Publications by authors named "Yifang Liu"

54 Publications

Defining cell types and lineage in the Drosophila midgut using single cell transcriptomics.

Curr Opin Insect Sci 2021 Feb 17;47:12-17. Epub 2021 Feb 17.

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, United States. Electronic address:

The Drosophila midgut has emerged in recent years as a model system to study stem cell renewal and differentiation and tissue homeostasis. Histological, genetic and gene expression studies have provided a wealth of information on gut cell types, regionalization, genes and pathways involved in cell proliferation and differentiation, stem cell renewal, and responses to changes in environmental factors such as the microbiota and nutrients. Here, we review the contribution of single cell transcriptomic methods to our understanding of gut cell type diversity, lineage and behavior.
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http://dx.doi.org/10.1016/j.cois.2021.02.008DOI Listing
February 2021

Rechargeable adhesive with calcium phosphate nanoparticles inhibited long-term dentin demineralization in a biofilm-challenged environment.

J Dent 2021 Jan 12;104:103529. Epub 2020 Nov 12.

State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China. Electronic address:

Objectives: This study aims to investigate the long-term demineralization-inhibition capability of a rechargeable adhesive with nanoparticles of amorphous calcium phosphate (NACP) on dentin in a biofilm-challenged environment.

Methods: The NACP adhesive was immersed in a pH 4 solution to exhaust calcium (Ca) and phosphate (P) ions and then recharged with Ca and P ions. Dentin samples were demineralized underStreptococcus mutans biofilms for 24 h and randomly divided into two groups: (1) dentin control, (2) dentin with recharged NACP adhesives. Each day, all the samples were immersed in brain heart infusion broth with 1% sucrose (BHIS) for 4 h, and then in artificial saliva (AS) for 20 h. This cycle was repeated for 10 days. The pH of BHIS, the Ca and P ions content of the BHIS and AS were measured daily. After 10 days, the lactic acid production and colony-forming units of the biofilms were tested. The changes of remineralization/demineralization were also analyzed.

Results: Dentin in the control group showed further demineralization. The recharged NACP adhesive neutralized acids, increasing the pH to above 5, and released large amounts of Ca and P ions each day. The recharged NACP adhesive decreased the production of lactic acid (P < 0.05), inhibited dentin demineralization and sustained the dentin hardness in the biofilm-challenged environment, showing an excellent long-term demineralization-inhibition capability.

Conclusions: The NACP adhesive could continuously inhibit dentin demineralization in a biofilm-challenged environment by recharging with Ca and P ions.

Significance: The rechargeable NACP adhesive could provide long-term dentin bond protection.
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http://dx.doi.org/10.1016/j.jdent.2020.103529DOI Listing
January 2021

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

The mutual benefits from Sino-Africa trade: Evidence on emission transfer along the global supply chain.

J Environ Manage 2020 Jun 17;263:110332. Epub 2020 Mar 17.

The Bartlett School of Construction and Project Management, University College London, London, WC1E 7HB, UK.

The carbon-emission transfer between two representative developing economies - China and Africa - behind the international trade has aroused quite a few controversies, which have not been fully estimated and understood yet. In this paper, the Multiregional Input-Output (MRIO) method is applied to the participants of Forum on China-Africa Cooperation (FOCAC) from the global perspective to reveal the roles both China and Africa have played in the global supply chain as either the original emitter or the final consumer, and to depict the evolution pattern of carbon transfer via Sino-Africa trade from the year 2000-2015. The findings are as follows: 1) China has played the role of net exporter of embodied carbon-emission in Sino-Africa trade, for the amount of emitted carbon China had born yet resulted by consumption in Africa well surpassed that vice versa. 2) Compared to the carbon-emission flows embodied in EU-Africa and US-Africa trades, China has shouldered more carbon-emission derived from Africa's consumption. 3) The sectoral contribution and intensities of embodied carbon-emission correspond to the trading pattern between China and Africa, which stems from the two parties' comparative advantages and economic complementarity. 4) The intensities of embodied carbon-emission on both sides are declining towards a rosy prospect, which indicates an improving carbon-emission efficiency of both economies. From a global perspective, both China and Africa play a positive part in carbon-emission reduction. The results in this study can facilitate low-carbon and high-efficiency trading link between the two economies.
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http://dx.doi.org/10.1016/j.jenvman.2020.110332DOI Listing
June 2020

Click chemistry-based amplification and detection of endogenous RNA and DNA molecules in situ using clampFISH probes.

Methods Enzymol 2020 15;641:459-476. Epub 2020 Jun 15.

Department of Bioengineering, Northeastern University, Boston, MA, United States. Electronic address:

Direct labeling and measurement of gene expression in single cells show the tremendous variability otherwise hidden in bulk measurements. Single-molecule RNA fluorescence in situ hybridization (FISH) has become a mainstay in laboratories worldwide for measuring gene expression with precision. However, this method remains relatively low throughput because the total fluorescent signal produced is weak and requires long exposure times and high magnification microscopy, which limits the total number of cells sampled in each image. As such, it is experimentally difficult and time-consuming to sample a large enough population of cells to visualize and quantify specific gene expression of rare cells directly. Several FISH-based tools were recently developed that retain single-molecule sensitivity and specificity while greatly amplifying the fluorescent signal, thus making FISH-based analysis possible using standard microscopes with low magnification objectives. These tools have also enabled the detection of smaller and more specific targets like splice junctions or single nucleotide polymorphisms. Here we will describe one such tool, clampFISH, an oligonucleotide-based fluorescence amplification strategy for visualizing genomic loci and individual RNA transcripts in fixed cells. ClampFISH maintains specificity while amplifying fluorescent signals, making it amenable to high throughput assays such as low magnification microscopy, spatial transcriptomics, and flow sorting. The clampFISH technique involves probing the target RNA or DNA using a series of C-shaped oligonucleotide probes, each with a 3' azide and a 5' alkyne. Hybridization of the probe with the target nucleic acid brings the azide and the alkyne in close proximity, allowing for ligation via bioorthogonal click chemistry (CuAAC). As a result, the probe forms a closed loop around the target sequence, thus enabling stringent washes to remove nonspecific binding in further rounds of amplification and retention of signal throughout liquid handling steps. Iterative rounds of hybridization with C-shaped, fluorescently labeled probes exponentially amplify the fluorescent signal. ClampFISH is simple to implement and expands the utility of in situ hybridization for multiple high throughput techniques such as low magnification microscopy, flow cytometry, and sorting based on RNA expression levels.
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http://dx.doi.org/10.1016/bs.mie.2020.04.049DOI Listing
June 2020

Resveratrol inhibits proliferation and promotes apoptosis of keloid fibroblasts by targeting HIF-1α.

J Plast Surg Hand Surg 2020 Oct 4;54(5):290-296. Epub 2020 Jun 4.

Department of Plastic Surgery, Peking Union Medical College Hospital, Beijing, China.

A keloid is characterized by red, tickling, hard, and irregular raised tissues, and it tends to outgrow its origin. It frequently occurs in young adults and appears to be refractory to prevailing therapies. Resveratrol is a new drug that has anti-proliferative effect. In this study, keloid-derived fibroblasts were cultured under hypoxia environment and was treated by resveratrol. CCK-8 assay and Annexin V-FITC were used to evaluate cell activity and apoptosis level. Western blot and RT-qPCR were also used to assess the expression of HIF-α, Collagen I and Collagen III. Besides, siRNA was also used to explore the mechanisms of resveratrol's effect. In this study, hypoxia promotes proliferation and inhibits apoptosis of keloid fibroblasts. These findings highlight the potential obstacle in treating keloids. Furthermore, we demonstrated that resveratrol could reverse the effect of hypoxia on keloids through down-regulation of HIF-1α. Moreover, collagen synthesis in keloid fibroblasts was also inhibited by resveratrol, which corresponded with HIF-1α suppression. These results provide evidence for resveratrol's treatment effect against keloids through inhibiting cell proliferation and promoting cell apoptosis, while, HIF-1α may play the key role in this process.
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http://dx.doi.org/10.1080/2000656X.2020.1771719DOI Listing
October 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.
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http://dx.doi.org/10.7554/eLife.54818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237219PMC
May 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.
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http://dx.doi.org/10.1073/pnas.1916820117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6983450PMC
January 2020

A two-step lineage reprogramming strategy to generate functionally competent human hepatocytes from fibroblasts.

Cell Res 2019 09 3;29(9):696-710. Epub 2019 Jul 3.

School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100191, China.

Terminally differentiated cells can be generated by lineage reprogramming, which is, however, hindered by incomplete conversion with residual initial cell identity and partial functionality. Here, we demonstrate a new reprogramming strategy by mimicking the natural regeneration route, which permits generating expandable hepatic progenitor cells and functionally competent human hepatocytes. Fibroblasts were first induced into human hepatic progenitor-like cells (hHPLCs), which could robustly expand in vitro and efficiently engraft in vivo. Moreover, hHPLCs could be efficiently induced into mature human hepatocytes (hiHeps) in vitro, whose molecular identity highly resembles primary human hepatocytes (PHHs). Most importantly, hiHeps could be generated in large quantity and were functionally competent to replace PHHs for drug-metabolism estimation, toxicity prediction and hepatitis B virus infection modeling. Our results highlight the advantages of the progenitor stage for successful lineage reprogramming. This strategy is promising for generating other mature human cell types by lineage reprogramming.
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http://dx.doi.org/10.1038/s41422-019-0196-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796870PMC
September 2019

Rabbit monoclonal E-cadherin antibody: A cost-effective alternative to mouse monoclonal antibody in distinguishing ductal carcinoma in situ from lobular carcinoma in situ.

Breast J 2019 09 4;25(5):813-822. Epub 2019 Jun 4.

Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, New York.

Rabbit monoclonal antibody (RabMAb) demonstrates higher sensitivity without sacrificing specificity than mouse monoclonal antibody (MMAb). MMAb against E-cadherin stain is heavily utilized in distinguishing ductal carcinoma in situ (DCIS) from lobular carcinoma in situ (LCIS). We aimed to compare the E-cadherin stain using RabMAb vs MMAb in distinguishing DCIS from LCIS. One hundred and seventeen in situ breast carcinomas (55 DCIS, 58 LCIS, and 4 DCIS and LCIS) were studied. Sections from a representative block of each were stained with RabMAb [EP700Y] and MMAb [36B5]. Scanned images of stained slides were compared in tandem. All DCIS cases (59/59) showed comparable staining by RabMAb and MMAb. Comparable staining was also observed in all but one case of LCIS (61/62; 98%). One case of pleomorphic LCIS showed mostly complete, weak to moderately intense membranous staining with RabMAb and fragmented, weak membranous staining with MMAb. Consistently better staining quality was observed in slides stained by RabMAb vs MMAb. RabMAb and MMAb against E-cadherin were diagnostically equivalent with the exception of one case where RabMAb may have led to diagnostic misinterpretation. However, the not insignificant cost savings and easier interpretation using RabMAb may justify the risk of misinterpretation of increased staining in rare cases, largely avertable with proper training.
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http://dx.doi.org/10.1111/tbj.13353DOI Listing
September 2019

Long-term functional maintenance of primary human hepatocytes in vitro.

Science 2019 04;364(6438):399-402

School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China.

The maintenance of terminally differentiated cells, especially hepatocytes, in vitro has proven challenging. Here we demonstrated the long-term in vitro maintenance of primary human hepatocytes (PHHs) by modulating cell signaling pathways with a combination of five chemicals (5C). 5C-cultured PHHs showed global gene expression profiles and hepatocyte-specific functions resembling those of freshly isolated counterparts. Furthermore, these cells efficiently recapitulated the entire course of hepatitis B virus (HBV) infection over 4 weeks with the production of infectious viral particles and formation of HBV covalently closed circular DNA. Our study demonstrates that, with a chemical approach, functional maintenance of PHHs supports long-term HBV infection in vitro, providing an efficient platform for investigating HBV cell biology and antiviral drug screening.
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http://dx.doi.org/10.1126/science.aau7307DOI Listing
April 2019

Targeting JNK pathway promotes human hematopoietic stem cell expansion.

Cell Discov 2019 8;5. Epub 2019 Jan 8.

1State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055 China.

The limited number of human hematopoietic stem cells (HSCs) has restrained their widespread clinical application. Despite great efforts in recent years, the in vitro expansion of HSCs remains a challenge due to incomplete understanding of the signaling networks underlying HSC self-renewal. Here, we show that culturing human cord blood (CB) CD34 cells with JNK-IN-8, an inhibitor of the JNK signaling pathway, can enhance the self-renewal of HSCs with a 3.88-fold increase in cell number. These cultured CD34 cells repopulated recipient mice for 21 weeks and can form secondary engraftment that lasted for more than 21 weeks. Knockdown of , a major downstream target in the JNK pathway, promoted the expansion of hematopoietic stem and progenitor cells (HSPCs). Our findings demonstrate a critical role of the JNK pathway in regulating HSC expansion, provide new insights into HSC self-renewal mechanism, and may lead to improved clinical application of HSCs.
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http://dx.doi.org/10.1038/s41421-018-0072-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323118PMC
January 2019

Necrostatin-1 protects against ischemia/reperfusion injury by inhibiting receptor-interacting protein 1 in a rat flap model.

J Plast Reconstr Aesthet Surg 2019 Feb 19;72(2):194-202. Epub 2018 Nov 19.

Department of Plastic Surgery, Peking Union Medical College Hospital, Beijing, China. Electronic address:

Introduction: The failure of reconstructive surgeries remains a challenge for plastic surgeons. Ischemia reperfusion (I/R) injury is considered to be one of the major problems in flap surgery. Necroptosis is a recently discovered and caspase-3-independent programed necrosis. Necrostatin-1 (Nec-1) is a specific inhibitor of necroptosis. Reports indicate that Nec-1 provides protection in ischemic models, such as brain, kidney, and heart. The aim of this study is to investigate the influence of Nec-1 on the I/R process in rat abdominal skin flaps.

Methods: Twenty male Sprague-Dawley rats, weighing 280-320 g, were randomly divided into three groups. The extended epigastric skin flap (6 cm × 9 cm) of rats was used. Three hours of complete ischemia was performed using a clamp, and the clamp was then removed to reperfusion the flap. Twenty-four hours after the onset of the reperfusion, the rats were assessed for flap survival and perfusion analysis. One sample (1 cm × 1 cm) was taken for H&E, TUNEL, electron microscopy, IHC staining for RIP-1, and ELISA analysis for caspase-3 activity.

Results: Compared to the CTL group, the flap in the Nec-1 group showed a higher survival rate and better blood perfusion. In histological observation, skin flap in the Nec-1 group showed less inflammatory infiltration than the CTL group. The AI in the CTL group was higher than that in the Nec-1 group and showed typical morphological changes of apoptotic cells. In IHC study, RIP-1 expression was higher in the CTL group. But there was no significant difference between the two groups in caspase-3 activity detection.

Conclusion: Nec-1 has a protective effect against I/R injury through the inhibition of RIP-1 on the skin flap model; this makes it a promising novel strategy in clinical setting.
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http://dx.doi.org/10.1016/j.bjps.2018.10.019DOI Listing
February 2019

Electrohydrodynamic Direct-Writing Micropatterns with Assisted Airflow.

Micromachines (Basel) 2018 Sep 11;9(9). Epub 2018 Sep 11.

Department of Instrumental and Electrical Engineering, Xiamen University, Xiamen 361102, China.

Electrohydrodynamic direct-writing (EDW) is a developing technology for high-resolution printing. How to decrease the line width and improve the deposition accuracy of direct-written patterns has been the key to the promotion for the further application of EDW. In this paper, an airflow-assisted spinneret for electrohydrodynamic direct-writing was designed. An assisted laminar airflow was introduced to the EDW process, which provided an additional stretching and constraining force on the jet to reduce the surrounding interferences and enhance jet stability. The flow field and the electric field around the spinneret were simulated to direct the structure design of the airflow-assisted spinneret. Then, a series of experiments were conducted, and the results verified the spinneret design and demonstrated a stable ejection of jet in the EDW process. With assisted airflow, the uniformity of printed patterns and the deposition position accuracy of a charged jet can be improved. Complex patterns with positioning errors of less than 5% have been printed and characterized, which provide an effective way to promote the integration of micro/nanosystems.
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http://dx.doi.org/10.3390/mi9090456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6187393PMC
September 2018

Electrospun Three-Dimensional Nanofibrous Structure via Probe Arrays Inducing.

Micromachines (Basel) 2018 Aug 24;9(9). Epub 2018 Aug 24.

Department of Instrumental and Electrical Engineering, Xiamen University, Xiamen 361102, China.

The fast and precise direct-printing of micro three-dimensional (3D) structures is the important development trend for micro/nano fabrication technique. A novel method with probe arrays was built up to realize the controllable deposition of 3D electrospun nanofibrous structures. Firstly, several 3D nanofibrous structures were built on a single probe and 2-, 3-probes, which indicated that the probe height and probe interval played a key role on the 3D structure morphology. Then, different stereo nanofibrous structures based on multiprobe arrays were achieved accurately and the effects of processing parameters, including the probe height, probe interval, applied voltage and flow rate on the deposition behaviors of electrospun nanofiber over the probe arrays were investigated. The deposition area of 3D electrospun nanofibrous structures decreased with the increase of probe interval, applied voltage, and flow rate. Several 3D nanofibrous structures of special shapes including convex, triangle wave, inverted cone and complex curved surface were demonstrated by controlling the configuration of probe arrays and electrospinning parameters. This work provides an effective and simple way for the construction of 3D electrospun nanofibrous structures, which has great potentials in various medical and industrial applications.
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http://dx.doi.org/10.3390/mi9090427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6187329PMC
August 2018

Controlling of Electrospray Deposition for Micropatterns.

Micromachines (Basel) 2018 Feb 6;9(2). Epub 2018 Feb 6.

School of Mathematical Sciences, Xiamen University, Xiamen 361005, China.

Based on the electrohydrodynamic (EHD) theory, a novel method of near-field electrospray is proposed to fabricate micropatterns with micro/nano-scale particles. Compared with conventional electrospray technology, the deposition area can be decreased to print a regular pattern according to the moving trajectory of the substrate by shortening the distance between the nozzle and the collector to several millimeters in near-field electrospray. The controlling strategies in the near-field electrospray deposition process were investigated. The line width of printed pattern increased with the increase of applied voltage, deposition time, and flow rate of solution. However, it decreased with the increase of motion velocity of the substrate. By applying a suitable matching of electrospray parameters, the regular patterns with a line width under 500 μm were printed controllably on the substrate. Thereby, atomized particles from near-field electrospray were successfully deposited in specific patterns. Characters of '2', '7', and '9' with uniform width and steady shape were patterned. This work provides an excellent way to promote the precision integrated manufacturing of electronic system.
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http://dx.doi.org/10.3390/mi9020072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6187448PMC
February 2018

Discovery of a periosteal stem cell mediating intramembranous bone formation.

Nature 2018 10 24;562(7725):133-139. Epub 2018 Sep 24.

Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.

Bone consists of separate inner endosteal and outer periosteal compartments, each with distinct contributions to bone physiology and each maintaining separate pools of cells owing to physical separation by the bone cortex. The skeletal stem cell that gives rise to endosteal osteoblasts has been extensively studied; however, the identity of periosteal stem cells remains unclear. Here we identify a periosteal stem cell (PSC) that is present in the long bones and calvarium of mice, displays clonal multipotency and self-renewal, and sits at the apex of a differentiation hierarchy. Single-cell and bulk transcriptional profiling show that PSCs display transcriptional signatures that are distinct from those of other skeletal stem cells and mature mesenchymal cells. Whereas other skeletal stem cells form bone via an initial cartilage template using the endochondral pathway, PSCs form bone via a direct intramembranous route, providing a cellular basis for the divergence between intramembranous versus endochondral developmental pathways. However, there is plasticity in this division, as PSCs acquire endochondral bone formation capacity in response to injury. Genetic blockade of the ability of PSCs to give rise to bone-forming osteoblasts results in selective impairments in cortical bone architecture and defects in fracture healing. A cell analogous to mouse PSCs is present in the human periosteum, raising the possibility that PSCs are attractive targets for drug and cellular therapy for skeletal disorders. The identification of PSCs provides evidence that bone contains multiple pools of stem cells, each with distinct physiologic functions.
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http://dx.doi.org/10.1038/s41586-018-0554-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6193396PMC
October 2018

Hyperbaric oxygen therapy can ameliorate the EMT phenomenon in keloid tissue.

Medicine (Baltimore) 2018 Jul;97(29):e11529

Department of Plastic Surgery, Peking Union Medical College Hospital Department of Plastic Surgery, China Meitan General Hospital Affiliated to North China University of Science and Technology, Beijing Department of Ear-Nose-Throat, Qingdao Huangdao District Hospital of Traditional Chinese Medicine, Qingdao, Shandong College of Life Science and Bioengineering, Beijing University of Technology Department of Hyperbaric Oxygen, Beijing Chao-Yang Hospital Department of Hyperbaric Oxygen, Navy General Hospital International education college, Beijing Vocational College of Agriculture, Beijing, China.

Background: Hyperbaric oxygen therapy (HBOT) has been widely used in the clinical setting. In this study, HBOT therapy was evaluated for its ability to ameliorate the epithelial-to-mesenchymal transition (EMT) phenomenon in keloid tissue.

Methods: Keloid patients were randomly divided into two groups: keloid patients (K group, 9 patients) and keloid patients receiving HBOT (O group, 9 patients). A third group with normal skin (S group, 9 patients) was established for control. Before HBOT and surgery, a laser Doppler flowmeter was used to measure the keloid blood supply of patients in the O group. Hematoxylin and eosin (H&E) staining was used to observe morphology. E-cadherin, ZO-1, vimentin, fibronectin, vascular endothelial growth factor (VEGF), and hypoxia inducible factor (HIF)-1α were measured by immunofluorescence staining and Western blot analysis. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to evaluate the mRNA expression level of these factors as well.

Results: In the O group, keloid blood perfusion was significantly reduced after patients received HBOT. Compared with the K group, lower expression levels of vimentin, vibronectin, VEGF, and HIF-1α were observed in the O group, whereas the expression of E-cadherin and ZO-1 was significantly higher. The mRNA expression of E-cadherin and ZO-1 was also increased after HBOT.

Conclusions: The expression levels of factors related to the EMT phenomenon were significantly reversed in keloid patients after they received HBOT, indicating that HBOT may be an effective therapy against the EMT phenomenon in keloid patients.
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http://dx.doi.org/10.1097/MD.0000000000011529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086457PMC
July 2018

Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming.

Cell Stem Cell 2018 Jul 21;23(1):31-45.e7. Epub 2018 Jun 21.

Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China; Shenzhen Stem Cell Engineering Laboratory, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China. Electronic address:

Chemical reprogramming provides a powerful platform for exploring the molecular dynamics that lead to pluripotency. Although previous studies have uncovered an intermediate extraembryonic endoderm (XEN)-like state during this process, the molecular underpinnings of pluripotency acquisition remain largely undefined. Here, we profile 36,199 single-cell transcriptomes at multiple time points throughout a highly efficient chemical reprogramming system using RNA-sequencing and reconstruct their progression trajectories. Through identifying sequential molecular events, we reveal that the dynamic early embryonic-like programs are key aspects of successful reprogramming from XEN-like state to pluripotency, including the concomitant transcriptomic signatures of two-cell (2C) embryonic-like and early pluripotency programs and the epigenetic signature of notable genome-wide DNA demethylation. Moreover, via enhancing the 2C-like program by fine-tuning chemical treatment, the reprogramming process is remarkably accelerated. Collectively, our findings offer a high-resolution dissection of cell fate dynamics during chemical reprogramming and shed light on mechanistic insights into the nature of induced pluripotency.
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http://dx.doi.org/10.1016/j.stem.2018.05.025DOI Listing
July 2018

Hot Spot and Whole-Tumor Enumeration of CD8 Tumor-Infiltrating Lymphocytes Utilizing Digital Image Analysis Is Prognostic in Triple-Negative Breast Cancer.

Clin Breast Cancer 2018 12 7;18(6):451-458.e1. Epub 2018 May 7.

Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY.

Background: CD8 tumor-infiltrating lymphocytes (TILs) have emerged as a prognostic indicator in triple-negative breast cancer (TNBC). There is debate surrounding the prognostic value of hot spots for CD8 TIL enumeration.

Methods: We compared hot spot versus whole-tumor CD8 TIL enumeration in prognosticating TNBC using immunohistochemistry on whole tissue sections and quantification by digital image analysis (Halo imaging analysis software; Indica Labs, Corrales, NM). A wide range of clinically relevant hot spot sizes was evaluated.

Results: CD8 TIL enumeration was independently statistically significant for all hot spot sizes and whole-tumor annotations for disease-free survival by multivariate analysis. A 10× objective (2.2 mm diameter) hot spot was found to correlate significantly with overall survival (P = .04), while the remaining hot spots and whole-tumor CD8 TIL enumeration did not (P > .05). Statistical significance was not demonstrated when comparing between hot spots and whole-tumor annotations, as the groups had overlapping confidence intervals.

Conclusion: CD8 TIL hot spot enumeration is equivalent to whole-tumor enumeration for prognostication in TNBC and may serve as a good alternative methodology in future studies and clinical practice.
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http://dx.doi.org/10.1016/j.clbc.2018.04.019DOI Listing
December 2018

Targeting skeletal endothelium to ameliorate bone loss.

Nat Med 2018 06 21;24(6):823-833. Epub 2018 May 21.

Department of Pathology and Laboratory Medicine, Cornell University, New York, NY, USA.

Recent studies have identified a specialized subset of CD31endomucin (CD31EMCN) vascular endothelium that positively regulates bone formation. However, it remains unclear how CD31EMCN endothelium levels are coupled to anabolic bone formation. Mice with an osteoblast-specific deletion of Shn3, which have markedly elevated bone formation, demonstrated an increase in CD31EMCN endothelium. Transcriptomic analysis identified SLIT3 as an osteoblast-derived, SHN3-regulated proangiogenic factor. Genetic deletion of Slit3 reduced skeletal CD31EMCN endothelium, resulted in low bone mass because of impaired bone formation and partially reversed the high bone mass phenotype of Shn3 mice. This coupling between osteoblasts and CD31EMCN endothelium is essential for bone healing, as shown by defective fracture repair in SLIT3-mutant mice and enhanced fracture repair in SHN3-mutant mice. Finally, administration of recombinant SLIT3 both enhanced bone fracture healing and counteracted bone loss in a mouse model of postmenopausal osteoporosis. Thus, drugs that target the SLIT3 pathway may represent a new approach for vascular-targeted osteoanabolic therapy to treat bone loss.
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http://dx.doi.org/10.1038/s41591-018-0020-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992080PMC
June 2018

Single-Image Super-Resolution Based on Rational Fractal Interpolation.

IEEE Trans Image Process 2018 Aug;27(8):3782-3797

This paper presents a novel single-image super-resolution (SR) procedure, which upscales a given low-resolution (LR) input image to a high-resolution image while preserving the textural and structural information. First, we construct a new type of bivariate rational fractal interpolation model and investigate its analytical properties. This model has different forms of expression with various values of the scaling factors and shape parameters; thus, it can be employed to better describe image features than current interpolation schemes. Furthermore, this model combines the advantages of rational interpolation and fractal interpolation, and its effectiveness is validated through theoretical analysis. Second, we develop a single-image SR algorithm based on the proposed model. The LR input image is divided into texture and non-texture regions, and then, the image is interpolated according to the characteristics of the local structure. Specifically, in the texture region, the scaling factor calculation is the critical step. We present a method to accurately calculate scaling factors based on local fractal analysis. Extensive experiments and comparisons with the other state-of-the-art methods show that our algorithm achieves competitive performance, with finer details and sharper edges.
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http://dx.doi.org/10.1109/TIP.2018.2826139DOI Listing
August 2018

3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations.

Nat Commun 2017 12 5;8(1):1937. Epub 2017 Dec 5.

Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China.

The Hi-C method is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. Here, we integrate Hi-C, whole-genome sequencing (WGS) and RNA-seq to study the 3D genome architecture of multiple myeloma (MM) and how it associates with genomic variation and gene expression. Our results show that Hi-C interaction matrices are biased by copy number variations (CNVs) and can be used to detect CNVs. Also, combining Hi-C and WGS data can improve the detection of translocations. We find that CNV breakpoints significantly overlap with topologically associating domain (TAD) boundaries. Compared to normal B cells, the numbers of TADs increases by 25% in MM, the average size of TADs is smaller, and about 20% of genomic regions switch their chromatin A/B compartment types. In summary, we report a 3D genome interaction map of aneuploid MM cells and reveal the relationship among CNVs, translocations, 3D genome reorganization, and gene expression regulation.
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http://dx.doi.org/10.1038/s41467-017-01793-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5715138PMC
December 2017

c-Jun N-Terminal Kinases (JNKs) Are Critical Mediators of Osteoblast Activity In Vivo.

J Bone Miner Res 2017 Sep;32(9):1811-1815

Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Cornell University, New York, NY, USA.

The c-Jun N-terminal kinases (JNKs) are ancient and evolutionarily conserved regulators of proliferation, differentiation, and cell death responses. Currently, in vitro studies offer conflicting data about whether the JNK pathway augments or represses osteoblast differentiation, and the contribution of the JNK pathway to regulation of bone mass in vivo remains unclear. Here we show that Jnk1 mice display severe osteopenia due to impaired bone formation, whereas Jnk2 mice display a mild osteopenia only evident in long bones. In order to both confirm that these effects were osteoblast intrinsic and assess whether redundancy with JNK1 masks a potential contribution of JNK2, mice with a conditional deletion of both JNK1 and JNK2 floxed conditional alleles in osteoblasts (Jnk1-2 ) were bred. These mice displayed a similar degree of osteopenia to Jnk1 mice due to decreased bone formation. In vitro, Jnk1 osteoblasts display a selective defect in the late stages of osteoblast differentiation with impaired mineralization activity. Downstream of JNK1, phosphorylation of JUN is impaired in Jnk1 osteoblasts. Transcriptome analysis showed that JNK1 is required for upregulation of several osteoblast-derived proangiogenic factors such as IGF2 and VEGFa. Accordingly, JNK1 deletion results in a significant reduction skeletal vasculature in mice. Taken together, this study establishes that JNK1 is a key mediator of osteoblast function in vivo and in vitro. © 2017 American Society for Bone and Mineral Research.
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http://dx.doi.org/10.1002/jbmr.3184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599178PMC
September 2017

Identification of a nucleoside analog active against adenosine kinase-expressing plasma cell malignancies.

J Clin Invest 2017 Jun 15;127(6):2066-2080. Epub 2017 May 15.

Department of Pathology and Laboratory Medicine.

Primary effusion lymphoma (PEL) is a largely incurable malignancy of B cell origin with plasmacytic differentiation. Here, we report the identification of a highly effective inhibitor of PEL. This compound, 6-ethylthioinosine (6-ETI), is a nucleoside analog with toxicity to PEL in vitro and in vivo, but not to other lymphoma cell lines tested. We developed and performed resistome analysis, an unbiased approach based on RNA sequencing of resistant subclones, to discover the molecular mechanisms of sensitivity. We found different adenosine kinase-inactivating (ADK-inactivating) alterations in all resistant clones and determined that ADK is required to phosphorylate and activate 6-ETI. Further, we observed that 6-ETI induces ATP depletion and cell death accompanied by S phase arrest and DNA damage only in ADK-expressing cells. Immunohistochemistry for ADK served as a biomarker approach to identify 6-ETI-sensitive tumors, which we documented for other lymphoid malignancies with plasmacytic features. Notably, multiple myeloma (MM) expresses high levels of ADK, and 6-ETI was toxic to MM cell lines and primary specimens and had a robust antitumor effect in a disseminated MM mouse model. Several nucleoside analogs are effective in treating leukemias and T cell lymphomas, and 6-ETI may fill this niche for the treatment of PEL, plasmablastic lymphoma, MM, and other ADK-expressing cancers.
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http://dx.doi.org/10.1172/JCI83936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451239PMC
June 2017

Folate Receptor Alpha Expression Is Associated With Increased Risk of Recurrence in Triple-negative Breast Cancer.

Clin Breast Cancer 2017 11 21;17(7):544-549. Epub 2017 Mar 21.

Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY.

Background: Folate receptor alpha (FOLR1) has been identified as a potential prognostic and therapeutic target in breast cancer. The limited studies evaluating the role of FOLR1 in breast cancer have shown that FOLR1 protein expression is enriched in triple-negative breast cancer (TNBC) and associated with poor prognosis in all breast cancer types. Newly developed anti-FOLR1 therapy could potentially be used in patients with TNBC for whom few therapeutic options exist. We sought to evaluate FOLR1 protein expression in a cohort of patients with TNBC to determine its prevalence and prognostic value.

Materials: Immunohistochemistry was performed for FOLR1 in 76 cases of primary TNBC. Membranous staining in ≥ 5% of cells was deemed positive in a given case. Statistical analyses correlating FOLR1 protein expression with clinicopathologic parameters and clinical outcome (disease-free survival and overall survival) were performed.

Results: A total of 76 cases of primary TNBC were studied. Most cases were negative for FOLR1 (80.3%; 61/76). FOLR1 expression did not correlate with any clinicopathologic parameters. FOLR1 expression was significantly correlated with decreased disease-free survival (hazard ratio, 2.61; 95% confidence interval, 0.96-7.09; P = .0497 log-rank test). Although FOLR1 expression trended towards decreased overall survival, it was not statistically significant (hazard ratio, 1.99; 95% confidence interval, 0.62-6.36; P > .05 log-rank test).

Conclusion: We found a lower incidence of FOLR1 expression in TNBC compared with other studies; however, these patients may benefit from anti-folate therapy as other targeted therapies are not available. Although no correlation between FOLR1 expression and standard clinicopathologic parameters was identified, our findings suggest that FOLR1 expression is prognostically significant in TNBC.
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http://dx.doi.org/10.1016/j.clbc.2017.03.007DOI Listing
November 2017

Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency.

Cell 2017 04;169(2):243-257.e25

Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China; Shenzhen Stem Cell Engineering Laboratory, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China. Electronic address:

Of all known cultured stem cell types, pluripotent stem cells (PSCs) sit atop the landscape of developmental potency and are characterized by their ability to generate all cell types of an adult organism. However, PSCs show limited contribution to the extraembryonic placental tissues in vivo. Here, we show that a chemical cocktail enables the derivation of stem cells with unique functional and molecular features from mice and humans, designated as extended pluripotent stem (EPS) cells, which are capable of chimerizing both embryonic and extraembryonic tissues. Notably, a single mouse EPS cell shows widespread chimeric contribution to both embryonic and extraembryonic lineages in vivo and permits generating single-EPS-cell-derived mice by tetraploid complementation. Furthermore, human EPS cells exhibit interspecies chimeric competency in mouse conceptuses. Our findings constitute a first step toward capturing pluripotent stem cells with extraembryonic developmental potentials in culture and open new avenues for basic and translational research. VIDEO ABSTRACT.
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http://dx.doi.org/10.1016/j.cell.2017.02.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679268PMC
April 2017

Inhibition of c-Jun N-terminal kinase signaling suppresses skin flap apoptosis in a rat ischemia and/or reperfusion model.

J Surg Res 2016 12 12;206(2):337-346. Epub 2016 Aug 12.

College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China.

Background: The goals of this study were to validate the role of c-Jun N-terminal kinase (JNK) activation in skin flap apoptosis in a rat model of abdomen skin ischemia and/or reperfusion (IR) and to compare the protective effect of SP600125 and hydrogen-rich saline in skin IR injury.

Methods: Male Sprague-Dawley rats were divided into five groups: one sham surgery group and four surgery groups. Before undergoing 3 h of IR management, the surgery groups were treated with normal saline (IR), dimethyl sulfoxide, SP600125 (SP), and hydrogen-rich saline (H). On the third postoperative day, blood perfusion of the flap was measured using Laser Doppler flowmeters. Hematoxylin and eosin staining was used to observe morphologic changes. Early apoptosis was observed using TdT-mediated dUTP-X nick end-labeling staining. pASK-1, pJNK, Bcl-2, and Bax were examined by immunodetection. Caspase-3 activity was also measured 24 h after reperfusion.

Results: Compared to the IR group and the dimethyl sulfoxide group, the SP group and the H group had larger skin flap survival area, more blood perfusion and lower levels of caspase-3 activity. The SP and the H groups had high expression levels of Bcl-2 and low expression levels of pASK-1 and pJNK. Bax was significantly decreased in the SP group. In addition, cell apoptosis was decreased in both the sham surgery and the H groups.

Conclusions: IR-induced JNK phosphorylation was reduced by SP600125, indicating that JNK mediates the apoptosis pathways in rat skin. In the SP and the H groups, the apoptotic factors measured showed similar expression levels, indicating that JNK inhibition during IR may be associated with H-mediated protection against skin IR apoptosis.
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http://dx.doi.org/10.1016/j.jss.2016.08.013DOI Listing
December 2016