Biology subjects

Lopes, R.

Publications and source records attributed to Lopes, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Tracking two decades of global dengue virus lineage dynamics

Dengue virus (DENV) is genetically diverse, consisting of four antigenically distinct serotypes and extensive sub-serotype variation that can influence epidemiology and control. As DENV continues to expand globally, there is an urgent need to characterize the dynamics of distinct DENV genetic lineages, including their persistence, establishment, and spread. Using a standardized DENV lineage nomenclature system and 37,828 publicly available DENV genomes sampled from 2000-2024, we classified sequences across nine global regions to construct a comprehensive resource of regional lineage distributions over time. We found marked regional differences in lineage diversity, with higher lineage richness in Southeast and East Asia than in the Americas. We further showed that COVID-19-related disruptions were associated with decreased regional lineage persistence and detection of new lineages during 2020-2021, followed by rebounds after 2022 and, in some regions, substantial lineage turnover. Finally, we identified a small set of globally expansive (cosmopolitan) lineages that are over-represented in available sequences, including five first-order minor lineages detected in at least seven of nine regions: 3III_B.3, 2II_F.1, 2II_A.1, 1III_A.3, and 1I_K.3. Together, these results demonstrate how standardized lineage classification enables global tracking of emerging DENV diversity and supports targeted genomic surveillance.

bioinformatics↗

bioRxiv2026

Phylodynamic analysis reveals asymmetric and accelerating global spread of dengue virus

Dengue virus (DENV) continues to expand globally, with increasing incidence in both endemic and non-endemic countries. Leveraging a large global dataset of DENV genomes starting from the 1940s, we reconstructed global and regional patterns of DENV spread using phylogeographic and phylodynamic methods. Our analyses reveal that the current global diversity of urban DENV originated in Asia in the first half of the 20th century. During the more than 100 years since, we find that the highest density of between-country spread occurs within Asia and the region continues to be a global source, seeding transmission in Africa and the Americas. Global spread is, however, not balanced. Even though there is more travel to South America, we show that DENV lineages primarily enter North America (mostly from South Asia) through a link defined by seasonal synchrony across the Northern Hemisphere. Along with a substantial increase in global travel starting ~2010, the rate of spread to the Americas is increasing, establishing new lineages associated with large recent outbreaks. DENV lineages do not frequently spread back to Asia from the Americas or Africa, and we posit this is due to higher genetic diversity in Asia, leading to stiffer competition for invading lineages. Within the Americas, the network of DENV dispersal initiates in North America, primarily the Caribbean, and then is maintained by major hubs in South America. Overall, we find that travel volume, rather than climate factors, is mostly responsible for long-term patterns of DENV spread globally and within the Americas. Our results highlight key nodes in the global dynamics of DENV lineages, and suggest spread will continue to accelerate in a more connected world.

genomics↗

bioRxiv2026

The cytokine structural homologs IL-1β and IL-1Ra have distinct dynamical character that potentially influence their roles in allosteric regulation of the IL-1 receptor.

Interleukin-1{beta} (IL-1{beta}) and the interleukin-1 receptor antagonist (IL-1Ra) share the {beta}-trefoil fold, engage the same receptor (IL-1R), but produce opposite biological outcomes. IL-1{beta} recruits the accessory protein IL-1RAcP to initiate inflammatory signaling while IL-1Ra occupies the receptor without supporting co-receptor recruitment. Seeking the origin of this divergence in properties not apparent from static structures, we used solution NMR relaxation to characterize fast internal motion in both proteins. Rigorous treatment of macromolecular tumbling shows both to be nearly maximally triaxial, which admits two near-degenerate axially symmetric solutions. This ambiguity was propagated throughout and found to have negligible impact. Complete replicate data sets from independently prepared IL-1{beta} samples establish the experimental precision directly. Backbone amide and methyl-bearing side chain order parameters are indistinguishable between the two proteins, the latter averaging 0.484 {+/-} 0.030 and 0.486 {+/-} 0.033, indicating essentially equivalent residual conformational entropy. Their spatial distributions are uncorrelated when projected onto the shared fold. Importantly, the difference between the proteins is concentrated at the receptor interface, where methyl probes lying on the IL-1{beta} footprint are considerably more mobile than those of IL-1Ra. It is therefore the agonist, not the antagonist, that presents an anomalously mobile binding surface. IL-1Ra also buries some 16% less surface while ostensibly binding IL-1R more tightly, the signature of an interface predisposed toward productive contact. Conformational entropy can thus distinguish protein function where structure and average flexibility are conserved, and the distinction resides not in how much entropy a protein has but in where it is kept.

biophysics↗

bioRxiv2026

Circulating Cell-Free Chromatin Particles Trigger a Unique Biphasic STING Signaling Program that Drives DNA Damage and Inflammation

Cell death, DNA damage, and inflammation are closely interconnected processes implicated in ageing, cancer, and inflammatory disorders, yet the endogenous mechanisms linking them remain unclear. We previously identified cell-free chromatin particles (cfChPs), released from dying cells, as biologically active entities that enter neighboring cells and induce DNA damage and inflammation. Here, we show that serum-derived circulating cfChPs are rapidly internalized by human peripheral blood mononuclear cells and trigger a previously unrecognized biphasic STING signaling response. An early phase involves rapid STING trafficking to the perinuclear region and nucleus, with activation of IRF3 and NF-{kappa}B preceding detectable DNA damage. This is followed by a later phase characterized by STING phosphorylation, puncta formation, persistent DNA damage, and robust inflammatory cytokine production. Pharmacological inhibition or genetic deletion of STING markedly attenuated these responses. These findings identify extracellular cfChPs as endogenous DNA-damaging agents and reveal biphasic STING signaling as a mechanistic link between cell death, DNA damage, and sterile inflammation. One-sentence summaryCirculating cell-free chromatin particles released from dying cells trigger a previously unrecognized biphasic STING signaling program that mechanistically links cell death to DNA damage and sterile inflammation, providing a potential basis for aging, cancer, and inflammatory diseases.

immunology↗

bioRxiv2026

Modulation of Avian Iridescence via Malanogenesis

The iridescent colors of birds originate in nanoscale feather structures that interact with light. Although the physical principles governing avian iridescence are well-established, the molecular mechanisms assembling these nanostructures into photonic materials remain unknown. Here, we integrated genomic, cellular, and optical approaches to investigate the molecular basis of iridescent color formation in birds. We leveraged mutations that arose in the domesticated Indian peafowl and natural color variation in wild birds. In peafowl, we identified eight genes underlying gains, losses, and shifts of iridescence, whereas in two wild species, we used single-cell transcriptomics to profile asymmetric feathers in which iridescent and non-iridescent barbules develop on opposite sides of the same feather. We found that all peafowl mutations mapped to melanogenesis genes, showing that variation in this pathway can modify diverse geometric features of feather photonic nanostructures. Mutations altering melanin composition collapsed multilayered photonic systems and yielded non-iridescent tissues, whereas changes in melanosome abundance, elongation, or deposition timing generated multilayer architectures with variable periodicity and color. We further show in peafowl that transitions from non-iridescent to iridescent plumage were associated with single-nucleotide mutations in a melanogenesis gene, suggesting that, in species already capable of forming multilayered nanostructures, iridescence can be gained by relatively small genetic changes. Single-cell transcriptomes from wild species also supported extensive melanocyte-centered regulatory rewiring associated with iridescence, including changes in melanosome maturation, trafficking, and intercellular signaling. Together, these results show that the nanoscale order underlying iridescence is developmentally plastic and highly responsive to the melanogenic environment. Significance StatementBird feathers can produce brilliant, shifting colors, but how these colors form during development has remained poorly understood. By comparing the genomes of color variants of domesticated peafowl and transcriptomes during feather development in wild birds, and combining these with chemical and optical analyses, we show that mutations in genes associated with melanogenesis can profoundly alter the amount, shape, and arrangement of the melanin granules inside feathers that interact with light and produce iridescence. These changes can switch feather appearance between dull and iridescent, or generate entirely new colors by restructuring how those granules are layered at the microscopic scale. Our results reveal a direct and flexible link between pigment production and the physical structures that generate iridescence in birds.

evolutionary biology↗

bioRxiv2026

Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology

Jamestown Canyon virus (JCV) is a re-emerging mosquito-borne virus of increasing concern in North America. It has been historically understudied, leading to significant gaps in our understanding of its evolutionary history, ecological maintenance, and transmission dynamics. Here, we generated 658 whole-genome JCV sequences from the Northeast United States, including 84% (500/597) of all JCV-positive mosquitoes detected in Connecticut from 1997-2022. Then we applied phylodynamic methods to demonstrate how mosquito phenology and host interaction structure the persistence and spread of JCV. Our phylogenetic analyses estimate that JCV was introduced in the Northeast by at least the early 1700s and the primary introductions of lineages A and B into Connecticut occurred during the mid-1800s to mid-1900s. Further, we estimate that JCV evolves at a rate of [~]3 x 10-5 s/s/y, making it one of the slowest evolving known RNA viruses, because the virus spends [~]10 months per year in evolutionary stasis while over-wintering in mosquito eggs. To investigate ecological drivers of JCV spread in Connecticut, we paired discrete trait and continuous phylogeographic reconstructions with mosquito surveillance data. We estimate that JCV has a low diffusion rate of [~]30-60 km2/year, which is more similar to slow-moving tick-borne viruses than other mosquito-borne viruses. We found that univoltine Aedes mosquitoes were likely to maintain the virus across years through overwintering in eggs, accounting for its slow evolution and dispersal, while multivoltine mosquitoes contribute to periodic bursts of spatial diffusion and amplification within seasons. By characterizing seasonal dynamics of JCV, we demonstrate the utility of dense sequencing and phylodynamics to disentangle complex transmission cycles, offering a framework to rapidly advance our evolutionary and ecological knowledge of understudied viruses.

ecology↗

bioRxiv2025

Apoptosis reveals human evolutionary heritage sequestered in non-coding DNA

Cell-free chromatin particles (cfChPs), primarily derived from non-coding DNA (ncDNA) and released from apoptotic cells into the bloodstream, can be horizontally transferred into living cells. However, their potential role in generating ncDNA within recipient cells remains unknown. We previously reported that cfChP- sized fragments generated upon sonicating high-molecular-weight DNA can indiscriminately transmit themselves into foreign cells across species and kingdom boundaries. We hypothesized that cfChP-like DNA-protein complexes generated following organismal death have been exchanged among species and have progressively accumulated to form a dense patchwork that now constitutes the ncDNA, and that apoptosis may dissociate these complexes, rendering them amenable to detection. To test this hypothesis, we used species-specific DNA fluorescent in situ hybridisation probes and antibodies against archaea, eubacteria, plants, algae, fungi, protozoa, Drosophila, fish, chicken, mouse, rat, pig, dog, and monkey on intact and apoptotic human cells. We detected no reactivity with intact cells but strong reactivity with the ncDNA component of apoptotic cells. These findings indicate that ncDNA represents a dense conglomeration of DNA-protein complexes derived from different species that become detectable following apoptosis. This suggests that human evolutionary heritage is conserved within ncDNA formed through progressive accumulation of genetic fragments transferred horizontally following organismal death.

evolutionary biology↗

bioRxiv2025

Bridging Gaps in Soil Ecology: Metagenomic Insights into Microbial Diversity and Functionality Across Brazil's Biomes.

Microorganisms participate in complex interactions involving different kingdoms, so rhizosphere biodiversity mapping is essential for understanding how microbes interact with each other in the soil and with roots. Although soil microbial communities are remarkably diverse and technological advances have provided a high capacity to acquire reliable sequence data, unique microbial taxa in soil, root and rhizosphere samples remain poorly described. For the first time, we organized a consortium to collect soil samples covering all Brazilian biomes, providing a comprehensive and unprecedented view of soil microbial diversity. This understanding is critical, especially within the context of climate change, which affects plant physiology, root exudation and, consequently, the composition and functionality of soil microbial communities. The interactions between soil, roots and rhizosphere are influenced by evolutionary and adaptive forces and shape the production of microbial natural products, which exhibit great therapeutic potential and Mapping and studying rhizosphere microbial biodiversity not only increases our knowledge of soil ecology but also offers valuable insights for developing sustainable practices. We employed both 16S/18S/ITS amplicon and metagenomic short-read shotgun sequencing methods to examine and catalogue the large-scale genomes of culture-independent rhizosphere microbes and their interactions with roots in six terrestrial Brazilian biomes, namely, the Amazon, Atlantic Forest, Cerrado, Caatinga, Pampa and Pantanal. Our results revealed the ubiquity of Proteobacteria, which reflects their adaptability to contrasting environments. Biomes with greater moisture availability, such as the Amazon and Pantanal, exhibited greater diversity and abundance of fast-growing bacteria, such as Proteobacteria, and nutrient cyclers, such as Thaumarchaeota. Arid and semiarid biomes, such as the Caatinga, were dominated by microorganisms tolerant to drought and nutrient-limited environments, such as Actinobacteria. Acidobacteria, which thrive in acidic, nutrient-poor soils, were very abundant in forest biomes. The Planctomycetes phylum also occurred more frequently in areas with a relatively high soil organic matter content, such as the Cerrado. Bacteroidetes was significantly more abundant in Pampa than in the other biomes. The results provide comprehensive insights into soil, root and rhizosphere biodiversity and not only enhance the knowledge of the fundamental biological processes sustaining plant life but also constitute a reliable sequencing databank to address present-day agricultural and environmental challenges.

microbiology↗

bioRxiv2024

Induction of pluripotent oncogenic stem cells from mouse fibroblasts

Natural biological agents that can transform normal somatic cells into cancer stem cells, have not been identified. We earlier reported that cell free chromatin particles (cfChPs) that circulate in blood of cancer patients can horizontally transfer themselves to healthy cells to induce dsDNA breaks and inflammation. Here we show that a single cell clone D5 developed from NIH3T3 mouse fibroblast cells treated with cfChPs isolated from sera of cancer patients exhibited upregulation of stemness related transcription factors and surface markers, and the ability to form spheroids in appropriate culture medium. Transcriptome analysis revealed upregulation of cancer related pathways including invasion, metastasis and stemness. Subcutaneous inoculation into SCID mice resulted in development of malignant tumors which expressed all three germline markers. Our results suggest the cfChPs that circulate in blood of cancer patients are oncogenic and can transform susceptible somatic cells into cancer stem cells with the potential to promote metastasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/622204v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@4288org.highwire.dtl.DTLVardef@1102d4borg.highwire.dtl.DTLVardef@10daaf6org.highwire.dtl.DTLVardef@53084d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Cell-free chromatin particles damage genomic DNA of healthy cells via an ROS-independent mechanism

Several hundred billion cells die daily in the human body, releasing cell-free chromatin particles (cfChPs) in the process, which then enter the blood circulation and get taken up by healthy cells. We have previously reported that, these internalized cfChPs damage genomic DNA as well cause physical damage to mitochondria, resulting in increased mitochondrial ROS production. In the current study, we evaluated the potential damaging effects of the cfChP-induced increase in ROS production on genomic DNA. NIH3T3 mouse fibroblast cells were treated with cfChPs isolated from the sera of healthy individuals (H-cfChPs) or patients with cancer (C-cfChPs) in the presence or absence of the ROS scavenger Mito-TEMPO. The pre-incubation of cfChP-treated cells with Mito-TEMPO abolished ROS production, but did not prevent genomic DNA damage induced by H-cfChPs and C-cfChPs. Our results suggest that cfChP-induced genomic DNA damage occurs in an ROS-independent manner. These findings align with emerging evidence suggesting that mitochondrial ROS may not be a direct cause of genomic DNA damage and suggest that DNA damage attributed to ROS may in-fact be induced by cfChPs. This possibility opens up new therapeutic approaches involving deactivation of cfChPs to retard ageing and other degenerative conditions traditionally attributed to oxidative stress.

cell biology↗

bioRxiv2024

Large-scale genomic analysis of SARS-CoV-2 Omicron BA.5 emergence in the United States

The COVID-19 pandemic is marked by the continuing emergence of novel SARS-CoV-2 variants. Questions remain about the mechanisms with which these lineages establish themselves in new geographical areas. In this study, we performed a discrete phylogeographic analysis on [~]19,000 SARS-CoV-2 sequences of Omicron BA.5 lineages between February and June 2022 to better understand how it emerged in different regions of the United States (U.S.). We found that the earliest introductions came from Africa, the putative origin of the variant, but the majority were from Europe, correlating with the high volume of air travelers. Additionally, the analysis revealed extensive domestic transmission between different regions of the U.S. driven by population size and cross-country transmission. Results suggest that most of the within-U.S. spread was between three regions that include California, New York, and Florida. Our results form a framework for understanding novel SARS-CoV-2 variant emergence in the U.S.

genomics↗

bioRxiv2023

Horizontally transferred cell-free chromatin particles function as miniature predatory genomes and vehicles for transposable elements within host cells

BackgroundHorizontal gene transfer (HGT) plays an important evolutionary role in prokaryotes, but it is thought to be less frequent in mammals. We previously reported that cell-free chromatin particles (cfChPs) - chromosomal fragments released from the billions of dying cells that circulate in human blood - are horizontally transferred to healthy cells with biological effects. However, the underlying mechanism and function of these effects remained unclear. MethodsWe treated NIH3T3 mouse fibroblasts cells with cfChPs isolated from human serum and serially passaged the cells. The intracellular activities of cfChPs were analysed using chromatin fibre fluorography, cytogenetic analysis, immuno-fluorescence and fluorescent in situ hybridisation. ResultsWe discovered that the internalised cfChPs were almost exclusively comprised of non-coding DNA, and the disparate DNA sequences contained within them had randomly combined to form complex concatemers some of which were ostensibly multi-mega base pairs in size. The concatemers exhibited variable and bizarre spatial relationships with the host cell interphase DNA with many remaining in the cytoplasm and others aligning themselves with the mouse chromosomal DNA. The concatemers autonomously performed many functions attributable to the nuclear genome. Being associated with DNA polymerase, the concatemers could synthesize DNA and autonomously replicate themselves without heed to the mitotic cycle of the host cell. They could synthesise RNA, RNA polymerase, ribosomal RNA, ribosomal proteins, and generate numerous human proteins, including oncogenes, within the mouse cells which manifested as complex and highly amplified multi-peptide fusion proteins. The concatemers harboured human LINE-1 and Alu elements, which being associated with DNA polymerase, reverse transcriptase and transposes could markedly amplify themselves and increase their copy number with time in culture with the potential to rearrange themselves within the mouse genome. The above findings were reproducible in four other cell lines derived from different species suggesting that horizontal transfer of cfChPs may be a universal phenomenon. ConclusionsOur results lead us to propose that: 1) a cell simultaneously harbours two autonomous genome forms: one that is inherited (hereditary genome) and numerous others that are acquired (satellite genomes); 2) satellite genomes may potentially have evolutionary functions given their ability to serve as vehicles for transposable elements and to generate a plethora of novel proteins; 3) transposable elements are "foreign" genetic elements that are acquired from dying cells via HGT; 4) non-coding DNA has many hidden biological functions that remain dormant but are activated following cellular apoptosis to become detectable in association with the cfChP concatemers; 5) "within-self" HGT occurs in mammals on a massive scale via the medium of cfChP concatemers that have undergone extensive and complex modifications resulting in their behaviour as "foreign" genetic elements. Video Abstracthttps://drive.google.com/file/d/1I6NbrYmT9BRM63ywYj47AU0O9WJ_NrcR/view?usp=drive_link

evolutionary biology↗

bioRxiv2023

Expanding the Drosophila toolkit for dual control of gene expression

The ability to independently control gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as the LexA-system or QF-system. Here, we describe a resource of reagents that facilitate combined use of the GAL4/UAS and a second binary system in various Drosophila tissues. Focusing on genes with well-characterizsed GAL4 expression patterns, we generated a set of more than 40 LexA-GAD and QF2 insertions by CRISPR knock-in and verified their tissue-specificity in larvae. We also built constructs that encode QF2 and LexA-GAD transcription factors in a single vector. Following successful integration of this construct into the fly genome, FLP/FRT recombination is used to isolate fly lines that express only QF2 or LexA-GAD. Finally, using new compatible shRNA vectors, we evaluated both LexA and QF systems for in vivo gene knockdown and are generating a library of such RNAi fly lines as a community resource. Together, these LexA and QF system vectors and fly lines will provide a new set of tools for researchers who need to activate or repress two different genes in an orthogonal manner in the same animal.

genetics↗

bioRxiv2023

Cell-free chromatin from dying cells trigger an immune response via the cGAS-STING pathway

It is long established that cell death and immune response are closely related, although the nature of this relationship has remained unclear. We earlier reported that cell-free chromatin particles (cfChPs) released from the billions of cells that die in the body every day to enter into the blood circulation, or those that are released locally from dying cells, can readily enter into healthy cells to induce DNA damage and activate inflammatory cytokines. In this study we investigated whether cfChPs from dying cells might be the missing link between cell death and immune response. We treated human lymphocytes with cfChPs isolated from sera of healthy individuals or with cfChPs released from hypoxia-induced dying lymphocytes. We observed that cfChPs from both sources readily entered into lymphocytes to accumulate in their nuclei within 2 h. This was associated with marked activation of CD69 and release of inflammatory cytokines, as well as of p-STING and cGAS expression. The addition of the STING protein inhibitor H151 to the cfChPs treated cells abolished the release of inflammatory cytokines. These findings lead us to suggest that cfChPs from dying cells are the critical triggers of immune response which act via cGAS-STING pathway.

immunology↗

bioRxiv2023

Cell-free chromatin particles activate immune checkpoints in human T cells: Implications for cancer therapy

Immune checkpoint blockade is an exciting breakthrough in cancer therapy, but how immune checkpoints are activated is unknown. We have earlier reported that cell-free chromatin particles (cfChPs) that circulate in the blood, or those that are released locally from dying cells, are readily internalized by healthy cells with biological consequences. Here we show that treatment of human lymphocytes with cfChPs isolated from sera of cancer patients led to marked activation of immune checkpoints viz. PD-1, CTLA-4, LAG-3, NKG2A, and TIM-3. Concurrently activated were stress-related markers cJun, cFos, JunB, FosB, NF[Kcy]B, and EGR1. The above immune checkpoints were also activated when lymphocytes were treated with cfChPs released from dying HeLa cells; the latter could be abrogated by three cfChPs deactivating agents. These results suggest that immune checkpoints are activated by lymphocytes as stress response to cfChPs. Simultaneous downregulation of multiple immune checkpoints may herald a new approach to immunotherapy of cancer. Statement of SignificanceWe show that cell-free chromatin particles (cfChPs) that circulate in the blood of cancer patients, or those released from dying cancer cells, simultaneously activate five immune checkpoints as a stress response by human lymphocytes. Activation of checkpoints was abrogated by cfChPs deactivating agents suggesting a novel approach to cancer treatment.

immunology↗

bioRxiv2022

Genetic and epigenetic driven variation in regulatory regions activitycontribute to adaptation and evolution under endocrine treatment

Comprehensive profiling of hormone-dependent breast cancer (HDBC) has identified hundreds of protein-coding alterations contributing to cancer initiation1, 2, but only a handful have been linked to endocrine therapy resistance, potentially contributing to 40% of relapses1, 3-9. If other mechanisms underlie the evolution of HDBC under adjuvant therapy is currently unknown. In this work, we employ integrative functional genomics to dissect the contribution of cis-regulatory elements (CREs) to cancer evolution by focusing on 12 megabases of non-coding DNA, including clonal enhancers10, gene promoters, and boundaries of topologically associating domains11. Massive parallel perturbation in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance12, 13 and endocrine therapy resistance9. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies non-coding changes involved in therapy resistance. Overall, our data uncover actionable transient transcriptional programs critical for dormant persister cells and unveil new regulatory nodes driving evolutionary trajectories towards disease progression.

cancer biology↗

bioRxiv2022

Probabilistic modeling of ambient noise in single-cell omics data

Droplet-based single-cell omics, including single-cell RNA sequencing (scRNAseq), single-cell CRISPR perturbations (e.g., CROP-seq), and single-cell protein and transcriptomic profiling (CITE-seq) hold great promise for comprehensive cell profiling and genetic screening at the single-cell resolution. However, these technologies suffer from substantial noise, among which ambient signals present in the cell suspension may be the predominant source. Current models to address this issue are highly technology-specific and relatively scRNAseq-centric. while a universal model to describe the noise across these technologies may reveal this common source, improving the denoising accuracy. To this end, we explicitly examined these unexpected signals in multiple datasets across droplet-based technologies, summarised a predictable pattern, and developed single-cell Ambient Remover (scAR) - a hypothesis-driven machine learning model to predict and remove ambient signals (including mRNA counts, protein counts, and sgRNA counts) at the molecular level. We benchmarked scAR on three technologies - single-cell CRISPR screens, CITE-seq, and scRNAseq along with the state-of-the-art single-technology-specific approaches. scAR showed high denoising accuracy for each type of dataset.

bioinformatics↗

bioRxiv2021

Cell-free chromatin particles released from dying cells inflict mitochondrial damage and ROS production in living cells

mtDNA damage and the resultant oxidative stress are associated with neurodegenerative diseases, ageing and cancer. However, what triggers mtDNA damage remains unclear. We have reported that cell-free chromatin particles (cfChPs) that are released from the billions of cells that die in the body every day can readily enter into healthy cells and damage their DNA. We show here that cfChPs isolated from sera of healthy individuals, or those that are released from dying cells, inflict direct physical damage mtDNA leading to marked activation of ROS. The latter could be abrogated by concurrent treatment with three different cfChPs deactivating agents. Given that 1x109-1x1012 cells die in the body every day, our findings suggest that cfChPs from dying cells are major physiological triggers for mtDNA damage and ROS production. Deactivation of cfChPs may provide a novel therapeutic approach to retard ageing and associated degenerative conditions that have been linked to oxidative stress.

biochemistry↗