Biology subjects

Dai, J.

Publications and source records attributed to Dai, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Morphological Identification of Ticks in district Swabi, Mardan, and Charsadda

Ticks are ectoparasitic arthropods that play a significant role in transmitting pathogens to humans and animals. This study aimed to address the research gap in understanding the morphological diversity and distribution of tick species in Swabi, Mardan, and Charsadda districts of Pakistan, where tick-borne diseases are prevalent but poorly documented. The primary objectives were to identify tick species, document their morphological characteristics, and map their distribution patterns across different habitats. Field surveys were conducted over nine months, collecting tick specimens from forests, grasslands, and residential areas. Specimens were preserved and analyzed using stereo-zoom microscopy and taxonomic keys for accurate classification. Key findings revealed a diverse tick fauna, including hard ticks (Ixodidae), with variations in body size, colour patterns, capitulum shape, and scutum features. Some species were widely distributed across all three districts, while others exhibited localized patterns. The study provides the first comprehensive morphological identification of tick species in these regions, highlighting their potential role in disease transmission. The implications of this research are significant for public health and disease control. The data can inform targeted interventions, enhance disease surveillance programs, and support the development of preventive measures to mitigate tick-borne diseases. By contributing to tick taxonomy and epidemiology, this study lays the groundwork for protecting public health in the study regions and beyond. This study addresses the lack of data on tick diversity in high-prevalence regions of Pakistan, providing critical insights for disease control and public health strategies. Limited information exists on the morphological diversity and distribution of tick species in Swabi, Mardan, and Charsadda districts. To identify tick species, document morphological characteristics, and map their distribution patterns in the study areas. Field surveys, specimen collection, stereo-zoom microscopy, and taxonomic classification were employed over nine months. Diverse tick fauna was identified, including hard ticks, with variations in morphology and distribution. Some species were widespread, while others were localized, highlighting potential disease transmission risks. The findings support targeted interventions, disease surveillance, and preventive measures, contributing to public health protection and tick-borne disease control in the region.

zoology↗

bioRxiv2025

Fast and accurate tree of blobs reconstruction under the network multispecies coalescent

Hybridization between species is an important force in evolution, commonly modeled by the network multispecies coalescent. Reconstructing evolutionary histories under this model is computationally challenging, even for level-1 networks where hybridization events are isolated. Divide-and-conquer is a promising path forward, but current methods with statistical guarantees rely on an estimated tree of blobs (TOB) for the network, which compresses the non-tree-like parts into single vertices. TOB reconstruction is itself challenging, with the only available method TINNiK having time complexity O(n5 + n4k) for k genes and n species. Here, we present a new framework for scalable TOB reconstruction with statistical guarantees. Our approach operates by (1) seeking a refinement of the TOB and then (2) contracting edges in it. For step (1), we show that any optimal solution to Weighted Quartet Consensus is a TOB refinement almost surely, as the number of genes goes to infinity, motivating the use of methods, such as ASTRAL or TREE-QMC. For step (2), we show that applying the same hypothesis tests as TINNiK to just O(n) four-taxon subsets around each edge is sufficient for statistical consistency when the underlying network is level-1. Leveraging TREE-QMC for the first step gives our method time complexity O(n3k) and its name: TOB-QMC. On simulated data, TOB-QMC typically matches or exceeds TINNiK in accuracy while being more scalable. TOB-QMC also enables fast exploration of non-tree-like evolution, as demonstrated through re-analysis of three phylogenomic data sets. Lastly, our study clarifies the theoretical utility of quartet-based species tree methods in the context of hybridization, which is critical given the recent result that ASTRAL can be misleading.

bioinformatics↗

bioRxiv2025

HIV-associated non-Hodgkin lymphoma tumor-microenvironment axes differ by EBV status across cellular origins

Non-Hodgkin Lymphoma (NHL) is the main cancer-related mortality for people living with HIV (PLWH). NHL genetic and molecular classifications have been intensely studied and correlated with clinical outcomes, but critical unanswered questions relevant to malignancy persist. For example, tumors positive for Epstein-Barr virus (EBV) are aggressive and account for 30-50% of HIV-associated NHLs, yet insights on the nature of EBV in NHL pathogenesis or potential therapeutic vulnerabilities have been limited. Here, we examined HIV-associated NHLs stratified by histopathologic classification, cell of origin (COO), molecular subtype, and EBV status using genome-wide spatial transcriptomic analyses. Tumor tissues in EBV+ HIV-NHLs displayed enriched expression of mitochondrial respiration and purine metabolism signatures versus EBV- tumors. Immune infiltration of EBV+ tumors was limited, and immune and stromal regions of EBV+ HIV-NHLs displayed upregulation of the gene for the iron exporter ferroportin (SLC40A1), indicating immunosuppressive macrophage polarization. An immunosuppressive SPP1-CD44 axis and oncogenic GAS6-AXL interaction between tumor and stroma were specifically predicted for EBV+ HIV-NHLs with plasmablastic features. Tumor microenvironment (TME) similarities to secondary lymphoid tissues such as inverse CXCL12-CXCL13 gradients and evidence of matching between tumor B cell phenotypes and reticular cell signatures were also observed. Finally, we developed a simple yet flexible approach to quantify expression gradients and cell proximity to annotated regions. Thus, this study highlights potential avenues for NHL therapy tailored by EBV status and provides a unique resource to examine tumor-TME interactions in the HIV-immunocompromised context. Key PointsO_LISpatial transcriptomic landscapes resolve cell-of-origin- and EBV-associated HIV-NHL heterogeneity including immunosuppressive myeloid responses to EBV+ tumors C_LIO_LISpatial gradients including CXCL12 and CXCL13 indicate that tumor-stromal interactions mimic lymphoid tissue organization and depend on B cell development stage C_LIO_LIDevelopment of a direction-agnostic method to calculate spatial expression gradients relative to annotated tissue and cell types of interest C_LIO_LIPredicted pharmacologic vulnerabilities in clinical samples are replicated in vitro and confirmed by small molecule screening C_LI

cancer biology↗

bioRxiv2025

IGP receptors act as redox sensors to mediate broad-spectrum disease resistance induced by cellooligomers

Cys-oxidation is a well-established post-translational regulator of intracellular protein function, yet its role in extracellular receptor-mediated signaling remains poorly understood. Here, we investigate the LRR-Malectin receptor-like kinase IGP1, a key receptor for plant cell wall damage-associated molecular patterns (DAMPs). We demonstrate that IGP1 directly recognizes cellooligomers with a degree of polymerization [≥] 3 via a conserved binding groove in its LRR domain, not the malectin domain as anticipated. Strikingly, a pair of cysteines within the malectin domain functions as a redox sensor, undergoing hydrogen peroxide-induced oxidation that sterically reduces ligand binding affinity and attenuates immune signaling. Phylogenetic analyses reveal that IGP originated after the terrestrialization of plants, and is an evolutionarily conserved redox sensor in land plants. Functional studies in Arabidopsis (Arabidopsis thaliana), wheat (Triticum aestivum), and soybean (Glycine max) confirm that the IGP-cellooligomer module confers broad-spectrum disease resistance. Our work uncovers a unique mechanism where ligand perception and redox sensing are integrated into a single receptor to regulate DAMP-triggered immunity.

plant biology↗

bioRxiv2025

Proteome profiling reveals HES1-driven mitotic catastrophe in ovarian serous carcinoma

Ovarian high-grade serous cancer (HGSC) is an aggressive subtype of epithelial ovarian cancer. Here, we identify BX-912, a phosphoinositide-dependent kinase 1 (PDPK1) inhibitor, as a promising therapeutic agent for HGSC. BX-912 suppressed HGSC growth as a single agent and synergized with olaparib independently of BRCA status. Unexpectedly, BX-912 treatment induced multinucleation, a phenotype not observed with other PDPK1 inhibitors. Proteome Integral Solubility Alteration (PISA) profiling revealed the transcription factor HES1 as a functional target of BX-912. Structural modeling showed that BX-912 binds the Orange domain of HES1, while its WRPW motif mediates interactions with protein partners, including the AP2 endocytic protein complex, coordinating their nuclear accumulation that leads to a mitotic catastrophe. Furthermore, cell cycle analyses showed that BX-912 combined with olaparib synergistically enhanced DNA damage and G2-M arrest. Our study demonstrates the value of proteomics for revealing hidden drug activities. It also identifies potential inhibition strategies for HES1, which is commonly overexpressed in HGSC. Additionally, this study proposes a novel strategy of targeting consecutive cell cycle phases to enhance treatment efficacy in HGSC.

cancer biology↗

bioRxiv2025

A single-cell transcriptomic atlas of the pigtail macaque placenta in late gestation

The placenta is a complex organ with multiple immune and non-immune cell types that promote fetal tolerance and facilitate the transfer of nutrients and oxygen. The nonhuman primate (NHP) is a key experimental model for studying human pregnancy complications, in part due to similarities in placental structure, which makes it essential to understand how single-cell populations compare across the human and NHP maternal-fetal interface. We constructed a single-cell RNA-Seq (scRNA-Seq) atlas of the placenta from the pigtail macaque (Macaca nemestrina) in the third trimester, comprising three different tissues at the maternal-fetal interface: the chorionic villi (placental disc), chorioamniotic membranes, and the maternal decidua. Each tissue was separately dissociated into single cells and processed through the 10X Genomics and Seurat pipeline, followed by aggregation, unsupervised clustering, and cluster annotation. Next, we determined the maternal-fetal origins of cell populations and analyzed single-cell RNA trajectory, Gene Ontology enrichment, and cell-cell communication. Single-cell populations in the pigtail macaque were strikingly similar in their identity and frequency to those found in the human placenta, including cells from trophoblast, stromal cell, immune, and macrophage lineages. An advantage of our approach was the deep sequencing of three tissues at the maternal-fetal interface, which yielded a rich diversity of common and rare single-cell populations. The third-trimester pigtail macaque single-cell atlas enables the identification of cellular subclusters analogous to those in humans and provides a powerful resource for understanding experimental perturbations on the NHP placenta.

genomics↗

bioRxiv2025

A spatiotemporal atlas of orchiectomy-induced androgen deprivation-mediated modulation of cellular composition and gene expression in the mouse prostate.

Androgen deprivation therapy (ADT) remains a cornerstone in the treatment of prostate cancer (PCa), yet most tumors eventually develop resistance. Murine models are widely used to study PCa progression and ADT response, but a detailed understanding of the prostates biological response to androgen deprivation in these models is lacking. Here, we present a comprehensive spatiotemporal analysis of cellular and transcriptional dynamics in the mouse prostate following orchiectomy (ORX)-induced androgen deprivation. We observed progressive involution across all prostate lobes (dorsal, ventral, lateral, and anterior) and distinct lobe-specific temporal gene expression changes post-ORX. Immune cell infiltration markedly increased over time, highlighting a shift in the prostates cellular landscape. Single-cell RNA sequencing uncovered a previously undescribed fibroblast subtype--termed ORX-induced fibroblast (OIF)-- characterized by high expression of Wnt2, Rorb, and Wif1, with distinct spatial localization. Pathway analysis revealed upregulation of amide and peptide binding functions, alongside suppression of peptidase and endopeptidase activity. Furthermore, dynamic changes in ligand-receptor interactions across lobes underscored the evolving intercellular communication in the post-ORX prostate. By integrating spatial transcriptomics with single-cell profiling, our study generates a high-resolution atlas of the murine prostates response to androgen deprivation. These findings provide a foundational resource for interpreting ADT responses in preclinical models of PCa.

cancer biology↗

bioRxiv2025

Cell modeling and rescue of a novel non-coding genetic cause of Glycogen Storage Disease IX

Delayed diagnosis of Mendelian disease substantially prevents early therapeutic intervention that could improve symptoms and prognosis. One major contributing challenge is the functional interpretation of non-coding variants that cause disease by altering splicing and/or gene expression. We identified two siblings with glycogen storage disease (GSD) type IX {gamma}2, both of whom had a classic clinical presentation, enzyme deficiency, and a known pathogenic splice acceptor variant on one allele of PHKG2. Despite the autosomal recessive nature of the disease, no variant on the second allele was identified by gene panel sequencing. To identify a potential missing second pathogenic variant, we completed whole genome sequencing (WGS) and detected putative deep intronic splicing variant in PHKG2 in both siblings. We confirmed the functional splicing effects of this variant using short-read and long-read RNA-seq on patient blood and a HEK293T cell model in which we installed the variant using CRISPR editing. Using the cell model, we demonstrated multiple biochemical and cellular impacts that are consistent with GSD IX {gamma}2, and a reversal of aberrant splicing using antisense splice-switching oligonucleotides. In doing so, we demonstrate a novel and robust pathway for detecting, validating, and reversing the impacts of novel non-coding causes of rare disease.

genetics↗

bioRxiv2025

ZMS-6659, a selective Polθ helicase inhibitor, demonstrates anti-tumor activity as monotherapy and synergy effect with PARP inhibitors and topoisomerase inhibitors

The repair of DNA double strand break (DSB) is crucial for genome stability. Homologous recombination (HR) is a high-fidelity, error-free DSB repair pathway, and its dysfunction leads to genome instability and can result in tumorigenesis. In HR deficient contexts, microhomology-mediated end joining (MMEJ), dependent on DNA polymerase theta (Pol{theta}), is up-regulated to serve as a backup pathway for DSB repair. Several studies have proved that Pol{theta} inhibition causes synthetic lethality with HR deficiency, and Pol{theta} emerges as a potential DNA damage repair (DDR) target for the treatment of HR deficient tumors both as single agent or in combination with PARP inhibitors (PARPi). In addition, evidences show that the blockage of Pol{theta} can enhance the sensitivity to DNA damage agents. Herein, we characterized ZMS-6659, a highly potent small-molecule Pol{theta} inhibitor targeting the helicase domain. ZMS-6659 induces synthetic lethality in HR deficient models, elicits synergistic effects with even low dose of PARPi and delays PARPi resistance without additional hematotoxicity. Besides, ZMS-6659 also enhance the sensitivity to topoisomerase inhibitors in HR proficient cell lines. These findings support the clinical exploration of ZMS-6659 in combination with PARPi in HR deficient tumors, and suggest a potential application expansion beyond HR deficiency.

cancer biology↗

bioRxiv2025

Single-Cell eQTL Mapping Reveals Cell Type-Specific Genetic Regulation in Lung Cancer

Genome-wide association studies (GWAS) have identified over 50 lung cancer risk loci; however, the precise cellular context of these genetic mechanisms remains unclear due to limitations in bulk tissue eQTL analyses. Here, we present the largest single-cell eQTL atlas of human lung tissue to date, profiling 222 donors using multiplexed scRNA-seq. We identified 16,785 eQTLs across 17 cell types, with over 90% of sc-eQTLs and 59% eGene being cell-type-specific, and fewer than 23% were detectable in paired bulk datasets. Integration with GWAS for non-small cell lung cancer highlighted epithelial and immune cells as key contributors to genetic susceptibility, identifying 28 candidate genes within known risk loci and 24 in novel regions. Notably, 47% of established NSCLC susceptibility loci exhibited cell-type-specific pleiotropic genetic regulation. This study provides a valuable resource of lung sc-eQTLs and illuminates how genetic variation modulates gene expression in a cell-type-specific fashion, contributing to lung cancer susceptibility.

genetics↗

bioRxiv2025

The photoreaction process of a large-Stokes-shift red fluorescence protein-LSSmCherry1

Large Stokes shift red fluorescent proteins are highly valued in fluorescence imaging due to their considerable spectral separation and minimal self-absorption. However, a notable gap remains in our understanding of these proteins excited-state dynamics. Unlocking this knowledge could potentially drive significant advancements in cellular and molecular biology. In this study, we systematically examine the excited-state dynamics of LSSmCherry1, a large Stokes shift red fluorescent protein, under varying isotopic compositions and temperatures. Our aim is to elucidate its distinctive spectral properties. Through steady fluorescence spectral experiments at different temperatures, we demonstrate that the large Stokes shift is significantly reduced by approximately 80 nm at low temperatures compared to room temperature. Using transient fluorescence and absorption spectroscopy, we dissect the excited-state dynamics of LSSmCherry1 in neutral environments. We also investigate the kinetic isotopic effect by comparing spectra in water and heavy water. These analyses allow us to delineate plausible photocyclic pathways. Our results reveal that the excited-state dynamics of LSSmCherry1 follow a model similar to that observed in other fluorescent proteins, such as Green Fluorescent Protein (GFP). Notably, we demonstrate that the excited-state proton transfer (ESPT) process is the primary origin of the large Stokes shift in LSSmCherry1. This ESPT process occurs rapidly, within approximately 365 fs after excitation in the neutral environment. This study provides crucial insights into the mechanisms underlying large Stokes shift fluorescent proteins, potentially paving the way for the development of improved fluorescent probes for biological imaging. TOC GraphicSome journals require a graphical entry for the Table of Contents. This should be laid out "print ready" so that the sizing of the text is correct. Inside the tocentry environment, the font used is Helvetica 8 pt, as required by Journal of the American Chemical Society. The surrounding frame is 9 cm by 3.5 cm, which is the maximum permitted for Journal of the American Chemical Society graphical table of content entries. The box will not resize if the content is too big: instead it will overflow the edge of the box. This box and the associated title will always be printed on a separate page at the end of the document.

biochemistry↗

bioRxiv2025

DiNovo: high-coverage, high-confidence de novo peptide sequencing using mirror proteases and deep learning

Despite the recent advancements driven by deep learning, de novo peptide sequencing is still constrained by incomplete peptide fragmentation and insufficient protein digestion in current single protease-based proteomic experiments. Here, we present a software system, named DiNovo, for high-coverage and confidence de novo peptide sequencing by leveraging the complementarity of mirror proteases. DiNovo is empowered by several innovative algorithms, including a mirror-spectra recognition algorithm independent of pre-sequencing, two sequencing algorithms based on deep learning and graph theory, respectively, and target-decoy mapping, a method for sequencing result evaluation free of prior peptide identification. Compared with the trypsin protease used alone, DiNovo using two pairs of mirror proteases led to two to three times high-confidence amino acids sequenced. Compared with previous single-protease de novo sequencing algorithms, DiNovo achieved much higher sequence coverages. DiNovo also showed great potential as a powerful complement or alternative to database search for peptide identification with quality control.

bioinformatics↗

bioRxiv2025

Quantitative phosphoproteomic analysis of testes from Iqcn-deficient mice highlights the significance of calmodulin signaling in spermiogenesis

Calmodulin (CaM) plays a crucial role in sperm function. Studies have reported that proteins containing IQ motif interact with CaM, subsequently engaging with downstream target proteins known as calmodulin-binding proteins (CaMBPs). It is reported that the loss of interaction between IQCN and CaM is mainly manifested as decreased motility, leading to fertilization failure and male infertility. However, no relevant reports have been published detailing which CaMBPs exist and the mechanisms by which they are regulated. In this study, we conducted a comprehensive quantitative proteomic and phosphoproteomic analysis of mouse testes from wild-type (WT) and Iqcn knockout (Iqcn-/-) mice. The results indicated that Iqcn deficiency substantially rewires the downstream phosphorylation signaling pathway, while not causing equivalent changes in protein levels. Among the total 577 differentially regulated phosphorylated sites in our results, most of them (494/577) belong to calmodulin-binding proteins (CaMBPs). Gene ontology analysis of these differentially phosphorylated CaMBPs showed enrichment in male gamete generation, actin cytoskeleton organization and microtubule cytoskeleton organization process, demonstrating IQCN regulates sperm function by interacting with CaM, which in turn affects the phosphorylation level of CaMBPs. Further kinase substrate network analysis revealed that most kinases with substrates phosphorylation sites up-regulated were tyrosine kinases, and the inhibition assay showed that FGFR4 and SYK tyrosine kinases are important for sperm motility and progressive motility. In summary, this study reveals the interaction between IQ motif-containing protein IQCN and CaM, which regulates the phosphorylation of downstream CaMBPs and is involved in the related processes of spermiogenesis and sperm function.

developmental biology↗

bioRxiv2025

AI-driven discovery of host thioredoxin as a CRISPR enhancer of phage-encoded miniature Cas12 hacker nuclease

The evolutionary arms race between bacteriophages and their bacterial hosts has driven the evolution of sophisticated adaptive immune systems, such as CRISPR-Cas, as a crucial defense mechanism. While bacteriophages have developed various anti-CRISPR strategies to counteract these immune systems, the role of bacterial host factors in enhancing CRISPR-Cas functions has been relatively unexplored. In this study, we employ an artificial intelligence (AI)-driven approach to systematically analyze potential interactions between Escherichia coli (E. coli) proteins and fifteen previously uncharacterized Cas12 proteins, generating 65,715 predicted binary complex structures. Our findings reveal a previously unknown dimension of CRISPR immunity, demonstrating that the hosts ubiquitous redox enzyme, thioredoxin (TrxA), significantly enhances the DNA cleavage efficiency of a phage-encoded, miniature Cas12 nuclease (termed Cas12 hacker). This synergistic relationship represents a strategic inversion, where a bacteriophage hijacks a host protein to reinforce its own genome degradation machinery, possibly targeting rival nucleic acids. Through comprehensive biochemical characterizations, structural analyses of the Cas12 hacker-TrxA-sgRNA-dsDNA quaternary complex, and in vivo bacterial defense assays, we uncover an intricate association in which thioredoxin binds to and activates the Cas12 hacker nuclease, intensifying its DNA cleavage capacity and bolstering CRISPR immunity. Our findings expand the understanding of the molecular interactions underlying host-phage conflicts and highlight the potential for harnessing endogenous host factors to enhance the capabilities of CRISPR-based genetic engineering tools.

microbiology↗

bioRxiv2024

Bipolar and schizophrenia risk gene AKAP11 encodes an autophagy receptor coupling the regulation of PKA kinase network homeostasis to synaptic transmission

Human genomic studies have identified protein-truncating variants in AKAP11 associated with both bipolar disorder (BD) and schizophrenia (SCZ), implicating a shared disease mechanism driven by loss-of-function. AKAP11, a protein kinase A (PKA) adaptor, plays a key role in degrading the PKA-RI complex through selective autophagy. However, the neuronal functions of AKAP11 and the impact of its loss-of-function remains largely uncharacterized. Through multi-omics approaches, cell biology, and electrophysiology analysis in mouse models and human induced neurons, we delineated a central role of AKAP11 in coupling PKA kinase network regulation to synaptic transmission. Loss of AKAP11 distorted compartment-specific PKA and GSK3/{beta} activities and impaired cellular functions that significantly overlap with pathways associated with BD and SCZ. Moreover, we identified interactions between AKAP11, the PKA-RI adaptor SPHKAP, and the ER-resident autophagy-related proteins VAPA/B, which co-adapt and mediate PKA-RI complex degradation in neurons. Notably, AKAP11 deficiency impaired neurotransmission, providing key insights into the mechanism underlying AKAP11-associated psychiatric diseases.

neuroscience↗

bioRxiv2024

Development of a novel peripherally acting alpha2A-adrenergic receptor antagonist for anti-diabetic

Yohimbine, a potent alpha2A-adrenergic receptor (2AAR) antagonist, was found therapeutic potential for type 2 diabetes through improving insulin release. However, the adverse side effects mediated by its actions in the brain hampered its use. Here, based on molecular docking analysis and structural modification, we have developed a novel peripherally acting yohimbine derivative (CDS479-2). CryoEM data found that yohimbine and CDS479-2 have similar interactions with the structure of 2AAR. Importantly, CDS479-2 shows similar 2AAR antagonist activity as yohimbine, but with very limited access to the brain, and thus avoiding the unwanted central effects such as hypertension and anxiety. Acute administration of CDS479-2 by injection or gavage lowered blood glucose levels and improved glucose tolerance in the high-fat diet-induced obesity (DIO) mice, an animal model for human type 2 diabetes. Remarkably, DIO mice received 2 weeks of daily administration of CDS479-2, but not yohimbine, exhibited sustained normoglycaemia, and increased density of the insulin-producing beta cells, in which important proliferation genes were found upregulated. Moreover, the overall protein expression levels of their pancreas were more similar to that of the healthy chow-fed mice. Thus, CDS479-2 may indicate a new direction for type 2 diabetes treatment. Importantly, the strategy we employed in this study will inspire the optimization for drugs that with both peripheral and central targets. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/628818v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d3d7corg.highwire.dtl.DTLVardef@1afbad3org.highwire.dtl.DTLVardef@12a1aborg.highwire.dtl.DTLVardef@1341a02_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

Assessment of DNA methylation from a single genomic region of ELOV2 is sufficient to predict chronological age

Estimation of chronological age is particularly informative in forensic contexts. Assessment of DNA methylation status allows for the prediction of age, though the accuracy and ease of manipulation may vary across different models. In this study, we started with a carefully designed discovery cohort recruiting more elderly subjects than other age categories, to diminish the effect of epigenetic drifting. We analyzed DNA methylation from a single genomic region of ELOV2, which was sufficient to construct an age-prediction model comprising 15 CpG sites. This model is further validated by an independent cohort as well as a multi-center test using trace dried bloodstains. The nature of our analytical pipeline, when combined the assessment of a single genomic locus with high-throughput sequencing, can easily be scaled up with low cost. Taken together, we propose a new age-prediction model featuring accuracy, ease of manipulation, high-throughput, and low cost. This model can be readily applied in both classic and newly emergent forensic contexts that require age estimation.

genetics↗

bioRxiv2024

Dynamic programming algorithms for fast and accurate cell lineage tree reconstruction from CRISPR-based lineage tracing data

CRISPR-based lineage tracing, coupled with single-cell RNA sequencing, has emerged as a promising approach for studying cell transformations during development as well as disease progression. However, the high ratio of cells to CRISPR-induced mutations, combined with missing data from silencing or dropout, make cell lineage tree (CLT) reconstruction difficult. As a result, this computational problem has attracted significant attention in recent years, including the introduction of Star Homoplasy Parsimony (SHP) in 2023 to model the specific properties of CRISPR-induced mutations, along with the Startle family of methods based on integer linear programming (ILP) or heuristic search (NNI). Here, we present Star-CDP, the first dynamic programming algorithm for SHP. Star-CDP solves SHP within a constrained search space {Sigma} defined by subsets of cells from which a solution CLT must draw its clades. When {Sigma} is the power set, Star-CDP is an exact exponential algorithm with time complexity O(nm |{Sigma}| 2), where n is the number of cells, m is the number of target sites, and |{Sigma} |= O(2n). We show that it is possible to build clade constraints that are polynomially-sized and effective in practice. Motivated by the technological challenges in producing consistent phylogenetic signal across the tree during lineage tracing, we also present algorithms to efficiently count, sample, and build consensus trees from all solutions to the clade-constrained SHP problem. In simulations, Star-CDPs strict consensus effectively reduced false positive branches while preserving many more true positives compared to the standard strict consensus implemented by PAUP*, a popular parsimony method from species phylogenetics. Likewise, Star-CDPs strict consensus achieved the same or higher accuracy (f1-score) on all but one of the 15 model conditions tested, often outperforming leading the methods, Startle-ILP and Startle-NNI, while also scaling to larger data sets than Startle-ILP. Lastly, we analyzed lineage tracing data from the KP-Tracer mouse model of lung adenocarcinoma, finding that Star-CDP produced plausible CLTs, often lowering the number of migration and reseeding events needed to explain metastases compared to Startle. Our analysis also showed, for the first time, that strategies for preprocessing cells with missing data--specifically cell pruning and deduplicating techniques--can have a substantial impact on CLTs reconstructed with the same method, even changing relative performance across methods compared to previously published results. The same was true of postprocessing trees with LAML, a maximum likelihood method designed for mixed-type missing data. By exploring these different pipelines, we recovered the most plausible CLT for the largest KP-Tracer metastatic tumor, reducing the number of reseeding events from 42 to 10 without increasing the number of migrations. Star-CDP is available on Github: https://github.com/molloy-lab/Star-CDP.

bioinformatics↗