Biology subjects

Chen, Z.

Publications and source records attributed to Chen, Z..

At least 469 records · Page 26Linked to original sources

bioRxiv2023

Programs, Origins, and Niches of Immunomodulatory Myeloid Cells in Gliomas

Gliomas are incurable malignancies notable for an immunosuppressive microenvironment with abundant myeloid cells whose immunomodulatory properties remain poorly defined. Here, utilizing scRNA-seq data for 183,062 myeloid cells from 85 human tumors, we discover that nearly all glioma-associated myeloid cells express at least one of four immunomodulatory activity programs: Scavenger Immunosuppressive, C1Q Immunosuppressive, CXCR4 Inflammatory, and IL1B Inflammatory. All four programs are present in IDH1 mutant and wild-type gliomas and are expressed in macrophages, monocytes, and microglia whether of blood or resident myeloid cell origins. Integrating our scRNA-seq data with mitochondrial DNA-based lineage tracing, spatial transcriptomics, and organoid explant systems that model peripheral monocyte infiltration, we show that these programs are driven by microenvironmental cues and therapies rather than myeloid cell type, origin, or mutation status. The C1Q Immunosuppressive program is driven by routinely administered dexamethasone. The Scavenger Immunosuppressive program includes ligands with established roles in T-cell suppression, is induced in hypoxic regions, and is associated with immunotherapy resistance. Both immunosuppressive programs are less prevalent in lower-grade gliomas, which are instead enriched for the CXCR4 Inflammatory program. Our study provides a framework to understand immunomodulatory myeloid cells in glioma, and a foundation to develop more effective immunotherapies.

cancer biology↗

bioRxiv2023

A Fuzzy sequencer for rapid DNA fragment counting and genotyping

High-throughput sequencing technologies generate a vast number of DNA sequence reads simultaneously, which are subsequently analyzed using the information contained within these fragmented reads. The assessment of sequencing technology relies on information efficiency, which measures the amount of information entropy produced per sequencing reaction cycle. In this study, we propose a fuzzy sequencing strategy that exhibits information efficiency more than twice of currently prevailing cyclic reversible terminator sequencing methods. To validate our approach, we developed a fully functional and high-throughput fuzzy sequencer. This sequencer implements a highly efficient fluorogenic sequencing-by-synthesis chemistry and underwent testing across various application scenarios, including copy-number variation detection, noninvasive prenatal testing, transcriptome profiling, mutation genotyping, and metagenomic profling. Our findings unequivocally demonstrate that the fuzzy sequencing strategy outperforms existing methods in terms of information efficiency and delivers accurate resequencing results with faster turnaround times. One Sentence SummaryA fuzzy sequencer can exceed current limit of information efficiency of DNA sequencers for resequencing applications.

genomics↗

bioRxiv2023

A Practical Approach for Targeting Structural Variants Genome-wide in Plasma Cell-free DNA

Interrogating gene mutations and aberrant DNA methylation in plasma cell-free DNA (cfDNA) has become increasingly common for monitoring tumor burden in cancer patients. However, no tests currently target chromosomal structural variants (SVs) genome-wide. Here, we report a simple molecular and sequencing workflow, Genome-wide Analysis of Palindrome Formation (GAPF-seq), to probe DNA palindromes, a type of SV that often demarcates gene amplification. Low-coverage next-generation sequencing of palindrome-enriched DNA uncovered skewed chromosomal distributions of high-coverage 1-kb bins (HCBs) in tumor DNA. When combined with traditional machine learning, GAPF-seq differentiated 39 breast tumors from matched control DNA with an Area Under the Curve (AUC) of 0.955. A proof-of-concept liquid biopsy study using cfDNA from 27 prostate cancer patients and 24 control individuals yielded an average AUC of 0.896. HCBs on the X chromosome emerged as a nearly decisive feature and were linked to androgen receptor gene amplification. As a simple and agnostic liquid biopsy approach, GAPF-seq could fill this technological gap, offering unique cancer-specific SV profiles.

cancer biology↗

bioRxiv2023

Addressing the dNTP bottleneck restricting prime editing activity

Prime editing efficiency is modest in cells that are quiescent or slowly proliferating where intracellular dNTP levels are tightly regulated. MMLV-reverse transcriptase - the prime editor polymerase subunit - requires high intracellular dNTPs levels for efficient polymerization. We report that prime editing efficiency in primary cells and in vivo is increased by mutations that enhance the enzymatic properties of MMLV-reverse transcriptase and can be further complemented by targeting SAMHD1 for degradation.

biochemistry↗

bioRxiv2023

Single-Molecule Morphology of Topologically Digested Olympic Networks

The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The evolution, replication and self-assembly of this structure are fascinating open questions in biology that can also inform us how to realise synthetic Olympic networks in vitro. To obtain a deeper understanding of the structure and assembly of kDNA networks, we sequenced the Crithidia fasciculata kDNA genome and performed high-resolution Atomic Force Microscopy (AFM) and analysis of kDNA networks that had been partially digested by selected restriction enzymes. We discovered that these topological perturbations lead to networks with significantly different geometrical features and morphologies with respect to the unperturbed kDNA, and that these changes are strongly dependent on the class of DNA circles targeted by the restriction enzymes. Specifically, cleaving maxicircles leads to a dramatic reduction in network size once adsorbed onto the surface, whilst cleaving both maxicircles and a minor class of minicircles yields non-circular and deformed structures. We argue that our results are a consequence of a precise positioning of the maxicircles at the boundary of the network, and we discuss our findings in the context of kDNA biogenesis, design of artificial Olympic networks and detection of in vivo perturbations.

biophysics↗

bioRxiv2023

Identification of new markers of angiogenic sprouting using transcriptomics: New role for RND3

BackgroundNew blood vessel formation requires endothelial cells to transition from a quiescent to an invasive phenotype. Transcriptional changes are vital for this switch, but a comprehensive genome-wide approach focused exclusively on endothelial cell sprout initiation has not been reported. Approach and ResultsUsing a model of human endothelial cell sprout initiation, we developed a protocol to physically separate cells that initiate the process of new blood vessel formation (invading cells) from non-invading cells. We used this model to perform multiple transcriptomics analyses from multiple donors to monitor endothelial gene expression changes. Single-cell Population Analyses, single-cell Cluster Analyses, and bulk RNA sequencing were used to delineate transcriptomic changes in invading cells. The results revealed a 39 gene signature that was consistent with activation of signal transduction, morphogenesis, and immune responses. Many of the genes were previously shown to regulate angiogenesis, and include multiple tip cell markers. Upregulation of SNAI1, PTGS2, and JUNB protein expression was confirmed in invading cells, and silencing JunB and SNAI1 significantly reduced invasion responses. Separate studies investigated Rounding 3 (RND3), also known as RhoE, which has not yet been implicated in angiogenesis. Silencing RND3 reduced endothelial invasion distance as well as filopodia length, fitting with a pathfinding role for RND3 via regulation of filopodial extensions. Analysis of in vivo retinal angiogenesis in Rnd3 heterozygous mice confirmed a decrease in filopodial length compared to wild type littermates. ConclusionValidation of multiple genes, including RND3, revealed a functional role for this gene signature early in the angiogenic process. This study expands the list of genes that are associated with the acquisition of a tip cell phenotype during endothelial cell sprout initiation. HIGHLIGHTSO_LITranscriptomic analyses identified 39 candidate genes that were upregulated at the onset of endothelial sprouting C_LIO_LIThe gene signature includes signal transduction, morphogenesis, and immune responses C_LIO_LINewly-identified RND3 is associated with filopodial extension and pathfinding C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/563021v1_ufig1.gif" ALT="Figure 1"> View larger version (92K): org.highwire.dtl.DTLVardef@1045439org.highwire.dtl.DTLVardef@1357703org.highwire.dtl.DTLVardef@1189cf2org.highwire.dtl.DTLVardef@e7d574_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Volumetric Compression Shifts Rho GTPase Balance and Induces Mechanobiological Cell State Transition

During development and disease progression, cells are subject to osmotic and mechanical stresses that modulate cell volume, which fundamentally influences cell homeostasis and has been linked to a variety of cellular functions. It is not well understood how the mechanobiological state of cells is programmed by the interplay of intracellular organization and complex extracellular mechanics when stimulated by cell volume modulation. Here, by controlling cell volume via osmotic pressure, we evaluate physical phenotypes (including cell shape, morphodynamics, traction force, and extracellular matrix (ECM) remodeling) and molecular signaling (YAP), and we uncover fundamental transitions in active biophysical states. We demonstrate that volumetric compression shifts the ratiometric balance of Rho GTPase activities, thereby altering mechanosensing and cytoskeletal organization in a reversible manner. Specifically, volumetric compression controls cell spreading, adhesion formation, and YAP nuclear translocation, while maintaining cell contractile activity. Furthermore, we show that on physiologically relevant fibrillar collagen I matrices, which are highly non-elastic, cells exhibit additional modes of cell volume-dependent mechanosensing that are not observable on elastic substrates. Notably, volumetric compression regulates the dynamics of cell-ECM interactions and irreversible ECM remodeling via Rac-directed protrusion dynamics, at both the single-cell level and the multicellular level. Our findings support that cell volume is a master biophysical regulator and reveal its roles in cell mechanical state transition, cell-ECM interactions, and biophysical tissue programming.

biophysics↗

bioRxiv2023

Adaptation to volumetric compression drives hepatoblastoma cells to an apoptosis-resistant and invasive phenotype

Liver cancer involves tumor cells rapidly growing within a packed tissue environment. Patient tumor tissues reveal densely packed and deformed cells, especially at tumor boundaries, indicative of physical crowding and compression. It is not well understood how these physical signals modulate tumor evolution and therapeutic susceptibility. Here we investigate the impact of volumetric compression on liver cancer (HepG2) behavior. We find that conditioning cells under a highly compressed state leads to major transcriptional reprogramming, notably the loss of hepatic markers, the epithelial-to-mesenchymal transition (EMT)-like changes, and altered calcium signaling-related gene expression, over the course of several days. Biophysically, compressed cells exhibit increased Rac1-mediated cell spreading and cell-extracellular matrix interactions, cytoskeletal reorganization, increased YAP and {beta}-catenin nuclear translocation, and dysfunction in cytoplasmic and mitochondrial calcium signaling. Furthermore, compressed cells are resistant to chemotherapeutics and desensitized to apoptosis signaling. Apoptosis sensitivity can be rescued by stimulated calcium signaling. Our study demonstrates that volumetric compression is a key microenvironmental factor that drives tumor evolution in multiple pathological directions and highlights potential countermeasures to re-sensitize therapy-resistant cells. Significance statementCompression can arise as cancer cells grow and navigate within the dense solid tumor microenvironment. It is unclear how compression mediates critical programs that drive tumor progression and therapeutic complications. Here, we take an integrative approach in investigating the impact of compression on liver cancer. We identify and characterize compressed subdomains within patient tumor tissues. Furthermore, using in vitro systems, we induce volumetric compression (primarily via osmotic pressure but also via mechanical force) on liver cancer cells and demonstrate significant molecular and biophysical changes in cell states, including in function, cytoskeletal signaling, proliferation, invasion, and chemoresistance. Importantly, our results show that compressed cells have impaired calcium signaling and acquire resistance to apoptosis, which can be countered via calcium mobilization.

cancer biology↗

bioRxiv2023

Hierarchical replay of multi-regional sequential spiking associated with working memory

How does millisecond-scale neural activity mediate behaviors over seconds? We recorded brain-wide activity in mice performing an olfactory working-memory task to decipher cross-region organization of activity. Spike-correlograms revealed millisecond within- and cross-region spike couplings, more prominent among neurons encoding similar memories. Spike coupling linked neurons into motifs of chains, single loops, and nested loops, especially among hippocampal and prefrontal-cortex neurons. Direction of spike coupling and activity chains was in line with that of memory-associated activity waves. Intriguingly, activity motifs were replayed before and after task performance, and during inter-trial intervals. Motifs were hierarchically organized, with progressively increasing time constants and the number of participating neurons. Thus, hierarchically organized and replayed cross-region spiking motifs are modulated on demand during delay period to mediate perceptual working memory. One Sentence SummaryNested activity motifs of chains, single loops, and nested loops, with progressively increasing time constants and number of participating neurons, are hierarchically organized and replayed to mediate perceptual working-memory maintenance.

neuroscience↗

bioRxiv2023

Pan-genome of pear provides insights into the differentiation of fruit quality traits between Asian and European pears

The pear (Pyrus spp.) is a remarkable fruit, well known for its diverse flavors, textures, culinary versatility, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid Yuluxiang pear and constructed the first pear pangenome of 1.15Gb by combining these two genomes with five previously published pear genomes. Using the constructed pangenome, we identified 21,224 gene PAVs and 1,158,812 SNPs in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, we found that PAV-based analysis provides additional insights into the pear population structure. In addition, we also revealed that some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhances sepal shedding in Xuehuali which is vital for pear quality. This research helps further capture the genetic diversity of pear populations and provides valuable genomic resources for accelerating pear breeding.

genomics↗

bioRxiv2023

Human disturbance increases spatiotemporal associations among mountain forest terrestrial mammal species

Spatial and temporal associations between sympatric species underpin biotic interactions, structure ecological assemblages, and sustain ecosystem functioning and stability. However, the resilience of interspecific spatiotemporal associations to human activity remains poorly understood, particularly in mountain forests where anthropogenic impacts are often pervasive. Here we applied context-dependent Joint Species Distribution Models to a systematic camera-trap survey dataset from a global biodiversity hotspot in eastern Himalaya to understand how prominent human activities in mountain forests influence species associations within terrestrial mammal communities. We obtained 10,388 independent detections of 17 focal species (12 carnivores and five ungulates) from 322 stations over 43,163 camera days of effort. We identified a higher incidence of positive associations in habitats with higher levels of human modification (87 %) and human presence (83 %) compared to those located in habitats with lower human modification (64 %) and human presence (65 %) levels. We also detected a significant reduction of pairwise encounter time at increasing levels of human disturbance, corresponding to more frequent encounters between pairs of species. Our findings indicate that human activities can push mammals together into more frequent encounters and associations, which likely influences the coexistence and persistence of wildlife, with potential far-ranging ecological consequences.

ecology↗

bioRxiv2023

Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos

In mammals, many retrotransposons are de-repressed during zygotic genome activation (ZGA). However, their functions in early development remain elusive largely due to the challenge to simultaneously manipulate thousands of retrotransposon insertions in embryos. Here, we employed epigenome editing to perturb the long terminal repeat (LTR) MT2_Mm, a well-known ZGA and totipotency marker that exists in [~]2667 insertions throughout the mouse genome. CRISPRi robustly repressed 2485 ([~] 93%) MT2_Mm insertions and 1090 ([~]55%) insertions of the closely related MT2C_Mm in 2-cell embryos. Remarkably, such perturbation caused down-regulation of hundreds of ZGA genes at the 2-cell stage and embryonic arrest mostly at the morula stage. Mechanistically, MT2_Mm/MT2C_Mm primarily served as alternative ZGA promoters activated by OBOX proteins. Thus, through unprecedented large-scale epigenome editing, we addressed to what extent MT2_Mm/MT2C_Mm regulates ZGA and preimplantation development. Our approach could be adapted to systematically perturb retrotransposons in other mammalian embryos as it doesnt require transgenic animals.

developmental biology↗

bioRxiv2023

Tissue-specific transfer-learning enables retasking of a general comprehensive model to a specific domain

Machine learning (ML) has proven successful in biological data analysis. However, may require massive training data. To allow broader use of ML in the full spectrum of biology and medicine, including sample-sparse domains, re-directing established models to specific tasks by add-on training via a moderate sample may be promising. Transfer learning (TL), a technique migrating pre-trained models to new tasks, fits in this requirement. Here, by TL, we retasked Enformer, a comprehensive model trained by massive data, tailored to breast cancers using breast-specific data. Its performance has been validated through statistical accuracy of predictions, annotation of genetic variants, and mapping of variants associated with breast cancer. By allowing the flexibility of adding dedicated training data, our TL protocol unlocks future discovery within specific domains with moderate add-on samples by standing on the shoulders of giant models.

bioinformatics↗

bioRxiv2023

Heteroscedastic Personalized Regression Unveils Genetic Basis of Alzheimer's Disease Stratified by Cognitive Level

In contemporary medical research, patient heterogeneity plays a pivotal role in comprehending intricate diseases such as Alzheimers disease and various forms of cancer. Specifically, in the genomic analysis of Alzheimers disease, individual patients may exhibit unique causal mutations that significantly influence their therapeutic trajectory. Conventional models that share numerous parameters across all individuals struggle to discern this heterogeneity and identify the influential factors for individuals. To tackle this challenge, we propose an innovative approach called Heteroscedastic Personalized Regression (Het-PR) to estimate the heterogeneity across samples and obtain personalized models for each sample. We demonstrate the effectiveness and robustness of Het-PR through both simulation and real data experiments. In the simulation experiment, we show that Het-PR outperforms other state-of-the-art models in capturing inter-sample heterogeneity. In the real data experiment, we apply Het-PR to Alzheimers data and show that it can identify persuasive selected genetic factors for each individual patient. Interestingly, our results suggest that there might be different associative SNPs for AD patients stratified by different cognitive levels. Author summaryIn medical research, it has been observed that causes of a disease vary significantly among individuals, especially when looking at complex diseases like Alzheimers disease and cancer. For Alzheimers disease, obesity, age, gender, and depression may play different roles across different patients. When studying the genes of Alzheimers patients, we find that each person might have their own unique genetic changes that can affect their treatment. For example, Alzheimers patients with different genetic mutations may respond differently to the same treatment. Traditional research methods often miss these individual differences and cant always pinpoint important personalized factors for each patient, because they usually use one model for all patients. To better understand these differences, weve introduced a new method, Heteroscedastic Personalized Regression (Het-PR), which generates a personalized model for each individual. Our experiments show that Het-PR is more effective than other leading methods in identifying these patient differences and recognizing Alzheimers genetic basis for each patient through both simulation and real data experiments. When we used Het-PR on real Alzheimers data, it helped us spot key genetic factors for each patient. Additionally, in our study, we excitedly find that different genetic markers in Alzheimers patients are possibly based on their cognitive abilities. Software for Heteroscedastic Personalized Regression is available in https://github.com/rong-hash/Het-PR.

bioinformatics↗

bioRxiv2023

Multilevel regulation of NF-kappa B signaling by NSD2 suppresses Kras-driven pancreatic tumorigenesis

Pancreatic ductal adenocarcinoma (PDAC) is a clinically challenging cancer with a dismal overall prognosis. NSD2 is an H3K36-specific di-methyltransferase which has been reported to play a crucial role in promoting tumorigenesis. Here, we demonstrate that NSD2 acts as a putative tumor suppressor in Kras-driven pancreatic tumorigenesis. Low level of NSD2 indicates aggressive feature of PDAC. NSD2 restrains the mice from inflammation and Kras-induced ductal metaplasia, while NSD2 loss facilitates pancreatic tumorigenesis. Mechanistically, NSD2-mediated H3K36me2 promotes the expression of I{kappa}B, which inhibits the phosphorylation of p65 and NF-{kappa}B nuclear translocation. More importantly, NSD2 interacts with the DNA binding domain of p65, attenuating NF-{kappa}B transcriptional activity. Furthermore, inhibition of NF-{kappa}B signaling relieves the symptoms of Nsd2-deficient mice. Together, our study reveals the important tumor suppressor role of NSD2 and multiple mechanisms by which NSD2 suppresses both p65 phosphorylation and downstream transcriptional activity during pancreatic tumorigenesis. This study contributes to understanding the pathogenesis of pancreatic tumorigenesis and identifies a novel negative regulator of NF-{kappa}B signaling.

cancer biology↗

bioRxiv2023

Pathogenic mitochondrial DNA mutations inhibit melanoma metastasis

Mitochondrial DNA (mtDNA) mutations are frequently observed in cancer, but their contribution to tumor progression is controversial. To evaluate the impact of mtDNA variants on tumor growth and metastasis, we created human melanoma cytoplasmic hybrid (cybrid) cell lines transplanted with wildtype mtDNA or pathogenic mtDNA encoding variants that partially or completely inhibit oxidative phosphorylation. Homoplasmic pathogenic mtDNA cybrids reliably established tumors despite dysfunctional oxidative phosphorylation. However, pathogenic mtDNA variants disrupted spontaneous metastasis of subcutaneous tumors and decreased the abundance of circulating melanoma cells in the blood. Pathogenic mtDNA did not induce anoikis or inhibit organ colonization of melanoma cells following intravenous injections. Instead, migration and invasion were reduced, indicating that limited circulation entry functions as a metastatic bottleneck amidst mtDNA dysfunction. Furthermore, analysis of selective pressure exerted on the mitochondrial genomes of heteroplasmic cybrid lines revealed a suppression of pathogenic mtDNA allelic frequency during melanoma growth. Collectively, these findings demonstrate that functional mtDNA is favored during melanoma growth and enables metastatic entry into the blood.

cancer biology↗

bioRxiv2023

Timing-dependent modulation of working memory by VTA dopamine release in medial prefrontal cortex

Dopamine significantly modulates working memory (WM)1-8, a fundamental cognitive function that maintains information during a brief delay period9-11. The temporal precision of dopaminergic modulation in WM and related neural mechanisms remain elusive. Here we unveiled the pivotal role of dopamine timing in WM performance with head-fixed mice engaged in learning an olfactory WM task. Through electrophysiology and optogenetics, we found that dopaminergic neurons in the ventral tegmental area (VTA) could encode WM information during the delay period, and manipulating dopaminergic neuronal activity bidirectionally modulated WM performance in an inverted U-shaped manner. Optogenetic manipulation of VTA activity also induced bidirectional changes in WM-related neural activity in the medial prefrontal cortex (mPFC). Imaging with a dopamine-sensitive GPCR-activation-based sensor (GRABDA)12,13 revealed transient dopamine peaks in the mPFC specifically during the early-delay period. Optogenetic stimulation of VTA-to-mPFC dopaminergic projections during the early- and late-delay period enhanced and impaired WM performance, respectively. Manipulations outside these periods or involving the nucleus accumbens had no effect. Single-unit recordings demonstrated that optogenetic excitation of VTA-to-mPFC projections could modulate mPFC neuronal activity in a manner consistent with behavioral modulation. Thus, the timing of dopamine release is critical in modulation of neuronal activity and behavior.

neuroscience↗

bioRxiv2023

Gut microbes contribute to variation in foraging intensity in the honey bee, Apis mellifera.

Gut microbiomes are increasingly recognized for mediating diverse biological aspects of their hosts, including complex behavioral phenotypes. While many studies have reported that experimental disruptions to the gut microbiome result in atypical host behavior, studies that address how gut microbes contribute to adaptive behavioral trait variation are rare. Eusocial insects represent a powerful model to test this, due to their simple microbiomes and complex division of labor characterized by colony-level variation in behavioral phenotypes. While previous studies report correlational differences in gut microbiome associated with division of labor, here, we provide evidence that gut microbes play a causal role in defining differences in foraging behavior between honey bees. Gut microbial community structure consistently differed between hive-based nurse bees and bees that leave the hive to forage for floral resources. These differences were associated with variation in the abundance of individual microbes, including Bifidobacterium asteroides, Bombilactobacillus mellis, and Lactobacillus melliventris. Manipulations of colony demography and individual foraging experience suggested that differences in microbiome composition were associated with task experience. Moreover, single microbe inoculations with B. asteroides, B. mellis, and L. melliventris caused changes in foraging intensity. These results demonstrate that gut microbes contribute to division of labor in a social insect, and support a role of gut microbes in modulating host behavioral phenotypic variation.

animal behavior and cognition↗