A5053600307- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- Gut microbiota and health
- Chromatin Remodeling and Cancer
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- RNA modifications and cancer
- Astronomy and Astrophysical Research
- Cancer Genomics and Diagnostics
- Galaxies: Formation, Evolution, Phenomena
- Stellar, planetary, and galactic studies
- Mechanisms of cancer metastasis
- Immune Response and Inflammation
- Infant Nutrition and Health
- Plant Pathogens and Resistance
- Oral microbiology and periodontitis research
- Immune cells in cancer
- Cancer, Hypoxia, and Metabolism
- Digestive system and related health
- MicroRNA in disease regulation
- Genomics and Chromatin Dynamics
- Cancer Cells and Metastasis
- S100 Proteins and Annexins
- Immune Cell Function and Interaction
- Protein Degradation and Inhibitors
Indiana University – Purdue University Indianapolis
2016-2025
Indiana University School of Medicine
2016-2025
Zhejiang University
2025
Capital Medical University
2024
University of Indianapolis
2022-2024
Indiana University
2018-2024
University School
2021-2024
Shanghai Jiao Tong University
2022-2024
Kunming University of Science and Technology
2024
Southern University of Science and Technology
2024
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in microbes occupy habitats such as gut, skin and vagina. Much this diversity remains unexplained, although diet, environment, host genetics early microbial exposure all been implicated. Accordingly, to characterize ecology human-associated communities, Human Microbiome Project has analysed largest cohort set distinct, clinically relevant body so far. We found abundance each habitat's signature vary...
A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in health disease. The National Institutes Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting broad range quality-controlled resources data including standardized methods for creating, processing interpreting distinct types high-throughput available scientific community. Here...
Characterizing the biogeography of microbiome healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from limited set subjects. Here, we analyzed one largest datasets to date and generated biogeographical map that annotates biodiversity, spatial relationships, temporal stability 22 habitats 279 humans.We identified 929 genera more than 24 million 16S rRNA gene sequences habitats, provide baseline inter-subject...
Sepsis is a dynamic state that progresses at variable rates and has life-threatening consequences. Staging patients along the sepsis timeline requires thorough knowledge of evolution cellular molecular events tissue level. Here, we investigated kidney, an organ central to pathophysiology sepsis. Single-cell RNA-sequencing in murine endotoxemia model revealed involvement various cell populations be temporally organized highly orchestrated. Endothelial stromal cells were first responders. At...
Abstract Background Determining bacterial abundance variation is the first step in understanding similarity between individuals. Categorization of communities into groups or community classes subsequent describing microbial distribution based on patterns. Here, we present an analysis groupings stool, nasal, skin, vaginal and oral habitats a healthy cohort 236 subjects from Human Microbiome Project. Results We identify distinct group patterns anterior nares, four skin sites, vagina at genus...
In response to vascular injury, smooth muscle cells (VSMCs) may switch from a contractile proliferative phenotype thereby contributing neointima formation. Previous studies showed that the long noncoding RNA (lncRNA)
Ischemic renal injury is a complex syndrome; multiple cellular abnormalities cause accelerating cycles of inflammation, damage, and sustained local ischemia. There no single therapy that effectively resolves the damage after However, infusions normal adult rat cells have been successful in several failure models. The broad benefit achieved by relatively few donor led to hypothesis extracellular vesicles (EV, largely exosomes) derived from these are therapeutic effector situ We now show EV...
Single-cell RNA sequencing (scRNA-seq) is an evolving technology used to elucidate the cellular architecture of adult organs. Previous scRNA-seq on breast tissue utilized reduction mammoplasty samples, which are often histologically abnormal. We report a rapid collection/processing protocol perform biopsies healthy women and identify 23 epithelial cell clusters. Putative cell-of-origin signatures derived from these clusters applied analyze transcriptomes ~3,000 cancers. Gene mature luminal...
Abstract The RNA-binding protein QKI belongs to the hnRNP K-homology domain family, a well-known regulator of pre-mRNA alternative splicing and is associated with several neurodevelopmental disorders. Qki found highly expressed in developing adult hearts. By employing human embryonic stem cell (hESC) cardiomyocyte differentiation system generating QKI-deficient hESCs (hESCs- del ) using CRISPR/Cas9 gene editing technology, we analyze physiological role differentiation, maturation,...
Despite IL-9 functioning as a pleiotropic cytokine in mucosal environments, the IL-9–responsive cell repertoire is still not well defined. Here, we found that mediates proallergic activities lungs by targeting lung macrophages. inhibits alveolar macrophage expansion and promotes recruitment of monocytes develop into CD11c + − interstitial populations. Interstitial macrophages were required for IL-9–dependent allergic responses. Mechanistically, affected function inducing Arg1 activity....
Asthma is a chronic inflammatory lung disease with intermittent flares predominately mediated through memory T cells. Yet, the identity of long-term cells that mediate allergic recall responses not well defined. In this report, using mouse model allergen exposure followed by an allergen-free rest period, we characterized subpopulation CD4+ secreted IL-9 as obligate effector cytokine. IL-9-secreting had resident cell phenotype, and blocking during challenge or deleting from significantly...
Most circulating endothelial cells are apoptotic, but rare colony-forming (C-ECFCs), also known as blood outgrowth cells, with proliferative and vasculogenic activity can be cultured; however, the origin naive function of these C-ECFCs remains obscure. Herein, detailed lineage tracing revealed murine emerged in early postnatal period, displayed high potential enriched frequency clonal compared tissue-resident ECFCs, were not committed to or derived from BM hematopoietic system ECFCs. In...
Abstract Background Microbial dysbiosis has emerged as an important element in the development and progression of various cancers, including breast cancer. However, microbial composition from healthy individuals, even relative to risk developing cancer, remains unclear. Here, we performed a comprehensive analysis microbiota normal tissue, which was analyzed relation tumor adjacent tissue. Methods The study cohorts included 403 cancer-free women (who donated tissue cores) 76 cancer patients...
A series of single genes protect soybean from the root and stem disease caused by oomycete pathogen Phytophthora sojae. In last two decades, Rps1-k has been most stable widely used resistance gene for major soybean-producing regions United States. Four highly similar encoding coiled coil-nucleotide binding-leucine rich repeat (CC-NB-LRR)-type proteins were isolated locus. These grouped into classes based on their sequence identity. Class I contains three with identical open reading frames...
A series of Rps (resistance to P ytophthora s ojae) genes have been protecting soybean from the root and stem rot disease caused by Oomycete pathogen, Phytophthora sojae. Five were mapped Rps1 locus located near 28 cM map position on molecular linkage group N composite genetic map. Among these five genes, Rps1-k was introgressed cultivar, Kingwa. has providing stable broad-spectrum resistance in major soybean-producing regions United States. isolated. More than one functional gene identified...
The human gut harbors thousands of bacterial taxa. A profusion metagenomic sequence data has been generated from stool samples in the last few years, raising question whether more taxa remain to be identified. We assessed by Human Microbiome Project Consortium determine if novel discovered healthy individuals. To do this, we established a rigorous bioinformatics pipeline that uses multiple platforms (Illumina GAIIX and Roche 454 FLX Titanium) approaches (whole-genome shotgun 16S rDNA...
Abstract Resistance of soybean against the oomycete pathogen Phytophthora sojae is conferred by a series Rps genes. We have characterized disease resistance gene-like sequence NBSRps4/6 that was introgressed into lines along with Rps4 or Rps6. High-resolution genetic mapping established cosegregates Rps4. Two mutants, M1 and M2, showing rearrangements in region were identified from analyses 82 F1's 201 selfed HARO4272 plants containing Fingerprints these mutants are identical to those for...
The exosome and its nuclear specific subunit Rrp6 form a 3'-5' exonuclease complex that regulates diverse aspects of RNA biology including 3' end processing degradation variety noncoding RNAs (ncRNAs) unstable transcripts. Known targets the include short (<1000 bp) RNAPII transcripts such as small (snRNAs), cryptic (CUTs), some stable unannotated (SUTs) are terminated by an Nrd1, Nab3, Sen1 (NNS) dependent mechanism. NNS-dependent termination is coupled to and/or Rrp6/exosome in yeast....
Abstract Kidney intercalated cells are involved in acid-base homeostasis via vacuolar ATPase expression. Here we report six human cell subtypes, including hybrid principal-intercalated identified from single transcriptomics. Phagosome maturation is a biological process that increases pathway analysis rank following exposure to uropathogenic Escherichia coli two of the subtypes. Real time confocal microscopy visualization murine renal tubules perfused with green fluorescent protein expressing...
Type 1 diabetes is a disorder of immune tolerance that leads to death insulin-producing islet β cells. We hypothesize inflammatory signaling within cells promotes progression autoimmunity the microenvironment. To test this hypothesis, we deleted proinflammatory gene encoding 12/15-lipoxygenase (Alox15) in non-obese diabetic mice at pre-diabetic time point when inflammation feature. Deletion Alox15 preservation cell mass, reduces populations infiltrating T cells, and protects against...
Introduction Due to a lack of spatial-temporal resolution at the single cell level, etiologies bone dysfunction caused by diseases such as normal aging, osteoporosis, and metabolic disease associated with chronic kidney (CKD) remain largely unknown. Methods To this end, flow cytometry scRNAseq were performed on long cells from Sost-cre/Ai9 + mice, pure osteolineage transcriptomes identified, including novel osteocyte-specific gene sets. Results Clustering analysis isolated osteoblast...
Abstract Osteocytes act within a hypoxic environment to control key steps in bone formation. FGF23, critical phosphate-regulating hormone, is stimulated by low oxygen/iron acute and chronic diseases, however the molecular mechanisms directing this process remain unclear. Our goal was identify osteocyte factors responsible for FGF23 production driven changes utilization. Hypoxia-inducible factor-prolyl hydroxylase inhibitors (HIF-PHI) which stabilize HIF transcription factors, increased Fgf23...