Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/109787/1/pmic7911.pd

Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.

Tens of thousands of splice isoforms of proteins have been catalogued as predicted sequences from transcripts in humans and other species. Relatively few have been characterized biochemically or structurally. With the extensive development of protein bioinformatics, the characterization and modeling of isoform features, isoform functions, and isoform-level networks have advanced notably. Here we present applications of the I-TASSER family of algorithms for folding and functional predictions and the IsoFunc, MIsoMine, and Hisonet data resources for isoform-level analyses of network and pathway-based functional predictions and protein-protein interactions. Hopefully, predictions and insights from protein bioinformatics will stimulate many experimental validation studies

IN SILICO DESIGN, SYNTHESIS, CHARACTERIZATION, IN VITRO ANTI-INFLAMMATORY, AND ANTIOXIDANT STUDIES OF 4-ARYL-4H-CHROMENE DERIVATIVES

Objective: The objective of the study was to explore in silico design, preparation, characterization, and evaluation in vitro of some novel 4H-chromene derivatives as anti-inflammatory and antioxidant agents.Methods: 4-phenyl-4H chromene derivatives were imperiled to in silico modeling studies at the molecular level. The ligands were docked against cyclooxygenase-2 (COX-2) receptor targets using Argus Lab. Based on the result, the derivatives were selected for wet lab synthesis. A highly efficient multicomponent reaction of 4H chromene was carried out by one-step condensation of aldehyde with malononitrile and resorcinol without catalyst in water under ultrasound irradiation. The prepared compounds were characterized by noting their melting point, ultraviolet (UV) spectroscopy, infrared (IR) spectroscopy, and thin layer chromatography (TLC) and were scrutinized for its in vitro anti-inflammatory and antioxidant activitives by in vitro cell culture studies. IR spectra of the two compounds were analyzed and studied. Thus, using melting point, TLC and UV spectroscopy the synthesized compounds were found to be pure and identified chemically. The synthesized compounds were then screened for in vitro antioxidant (by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and hydrogen peroxide free radical scavenging) activity and anti-inflammatory activity by Raw 264.7 cell lines.Result: From the study, it was noticed that chemical structure-2 showed better antioxidant and anti-inflammatory activitives than chemical structure. In the 4-phenyl-4H chromene derivatives, hydroxyl substitution at 7th position and electronegative halogen at 4th position showed better antioxidant and anti-inflammatory activities.Conclusion: The results disclosed that these synthesized derivatives be likely to have moderate action against COX-2 mediated diseases, thereby it may lessen inflammation and agony because of its antioxidant and anti-inflammatory activitives

Sodium glucose co-transporter 2 inhibition increases epidermal growth factor expression and improves outcomes in patients with type 2 diabetes

Underlying molecular mechanisms of the kidney protective effects of sodium glucose co-transporter 2 (SGLT2) inhibitors are not fully elucidated. Therefore, we studied the association between urinary epidermal growth factor (uEGF), a mitogenic factor involved in kidney repair, and kidney outcomes in patients with type 2 diabetes (T2D). The underlying molecular mechanisms of the SGLT2 inhibitor canagliflozin on EGF using single-cell RNA sequencing from kidney tissue were examined. Urinary EGF-to-creatinine ratio (uEGF/Cr) was measured in 3521 CANagliflozin cardioVascular Assessment Study (CANVAS) participants at baseline and week 52. Associations of uEGF/Cr with kidney outcome were assessed using multivariable-adjusted Cox regression models. Single-cell RNA sequencing was performed using protocol kidney biopsy tissue from ten young patients with T2D on SGLT2i, six patients with T2D on standard care only, and six healthy controls (HCs). In CANVAS, each doubling in baseline uEGF/Cr was associated with a 12% (95% confidence interval 1-22) decreased risk of kidney outcome. uEGF/Cr decreased after 52 weeks with placebo and remained stable with canagliflozin (between-group difference +7.3% (2.0-12.8). In young persons with T2D, EGF mRNA was primarily expressed in the thick ascending loop of Henle. Expression in biopsies from T2D without SGLT2i was significantly lower compared to HCs, whereas treatment with SGLT2i increased EGF levels closer to the healthy state. In young persons with T2D without SGLT2i, endothelin-1 emerged as a key regulator of the EGF co-expression network. SGLT2i treatment was associated with a shift towards normal EGF expression. Thus, decreased uEGF represents increased risk of kidney disease progression in patients with T2D. Canagliflozin increased kidney tissue expression of EGF and was associated with a downstream signaling cascade linked to tubular repair and reversal of tubular injury.</p

Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker

To define cellular mechanisms underlying kidney function and failure, the KPMP analyzes biopsy tissue in a multicenter research network to build cell-level process maps of the kidney. This study aimed to establish a single cell RNA sequencing strategy to use cell-level transcriptional profiles from kidney biopsies in KPMP to define molecular subtypes in glomerular diseases. Using multiple sources of adult human kidney reference tissue samples, 22,268 single cell profiles passed KPMP quality control parameters. Unbiased clustering resulted in 31 distinct cell clusters that were linked to kidney and immune cell types using specific cell markers. Focusing on endothelial cell phenotypes, in silico and in situ hybridization methods assigned 3 discrete endothelial cell clusters to distinct renal vascular beds. Transcripts defining glomerular endothelial cells (GEC) were evaluated in biopsies from patients with 10 different glomerular diseases in the NEPTUNE and European Renal cDNA Bank (ERCB) cohort studies. Highest GEC scores were observed in patients with focal segmental glomerulosclerosis (FSGS). Molecular endothelial signatures suggested 2 distinct FSGS patient subgroups with α-2 macroglobulin (A2M) as a key downstream mediator of the endothelial cell phenotype. Finally, glomerular A2M transcript levels associated with lower proteinuria remission rates, linking endothelial function with long-term outcome in FSGS

Effects of Antioxidants in Human Cancers: Differential Effects on Non-Coding Intronic RNA Expression

The notion that dietary antioxidants can help fight cancer is popular. However, the mechanism(s) behind the effect of antioxidants in cancer is still unclear. Previous studies indicate that supplements can influence gene expression; however, all of these studies were focused on the coding/exonic gene expression. Studies are now emerging to highlight critical functional roles for RNAs expressed from the non-coding regions. This project was designed to study the effect of antioxidant supplements on non-coding intronic RNA expression in human cancers. Vitamin E, N-Acetyl cysteine (NAC) and Sulforaphane are commonly used supplements to prevent diseases including cancers. We studied the effect of these antioxidant supplements on the non-coding intronic RNA expression using publicly available datasets from a mouse model for lung cancer and prostate cancer cell lines. Although high throughput polyA-enriched RNA-Seq data characterize spliced coding mRNA regions, recent studies reveal the expression of reads from the non-coding intronic regions. Our analyses indicate that cancer cells have higher expression of introns compared to that of normal cells and that treatment with antioxidant supplements reduces the increased expression of introns of several genes. However, we did find high expression of introns of multiple genes including many oncogenes in the supplement treated groups compared to that of the control; this effect was distinct depending on the cell type and the supplement studied. Using RT-PCRs, we validated the expression of introns of two oncogenes, DLK1 and LRG1, known to be key players in lung cancer progression, and demonstrate changed intronic expression with supplement treatment in cancer cells. With regard to the antioxidant system, supplements did not change the intronic RNAs for endogenous antioxidant enzymes except for a significant decrease in the expression of superoxide dismutase (SOD) intronic RNA. Concurrently, we also found that a prolonged (48 h) exposure to Vitamin C, Vitamin E and Green tea extract reduced the enzymatic activity of SOD in lung cancer cells. The results from this study reveal that the antioxidant supplements have a significant effect on the intronic RNA expression of many genes including cancer genes that are not directly linked to the body’s antioxidant system. It is important to study this novel effect of antioxidant supplements in detail as it may have a significant role in disease progression

Generalised image processing method for quantitative analysis of nucleus, cell and focal adhesion clusters

Focal adhesion clusters (FAC) are dynamic and complex structures that help cells to sense physicochemical properties of their environment. Research in biomaterials, cell adhesion or cell migration often involves the visualization of FAC by fluorescence staining and microscopy, which necessitates quantitative analysis of FAC and other cell features in microscopy images using image processing. Fluorescence microscopy images of human umbilical vein endothelial cells (HUVEC) obtained at 63x magnification were quantitatively analysed using ImageJ software. A generalised algorithm for selective segmentation and morphological analysis of FAC, nucleus and cell morphology is implemented. Further, a method for discrimination of FACnear the nucleus and around the periphery is implemented using masks. Our algorithm is able to effectively quantify different morphological characteristics of cell components and shows a high sensitivity and specificity while providing a modular software implementation

M2 - Endocrine, Winter 2008

The Endocrine Sequence is a two-week unit designed to teach the basic principles of hormone secretion and action and the clinical disorders which result from abnormalities of hormonal activities. Students are expected to be familiar with the functions of the endocrine glands, the structure, secretion and action of the important hormones, and the major clinical endocrine disorders. Emphasis will be placed on understanding pathophysiology and being able to use general principles in endocrine physiology (e.g. negative feedback) or in the management of endocrine disorders (e.g., insulin management) in consideration of specific circumstances and clinical cases.http://deepblue.lib.umich.edu/bitstream/2027.42/64949/5/GHammer-AdrenalLectures08.ppthttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/6/RLash-Thyroid08.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/7/EOral-Obesity.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/8/RLash-Thyroid08.ppthttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/9/GHammer-AdrenalLectures08.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/10/RMenon-AbnormalDevelopment08.ppthttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/11/RMenon-AbnormalDevelopment08.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/12/EOral-Obesity.ppthttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/13/EOral-Obesity.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/14/EOral-Obesity.dochttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/15/EOral-obesity-NIHguide.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/16/EOral-obesity-NIH-WIN.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/64949/17/m2endocrine-winter2008.zi