Biology subjects

Yi, T.

Publications and source records attributed to Yi, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Transcriptomic analysis of cecal mucosal immunity in SPF White Leghorn chicks infected with precocious and parent strains of Eimeria tenella

Eimeria tenella (E. tenella) preferentially invades the cecum of young chickens and causes enormous economic losses to the global poultry industry. In this study, chick infection models of virulent parent strain and precocious attenuated line were established with schizogony (2 dpi) and gametogony (6 dpi) as two critical sampling time points. Combined with pathogenicity detection, transcriptome sequencing, mucosal immune index measurement and homologous challenge protection assays, we systematically deciphered the differential molecular mechanisms underlying pathogenicity and immune regulation between the two strains. Pathogenicity results showed that increased infection dosages suppressed weight gain and aggravated bloody diarrhea and oocyst shedding in both strains. In particular, infection with 1 x 105 sporulated oocysts of the parent strain caused massive chick mortality, while the precocious line exhibited markedly lower virulence. Transcriptomic data revealed that gametogony (6 dpi) represented the peak of host immune response. The parent strain persistently overactivated the NF- {kappa}B - mediated positive feedback cascade of coagulation and complement as well as ECM remodeling, triggering steroid metabolic disorder and antioxidant exhaustion, which ultimately induced severe hemorrhagic necrosis of the cecum. By contrast, the precocious line specifically activated the PPAR - {gamma} signaling pathway to negatively restrain excessive inflammation, accompanied by enriched TLR signaling and leukocyte transendothelial migration pathways, thereby forming an immune cascade of "lipid anti - inflammation - pathogen elimination - mucosal repair". Immunoprotection trials verified that priming with 1 x 104 sporulated oocysts of the precocious line significantly alleviated cecal lesions and reduced oocyst output upon secondary challenge, conferring stable mucosal immune protection. The expression trends of seven hub genes (PPARG, PLIN1, CYP1A1, THBS1, FMO4, CYP2C18, CYP14) detected via qRT - PCR were consistent with RNA - seq data. This study identified a dual regulatory paradigm consisting of NF - {kappa}B - mediated tissue injury and PPAR - {gamma} - dependent anti - inflammatory responses, refined the mucosal immune theoretical framework for commercially available precocious attenuated strains, and provided candidate molecular targets for targeted anti - coccidial intervention in chickens.

microbiology↗

bioRxiv2026

AMPKγ2 Deacetylation Drives Nuclear Translocation and Doxorubicin-Induced Cardiomyopathy via Nucleolar Stress Signaling

Doxorubicin (Dox)-induced cardiomyopathy (DIC), characterized by cardiomyocyte apoptosis, remains a major clinical challenge in chemotherapy. The regulatory {gamma}2 subunit of AMP-activated protein kinase (AMPK{gamma}2) plays a key role in cardiovascular diseases, but its function in DIC is poorly understood. Here, we report that Dox induces isoform-specific deacetylation and nuclear accumulation of {gamma}2, triggering nucleolar stress and p53-mediated apoptosis. Mechanistically, HDAC3 and TIP60 interact with {gamma}2 and modulate the acetylation of multiple lysine residues within its nuclear localization signal (NLS), controlling its nucleocytoplasmic shuttling. Dox enhances HDAC3-mediated {gamma}2 deacetylation, thereby driving nuclear accumulation of the {gamma}2-containing AMPK ({gamma}2-AMPK) while suppressing the cytosolic AMPK activity. Nuclear {gamma}2-AMPK phosphorylates and inactivates TIF-IA, a key RNA polymerase I-specific transcription initiation factor, leading to nucleolar stress through inhibition of rRNA transcription. rRNA deficit triggers release of free ribosomal proteins (RPs), which bind to and inhibit the E3 ubiquitin ligase MDM2, resulting in p53 stabilization and activation of apoptotic signaling. Using genetically engineered cardiomyocytes and a DIC mouse model, we found that a deacetyl-mimetic {gamma}2 mutant (6KR) exacerbated DIC, whereas an acetyl-mimetic mutant (6KQ) was cardioprotective. Collectively, our findings establish acetylation-driven nuclear translocation of {gamma}2 as a critical node linking Dox-induced nucleolar stress to p53-dependent apoptosis and suggest a promising cardio-oncology strategy that combines HDAC inhibitors with Dox to mitigate DIC. Significance statementDoxorubicin is an effective cancer drug, but its use is limited by cardiomyopathy. Our study reveals that doxorubicin drives HDAC3-mediated deacetylation of AMPK{gamma}2, exposing its nuclear localization signal and redirecting {gamma}2-containing AMPK from the cytoplasm to the nucleus. Nuclear AMPK{gamma}2 phosphorylates TIF-IA, suppresses ribosomal RNA synthesis, and activates a nucleolar stress pathway that stabilizes p53 and promotes cardiomyocyte apoptosis. In mice, a deacetylation-mimetic AMPK{gamma}2 mutant worsens doxorubicin-induced cardiomyopathy, whereas an acetylation-mimetic mutant is protective. These findings uncover an acetylation-controlled spatial switch in AMPK signaling and identify the AMPK{gamma}2 deacetylation-nucleolar stress axis as a potential target for reducing chemotherapy-associated cardiac injury.

cell biology↗

bioRxiv2026

Comparison of Four Density Gradient Centrifugation Protocols for Purification of Toxoplasma gondii PRU Brain Cysts

Toxoplasma gondii is an obligate intracellular zoonotic protozoan that establishes persistent brain cysts in infected hosts, causing chronic infection and neuropathological damage. Efficient isolation and purification of brain cysts are essential for studying its biological characteristics and developing effective control strategies. The present study aimed to establish a reliable method for purifying brain cysts of the T. gondii PRU strain with high yield, viability, and practicality. Brain cysts harvested from experimentally infected ICR mice were purified using four different density gradient centrifugation methods: lymphocyte separation medium (LSM), Percoll, cesium chloride (CsCl), and sucrose. Purification efficiency was systematically evaluated, and the infection model was validated via brain histopathology. Cyst counts and purification yields were quantified, while cyst and bradyzoite viability were assessed using FDA/PI staining, trypan blue exclusion, and in vivo infectivity assays. Infected mice displayed the most severe clinical signs at 15 days post-infection (dpi), accompanied by significantly reduced body weight compared with uninfected controls (P < 0.05) and prominent perivascular inflammatory infiltration in the brain. Among the four purification methods, Percoll, CsCl, and sucrose gradients yielded significantly higher cyst numbers than LSM (P < 0.001), with no significant differences observed among the three gradient-based methods. Cysts purified by Percoll and LSM retained high viability and remained fully infectious in mice. Sucrose-purified cysts exhibited decreased viability, but their bradyzoites remained infective. In contrast, cysts and bradyzoites purified by CsCl were completely non-viable. These results clarify the advantages and limitations of each protocol and provide an optimized technical reference for T. gondii brain cyst research, supporting the development of toxoplasmosis prevention and control measures.

microbiology↗

bioRxiv2026

Progranulin deficiency induces lipid droplet accumulation in microglia via a STAT3-GPAT3 axis

Heterozygous mutations in the progranulin (PGRN) encoding gene GRN cause frontotemporal dementia (FTD), whereas homozygous GRN mutations lead to neuronal ceroid lipofuscinosis (NCL). However, the mechanisms underlying neurodegeneration due to PGRN deficiency remain unclear. In the aged brains or under neurodegenerative conditions, the accumulation of lipid droplets (LDs) in microglia contributes to cellular dysfunction and pro-inflammatory responses, exacerbating neurodegenerative pathology. Here, we investigated how PGRN deficiency induces LD accumulation in microglia. We found that PGRN ablation significantly upregulated triglycerol-3-phosphate acyltransferase 3 (GPAT3), the first and rate-limiting enzyme for triacylglycerol biosynthesis, and increased LD formation in both Grn-/- BV2 microglial cells and Grn-/-mouse brains. Mechanistic study revealed that PGRN deficiency upregulates GPAT3 via stimulating signal transduction and activator of transcription factor 3 (STAT3) signaling. Silencing Gpat3, inhibiting GPAT3 activity with the small molecule inhibitor FSG67, or PGRN restoration reduced LD accumulation and rescued the cytotoxicity of Grn-/- microglia conditional medium (MCM) toward N2a cells. Notably, intraperitoneal administration of FSG67 or AAV-MG1.2-mCx3cr1-mGrn-eGFP-mediated microglia-specific gene therapy reduced microglial LDs and ameliorated behavior phenotypes in Grn-/- mice. Our study elucidates the role of PGRN loss in microglial lipid homeostasis and identifies the STAT3-GPAT3 axis as a potential therapeutic target for LD-associated neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Elevated neuronal TAF15 expression leads to FTD-like phenotype

TAF15, a DNA/RNA-binding protein whose dysfunction in alternative splicing impairs NMDA receptor signaling, can form amyloid fibrils that contribute to neurodegeneration in the neurodegenerative diseases like FTD and ALS, indicating a close involvement of TAF15 in both neuronal physiological function and activation of pathological pathways. However, the relationship between TAF15 expression levels and neurodegeneration, as well as the specific downstream pathways mediating its neurotoxicity, remains unclear. Here, we found a consistent upregulation of TAF15 in prefrontal cortex neurons from patients across multiple FTD and ALS subtypes. Both in vitro and in vivo experiments demonstrated that neuronal TAF15 overexpression triggered oxidative stress, evidenced by reactive oxygen species (ROS) production, leading to neurotoxicity and gliosis. Mice overexpressing TAF15 in medial prefrontal cortex (mPFC) neurons exhibited heightened anxiety and impaired fear memory, mimicking some key features of FTD behavioral abnormalities. Notably, these pathological and behavioral phenotypes are rescued by the antioxidant N-acetylcysteine amide (NACA), indicating that elevated TAF15 level exacerbates neurodegeneration primarily by activating oxidative stress pathways. Together, this work elucidates a novel TAF15-oxidative stress axis in FTD-associated neurodegeneration, providing a conceptual framework for future therapeutic development. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/694105v1_ufig1.gif" ALT="Figure 1000"> View larger version (35K): org.highwire.dtl.DTLVardef@cc581eorg.highwire.dtl.DTLVardef@1ad2129org.highwire.dtl.DTLVardef@15c0fb5org.highwire.dtl.DTLVardef@10b57a6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsTAF15 is upregulated in prefrontal cortex neurons of patients with FTD and ALS across different subtypes. Elevated TAF15 expression provokes ROS elevation, leading to neurotoxicity and gliosis. Neuronal TAF15 overexpression in the mouse mPFC results in FTD-like anxiety and impaired fear-memory phenotype. Reducing oxidative stress can rescue FTD-like phenotype caused by TAF15 upregulation.

neuroscience↗

bioRxiv2025

Nanoprotrusion enlargement conducts cytocapsular tube elongation along the path of least resistance

Cancer metastasis is a major source of cancer lethality. Recently, we reported that the ATP-dependent calcium pump PMCA2 is enriched in cytocapsular membranes as biomarker of native malignant tumors. Cytocapsular tubes (CCTs) provide membrane-enclosed freeways for protected and bi-directional cancer metastasis in cytocapsular tumor network systems (CTNSs). It is obscure how CCTs initiate and elongate in heterogeneous human tissues and organs against diverse blocks of resistance. Here, we report that thin CCT nanoprotrusions (NPs) enlarge in directions of least resistance to grow into enlarged NPs. Subsequently, enlarged NPs develop into initial CCTs (ICCTs) followed by development into full CCTs. The full CCTs elongate in paths of least resistance over long distances, as observed in 34 kinds of human tissues and organs. Sideways CCT branching proceeds via a NP bifid format, which increases CCT numbers and expands 3D CCT networks in tissues. CCT regeneration additionally drives repeated cancer metastasis. CCT superstructures facilitate full cancer metastasis. This study demonstrated nanoprotrusion-conducted CCT elongation along the path of least resistance and branching morphogenesis in bifid branching style. The cytocapsular membrane system expansion mechanics of CCTs and CCT networks described here may open new avenues for native cancer research and CTNS-targeted effective cancer cure. (200 words) Significance statementThe recent identification of PMCA2 as a biomarker for malignant tumors, allows imaging very early native cancer growths on culture plates in vitro and in human bodies as revealed from snapshot images of numerous cancer biopsies in vivo. Aggressive cancer metastasis, cancer progression, repeated cancer relapse, limited cancer therapy outcomes, pan-cancer drug resistance, immune cell attack escape, and immunotherapy non-responsive "cold" tumors are unmet challenges in clinical cancer therapy. However, the cytocapsular tube (CCT) elongation mechanisms in human tissues/organs with heterogeneous resistances are still unclear. Here, we report that CCT nanoprotrusions (NPs) extend into enlarged NPs apparently towards tissue of least resistance and subsequently develop into initial CCTs. Intracytocapsular oncocells released cytocapsulasomes to fuse into the membranes of initial CCTs and increase cytocapsular membrane areas. This enables oncocells to push and deform initial CCT membranes and to generate new CCTs with new nanoprotrusion layers. Furthermore, CCT branching morphogenesis develops in a bifid format, significantly increasing CCT numbers and expanding 3D CCT networks in all kinds of human tissues. CCT superstructures promote complete cancer metastasis in AMCC complexes. Repeated CCT regeneration drives repeated cancer relapses. This study reveals the CCT elongation laws, and elucidates that CCT elongation and branching morphogenesis drives cytocapsular membrane protected cancer metastasis, and that repeated CCT regeneration promotes repeated tumor relapses in vivo.

cancer biology↗

bioRxiv2024

Role of non-coding RNA hsa_circ_0001495 in 16HBE cellular inflammation induced by PM2.5 and O3 combined exposure

BackgroundPM2.5 and O3 are the main air pollutants in China, and inflammation of the respiratory system is one of their main toxic effects. Cyclic RNAs are involved in many pathophysiological processes, but their relationship to the combined exposure to PM2.5 and O3 has not yet been investigated. ObjectiveTo elucidate the biological function played by hsa_circ_0001495 in the induction of 16HBE cellular inflammation by combined exposure to PM2.5 and O3. MethodDetection of cell survival after 24h exposure of 16HBE cells to a combination of PM2.5 and O3 by CCK8. RT-qPCR and ELISA were used to detect inflammatory factors in 16HBE cells after co-exposing to PM2.5 and O3. CircRNA was screened using high throughput sequencing and bioinformatics analysis approaches. RNaseR experiments were carried out to verify the circular RNA properties of the circRNAs. Cytoplasmic-nuclear subcellular localisation assays and fish assays were used to verify the distribution of circRNAs in the nucleus versus the cytoplasm of the cell. To validate functions related with circRNA,RT-qPCR and ELISA were employed. ResultCombined exposure to PM2.5 and O3 resulted in decreased cell viability.Combined exposure to PM2.5 and O3 resulted in 16HBE inflammation. High throughput sequencing and RT-qPCR results showed that the expression of hsa_circ_0001495 was significantly downregulated in 16HBE exposed to PM2.5 and O3 in combination. Hsa_circ_0001495 is not easily digested by RNaseR enzymes and has the properties of a circular RNA. Hsa_circ_0001495 is expressed in the cytoplasm as well as in the nucleus, but its distribution is predominantly in the cytoplasm. ConclusionIn 16HBE cells, combined exposure to PM2.5 and O3 can induce an inflammatory response.hsa_circ_0001495 plays an inhibitory role in the inflammatory response of 16HBE cells that can be induced by combined exposure to PM2.5 and O3.

molecular biology↗

bioRxiv2023

Activating SRC/MAPK signaling via 5-HT1A receptor contributes to the effect of vilazodone on improving thrombocytopenia

Thrombocytopenia caused by long-term radiotherapy and chemotherapy exists in cancer treatment. Previous research demonstrates that 5-Hydroxtrayptamine (5-HT) and its receptors induces the formation of megakaryocytes (MKs) and platelets. However, the relationships between 5-HT1A receptor (5-HTR1A) and MKs is unclear so far. We screened and investigated the mechanism of vilazodone as a 5-HTR1A partial agonist in promoting MK differentiation and evaluated its therapeutic effect in thrombocytopenia. We employed a drug screening model based on machine learning (ML) to screen the megakaryocytopoiesis activity of VLZ. The effects of Vilazodone (VLZ) on megakaryocytopoiesis were verified in HEL and Meg-01 cells. Tg (itga2b: eGFP) zebrafish was performed to analyze the alterations in thrombopoiesis. Moreover, we established a thrombocytopenia mice model to investigate VLZ administration accelerates platelet recovery and function. We carried out network pharmacology, Western blot and immunofluorescence to demonstrate the potential targets and pathway of VLZ. VLZ has been predicted to have a potential biological action. Meanwhile, VLZ administration promotes MK differentiation and thrombopoiesis in cells and zebrafish models. Progressive experiments showed that VLZ has a potential therapeutic effect on radiation-induced thrombocytopenia in vivo. The network pharmacology and associated mechanism study indicated that SRC and MAPK signaling are both involved in the processes of megakaryopoiesis facilitated by VLZ. Furthermore, the expression of 5-HTR1A during megakaryocyte differentiation is closely related to the activation of SRC and MAPK. Our findings demonstrated that the expression of 5-HTR1A on MK, VLZ could bind to the 5-HTR1A receptor and further regulate the SRC/MAPK signaling pathway to facilitate megakaryocyte differentiation and platelet production, which provides new insights into the alternative therapeutic options for thrombocytopenia.

pharmacology and toxicology↗

bioRxiv2023

Presence of NCOR1+/CD4+ T cells in tertiary lymphoid organ predicts favorable prognosis in pancreatic ductal adenocarcinoma

CD4+ T cells have critical roles in anti-tumour immunity and its differentiation is known to be regulated by the nuclear receptor co-repressor 1 (NCOR1). Previous studies suggested that high CD4+ T cells are associated with a favourable prognosis in patients with pancreatic ductal adenocarcinoma (PDAC). However, the prognostic significance of NCOR1 in PDAC is still missing. In this study, the pathological impact of NCOR1 and CD4 has been analysed by multiplex immunohistochemistry in 100 PADC patients. NCOR1 expression in tertiary lymphoid organs is positively associated with the good prognosis of PDAC patients, while its expression in tumour tissue is not. Furthermore, the presence of NCOR1+/CD4+ T cells in tertiary lymphoid organs predicts a favourable prognosis in PDAC. Mechanistically, upregulation of NCOR1 expression in CD4+ T cells increases the release of TNF-, which induces the apoptosis of the tumor cells in vitro. Together, our data highlighted the tumour suppressive role of NCOR1+/CD4+ T cells in PDAC.

cancer biology↗

bioRxiv2023

Cytocapsular oncocells drive membrane-sheltered cancer progression

Cancer is a leading source of human lethality but current therapies have had limited efficacy in many cancers, which highlights an unmet need to assess the underlying mechanisms that govern cancer progression in vivo. Here we show that, upon malignant transformation, aggressive oncocells generate extracellular membranous compartments, cytocapsulas or cytocapsular tubes (CCTs), to enclose oncocells and engender cytocapsular oncocells in vivo. Cytocapsular oncocells are universally present in solid cancers and appear in hematologic cancers in the immune organs. Networks of cytocapsular tubes provide membrane-enclosed freeways for protected cancer metastasis. CCT networks interconnect cytocapsular tumors creating cytocapsular tumor network systems. Our findings suggest that cytocapsular oncocells drive membrane-encompassed cancer progression. Thus, interconnected cytocapsular oncocells, CCT networks and cytocapsular tumor network systems coordinate cancer progression in the integrated cytocapsular membrane systems.

cancer biology↗

bioRxiv2023

Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales

O_LIFlowering plant lineages display remarkable diversity in life history and morphological form. However our understanding of how this phenotypic diversity or disparity, arises and what, if any, relation there is to processes such as gene and genome duplication remains unlcear. C_LIO_LIHere we investigate the relationship between phenotypic and genomic evolution in the angiosperm order Fagales, a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous. To this end, we examine newly generated trait and transcriptomic datasets spanning the phylogenetic breadth of the order, including most extant genera as well as a rich diversity of Cretaceous fossil representatives. C_LIO_LIOur phylogenomic analyses resolved the location of an ancient polyploidization event in Juglandaceae and identified hotspots of gene-duplication and genomic conflict across the order. Examinations of phenotypic evolution (including morphospace occupancy and rate shifts) show that the morphospace occupied by Fagales was filled by the early Cenozoic and rates of evolution were highest during the early radiation of the Fagales crown and its major families. Many instances of phenotypic rates also correspond to hotspots of gene duplication. C_LIO_LIOur results show that Fagales conform to an "early burst" model of phenotypic diversification, with morphospace being filled early in the groups evolutionary history. Our study is consistent with others showing a decoupling of species diversification with other biological processes (e.g., phenotypic and genomic evolution), underscoring the complexity of understanding the major drivers of plant evolution over broad timescales. C_LI

evolutionary biology↗

bioRxiv2023

Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae)

AO_SCPLOWBSTRACTC_SCPLOWOaks (Quercus), one of the most species-rich and ecologically dominant woody plant clades in the Northern Hemisphere, are well known for their propensity to hybridize and form syngameons, complexes where alleles are readily exchanged among closely related species. While hybridization has been extensively studied towards the tips of the oak phylogeny, the extent, timeline, and evolutionary scenarios of hybridization during the early radiation of oaks and related genera (Quercoideae) remain poorly known. Using an expansive new dataset of nuclear and chloroplast sequences (including up to 431 spp.), we conducted a multifaceted phylogenomic investigation of Quercus aimed at characterizing gene-tree and cytonuclear (chloroplast-nuclear) discordance and identifying ancient reticulation in the early evolution of the group. We document extensive nuclear gene-tree and cytonuclear discordance at deep nodes in Quercus and Quercoideae, with Quercus recovered as non-monophyletic in the chloroplast phylogeny. Analyses recovered clear signatures of gene flow against a backdrop of incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and Quercoideae during their initial radiation, dated to the early-middle Eocene. Ancestral reconstructions including fossil data suggest that the ancestors of Castanea+Castanopsis, Lithocarpus, and the Old World oak clade co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Following this initial phase of radiation and reticulation, we detected multiple niche shifts in Quercus and other Quercoideae genera that likely facilitated their expansion into new habitats arising from post-Eocene climatic changes. Our study shows that hybridization--perhaps in the form of ancient syngameons similar to those seen today--has been a common and important process throughout the evolutionary history of oaks and their close relatives.

evolutionary biology↗

bioRxiv2023

Comparative Phylogenomics and Phylotranscriptomics Provide Insights into the Genetic Complexity of Nitrogen Fixing Root Nodule Symbiosis

Plant root nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. It is widely accepted that nodulation originated through the assembly of modules recruited from existing functions, such as mycorrhizal symbiosis, polar growth, and lateral root development. Because nodulating species are scattered within the NFNC, the number of times nodulation has evolved or has been lost has been a matter of considerable speculation. This interesting evolutionary question has practical implications concerning the ease with which nodulation might be engineered in non-nodulating crop plants. Nodulating species share many commonalities, due either to divergence from a common ancestor over 100 million years ago or to convergence or deep homology following independent origins over that same time period. In either case, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation--what must be acquired or cannot be lost for a functional symbiosis--and what the latitude is for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here we present new information across the spectrum of nodulating groups. We find no evidence for convergence at the level of amino acid residues or gene family expansion across the NFNC. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor, NIN, as a master regulator of nodulation, and identify key mutations affecting its function across the NFNC. We find that nodulation genes are over-represented among orthologous gene groups (OGs) present in the NFNC common ancestor, but that lineage-specific OGs play major roles in nodulation. We identified over 900,000 conserved noncoding elements (CNEs), of which over 300,000 were unique to NFNC species. A significant proportion of these are associated with nodulation-related genes and thus are candidates for transcriptional regulators.

evolutionary biology↗

bioRxiv2022

Two shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

Root nodule symbiosis (RNS) allows plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. RNS is a complex trait requiring coordination from both the plant host and the bacterial symbiont, and pinpointing the evolutionary origins of root nodules is critical for understanding the genetic basis of RNS. This endeavor is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for all major lineages of the NFC and an enhanced root nodule trait database to reconstruct the evolution of RNS. Through identification of the evolutionary pathway to RNS gain, we show that shifts among heterogeneous evolutionary rates can explain how a complex trait such as RNS can arise many times across a large phylogeny. Our analysis identifies a two-step process in which an ancestral precursor state gave rise to a more labile state from which RNS was quickly gained at specific points in the NFC. Our rigorous reconstruction of ancestral states illustrates how a two-step pathway could have led to multiple independent gains and losses of RNS, contrary to recent hypotheses invoking just a single gain and numerous losses. RNS may be an example of multi-level convergent evolution, thus requiring a broader phylogenetic and genetic scope for genome-phenome mapping to elucidate mechanisms enabling fully functional RNS.

evolutionary biology↗

bioRxiv2022

Cytocapsular cancer evolution analyses of 311 kinds of cancers

Cancer is a leading cause of human lethality. Cytocapsular tube, a newly discovered cancer cell specific organelle in vivo, plays pleiotropic biological functions and its generation distinguishes incomplete from complete cancer cells. It is essential for complete malignant tumor growth, cancer metastasis, conventional cancer drug pan-resistance, and cancer relapse. However, mechanisms of cytocapsular cancer evolution are still elusive. Here, we investigated cytocapsular cancer evolution in 311 kinds/subtype of cancers, including 265 types/subtypes of solid cancers and 46 types/subtypes of liquid/hematological cancers. We analyzed 9,856 pieces of annotated clinical tissue samples from 9,682 cancer patients in the asymptotic early stage, Stages I-IV, and before, during and after cancer treatments. We discovered that cytocapsular cancer evolution in solid cancers includes: transformation, formation of incomplete cancer cells, transition to complete cancer cells surrounded by cytocapsulae (CC), merging of complete cancer cells by devolution, formation of cytocapsular tubes (CCTs) and complete malignant tumors in superlarge CC. This is followed by generation of CCT networks, cancer metastasis, CCT network-tumor system (CNTS), CCT degradation and decomposition, and spatiotemporal moving CNTS. In addition, cytocapsular cancer evolution related to liquid (hematological) cancers including bone marrow, thymus, lymph nodes, and spleen, mirrors the process in solid cancers, except that cancer cells in the blood only form CCs but not CCTs. In summary, our study established a cytocapsular cancer evolution atlas, which may pave an avenue for the research on therapy of both solid and liquid cancers.

cancer biology↗

bioRxiv2022

Cytocapsulae and cytocapsular tubes are golden targets for precise, effective and efficient cancer diagnosis and therapy in 307 kinds of liquid and solid cancers

Cancer is a leading cause of human lethality worldwide. A cancer cell is not only the cytoplasm and nucleus enclosed in the cell membrane. A malignant tumor is not only a mass of cancer cells. Cancer in a patient is not only isolated tumors distributed in tissues and organs. The comprehensive understanding of the complete structural compartments and their biological functions of cancer cells, malignant tumors and tumor systems in patients in vivo is an indispensable prerequisite for effective drug development and efficient clinical cancer pharmacotherapies. However, there remains an open question for a long time: what are the complete structural compartments of cancer cells, malignant tumors and tumor systems in the patient body? Here, we comprehensively and systematically investigated the complete structural compartments of cancer cells, malignant tumors and cytocapsular tube (CCT) network-tumor system (CNTS) of 307 types/subtypes of cancers in 33 kinds of tissues and organs by biochemistry and molecular biology assays with 9,811 clinical cancer tissue specimens from 9,637 cancer patients and >110,000 immunohistochemistry (IHC) fluorescence staining images. We discovered the complete structural compartments of cancer cells, malignant tumors and CNTSs in 307 kinds of cancers, elucidated mechanisms of cytocapsular growth and CCT elongation, and identified the comprehensive procedures of cancer evolution in patients. This study paves avenues for curing all kinds of cancers.

cancer biology↗

bioRxiv2022

Cytocapsular tube network-tumor system is an integrated physical target for the highly effective and efficient pharmacotherapy of solid cancers

Cancer is a leading cause of human lethality and cancer drug pan-resistant tumor metastasis (cdp-rtm) is a major source of cancer death. The integrated cytocapsular tube (CCT) networktumor system (CNTS) is essential for cancer evolution procedures including cancer cell proliferation, migration and dissemination in CCT networks, new tumor growth in CCT terminals, conventional cancer drug pan-resistance, and tumor relapse. The preclinical screening experimentations with CCTs and networks are necessary prerequisites for the discovery and development of cancer drug candidates for efficient clinical trials, and effective and precise clinical cancer pharmacotherapy. However, it is unknown whether the popularly employed conventional mouse experimentations for preclinical therapeutic development generate CCTs and networks. Here, we comprehensively investigated the cancer cell line derived xenografts (CDX) of 8 kinds of cancer cell lines, and patient cancer cells derived-xenografts (PDX) with 16 kinds of clinical primary and metastatic malignant tumor cells in multiple cancer stages by immunohistochemistry staining assays with CCT marker protein antibodies of anti-CM-01 antibodies. We found that there are no CCTs or CCT networks in all these examined 16 CDX and 22 PDX transplanted tumors. Our data evidenced that the conventional transplantation tumors for preclinical therapeutic development do not engender CCTs or CNTS, which is consistent with and provides an explanation of the poor clinical outcomes of the marketed cancer drugs. This study demonstrated that CCT network-tumor system (CNTS) is an integrated physical target for pharmacotherapy, and that preclinical experimentations engendering CNTS (such as CCT xenograft, CCTX) should be employed for the discovery and development of highly effective and efficient cancer drugs aimed for cure of solid cancers.

cancer biology↗

bioRxiv2022

Cytocapsular tubes and networks function as physical superdefence freeway systems conducting conventional cancer drug pan-resistant tumor metastasis

Cancer drug pan-resistant tumor metastasis (cdp-rtm) is a major source of cancer lethality. Cytocapsular tubes (CCTs) and their networks are physical membrane-enclosed freeway systems for cancer cell dissemination across tissues and organs in vivo. Whether cytocapsular tube superlarge biomembranes function as superdenfence and conduct cdp-rtm is unknown. It is also unknown whether conventional cancer drug development methods, including cancer cell line derived xenograft (CDX) and patient cancer cell derived xenograft (PDX), generate cytocapsular tubes (CCTs). It is also unclear whether xenografts can be created that contain CCTs for efficient cancer drug development. Here, we investigated CCT functions related to cancer drug resistance, CCTs in CDX and PDX and CCT xenograft (CCTX). Using clinical cancer tissues, we discovered that CCTs potently shielded against multiple chemotherapy treatments with diverse conventional cancer drugs. Next, our quantitative analyses show that CCT biomembrane drug barriers significantly increase cancer drug resistance by 6.6-folds to14-folds. We found that conventional CDX and PDX animal models do not generate CCTs in these xenografts. By mimicking in vivo cancer cell environments for cancer patient cancer cell culturing, we have successfully isolated CH-5high/CH-6high subpopulations of patient breast cancer cells and pancreas cancer cells that are propertied with cytocapsular tube generation capacities and engender large quantities of CCTs in mouse xenografts. Biochemical and immunohistochemistry analyses demonstrated that CCTs in these xenografts are similar to those in clinical cancer tissues. In summary, our research has identified that CCTs and networks function as physical superdefence freeway systems conducting conventional cancer drug pan-resistant tumor metastasis, and developed a CCTX platform for highly efficient cancer drug development, which pave avenues for more efficient development of effective and precise cancer drugs for tumor cure at both personal and broad-spectrum levels.

cancer biology↗