Biology subjects

Lu, K.

Publications and source records attributed to Lu, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Long-term combination therapy with Metformin and Oxymetholone in a Fanconi Anemia mouse model

Fanconi Anemia (FA) is a disease caused by defective DNA repair which manifests as bone marrow failure, cancer predisposition, and developmental defects. Mice containing inactivating mutations in one or more genes in the FA pathway partially mimic the human disease. We previously reported that monotherapy with either metformin (MET) or oxymetholone (OXM) improved peripheral blood (PB) counts and the number and functionality of bone marrow (BM) hematopoietic stem progenitor cells (HSPCs) number in Fancd2-/- mice. To evaluate whether the combination treatment of these drugs has a synergistic effect to prevent bone marrow failure in FA, we treated cohorts of Fancd2-/- mice and wild-type controls with either MET alone, OXM alone, MET+OXM or placebo diet. Both male and female mice were treated from age 3 weeks to 18 months. The OXM treated animals showed modest improvements in blood parameters including platelet count (p=0.01) and hemoglobin levels (p<0.05). In addition, the percentage of quiescent HSC (LSK) was significantly increased (p=0.001) by long-term treatment with MET alone. However, the absolute number of progenitors, measured by LSK frequency or CFU-S, was not significantly altered by MET therapy. The combination of metformin and oxymetholone did not result in a significant synergistic effect on any parameter. Male animals on MET+OXM or MET alone were significantly leaner than controls at 18 months, regardless of genotype. Gene expression analysis of liver tissue from these animals showed that some of the expression changes caused by Fancd2 deletion were partially normalized by metformin treatment. Importantly, no adverse effects of the individual or combination therapies were observed, despite the long-term administration. Highlights- Long-term coadministration of metformin in combination oxymetholone is well tolerated by Fancd2-/- mice. - HSC quiescence in mutant mice was enhanced by treatment with metformin alone. - Metformin treatment caused a partial normalization of gene expression in the livers of mutant mice.

genetics↗

bioRxiv2023

Propionyl-CoA carboxylase subunit B modulates PIK3CA-regulated immune-surveillance in a pancreatic cancer mouse model

Most human pancreatic ductal adenocarcinoma (PDAC) are not infiltrated with cytotoxic T cells and are highly resistant to immunotherapy. Over 90% of PDAC have oncogenic KRAS mutations, and phosphoinositide 3-kinases (PI3Ks) are direct effectors of KRAS. Our previous study demonstrated that ablation of Pik3ca in KPC (KrasG12D; Trp53R172H; Pdx1-Cre) pancreatic cancer cells induced host T cells to infiltrate and completely eliminate the tumors in a syngeneic orthotopic implantation mouse model. Now, we show that implantation of Pik3ca-/- KPC (named KO) cancer cells induces clonal expansion of cytotoxic T cells infiltrating the pancreatic tumors. To identify potential molecules that can regulate the activity of these anti-tumor T cells, we conducted an in vivo genome-wide gene-deletion screen using KO cells implanted in the mouse pancreas. The result shows that deletion of propionyl-CoA carboxylase subunit B gene (Pccb) in KO cells (named p-KO) leads to immune evasion, tumor progression and death of host mice. Surprisingly, p-KO tumors are still infiltrated with clonally expanded CD8+ T cells but they are inactive against tumor cells. However, blockade of PD-L1/PD1 interaction reactivated these clonally expanded T cells infiltrating p-KO tumors, leading to slower tumor progression and improve survival of host mice. These results indicate that Pccb can modulate the activity of cytotoxic T cells infiltrating some pancreatic cancers and this understanding may lead to improvement in immunotherapy for this difficult-to-treat cancer.

cancer biology↗

bioRxiv2023

Integration of eQTL and Machine Learning Methods to Dissect Causal Genes with Pleiotropic effects in Genetic Regulation Networks of Seed Cotton Yield

Expression quantitative trait loci (eQTL) provide a powerful means of investigating the biological basis of genome-wide association study (GWAS) results and exploring complex traits or phenotypes. In addition to identifying the causal gene in cis, eQTL analysis also reveals a large number of trans-regulated genes located on different chromosomes, which form a gene regulatory network (GRN) that complements the GWAS locus. However, the dissection of a GRN and the crosstalk underlying multiple agronomical traits, along with prioritizing important genes in eQTL-derived GRNs, remains a major challenge. In this study, we generated 558 transcriptional profiles of lint-bearing ovules at one day post-anthesis (DPA) from a selective core cotton germplasm, from which we identified 12,207 eQTLs. By integrating with a GWAS catalog, we found that 66 out of 187 (35.29%) known phenotypic GWAS loci are colocalized with 1,090 eQTLs, forming 38 major functional GRNs predominantly (30 out of 38) associated with seed size-related phenotypes. Of the eGenes, 34 were shared between at least two functional GRNs, exhibiting pleiotropic effects, such as NF-YB3, GRDP1, and IDD7. Narrow-sense heritability analysis showed that the heritability increased with combining the eQTLs with GRNs compared to those with previous yield trait GWAS loci. The extreme gradient boosting (XGBoost) machine learning approach was then applied to predict seed cotton yield phenotypes based on gene expression. Top-ranking eGenes (NF-YB3, FLA2, and GRDP1) derived by XGBoost with pleiotropic effects on yield traits were validated, along with their potential roles by correlation analysis, domestication selection analysis, and transgenic plants. This study provides insights into the mining of GRNs in relation to the pleiotropy of phenotype. The combination of eQTL and machine learning approaches is efficient in improving the genetic dissection of agricultural traits.

genetics↗

bioRxiv2023

The BTB-ZF gene Bm-mamo regulate pigmentation in caterpillars

The color pattern of insects is one of the most diverse adaptive evolutionary phenotypes. However, the molecular regulation of this color pattern is not fully understood. In this study, we found that the transcription factor Bm-mamo is responsible for black dilute (bd) allele mutations in the silkworm. Bm-mamo belongs to the BTB zinc finger family and is orthologous to mamo in Drosophila melanogaster. This gene has a conserved function in gamete production in Drosophila and silkworms and has evolved a pleiotropic function in the regulation of color patterns in caterpillars. Using RNAi and clustered regularly interspaced short palindromic repeats (CRISPR) technology, we showed that Bm-mamo is a repressor or has dark melanin patterns in the larval epidermis. Using in vitro binding assays and gene expression profiling in wild-type and mutant larvae, we also showed that Bm-mamo likely regulates the expression of related pigment synthesis and cuticular protein genes in a coordinated manner to mediate its role in color pattern formation. This mechanism is consistent with the dual role of this transcription factor in regulating both the structure and shape of the cuticle and the pigments that are embedded within it. This study provides new insight into the regulation of color patterns as well as into the construction of more complex epidermis features in some insects.

genetics↗

bioRxiv2023

Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancer

KRAS is the archetypal oncogenic driver of pancreatic cancer. To identify new modulators of KRAS activity in human pancreatic ductal adenocarcinoma (PDAC), we performed regulatory network analysis on a large collection of expression profiles from laser capture microdissected samples of PDAC and benign controls. We discovered that BMAL2, a member of the PAS family of transcription factors, promotes tumor initiation, progression, and post-resection survival, and is highly correlated with KRAS activity. Functional analysis of BMAL2 target genes suggested a role in regulating the hypoxia response, a hallmark of PDAC. Knockout of BMAL2 in multiple human PDAC cell lines reduced cancer cell viability, invasion, and glycolysis, leading to broad dysregulation of cellular metabolism, particularly under hypoxic conditions. We find that BMAL2 directly regulates hypoxia-responsive target genes and is necessary for the stabilization of HIF1A under low oxygen conditions, while simultaneously destabilizing HIF2A. Notably, in vivo xenograft studies demonstrated that BMAL2 loss significantly impairs tumor growth and reduces tumor volume, underscoring its functional importance in tumor progression. We conclude that BMAL2 is a master transcriptional regulator of hypoxia responses in PDAC that works downstream of KRAS signaling, possibly serving as a long-sought molecular switch that distinguishes HIF1A- and HIF2A-dependent modes of hypoxic metabolism. Statement of SignificanceWe annotate the landscape of KRAS-associated transcriptional drivers of pancreatic cancer initiation, progression, and overall survival, leading to the identification of BMAL2 as a novel regulator of hypoxic metabolism. BMAL2 helps execute the oncogenic transcriptional programs of KRAS and serves as a long-sought switch between HIF1A- and HIF2A-dependent modes of hypoxic metabolism.

cancer biology↗

bioRxiv2023

Excessive apoptosis of naïve T cells resulting hyperactivation as a cause of mammalian aging

In mammals, the most remarkable T cell variations with aging are the shrinking of naive T cell pool and enlargement of memory T cell pool, which are partially caused by thymic involution. However, it remains an enigma whether these T-cell-related changes are consequences or causes of mammalian aging. In this study, we find that the T-cell specific Rip1 KO mice present similar age-related T cell changes and exhibit signs of accelerated aging, including inflammation, multiple age-related diseases and a shorter lifespan. Mechanistically, T cells lacking RIP1 displayed excessive apoptosis, leading to T cell compensatory proliferation, hyperactivation, increased inflammation, and ultimately premature death. Consistent with this, blocking apoptosis by co-deletion of Fadd in Rip1 deficient T cells significantly recovered the lymphopenia and imbalance between naive and memory T cell, substantially restored ageing-related phenotypes, and prolonged life span in T-cell specific Rip1 KO mice. These results suggest that changes in T cells play a causal role in mammalian aging. Therefore, replenishing or blocking apoptosis of naive T cells could offer new therapeutic approaches for aging and age-related diseases.

immunology↗

bioRxiv2023

Sustained Delivery of GLP-1 Receptor Agonists from Injectable Biomimetic Hydrogels Improves Treatment of Diabetes

Glucagon-like peptide-1 (GLP-1) is an incretin hormone and neurotransmitter secreted from intestinal L-cells in response to nutrients to stimulate insulin and block glucagon secretion in a glucose-dependent manner. GLP-1 in itself is rapidly degraded, but long-acting GLP-1 receptor agonists (GLP-1 RAs) have become central in the treatment of T2D because of the beneficial effects extending also beyond glucose control. Currently, these therapeutics must be injected either daily or weekly or taken daily orally, leaving room for technological innovations that enable less frequent administrations, which will reduce patient burden and increase patient compliance. An ideal GLP-1 RA drug product would provide continuous therapy for upwards of four months from a single administration to match the cadence with which T2D patients typically visit their physician. In this work, we leveraged an injectable hydrogel depot technology to develop a long-acting GLP-1 RA drug product. By modulating the hydrogel properties to tune GLP-1 RA retention within the hydrogel depot, we engineered formulations capable of months-long GLP-1 RA delivery. Using a rat model of T2D, we confirmed that a single injection of hydrogel-based therapies exhibits sustained exposure of GLP-1 RA over 42 days, corresponding to a once-every four month therapy in humans. Moreover, these hydrogel therapies maintained optimal management of blood glucose and weight comparable to daily injections of a leading GLP-1 RA drug molecule. The pharmacokinetics and pharmacodynamics of these hydrogel-based long-acting GLP-1 RA treatments are promising for development of novel therapies reducing treatment burden for more effective management of T2D. Progress and PotentialWhile insufficient access to quality healthcare is problematic for consistent management of Type II diabetes (T2D), poor adherence to burdensome treatment regimens is one of the greatest challenges for disease management. Glucagon-like peptide 1 (GLP1) drugs have become central to the treatment of T2D due to their many beneficial effects beyond improving glucose control. Unfortunately, while optimization of GLP1 drugs has reduced treatment frequency from daily to weekly, significant patient burden still leads to poor patience compliance. In this work we developed an injectable hydrogel technology to enable GLP1 drugs only requiring administration once every four months. We showed in a rat model of T2D that one injection of a hydrogel-based therapy improves management of blood glucose and weight when compared with daily injections of the leading drug used clinically. These hydrogel-based GLP1 treatments are promising for reducing treatment burden and more effectively managing T2D. Future ImpactA GLP-1-based drug product providing four months of continuous therapy per administration could be transformational for the management of Type II diabetes (T2D). One of the most challenging aspects of diabetes management with GLP-1 mimics is maintenance of consistent levels of the drugs in the body, which is complicated by poor patient compliance on account of the high frequency of dosing required for current treatments. By leveraging a unique sustained release hydrogel depot technology we develop a months-long GLP-1 drug product candidate that has the potential to reduce patient burden and improving diabetes management. Overall, the hydrogel technology we describe here can dramatically reduce the frequency of therapeutic interventions, significantly increasing patient quality of life and reducing complications of diabetes management. Our next steps will focus on optimization of the drug formulations in a swine model of T2D, which is the most advanced and translationally-relevant animal model for these types of therapeutics. The long-term vision for this work is to translate lead candidate drug products towards clinical evaluation, which will also require comprehensive safety evaluation in multiple species and manufacturing our these materials according to Good Manufacturing Practices. The months-long-acting GLP-1 drug product that will come from this work has the potential to afford thus far unrealized therapeutic impact for the hundreds of millions of people with diabetes worldwide.

bioengineering↗

bioRxiv2022

Antimicrobial copper as an effective and practical deterrent to surface transmission of SARS-CoV-2

The aerosols are critical for SARS-CoV-2 transmission, however in areas with high confluence of people the contaminated surfaces take an important role that we could attack using antimicrobial surfaces including copper. In this study, we wanted to challenge infectious SARS-CoV-2 with two samples of copper surfaces and one plastic surface as control at different direct times contact. To evaluate and quantify virucidal activity of copper against SARS-CoV-2, two methods of experimental infection were performed, TCID50 and plaque assays on VeroE6 cells, showing significant inactivation of high titer of SARS-CoV-2 within minutes reaching 99.9 % of inactivation of infectivity on both copper surfaces. Daily high demand surfaces contamination is an issue that we have to worry about not only during the actual pandemic time but also for future, where copper or its alloys will have a pivotal role. ImportanceQuantitative data obtained of TCID50 and plaque assay with infectious SARS-CoV-2 virus showed that after direct contact with copper or copper alloys, viruses were inactivated within minutes. Notably, the SARS-CoV-2 virus used in these assays was in high titer (106 PFU/mL) showing strong copper inactivation of the infectious SARS-CoV-2.

microbiology↗

bioRxiv2022

Multiple Cullin-Associated E3 Ligases Regulate Cyclin D1 Protein Stability

Cyclin D1 is a key regulator of cell cycle progression, which forms a complex with CDK4/6 to regulate G1/S phase transition during cell cycle progression. Cyclin D1 has been recognized as an oncogene since it was upregulated in several different types of cancers. It is known that the post-translational regulation of cyclin D1 is controlled by ubiquitination/ proteasome degradation system in a phosphorylation-dependent manner. A few cullin-associated F-box E3 ligases have been shown to regulate cyclin D1 degradation; however, it is not known if additional cullin-associated E3 ligases participate in the regulation of cyclin D1 protein stability. In this study, we have screened a siRNA library containing siRNAs specific for 154 ligase subunits, including F-box, SOCS, BTB-containing proteins and DDB proteins. We found that multiple cullin-associated E3 ligases regulate cyclin D1 activity, including Keap1, DDB2, WSB2 and Rbx1. We found that these E3 ligases directly interact with cyclin D1, regulate cyclin D1 ubiquitination and proteasome degradation in a phosphorylation-dependent manner. These E3 ligases also control cell cycle progression and cell proliferation through regulation of cyclin D1 protein stability. Our study provides novel insights into regulatory mechanisms of cyclin D1 protein stability and function.

molecular biology↗

bioRxiv2021

Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in PSC.

ObjectiveConflicting microbiota data exist for primary sclerosing cholangitis (PSC) and experimental models. Goal: Define complex interactions between resident microbes and their association in PSC patients by studying antibiotic-treated specific pathogen-free (SPF) and germ-free (GF) multi-drug-resistant 2 deficient (mdr2-/-) mice. DesignWe measured weights, liver enzymes, RNA expression, histological, immunohistochemical and fibrotic biochemical parameters, fecal 16s rRNA gene profiling, and metabolomic endpoints in gnotobiotic and antibiotic-treated SPF mdr2-/- mice and targeted metagenomic analysis in PSC patients. ResultsGF mdr2-/- mice had exaggerated hepatic inflammation and fibrosis with 100% mortality by 8 weeks; early SPF autologous stool transplantation rescued liver-related mortality. Broad-spectrum antibiotics and vancomycin alone accelerated disease in weanling SPF mdr2-/- mice, indicating that vancomycin-sensitive resident microbiota protect against hepatobiliary disease. Vancomycin treatment selectively decreased Lachnospiraceae and short-chain fatty acids (SCFAs) but expanded Enterococcus and Enterobacteriaceae. Antibiotics increased cytolysin-expressing E. faecalis and E. coli liver translocation; colonization of gnotobiotic mdr2-/- mice with translocated E. faecalis and E. coli strains accelerated liver inflammation and mortality. Lachnospiraceae colonization of antibiotic pre-treated mdr2-/- mice reduced liver fibrosis, inflammation and translocation of pathobionts, while Lachnospiraceae-produced SCFA decreased fibrosis. Fecal E. faecalis/ Enterobacteriaceae was positively and Lachnospiraceae was negatively associated with PSC patients clinical severity Mayo risk scores. ConclusionsWe identified specific functionally protective and detrimental resident bacterial species in mdr2-/- mice and PSC patients with associated clinical outcomes. These insights may guide personalized targeted therapeutic interventions in PSC patients.

microbiology↗

bioRxiv2021

Reference genomes of 545 silkworms enable high-throughput exploring genotype-phenotype relationships

The silkworm Bombyx mori is a domestic insect for silk production and a lepidopteran model. The currently available genomes limit a full understanding of its genetic and phenotypic diversity. Here we assembled long-read genomes of 545 domestic and wild silkworms and constructed a high-resolution pan-genome dataset. We found that the silkworm population harbors extremely variable genomes containing 7,308 new gene families, 4,260 (22%) core gene families, and 3,432,266 non-redundant SVs. We deciphered a series of causal genes and variants associated with domestication, breeding, and ecological adaptation traits, and experimentally validated two of those genes using CRISPR-Cas9 or RNA interference. This unprecedented large-scale genomic resource allows for high-throughput screening of interesting traits for functional genomic research and breeding improvement of silkworms and may serve as a guideline for traits decoding in other species.

genomics↗

bioRxiv2021

Iba1+ cell density and morphology classification at postnatal day 10 in four hippocampal subregions of female and male C57BL/6J mice

Microglia, the resident immune cells of the brain, support normal brain function and the brains response to disease and injury. The hippocampal dentate gyrus (DG) is an area of microglial study due to its central role in many behavioral and cognitive functions. Interestingly, microglia and related cells are distinct in female vs. male rodents, even in early life. Indeed, postnatal day (P)-dependent sex differences in number, density, and morphology of microglia have been reported in certain hippocampal subregions at specific ages. However, sex differences in the DG have not yet been assessed at P10, a rodent developmental time point translationally relevant to human term gestation. To address this knowledge gap, Iba1+ cells in the DG (which are enriched in the Hilus and Molecular Layer) in female and male C57BL/6J mice were analyzed for their number (via stereology) and density (via stereology and via sampling). Next, Iba1+ cells were classified into published morphology categories. Finally, the percent of Iba1+ cells in each morphology category was multiplied by total cell number to generate a total number of Iba1+ cells in each morphological category. Results show no sex difference in Iba1+ cell number, density, or morphology in the P10 Hilus or Molecular Layer. The lack of sex difference in Iba1+ cells in P10 DG using commonly-employed methodologies (sampling, stereology, morphology classification) provides a baseline from which to interpret microglia changes seen after injury. HIGHLIGHTSO_LISex differences in Iba1+ cells were assessed in the dentate gyrus (DG) of P10 mice C_LIO_LIIba1+ cells were assessed in DG microglia-rich subregions: Hilus and Molecular Layer C_LIO_LIBoth stereology and sampling approaches were used to quantify Iba1+ cells C_LIO_LINo sex difference found in Iba1+ cell number, density, or morphology in P10 mice DG C_LI

neuroscience↗

bioRxiv2021

Cinnamoyl-CoA Reductase 1 (CCR1) and CCR2 Function Divergently in Tissue Lignification, Flux Control and Cross-talk with Glucosinolate Pathway in Brassica napus

Cinnamoyl-CoA reductase (CCR) is the entry point of lignin pathway and a crucial locus in dissection and manipulation of associated traits, but its functional dissection in Brassicaceae plants is largely lagged behind though Arabidopsis thaliana CCR1 has been characterized to certain extent. Here, 16 CCR genes are identified from Brassica napus and its parental species B. rapa and B. oleracea. Brassicaceae CCR genes are divided into CCR1 subfamily and CCR2 subfamily with divergent organ-specificity, yellow-seed trait participation and stresses responsiveness. CCR1 is preferential in G- and H-lignins biosynthesis and vascular development, while CCR2 has a deviation to S-lignin biosynthesis and interfascicular fiber development. CCR1 has stronger effects on lignification-related development, lodging resistance, phenylpropanoid flux control and seed coat pigmentation, whereas CCR2 controls sinapates levels. CCR1 upregulation could delay bolting and flowering time, while CCR2 upregulation weakens vascular system in leaf due to suppressed G lignin accumulation. Besides, CCR1 and CCR2 are deeply but almost oppositely linked with glucosinolates metabolism through inter-pathway crosstalk. Strangely, upregulation of both CCR1 and CCR2 could not enhance resistance to UV-B and S. sclerotiorum though CCR2 is sharply induced by them. These results provide systemic dissection on Brassica CCRs and CCR1-CCR2 divergence in Brassicaceae. HighlightBrassicaceae contains two types of Cinnamoyl-CoA reductase. As revealed in Brassica napus, they are divergently involved in lignin monomer biosynthesis, tissue lignification, phenylpropanoid flux control, and inter-pathway crosstalk with glucosinolates.

plant biology↗

bioRxiv2021

Cardiac Nmnat/NAD+/SIR2 pathways activation mediates endurance exercise resistance to heart defects induced by a high-fat diet in aging Drosophila

Endurance exercise is an important way to resist and treat a high-fat-diet(HFD)-induced heart defects, but the underlying molecular mechanisms are poorly understood. Here, we used Drosophila to identify whether cardiac Nmnat/NAD+/SIR2 pathways activation could mediate endurance exercise resistance to heart defects. The results showed that endurance exercise activated the cardiac Nmnat/NAD+/SIR2/FOXO pathway and Nmnat/NAD+/SIR2/PGC-1 pathway, including up-regulating cardiac Nmnat, SIR2, FOXO, PGC-1 expression, SOD activity, and NAD+ level, and it prevented HFD-induced or cardiac Nmnat knock-down-induced cardiac lipid accumulation, MDA content and fibrillation increase, and fractional shortening decrease. Cardiac Nmnat overexpression activated heart Nmnat/NAD+/SIR2 pathways and resisted HFD-induced cardiac malfunction, but it could not protect against HFD-induced lifespan reduction and locomotor impairment. Exercise improved lifespan and mobility in cardiac Nmnat knockdown flies. Therefore, current results confirmed that cardiac Nmnat/NAD+/SIR2 pathways were important antagonists of HFD-induced heart defects. The cardiac Nmnat/NAD+/SIR2 pathways activation was the important underlying molecular mechanism of endurance exercise and cardiac Nmnat overexpression against heart defects in Drosophila.

genetics↗

bioRxiv2020

Improved microbial community characterization of 16S rRNA via metagenome hybridization capture enrichment

Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases. However, shotgun metagenomic sequencing is much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having < 80% sequence similarity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average >400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely in part to the extent and curation of the reference databases considered.

microbiology↗

bioRxiv2020

Primate heart regeneration via migration and fibroblast repulsion by human heart progenitors

SUMMARYHuman heart regeneration is one of the most critical unmet clinical needs at a global level1. Muscular regeneration is hampered both by the limited renewing capacity of adult cardiomyocytes2-4 and the onset of cardiac fibrosis5,6, resulting in reduced compliance of the tissue. Primate have proven to be ideal models for pluripotent stem cell strategies for heart regeneration, but unravelling specific approaches to drive cell migration to the site of injury and inhibition of subsequent fibrosis have been elusive. Herein, by combining human cardiac progenitor lineage tracing and single-cell transcriptomics in injured non-human primate heart bio-mimics, we uncover the coordinated muscular regeneration of the primate heart via directed migration of human ventricular progenitors to sites of injury, subsequent fibroblast repulsion targeting fibrosis, and ultimate functional replacement of damaged cardiac muscle by differentiation and electromechanical integration. Single-cell RNAseq captured distinct modes of action, uncovering chemoattraction mediated by CXCL12/CXCR4 signalling and fibroblast repulsion regulated by SLIT2/ROBO1 guidance in organizing cytoskeletal dynamics. Moreover, transplantation of human cardiac progenitors into hypo-immunogenic CAG-LEA29Y transgenic porcine hearts following injury proved their chemotactic response and their ability to generate a remuscularized scar without the risk of arrhythmogenesis in vivo. Our study demonstrates that inherent developmental programs within cardiac progenitors are sequentially activated in the context of disease, allowing the cells to sense and counteract injury. As such, they may represent an ideal bio-therapeutic for functional heart rejuvenation.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗

bioRxiv2020

Cryo-EM structure of C9ORF72-SMCR8-WDR41 reveals the role as a GAP for Rab8a and Rab11a

A massive intronic hexanucleotide repeat (GGGGCC) expansion in C9ORF72 is a genetic origin of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recently, C9ORF72, together with SMCR8 and WDR41, has been shown to regulate autophagy and function as Rab GEF. However, the precise function of C9ORF72 remains unclear. Here, we report the cryo-EM structure of the human C9ORF72-SMCR8-WDR41 complex at a resolution of 3.2 [A]. The structure reveals the dimeric assembly of a heterotrimer of C9ORF72-SMCR8-WDR41. Notably, the C-terminal tail of C9ORF72 and the DENN domain of SMCR8 play critical roles in the dimerization of the two protomers of the C9ORF72-SMCR8-WDR41 complex. In the protomer, C9ORF72 and WDR41 are joined by SMCR8 without direct interaction. WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix. Interestingly, the prominent structural feature of C9ORF72-SMCR8 resembles that of the FLNC-FNIP2 complex, the GTPase activating protein (GAP) of RagC/D. Structural comparison and sequence alignment revealed that Arg147 of SMCR8 is conserved and corresponds to the arginine finger of FLCN, and biochemical analysis indicated that the Arg147 of SMCR8 is critical to the stimulatory effect of the C9ORF72-SMCR8 complex on Rab8a and Rab11a. Our study not only illustrates the basis of C9ORF72-SMCR8-WDR41 complex assembly but also reveals the GAP activity of the C9ORF72-SMCR8 complex. Significance StatementC9ORF72, together with SMCR8 and WDR41, has been shown to form a stable complex that participates in the regulation of membrane trafficking. We report the cryo-EM structure of the C9ORF72-SMCR8-WDR41 complex at atomic resolution. Notably, the stoichiometry of the three subunits in the C9ORF72-SMCR8-WDR41 complex is 2:2:2. Interestingly, the C-termini of C9ORF72 and the DENN domain of SMCR8 mediate the dimerization of the two C9ORF72-SMCR8-WDR41 protomers in the complex. Moreover, WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix without direct contact with C9ORF72. Most importantly, the C9ORF72-SMCR8 complex works as a GAP for Rab8a and Rab11a in vitro, and the Arg147 of SMCR8 is the arginine finger.

biochemistry↗

bioRxiv2020

CReSCENT: CanceR Single Cell ExpressioN Toolkit

CReSCENTCanceR Single Cell ExpressioN Toolkit (https://crescent.cloud), is an intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA sequencing (scRNA-seq) data. While scRNA-seq data for tumour specimens are readily generated, subsequent analysis requires high-performance computing infrastructure and user expertise to build analysis pipelines and tailor interpretation for cancer biology. CReSCENT uses public data sets and preconfigured pipelines that are accessible to computational biology non-experts and are user-editable to allow optimization, comparison, and reanalysis for specific experiments. Users can also upload their own scRNA-seq data for analysis and results can be kept private or shared with other users.

bioinformatics↗