David Hong

Columbia College

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Frank A. Witzmann

Indiana University School of Medicine

S. B. Mason

Great Ormond Street Hospital

Robert L. Bacallao

Richard L. Roudebush VA Medical Center

Bonnie L. Blazer‐Yost

Indiana University – Purdue University Indianapolis

Seth Lederman

Tonix Pharmaceuticals (United States)

Xianyin Lai

Eli Lilly (United States)

Ghislaine Jumonville

Columbia University

Chunhua Weng

Columbia University

Zheng-sheng Ye

Massachusetts Institute of Technology

Samya Z. Nasr

Townsville Hospital

Cooperative Institutions

Columbia University

Columbia University Irving Medical Center

Indiana University School of Medicine

Indiana University – Purdue University Indianapolis

Indiana University

Laboratoire d’immunologie intégrative du cancer

University of California, Los Angeles

New York Genome Center

Royal College of Physicians

Rockefeller University

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Renal cyst fluid proteomics in autosomal dominant polycystic kidney disease (ADPKD)

The FASEB Journal (2008)

Xianyin Lai Robert L. Bacallao Bonnie L. Blazer‐Yost David Hong S. B. Mason

ADPKD is characterized by localized autonomous cellular proliferation, fluid accumulation within the cysts, and intraparenchymal fibrosis of the kidney. Little is known about the cyst fluid's protein composition. We hypothesized that the complex collection of cystic fluid proteins (cystic proteome) plabys a major role in cyst formation/maintenance and contains yet unknown diagnostic and mechanistic features that are common to all forms of PKD. We analyzed five kidney cyst fluids from four patients with ADPKD. Tryptic peptides from plasma‐protein immunodepleted (ProteoPrep ® ) and undepleted cyst fluid samples were analyzed by LC‐MS/MS. The proteins were identified by SEQUEST and validated via Trans‐Proteomic Pipeline. 391 proteins were identified with >90% confidence; 251 of them in undepleted and 362 in immunodepleted samples. Immunodepletion removed >98% of the cyst fluid protein. A surprisingly large and functionally diverse number of proteins common to all 5 cysts was identified. These proteins may be of mechanistic interest and include Ig γ κ and fragments; complement components; vitronectin; orosomucoid; prostaglandin D2 synthase; and vitamin D‐binding protein. Supported by AFOSR Grant FA9550‐06‐1‐0083.

PKD1

Proteome

10.1096/fasebj.22.1_supplement.942.1

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Quantitative Mass Spectrometry to Determine Effects of Diabetic Dyslipidemia and Exercise on the plasma Low Density Lipoproteome

The FASEB Journal (2007)

Matthew R. Richardson David Hong Michael Sturek Mu Wang Frank A. Witzmann

There is a predominant role for LDL in atherogenesis. Coronary vascular dysfunction in the Yucatan swine model of diabetic dyslipidemia (DD) was prevented by aerobic exercise training (DDX) without altering total LDL concentration (Mokelke et al. J. Appl. Physiol. 95:, 2003). Attenuation of the DD induced changes in the quantitative and/or qualitative properties of LDL may explain the cardioprotective effects of exercise. We used quantitative mass spectrometry to determine these changes in the complex LDL particle in plasma of healthy control, DD, and DDX pigs. The LDL fraction of the plasma was isolated via FPLC, and the tryptically digested LDL peptides were analyzed serially via linear ion-trap LC-MS/MS. Proteins were identified using SEQUEST and X!Tandem, while protein quantification was carried out based on total ion chromatograms using the proprietary technology of Indiana Centers for Applied Protein Sciences. In this approach, the integral volume under each selected peptide peak was measured, normalized, and compared for relative abundance. In this study, 434 proteins were identified and quantified. Of these, 210 were identified with high confidence, including porcine apolipoproteins B100, D, E, CIII, N, R, AIV and AI. To our knowledge this is the largest number of proteins in the LDL particle ever identified with high confidence. Supported by NIH RR013223, HL062552 (MS) and AA015698 (FAW).

Dyslipidemia

Lipoprotein particle

10.1096/fasebj.21.6.a855-a

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A single gene for human TRAF-3 at chromosome 14q32.3 encodes a variety of mRNA species by alternative polyadenylation, mRNA splicing and transcription initiation

Molecular Immunology (1998)

W.G van Eyndhoven Dale Frank Sergey Kalachikov Alan Cleary David Hong

Human TRAF-3 is a signaling molecule that interacts with the cytoplasmic tails of CD40 and other TNF-receptor family members. TRAF-3 mRNA is expressed as two major classes of approximately 2 and 8 kb and a number of TRAF-3 encoding cDNA clones differ in discrete gene segments. Because this variety of mRNA species could result from mRNA processing events and/or multiple genes, the structure and localization of TRAF-3 encoding gene elements were determined. FISH and radiation hybrid mapping demonstrated that TRAF-3 is located at chromosome 14q32.3, approximately 1 Mb centromeric to the Ig heavy chain gene complex. Physical mapping of four overlapping genomic PAC clones established that TRAF-3 transcripts are encoded by a single gene, comprised of 13 exons and spanning 130 kb. Alternative polyadenylation in the mRNA segment encoded by exon 12 accounts for the difference between the 2 kb and the 8 kb classes of transcripts. Alternative mRNA splicing in the coding region (encoded by exons 3–12) generates transcripts which delete exons 8 (75 nt), 7+8 (156 nt) or 8+9 (168 nt) and that encode distinct protein isoforms (Δ25, Δ52 and Δ56 aa, respectively). Alternative splicing of exon 2 (139 nt) and alternative transcriptional initiation result in mRNA species with distinct 5′UTRs. Together, these data indicate that a single TRAF-3 gene encodes a variety of mRNA species by a combination of alternative polyadenylation, alternative mRNA splicing and/or alternative initiation.

Transcription

10.1016/s0161-5890(98)00099-6

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Citations (15)

Characterization of the renal cyst fluid proteome in autosomal dominant polycystic kidney disease (ADPKD) patients

PROTEOMICS - CLINICAL APPLICATIONS (2008)

Xianyin Lai Robert L. Bacallao Bonnie L. Blazer‐Yost David Hong S. B. Mason

Autosomal dominant polycystic kidney disease (ADPKD) is characterized by localized autonomous cellular proliferation, fluid accumulation within the cysts, and intraparenchymal fibrosis of the kidney. Little is known about the cyst fluid's protein composition. We hypothesized that the complex collection of cyst fluid proteins (cyst fluid proteome) plays a major role in cyst formation/maintenance and contains yet unknown diagnostic and mechanistic features that are common to all forms of PKD. We analyzed five kidney cyst fluids from four patients with ADPKD. Tryptic peptides from plasma-protein immunodepleted (ProteoPrep(R)) and undepleted cyst fluid samples were analyzed by LC-MS/MS. Proteins were identified by SEQUEST and validated via the Trans-Proteomic Pipeline; 391 proteins were identified with >90% confidence; 251 of them in undepleted and 362 in immunodepleted samples. Immunodepletion removed >94% of the cyst fluid protein. A surprisingly large and functionally diverse number of proteins common to most cysts were identified. These proteins may be of mechanistic interest and include Ig gamma, kappa, and fragments; complement components; vitronectin; orosomucoid; prostaglandin D2 synthase; vitamin D-binding protein; clusterin; SERPIN family proteins; hemopexin; and fetuin-A. Additionally, these results suggest that further prefractionation and enhanced chromatographic separation of tryptic peptides is likely to expose an even greater number of relevant proteins.

PKD1

Hemopexin

Proteome

Clusterin

Haptoglobin

10.1002/prca.200780140

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Citations (55)

Involvement of CRAF1, a relative of TRAF, in CD40 signaling

Science (1995)

Genhong Cheng Aileen M. Cleary Zheng-sheng Ye David Hong Seth Lederman

CD40 is a receptor on the surface of B lymphocytes, the activation of which leads to B cell survival, growth, and differentiation. A yeast two-hybrid screen identified a gene, CRAF1 , encoding a protein that interacts directly with the CD40 cytoplasmic tail through a region of similarity to the tumor necrosis factor-α (TNF-α) receptor-associated factors. Overexpression of a truncated CRAF1 gene inhibited CD40-mediated up-regulation of CD23. A region of CRAF1 was similar to the TNF-α receptor-associated factors TRAF1 and TRAF2 and so defined a shared TRAF-C domain that was necessary and sufficient for CD40 binding and homodimerization. The CRAF1 sequence also predicted a long amphipathic helix, a pattern of five zinc fingers, and a zinc ring finger. It is likely that other members of the TNF receptor superfamily use CRAF -related proteins in their signal transduction processes.

CD23

10.1126/science.7533327

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Citations (454)

Digital biobanks are underutilized in dermatology and create opportunities to reduce the burden of skin disease

British Journal of Dermatology (2023)

Ghislaine Jumonville David Hong Atlas Khan Andrew T. DeWan Suzanne M. Leal

Digital biobanks that integrate genetic data with health data captured by digital sources are used routinely to discover genes, biomarkers, gene–environment interactions and pharmacogenetic relationships across many clinical areas. There remain many opportunities in dermatology to further use biobank data to increase our knowledge about the genetic architecture of skin disease, to resolve disease mechanisms that can be modulated by medical interventions and to discover genetically derived disease relationships that inform on drug repurposing and adverse events. Such knowledge promises to reduce the global burden of skin disease and facilitates the development of tailored medical care.

Repurposing

Pharmacogenomics

Drug repositioning

10.1093/bjd/ljad439

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Citations (1)