal DNA binding domain of GlnR (GlnR_DBD) and its regulatory cis-element DNA, and a cryo-EM structure of GlnR-TAC comprising of Mycobacterium tuberculosis RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures show four GlnR protomers coordinately engage promoter DNA in a head-to-tail manner, with two N-terminal receiver domains of GlnR (GlnR-RECs) jointly act as a bridge to connect RNAP NTD with the upstream GlnR_DBD. GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved {beta} flap, {sigma}AR4, CTD, NTD domains of RNAP. These are in good agreement with our mutational and kinetic single-molecule fluorescence assays. Altogether, our results reveal a general transcription activation mechanism for the global regulator GlnR and other OmpR/PhoB subfamily proteins, and present a unique mode of bacterial transcription regulation. Significance statementIn low-GC gram-negative bacteria, the typical two component system NtrB/NtrC accounts for the expression of genes related to nitrogen metabolism. In high-GC gram-positive actinobacteria, GlnR, an atypical and orphan response regulator (RR) of the OmpR/PhoB subfamily proteins, globally coordinates transcription of genes involved in nitrogen, carbon and phosphate metabolism. Here, using crystallography, cryo-electron microscopy, and single-molecule fluorescence assays, we show that GlnR activates transcription by contacting DNA between the -10 and -35 elements and further upstream through contacting {sigma} region 4 and RNAP {beta} flap subunit. We also identify a previously unobserved cooperative engagement of four GlnR protomers to the promoter DNA, which not only makes the transcription initiation complex (RPo) more stable, but also provides better transcription activities.

biochemistry↗

bioRxiv2023

Fluorescence Image Data with Sparse and Low-Rank Poisson Regression

Multispectral biological fluorescence microscopy has enabled the identification of multiple targets in complex samples. The accuracy in the unmixing result degrades (1) as the number of fluorophores used in any experiment increases and (2) as the signal-to-noise ratio in the recorded images decreases. Further, the availability of prior knowledge regarding the expected spatial distributions of fluorophores in images of labeled cells provides an opportunity to improve the accuracy of fluorophore identification and abundance. We propose a regularized sparse and low-rank Poisson unmixing approach (SL-PRU) to deconvolve spectral images labeled with highly overlapping fluorophores which are recorded in low signal-to-noise regimes. Firstly, SL-PRU implements multi-penalty terms when pursuing sparseness and spatial correlation of the resulting abundances in small neighborhoods simultaneously. Secondly, SL-PRU makes use of Poisson regression for unmixing instead of least squares regression to better estimate photon abundance. Thirdly, we propose a method to tune the SL-PRU parameters involved in the unmixing procedure in the absence of knowledge of the ground truth abundance information in a recorded image. By validating on simulated and real-world images, we show that our proposed method leads to improved accuracy in unmixing fluorophores with highly overlapping spectra.

bioinformatics↗

bioRxiv2023

Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila

Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases and catalyze the transition of 5mC to 5hmC in DNA. These enzymes have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila as Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by mapping one, Tet DNA-binding sites throughout the genome and two, the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC modifications are distributed along the entire transcript, while Tet DNA-binding sites are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are preferentially involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs primarily in cells of the nervous system.

neuroscience↗

bioRxiv2023

Multi-omics analysis reveals the regulatory mechanism of flavonol biosynthesis during the formation of petal color in Camellia nitidissima

Camellia nitidissima is a prized woody flower with golden-yellow flowers, and has high ornamental, medicinal and economic value. Previous works indicated that the content of flavonol accumulated greatly during golden petal formation. However, the molecular mechanism of golden flower formation in C. nitidissima remains largely unknown. In this study, we performed an integrative anlysis of transcriptome, proteome and metablome of petals at five developmental stages to construct the regulatory network during golden flower formation in C. nitidissima. Metablome anlysis showed that two flavonols, the quercetin and kaempferol glycosides, were highly accumulated in the golden petals. Furthermore, transcriptome and proteome sequencing suggested that the expression of flavonol biosynthesis genes or proteins was increased in golden petal stage, whereas expression of anthocyanin and proanthocyanidin genes or proteins were decreased. Six MYB and 20 bHLH genes were identified as potentially involved in flavonoid biosynthesis, and the brassinosteroid (BR) and jasmonate (JA) pathways were positively and negatively corretated with flavonol biosynthesis, respectively. Network correlation analysis suggested close relationships among BR and JA, MYB and bHLH, and the flavonoid pathway and flavonoid metabolites. Overall, this study shows a potential regulatory mechanism of flavonol biosynthesis duing golden petal formation in C. nitidissima. HighlightThe BR and JA pathway may positively and negatively regulate flavonol synthesis in Camellia nitidissima, respectively.

molecular biology↗

bioRxiv2022

Hematopoietic-specific heterozygous loss of Dnmt3a exacerbates colitis-associated colon cancer

Clonal hematopoiesis (CH) is defined as clonal expansion of mutant hematopoietic stem cells absent diagnosis of a hematologic malignancy. Presence of CH in solid tumor patients, including colon cancer, correlates with shorter survival. We hypothesized that bone marrow-derived cells with heterozygous loss-of-function mutations of DNMT3A, the most common genetic alteration in CH, contribute to the pathogenesis of colon cancer. In a mouse model that combines colitis-associated colon cancer with experimental CH driven by Dnmt3a+/{Delta}, we found higher tumor penetrance and increased tumor burden compared to controls. Histopathological analysis revealed accentuated colonic epithelium injury, dysplasia and adenocarcinoma formation. Transcriptome profiling of colon tumors identified enrichment of gene signatures associated with carcinogenesis, including angiogenesis. Treatment with the angiogenesis inhibitor axitinib eliminated the colon tumor-promoting effect of experimental CH driven by Dnmt3a haploinsufficiency. This study provides conceptually novel insights into non-tumor-cell-autonomous effect of hematopoietic alterations on colon carcinogenesis and identifies potential therapeutic strategies. SUMMARYA pre-clinical mouse model demonstrates that genetic alterations in the blood system characteristic of clonal hematopoiesis (CH) contribute to an aggressive solid tumor phenotype. It further identifies cancer angiogenesis as a potential therapeutic target to mitigate adverse CH effects.

cancer biology↗

bioRxiv2022

New mitochondrial genomes of leptosporangiate ferns allow modeling the mitogenomic inflation syndrome across all land plant lineages

Plants mitochondrial genomes (mitogenome) evolve in a hard-to-predict fashion. To reconstruct the evolutionary trajectories of land plant mitogenomes, we, here, filled the last major mitogenomic gap within land plants by assembling the mitogenomes of the leptosporangiate ferns Azolla filiculoides and Pteridium revolutum and, secondly, analyzed the mitogenomic evolutionary regime shifts across land plants. By testing various Ornstein-Uhlenbeck stabilizing selection models in an a priori-free analysis of five selected mitogenomic traits, we observed 71 evolutionary regime shifts across 218 land plant species. These shifts can lead to genomic convergence, in which certain traits such as size, GC content, and the proportion of non-coding DNA converge, or non-converging regimes, which are characterized by exceptional paths of genomic evolution such as extreme GC content or size. We also found that non-seed plants have a slightly, but significantly, higher rate of synonymous substitutions across all gene classes than seed plants, and that ferns differ significantly in the number of nonsynonymous and synonymous changes compared with other non-seed and seed plants. This pattern matches an outstandingly high rate of RNA editing in the small but repeat-rich mitogenomes of leptosporangiate ferns. In sum, our study highlights the considerable changes in mito-chromosomal architecture that occur during land plant evolution and suggests that these changes may be related to increases in error-prone repair mechanisms. Further study of underrepresented plant groups such as ferns and lycophytes is needed to understand the mechanisms and dominating forces behind the evolutionary dynamics and the mitogenomic inflation syndrome. Significance StatementOur study provides new insights into the complexity and diversity of land plant mitogenome evolution and reveals that they take many turns of molecular evolutionary directions across 218 land plant species. Our results have the potential to inform future research in this area and to advance our understanding of the mitogenomic inflation syndrome during plant evolution.

evolutionary biology↗

bioRxiv2022

Benchmarking single-cell hashtag oligo demultiplexing methods

Sample multiplexing is often used to reduce cost and limit batch effects in single-cell RNA sequencing (scRNA-seq) experiments. A commonly used multiplexing technique involves tagging cells prior to pooling with a hashtag oligo (HTO) that can be sequenced along with the cells RNA to determine their sample of origin. Several tools have been developed to demultiplex HTO sequencing data and assign cells to samples. In this study, we critically assess the performance of seven HTO demultiplexing tools: hashedDrops, HTODemux, GMM-Demux, demuxmix, deMULTIplex, BFF and HashSolo. The comparison uses data sets where each sample has also been demultiplexed using genetic variants from the RNA, enabling comparison of HTO demultiplexing techniques against complementary data from the genetic "ground truth". We find that all methods perform similarly where HTO labelling is of high quality, but methods that assume a bimodal counts distribution perform poorly on lower quality data. We also suggest heuristic approaches for assessing the quality of HTO counts in a scRNA-seq experiment.

bioinformatics↗