Publications by authors named "Yanhui Hu"

126 Publications

Spacer-based gap balancing is useful in total knee arthroplasty: a 3-year follow-up of a retrospective study.

J Orthop Surg Res 2021 Oct 21;16(1):633. Epub 2021 Oct 21.

Department of Orthopaedics, Liaocheng People's Hospital, 67 Dongchang West Road, Liaocheng, 252000, Shandong, China.

Background: Which technique, gap balancing or measured resection, can obtain better femoral component alignment and soft tissue balance in total knee arthroplasty (TKA) is still controversial. This study aimed to determine whether the gap balancing technique using a modified spacer block in TKA can result in better postoperative clinical outcomes than the measured resection technique.

Methods: A total of 124 patients who underwent consecutive primary TKA between May 2016 and August 2018 were retrospectively reviewed. The gap balancing technique assisted by a modified spacer block was used in 61 patients, and the measured resection technique was used in 63 patients. The surgical, imaging and knee function outcomes of the two groups were compared.

Results: The thickness of the posterior medial condyle bone resection using the modified spacer block tool in gap balancing was significantly larger than that of the MR technique (P = 0.001). Compared with the measured resection group, the gap balancing group had a greater external rotation resection angle of the femur (4.06 ± 1.10° vs. 3.19 ± 0.59°, P < 0.001°). Despite these differences, the mean ROM, KSS scores, and WOMAC scores at the 6-week, 1-year, and 2-year follow-ups were not significantly different. Postoperatively, there was no significant difference between the two groups in mechanical axis measurements (P = 0.275), the number of HKA outliers (P = 0.795) or the joint line displacement (P = 0.270).

Conclusion: The functional outcomes of the gap balancing technique based on the modified spacer are similar to those of measured resection at 3 years. Compared with the MR technique, the GB technique resulted in a greater external rotation resection angle and thicker posterior medial condylar cuts in TKA with knee varus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13018-021-02788-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8532342PMC
October 2021

Coordination of tumor growth and host wasting by tumor-derived Upd3.

Cell Rep 2021 Aug;36(7):109553

Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, PR China; Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, PR China; Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, PR China. Electronic address:

yki-induced gut tumors in Drosophila are associated with host wasting, including muscle dysfunction, lipid loss, and hyperglycemia, a condition reminiscent of human cancer cachexia. We previously used this model to identify tumor-derived ligands that contribute to host wasting. To identify additional molecular networks involved in host-tumor interactions, we develop PathON, a web-based tool analyzing the major signaling pathways in Drosophila, and uncover the Upd3/Jak/Stat axis as an important modulator. We find that yki-gut tumors secrete Upd3 to promote self-overproliferation and enhance Jak/Stat signaling in host organs to cause wasting, including muscle dysfunction, lipid loss, and hyperglycemia. We further reveal that Upd3/Jak/Stat signaling in the host organs directly triggers the expression of ImpL2, an antagonistic binding protein for insulin-like peptides, to impair insulin signaling and energy balance. Altogether, our results demonstrate that yki-gut tumors produce a Jak/Stat pathway ligand, Upd3, that regulates both self-growth and host wasting.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2021.109553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8410949PMC
August 2021

TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.

Nucleic Acids Res 2021 07;49(W1):W641-W653

Center for Computational and Molecular Biology, Brown University, Providence, RI 02912, USA.

Uncovering how transcription factors regulate their targets at DNA, RNA and protein levels over time is critical to define gene regulatory networks (GRNs) and assign mechanisms in normal and diseased states. RNA-seq is a standard method measuring gene regulation using an established set of analysis stages. However, none of the currently available pipeline methods for interpreting ordered genomic data (in time or space) use time-series models to assign cause and effect relationships within GRNs, are adaptive to diverse experimental designs, or enable user interpretation through a web-based platform. Furthermore, methods integrating ordered RNA-seq data with protein-DNA binding data to distinguish direct from indirect interactions are urgently needed. We present TIMEOR (Trajectory Inference and Mechanism Exploration with Omics data in R), the first web-based and adaptive time-series multi-omics pipeline method which infers the relationship between gene regulatory events across time. TIMEOR addresses the critical need for methods to determine causal regulatory mechanism networks by leveraging time-series RNA-seq, motif analysis, protein-DNA binding data, and protein-protein interaction networks. TIMEOR's user-catered approach helps non-coders generate new hypotheses and validate known mechanisms. We used TIMEOR to identify a novel link between insulin stimulation and the circadian rhythm cycle. TIMEOR is available at https://github.com/ashleymaeconard/TIMEOR.git and http://timeor.brown.edu.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkab384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262710PMC
July 2021

DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species.

Comput Struct Biotechnol J 2021 11;19:2018-2026. Epub 2021 Apr 11.

Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

With the advent of single-cell RNA sequencing (scRNA-seq) technologies, there has been a spike in studies involving scRNA-seq of several tissues across diverse species including . Although a few databases exist for users to query genes of interest within the scRNA-seq studies, search tools that enable users to find orthologous genes and their cell type-specific expression patterns across species are limited. Here, we built a new search database, DRscDB (https://www.flyrnai.org/tools/single_cell/web/), to address this need. DRscDB serves as a comprehensive repository for published scRNA-seq datasets for and relevant datasets from human and other model organisms. DRscDB is based on manual curation of scRNA-seq studies of various tissue types and their corresponding analogous tissues in vertebrates including zebrafish, mouse, and human. Of note, our search database provides most of the literature-derived marker genes, thus preserving the original analysis of the published scRNA-seq datasets. Finally, DRscDB serves as a web-based user interface that allows users to mine gene expression data from scRNA-seq studies and perform cell cluster enrichment analyses pertaining to various scRNA-seq studies, both within and across species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.csbj.2021.04.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085783PMC
April 2021

Proteomics of protein trafficking by in vivo tissue-specific labeling.

Nat Commun 2021 04 22;12(1):2382. Epub 2021 Apr 22.

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.

Conventional approaches to identify secreted factors that regulate homeostasis are limited in their abilities to identify the tissues/cells of origin and destination. We established a platform to identify secreted protein trafficking between organs using an engineered biotin ligase (BirA*G3) that biotinylates, promiscuously, proteins in a subcellular compartment of one tissue. Subsequently, biotinylated proteins are affinity-enriched and identified from distal organs using quantitative mass spectrometry. Applying this approach in Drosophila, we identify 51 muscle-secreted proteins from heads and 269 fat body-secreted proteins from legs/muscles, including CG2145 (human ortholog ENDOU) that binds directly to muscles and promotes activity. In addition, in mice, we identify 291 serum proteins secreted from conditional BirA*G3 embryo stem cell-derived teratomas, including low-abundance proteins with hormonal properties. Our findings indicate that the communication network of secreted proteins is vast. This approach has broad potential across different model systems to identify cell-specific secretomes and mediators of interorgan communication in health or disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-021-22599-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8062696PMC
April 2021

The role of the PI3K/AKT signalling pathway in bFGF/PDGF composite hydrogel promoting the repair of spinal cord injuries.

Ann Ital Chir 2021 ;92:92-97

Objective: This study aimed to explore the role of the PI3K/AKT signaling pathway in bFGF/PDGF composite hydrogel promoting the repair of spinal cord injuries.

Methods: In this study, the spinal cord injury rat model was established using Allen's punch method. Healthy male Sprague Dawley rats of the clean grade were randomly divided into four groups (n=18, each): sham operation group (group S), bFGF/PDGF composite hydrogel group (group A), bFGF/PDGF composite hydrogel + LY294002 (PI3K/AKT signaling pathway inhibitor) group (group B) and bFGF/PDGF composite hydrogel + IGF-1 (PI3K/AKT signaling pathway agonist) group (group C). After the operation, the motor function of the posterior limbs, the apoptosis of the spinal cord cells and the expression of PI3K, Akt and phosphorylated Akt (p-Akt) in the spinal cord tissues of the rats in each group were detected.

Results: BBB joint score were significantly higher (P<0.05).

Conclusion: BFGF/PDGF composite hydrogel can significantly promote the repair of spinal cord injuries and the mechanism is closely correlated to the activation of the PI3K/AKT signaling pathway.

Key Words: BFGF, Cell apoptosis, PDGF, PI3K/Akt signaling pathway, Spinal cord injury.
View Article and Find Full Text PDF

Download full-text PDF

Source
August 2021

Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila.

Genetics 2021 04;217(4)

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.

Single-cell RNA sequencing (scRNAseq) experiments provide a powerful means to identify clusters of cells that share common gene expression signatures. A major challenge in scRNAseq studies is to map the clusters to specific anatomical regions along the body and within tissues. Existing data, such as information obtained from large-scale in situ RNA hybridization studies, cell type specific transcriptomics, gene expression reporters, antibody stainings, and fluorescent tagged proteins, can help to map clusters to anatomy. However, in many cases, additional validation is needed to precisely map the spatial location of cells in clusters. Several approaches are available for spatial resolution in Drosophila, including mining of existing datasets, and use of existing or new tools for direct or indirect detection of RNA, or direct detection of proteins. Here, we review available resources and emerging technologies that will facilitate spatial mapping of scRNAseq clusters at high resolution in Drosophila. Importantly, we discuss the need, available approaches, and reagents for multiplexing gene expression detection in situ, as in most cases scRNAseq clusters are defined by the unique coexpression of sets of genes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/genetics/iyab019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8049553PMC
April 2021

mTORC1-chaperonin CCT signaling regulates mA RNA methylation to suppress autophagy.

Proc Natl Acad Sci U S A 2021 03;118(10)

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;

Mechanistic Target of Rapamycin Complex 1 (mTORC1) is a central regulator of cell growth and metabolism that senses and integrates nutritional and environmental cues with cellular responses. Recent studies have revealed critical roles of mTORC1 in RNA biogenesis and processing. Here, we find that the mA methyltransferase complex (MTC) is a downstream effector of mTORC1 during autophagy in and human cells. Furthermore, we show that the Chaperonin Containing Tailless complex polypeptide 1 (CCT) complex, which facilitates protein folding, acts as a link between mTORC1 and MTC. The mTORC1 activates the chaperonin CCT complex to stabilize MTC, thereby increasing mA levels on the messenger RNAs encoding autophagy-related genes, leading to their degradation and suppression of autophagy. Altogether, our study reveals an evolutionarily conserved mechanism linking mTORC1 signaling with mA RNA methylation and demonstrates their roles in suppressing autophagy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.2021945118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7958400PMC
March 2021

Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells.

PLoS Genet 2021 02 16;17(2):e1009354. Epub 2021 Feb 16.

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America.

The RB1 tumor suppressor is recurrently mutated in a variety of cancers including retinoblastomas, small cell lung cancers, triple-negative breast cancers, prostate cancers, and osteosarcomas. Finding new synthetic lethal (SL) interactions with RB1 could lead to new approaches to treating cancers with inactivated RB1. We identified 95 SL partners of RB1 based on a Drosophila screen for genetic modifiers of the eye phenotype caused by defects in the RB1 ortholog, Rbf1. We validated 38 mammalian orthologs of Rbf1 modifiers as RB1 SL partners in human cancer cell lines with defective RB1 alleles. We further show that for many of the RB1 SL genes validated in human cancer cell lines, low activity of the SL gene in human tumors, when concurrent with low levels of RB1 was associated with improved patient survival. We investigated higher order combinatorial gene interactions by creating a novel Drosophila cancer model with co-occurring Rbf1, Pten and Ras mutations, and found that targeting RB1 SL genes in this background suppressed the dramatic tumor growth and rescued fly survival whilst having minimal effects on wild-type cells. Finally, we found that drugs targeting the identified RB1 interacting genes/pathways, such as UNC3230, PYR-41, TAK-243, isoginkgetin, madrasin, and celastrol also elicit SL in human cancer cell lines. In summary, we identified several high confidence, evolutionarily conserved, novel targets for RB1-deficient cells that may be further adapted for the treatment of human cancer.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1009354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7909629PMC
February 2021

A Retrospective Observational Study of Anlotinib in Patients with Platinum-Resistant or Platinum-Refractory Epithelial Ovarian Cancer.

Drug Des Devel Ther 2021 27;15:339-347. Epub 2021 Jan 27.

Department of Integrated Traditional and Western Medicine, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou City, Henan Province, People's Republic of China.

Objective: Anlotinib, an oral small-molecular tyrosine kinase inhibitor (TKI) on tumor angiogenesis and growth, has a wide spectrum of inhibitory effects on targets such as vascular endothelial growth factor receptors 2/3 (VEGFR2/3), etc. The efficacy and safety of anlotinib in the treatment of platinum-resistant or platinum-refractory ovarian cancer were evaluated.

Patients And Methods: Patients with platinum-resistant or platinum-refractory ovarian cancer that treated with anlotinib in the Affiliated Cancer Hospital of Zhengzhou University from May 2018 to March 2020 were included. Medical records were reviewed in terms of objective response, survival outcomes, and safety.

Results: A total of 38 patients were analyzed. The median progression-free survival and the median overall survival were 7.7 months (95% CI: 6.7-8.7) and 16.5 months (95% CI: 13.3-19.7), respectively. About 17 patients received anlotinib monotherapy, and the median progression-free survival was 7.7 months (95% CI: 6.3-9.1). A total of 19 cases received anlotinib plus chemotherapy with a median progression-free survival of 8.0 months (95% CI: 4.8-11.2). A total of 2 cases received anlotinib plus anti-PD-1 antibody pembrolizumab, and 1 case had partial response, the other progressive disease. The objective response rate was 42.1% while the disease control rate was 86.8%. A total of 5 patients experienced dose reduction from 12 mg to 10 mg because of adverse effects. The most common adverse effects were hypertension (31.6%), fatigue (28.9%), anorexia (26.3%) and hand-foot syndrome (23.7%). No treatment-related deaths were recorded.

Conclusion: Anlotinib produced moderate improvements in progression-free survival and overall survival in patients with platinum-resistant or platinum-refractory ovarian cancer. It indicates that anlotinib maybe a new treatment option for patients with platinum-resistant or platinum-refractory ovarian cancer.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2147/DDDT.S286529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7850384PMC
September 2021

Publisher Correction: Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging.

Nat Methods 2021 Feb;18(2):220

State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41592-021-01066-xDOI Listing
February 2021

Miniature two-photon microscopy for enlarged field-of-view, multi-plane and long-term brain imaging.

Nat Methods 2021 01 6;18(1):46-49. Epub 2021 Jan 6.

State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China.

We have developed a miniature two-photon microscope equipped with an axial scanning mechanism and a long-working-distance miniature objective to enable multi-plane imaging over a volume of 420 × 420 × 180 μm at a lateral resolution of ~1 μm. Together with the detachable design that permits long-term recurring imaging, our miniature two-photon microscope can help decipher neuronal mechanisms in freely behaving animals.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41592-020-01024-zDOI Listing
January 2021

QNAR modeling of cytotoxicity of mixing nano-TiO and heavy metals.

Ecotoxicol Environ Saf 2021 Jan 18;208:111634. Epub 2020 Nov 18.

Safety Assessment and Research Center for Drug, Pesticide and Veterinary Drug of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu, China. Electronic address:

The Quantitative Structure-Activity Relationship (QSAR) has been used to investigate organic mixtures but QSAR in the nanomaterial field (QNAR) is still new. Toxicity is a result of the interaction of many substances. QNAR research focuses on a single nanomaterial in the long-term. It is difficult to find an appropriate descriptor to build a model due to the complexity of the mixture. Here, we attempt to build a QNAR model to predict cell viability for HK-2 cells exposed to a mixture containing nano-TiO and heavy metals. HK-2 cells were exposed to four groups of mixtures containing heavy-metals and nanomaterials and CCK8 was added to obtain the number of living cells. At the same time, ROS was investigated to study this mechanism. Each descriptor of the components and mixtures were obtained using the formula D= [Formula: see text] respectively. We used the Multiple Partial Least Squares Regression (PLS) and Random Forest Regression (RF) to build a QNAR model. Both models reliably predict and assess viability of HK-2 cells exposed to the mixture. The RF model showed greater stability and higher precision in toxicity predictability and can be applied to environmental nano-toxicology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ecoenv.2020.111634DOI Listing
January 2021

Sevoflurane postconditioning reduces myocardial ischemia reperfusion injury-induced necroptosis by up-regulation of OGT-mediated O-GlcNAcylated RIPK3.

Aging (Albany NY) 2020 11 20;12(24):25452-25468. Epub 2020 Nov 20.

Department of Anesthesiology, The Second Affiliate Hospital of Nanchang University, Nanchang 330006, China.

Inhalation anesthetics have been demonstrated to have protective effects against myocardial ischemia reperfusion injury (MIRI). O-linked GlcNAcylation (O-GlcNAc) modifications have been shown to protect against MIRI. This study aimed to investigate whether O-GlcNAcylation and necroptosis signaling were important for sevoflurane postconditioning (SPC) induced cardioprotective effects. Apart from rats in the SHAM and sevoflurane (SEVO) group, rats underwent 30 min ischemia followed by 2 h reperfusion. Cardiac hemodynamics and function were determined. In addition, myocardial infarction size, cardiac function parameters, myocardial lactic dehydrogenase (LDH) content, myocardium histopathological changes, necrotic myocardium, O-GlcNAcylation, and protein expression levels of necroptosis biomarkers were measured, together with co-immunoprecipitation experiments using proteins associated with the necroptosis pathway and O-GlcNAcylation. SPC reduced myocardial infarction size, ameliorated cardiac function, restored hemodynamic performance, improved histopathological changes, and reduced receptor-interacting protein kinase 1 (RIPK1)/receptor-interacting protein kinase 3 (RIPK3)/mixed lineage kinase domain-like (MLKL) mediated necroptosis. In addition, SPC up-regulated O-GlcNAc transferase (OGT) mediated O-GlcNAcylation, increased O-GlcNAcylated RIPK3, and inhibited the association of RIPK3 and MLKL. However, OSMI-1, an OGT inhibitor, abolished SPC mediated cardioprotective effects and inhibited OGT mediated up-regulation of O-GlcNAcylation and down-regulation of RIPK3 and MLKL proteins induced by SPC. Our study demonstrated that SPC restrained MIRI induced necroptosis via regulating OGT mediated O-GlcNAcylation of RIPK3 and lessening the formulation of RIPK3/MLKL complex.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18632/aging.104146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7803485PMC
November 2020

PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity.

Elife 2020 10 27;9. Epub 2020 Oct 27.

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States.

PDGF/VEGF ligands regulate a plethora of biological processes in multicellular organisms via autocrine, paracrine, and endocrine mechanisms. We investigated organ-specific metabolic roles of PDGF/VEGF-like factors (Pvfs). We combine genetic approaches and single-nuclei sequencing to demonstrate that muscle-derived Pvf1 signals to the hepatocyte-like cells/oenocytes to suppress lipid synthesis by activating the Pi3K/Akt1/TOR signaling cascade in the oenocytes. Functionally, this signaling axis regulates expansion of adipose tissue lipid stores in newly eclosed flies. Flies emerge after pupation with limited adipose tissue lipid stores and lipid level is progressively accumulated via lipid synthesis. We find that adult muscle-specific expression of increases rapidly during this stage and that muscle-to-oenocyte Pvf1 signaling inhibits expansion of adipose tissue lipid stores as the process reaches completion. Our findings provide the first evidence in a metazoan of a PDGF/VEGF ligand acting as a myokine that regulates systemic lipid homeostasis by activating TOR in hepatocyte-like cells.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.56969DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7752135PMC
October 2020

FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update.

Nucleic Acids Res 2021 01;49(D1):D908-D915

Department of Genetics, Blavatnik Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog mapping and mining of information about orthologs in common genetic model species; reagent-centric resources that help researchers identify RNAi and CRISPR sgRNA reagents or designs; and data-centric resources that facilitate visualization and mining of transcriptomics data, protein modification data, protein interactions, and more. Here, we discuss updated and new features that help biological and biomedical researchers efficiently identify, visualize, analyze, and integrate information and data for Drosophila and other species. Together, these resources facilitate multiple steps in functional genomics workflows, from building gene and reagent lists to management, analysis, and integration of data.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkaa936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778949PMC
January 2021

BioLitMine: Advanced Mining of Biomedical and Biological Literature About Human Genes and Genes from Major Model Organisms.

G3 (Bethesda) 2020 12 3;10(12):4531-4539. Epub 2020 Dec 3.

Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115.

The accumulation of biological and biomedical literature outpaces the ability of most researchers and clinicians to stay abreast of their own immediate fields, let alone a broader range of topics. Although available search tools support identification of relevant literature, finding relevant and key publications is not always straightforward. For example, important publications might be missed in searches with an official gene name due to gene synonyms. Moreover, ambiguity of gene names can result in retrieval of a large number of irrelevant publications. To address these issues and help researchers and physicians quickly identify relevant publications, we developed BioLitMine, an advanced literature mining tool that takes advantage of the medical subject heading (MeSH) index and gene-to-publication annotations already available for PubMed literature. Using BioLitMine, a user can identify what MeSH terms are represented in the set of publications associated with a given gene of the interest, or start with a term and identify relevant publications. Users can also use the tool to find co-cited genes and a build a literature co-citation network. In addition, BioLitMine can help users build a gene list relevant to a MeSH term, such as a list of genes relevant to "stem cells" or "breast neoplasms." Users can also start with a gene or pathway of interest and identify authors associated with that gene or pathway, a feature that makes it easier to identify experts who might serve as collaborators or reviewers. Altogether, BioLitMine extends the value of PubMed-indexed literature and its existing expert curation by providing a robust and gene-centric approach to retrieval of relevant information.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1534/g3.120.401775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7718760PMC
December 2020

Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila.

Nat Commun 2020 09 8;11(1):4483. Epub 2020 Sep 8.

Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea.

The Drosophila lymph gland, the larval hematopoietic organ comprised of prohemocytes and mature hemocytes, has been a valuable model for understanding mechanisms underlying hematopoiesis and immunity. Three types of mature hemocytes have been characterized in the lymph gland: plasmatocytes, lamellocytes, and crystal cells, which are analogous to vertebrate myeloid cells, yet molecular underpinnings of the lymph gland hemocytes have been less investigated. Here, we use single-cell RNA sequencing to comprehensively analyze heterogeneity of developing hemocytes in the lymph gland, and discover previously undescribed hemocyte types including adipohemocytes, stem-like prohemocytes, and intermediate prohemocytes. Additionally, we identify the developmental trajectory of hemocytes during normal development as well as the emergence of the lamellocyte lineage following active cellular immunity caused by wasp infestation. Finally, we establish similarities and differences between embryonically derived- and larval lymph gland hemocytes. Altogether, our study provides detailed insights into the hemocyte development and cellular immune responses at single-cell resolution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-020-18135-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7479620PMC
September 2020

A single-cell survey of blood.

Elife 2020 05 12;9. Epub 2020 May 12.

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States.

blood cells, called hemocytes, are classified into plasmatocytes, crystal cells, and lamellocytes based on the expression of a few marker genes and cell morphologies, which are inadequate to classify the complete hemocyte repertoire. Here, we used single-cell RNA sequencing (scRNA-seq) to map hemocytes across different inflammatory conditions in larvae. We resolved plasmatocytes into different states based on the expression of genes involved in cell cycle, antimicrobial response, and metabolism together with the identification of intermediate states. Further, we discovered rare subsets within crystal cells and lamellocytes that express fibroblast growth factor (FGF) ligand and receptor , respectively. We demonstrate that these FGF components are required for mediating effective immune responses against parasitoid wasp eggs, highlighting a novel role for FGF signaling in inter-hemocyte crosstalk. Our scRNA-seq analysis reveals the diversity of hemocytes and provides a rich resource of gene expression profiles for a systems-level understanding of their functions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7554/eLife.54818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237219PMC
May 2020

Dexmedetomidine alleviates postoperative cognitive dysfunction through circular RNA in aged rats.

3 Biotech 2020 Apr 24;10(4):176. Epub 2020 Mar 24.

Department of Anesthesiology, Donghu District, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006 Jiangxi China.

Circular RNA (circRNA) has been well studied in many diseases, whereas their role in patients with postoperative cognitive dysfunction (POCD) remains largely unclear. Here, we investigated the therapeutic effects of dexmedetomidine (Dex) on POCD and analyzed the role of circRNA as well as the pathways that may be involved. The Morris water maze test demonstrated that POCD rats have a longer incubation period than the normal group, but the latency of POCD rats was significantly lower after Dex treatment. Moreover, HE staining showed that Dex improved hippocampal pathological changes. RNA sequencing showed 164 differentially expressed circRNAs between POCD and Dex groups; 74 were upregulated and 90 were downregulated in the Dex group. A total of 20,790 target genes for differentially expressed circRNAs were observed in RNAhybrid and Miranda databases. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the target genes of differentially expressed circRNAs are mainly focused on positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage, negative regulation of cell adhesion mediated by integrin, and response to cytokines and other function of life activities and involved in the P53 signaling pathway and nuclear factor kappa B (NF-κB) signaling pathway. Furthermore, the expression of five candidate circRNAs (circ-Shank3, circ-Cdc42bpa, circ-chrx-24658, cir-chr17-3642 and circ-Sgsm1) and target genes were consistent with the RNA sequencing results, which was verified by quantitative real-time polymerase chain reaction (qRT-PCR). These results indicate that circ-Shank3 participate in the process of Dex improved POCD through regulating the P53 and NF-κB signaling pathways and may potentially facilitate POCD treatment through the development of clinical drugs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13205-020-2163-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7093639PMC
April 2020

Large-Scale Transgenic Resource Collections for Loss- and Gain-of-Function Studies.

Genetics 2020 04 18;214(4):755-767. Epub 2020 Feb 18.

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115.

The Transgenic RNAi Project (TRiP), a functional genomics platform at Harvard Medical School, was initiated in 2008 to generate and distribute a genome-scale collection of RNA interference (RNAi) fly stocks. To date, it has generated >15,000 RNAi fly stocks. As this covers most genes, we have largely transitioned to development of new resources based on CRISPR technology. Here, we present an update on our libraries of publicly available RNAi and CRISPR fly stocks, and focus on the TRiP-CRISPR overexpression (TRiP-OE) and TRiP-CRISPR knockout (TRiP-KO) collections. TRiP-OE stocks express single guide RNAs targeting upstream of a gene transcription start site. Gene activation is triggered by coexpression of catalytically dead Cas9 fused to an activator domain, either VP64-p65-Rta or Synergistic Activation Mediator. TRiP-KO stocks express one or two single guide RNAs targeting the coding sequence of a gene or genes. Cutting is triggered by coexpression of Cas9, allowing for generation of indels in both germline and somatic tissue. To date, we have generated >5000 TRiP-OE or TRiP-KO stocks for the community. These resources provide versatile, transformative tools for gene activation, gene repression, and genome engineering.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.119.302964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153935PMC
April 2020

Metabolomics Reveals that Cysteine Metabolism Plays a Role in Celastrol-Induced Mitochondrial Apoptosis in HL-60 and NB-4 Cells.

Sci Rep 2020 01 16;10(1):471. Epub 2020 Jan 16.

Department of Hygienic Analysis and Detection, Nanjing Medical University, Nanjing, 211166, China.

Recently, celastrol has shown great potential for inducing apoptosis in acute myeloid leukemia cells, especially acute promyelocytic leukaemia cells. However, the mechanism is poorly understood. Metabolomics provides an overall understanding of metabolic mechanisms to illustrate celastrol's mechanism of action. We treated both nude mice bearing HL-60 cell xenografts in vivo and HL-60 cells as well as NB-4 cells in vitro with celastrol. Ultra-performance liquid chromatography coupled with mass spectrometry was used for metabolomics analysis of HL-60 cells in vivo and for targeted L-cysteine analysis in HL-60 and NB-4 cells in vitro. Flow cytometric analysis was performed to assess mitochondrial membrane potential, reactive oxygen species and apoptosis. Western blotting was conducted to detect the p53, Bax, cleaved caspase 9 and cleaved caspase 3 proteins. Celastrol inhibited tumour growth, induced apoptosis, and upregulated pro-apoptotic proteins in the xenograft tumour mouse model. Metabolomics showed that cysteine metabolism was the key metabolic alteration after celastrol treatment in HL-60 cells in vivo. Celastrol decreased L-cysteine in HL-60 cells. Acetylcysteine supplementation reversed reactive oxygen species accumulation and apoptosis induced by celastrol and reversed the dramatic decrease in the mitochondrial membrane potential and upregulation of pro-apoptotic proteins in HL-60 cells. In NB-4 cells, celastrol decreased L-cysteine, and acetylcysteine reversed celastrol-induced reactive oxygen species accumulation and apoptosis. We are the first to identify the involvement of a cysteine metabolism/reactive oxygen species/p53/Bax/caspase 9/caspase 3 pathway in celastrol-triggered mitochondrial apoptosis in HL-60 and NB-4 cells, providing a novel underlying mechanism through which celastrol could be used to treat acute myeloid leukaemia, especially acute promyelocytic leukaemia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-57312-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6965619PMC
January 2020

A cell atlas of the adult midgut.

Proc Natl Acad Sci U S A 2020 01 8;117(3):1514-1523. Epub 2020 Jan 8.

Department of Genetics, Harvard Medical School, Boston, MA 02115;

Studies of the adult midgut have led to many insights in our understanding of cell-type diversity, stem cell regeneration, tissue homeostasis, and cell fate decision. Advances in single-cell RNA sequencing provide opportunities to identify new cell types and molecular features. We used single-cell RNA sequencing to characterize the transcriptome of midgut epithelial cells and identified 22 distinct clusters representing intestinal stem cells, enteroblasts, enteroendocrine cells (EEs), and enterocytes. This unbiased approach recovered most of the known intestinal stem cells/enteroblast and EE markers, highlighting the high quality of the dataset, and led to insights on intestinal stem cell biology, cell type-specific organelle features, the roles of new transcription factors in progenitors and regional variation along the gut, 5 additional EE gut hormones, EE hormonal expression diversity, and paracrine function of EEs. To facilitate mining of this rich dataset, we provide a web-based resource for visualization of gene expression in single cells. Altogether, our study provides a comprehensive resource for addressing functions of genes in the midgut epithelium.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1916820117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6983450PMC
January 2020

Use of the CRISPR-Cas9 System in Drosophila Cultured Cells to Introduce Fluorescent Tags into Endogenous Genes.

Curr Protoc Mol Biol 2020 03;130(1):e112

Department of Genetics, Harvard Medical School, Boston, Massachusetts.

The CRISPR-Cas9 system makes it possible to cause double-strand breaks in specific regions, inducing repair. In the presence of a donor construct, repair can involve insertion or 'knock-in' of an exogenous cassette. One common application of knock-in technology is to generate cell lines expressing fluorescently tagged endogenous proteins. The standard approach relies on production of a donor plasmid with ∼500 to 1000 bp of homology on either side of an insertion cassette that contains the fluorescent protein open reading frame (ORF). We present two alternative methods for knock-in of fluorescent protein ORFs into Cas9-expressing Drosophila S2R+ cultured cells, the single-stranded DNA (ssDNA) Drop-In method and the CRISPaint universal donor method. Both methods eliminate the need to clone a large plasmid donor for each target. We discuss the advantages and limitations of the standard, ssDNA Drop-In, and CRISPaint methods for fluorescent protein tagging in Drosophila cultured cells. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Knock-in into Cas9-positive S2R+ cells using the ssDNA Drop-In approach Basic Protocol 2: Knock-in into Cas9-positive S2R+ cells by homology-independent insertion of universal donor plasmids that provide mNeonGreen (CRISPaint method) Support Protocol 1: sgRNA design and cloning Support Protocol 2: ssDNA donor synthesis Support Protocol 3: Transfection using Effectene Support Protocol 4: Electroporation of S2R+-MT::Cas9 Drosophila cells Support Protocol 5: Single-cell isolation of fluorescent cells using FACS.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/cpmb.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7213786PMC
March 2020

An in vivo RNAi screen uncovers the role of AdoR signaling and adenosine deaminase in controlling intestinal stem cell activity.

Proc Natl Acad Sci U S A 2020 01 18;117(1):464-471. Epub 2019 Dec 18.

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;

Metabolites are increasingly appreciated for their roles as signaling molecules. To dissect the roles of metabolites, it is essential to understand their signaling pathways and their enzymatic regulations. From an RNA interference (RNAi) screen for regulators of intestinal stem cell (ISC) activity in the midgut, we identified () as a top candidate gene required for ISC proliferation. We demonstrate that Ras/MAPK and Protein Kinase A (PKA) signaling act downstream of AdoR and that Ras/MAPK mediates the major effect of AdoR on ISC proliferation. Extracellular adenosine, the ligand for AdoR, is a small metabolite that can be released by various cell types and degraded in the extracellular space by secreted adenosine deaminase. Interestingly, down-regulation of () from enterocytes is necessary for extracellular adenosine to activate AdoR and induce ISC overproliferation. As expression and its enzymatic activity decrease following tissue damage, our study provides important insights into how the enzymatic regulation of extracellular adenosine levels under tissue-damage conditions facilitates ISC proliferation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1900103117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955304PMC
January 2020

SNP-CRISPR: A Web Tool for SNP-Specific Genome Editing.

G3 (Bethesda) 2020 02 6;10(2):489-494. Epub 2020 Feb 6.

Department of Genetics,

CRISPR-Cas9 is a powerful genome editing technology in which a single guide RNA (sgRNA) confers target site specificity to achieve Cas9-mediated genome editing. Numerous sgRNA design tools have been developed based on reference genomes for humans and model organisms. However, existing resources are not optimal as genetic mutations or single nucleotide polymorphisms (SNPs) within the targeting region affect the efficiency of CRISPR-based approaches by interfering with guide-target complementarity. To facilitate identification of sgRNAs (1) in non-reference genomes, (2) across varying genetic backgrounds, or (3) for specific targeting of SNP-containing alleles, for example, disease relevant mutations, we developed a web tool, SNP-CRISPR (https://www.flyrnai.org/tools/snp_crispr/). SNP-CRISPR can be used to design sgRNAs based on public variant data sets or user-identified variants. In addition, the tool computes efficiency and specificity scores for sgRNA designs targeting both the variant and the reference. Moreover, SNP-CRISPR provides the option to upload multiple SNPs and target single or multiple nearby base changes simultaneously with a single sgRNA design. Given these capabilities, SNP-CRISPR has a wide range of potential research applications in model systems and for design of sgRNAs for disease-associated variant correction.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1534/g3.119.400904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7003079PMC
February 2020

Intestinal response to dietary manganese depletion in Drosophila.

Metallomics 2020 02 4;12(2):218-240. Epub 2019 Dec 4.

Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados, Av. IPN 2508, Mexico City, 07360, Mexico.

Manganese is considered essential for animal growth. Manganese ions serve as cofactors to three mitochondrial enzymes: superoxide dismutase (Sod2), arginase and glutamine synthase, and to glycosyltransferases residing in the Golgi. In Drosophila melanogaster, manganese has also been implicated in the formation of ceramide phosphoethanolamine, the insect's sphingomyelin analogue, a structural component of cellular membranes. Manganese overload leads to neurodegeneration and toxicity in both humans and Drosophila. Here, we report specific absorption and accumulation of manganese during the first week of adulthood in flies, which correlates with an increase in Sod2 activity during the same period. To test the requirement of dietary manganese for this accumulation, we generated a Drosophila model of manganese deficiency. Due to the lack of manganese-specific chelators, we used chemically defined media to grow the flies and deplete them of the metal. Dietary manganese depletion reduced Sod2 activity. We then examined gene and protein expression changes in the intestines of manganese depleted flies. We found adaptive responses to the presumed loss of known manganese-dependent enzymatic activities: less glutamine synthase activity (amination of glutamate to glutamine) was compensated by 50% reduction in glutaminase (deamination of glutamine to glutamate); less glycosyltransferase activity, predicted to reduce protein glycosylation, was compensated by 30% reduction in lysosomal mannosidases (protein deglycosylating enzymes); less ceramide phosphoethanolamine synthase activity was compensated by 30% reduction in the Drosophila sphingomyeline phospodiesterase, which could catabolize ceramide phosphoethanolamine in flies. Reduced Sod2 activity, predicted to cause superoxide-dependent iron-sulphur cluster damage, resulted in cellular iron misregulation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1039/c9mt00218aDOI Listing
February 2020

Pooled CRISPR Screens in Drosophila Cells.

Curr Protoc Mol Biol 2019 12;129(1):e111

Department of Genetics, Harvard Medical School, Boston, Massachusetts.

High-throughput screens in Drosophila melanogaster cell lines have led to discovery of conserved gene functions related to signal transduction, host-pathogen interactions, ion transport, and more. CRISPR/Cas9 technology has opened the door to new types of large-scale cell-based screens. Whereas array-format screens require liquid handling automation and assay miniaturization, pooled-format screens, in which reagents are introduced at random and in bulk, can be done in a standard lab setting. We provide a detailed protocol for conducting and evaluating genome-wide CRISPR single guide RNA (sgRNA) pooled screens in Drosophila S2R+ cultured cells. Specifically, we provide step-by-step instructions for library design and production, optimization of cytotoxin-based selection assays, genome-scale screening, and data analysis. This type of project takes ∼3 months to complete. Results can be used in follow-up studies performed in vivo in Drosophila, mammalian cells, and/or other systems. © 2019 by John Wiley & Sons, Inc. Basic Protocol: Pooled-format screening with Cas9-expressing Drosophila S2R+ cells in the presence of cytotoxin Support Protocol 1: Optimization of cytotoxin concentration for Drosophila cell screening Support Protocol 2: CRISPR sgRNA library design and production for Drosophila cell screening Support Protocol 3: Barcode deconvolution and analysis of screening data.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/cpmb.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6961806PMC
December 2019

SREBP2-STARD4 is involved in synthesis of cholesteryl ester stimulated by mono-butyl phthalate in MLTC-1 cells.

Environ Toxicol 2020 Mar 9;35(3):377-384. Epub 2019 Nov 9.

The Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.

Sterol is synthesized from cholesterol which is from the hydrolysis of stored cholesteryl esters. The process of maintaining cholesterol homeostasis is regulated by SREBP2-STARD4. Lots of researches demonstrated that male steroidogenesis could be interfered by di-n-butyl phthalate (DBP) or monobutyl phthalate (MBP). However, mechanisms of MBP exposure in this process have not been uncovered clearly. The objectiveof this study was to explore roles of SREBP2 and STARD4 in cholesteryl estersynthesis stimulated by MBP in mouse Leydig tumor cells (MLTC-1). MLTC-1 exposedto 10-8, 10-7, 10-6, 10-5 M MBP showed that levels of cholestery ester were increased significantly at 10-7 M MBP. Besides, cholesteryl ester synthesis stimulated by MBP was down-regulate when STARD4 or SREBP2 were inhibited. Activity of SREBP2 binding to the promoter of STARD4 was increased after MBP exposure. This study suggests that MBP can increase cholesteryl ester synthesis through SREBP2-STARD4 signal pathway in MLTC-1 cells.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/tox.22874DOI Listing
March 2020
-->