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Dive into the research topics where Debabrata Patra is active.

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Featured researches published by Debabrata Patra.


Osteoarthritis and Cartilage | 2008

Exuberant expression of chemokine genes by adult human articular chondrocytes in response to IL-1β

Linda J. Sandell; Xiaoyun Xing; Carl J. Franz; Sherri R. Davies; Li-Wei Chang; Debabrata Patra

OBJECTIVE To provide a more complete picture of the effect of interleukin-1 beta (IL-1beta) on adult human articular chondrocyte gene expression, in contrast to the candidate gene approach. DESIGN Chondrocytes from human knee cartilage were cultured in medium containing IL-1beta. Changes in gene expression were analyzed by microarray and reverse transcriptase-polymerase chain reaction analysis. The ability of transforming growth factor beta-1 (TGF-beta1), fibroblast growth factor (FGF)-18, and bone morphogenetic protein 2 (BMP-2) to alter the effects of IL-1beta was analyzed. Computational analysis of the promoter regions of differentially expressed genes for transcription factor binding motifs was performed. RESULTS IL-1beta-treated human chondrocytes showed significant increases in the expression of granulocyte colony stimulating factor-3, endothelial leukocyte adhesion molecule 1 and leukemia inhibitory factor as well as for a large group of chemokines that include CXCL1, CXCL2, CXCL3, CXCL5, CXCL6, CXCL8, CCL2, CCL3, CCL4, CCL5, CCL8, CCL20, CCL3L1, CX3CL1 and the cytokine IL-6. As expected, the mRNA for matrix metalloproteinase (MMP)-13 and BMP-2 also increased while mRNA for the matrix genes COL2A1 and aggrecan was down-regulated. A subset of chemokines increased rapidly at very low levels of IL-1beta. The phenotype induced by IL-1beta was partially reversed by TGF-beta1, but not by BMP-2. In the presence of IL-1beta, FGF-18 increased expression of ADAMTS-4, aggrecan, BMP-2, COL2A1, CCL3, CCL4, CCL20, CXCL1, CXCL3, CXCL6, IL-1beta, IL-6, and IL-8 and decreased ADAMTS-5, MMP-13, CCL2, and CCL8. Computational analysis revealed a high likelihood that the most up-regulated chemokines are regulated by the transcription factors myocyte enhancer binding factor-3 (MEF-3), CCAAT/enhancer binding protein (C/EBP) and nuclear factor-kappa B (NF-kappaB). CONCLUSION IL-1beta has a diverse effect on gene expression profile in human chondrocytes affecting matrix genes as well as chemokines and cytokines. TGF-beta1 has the ability to antagonize some of the phenotype induced by IL-1beta.


Expert Reviews in Molecular Medicine | 2012

Antiangiogenic and anticancer molecules in cartilage

Debabrata Patra; Linda J. Sandell

Cartilage is one of the very few naturally occurring avascular tissues where lack of angiogenesis is the guiding principle for its structure and function. This has attracted investigators who have sought to understand the biochemical basis for its avascular nature, hypothesising that it could be used in designing therapies for treating cancer and related malignancies in humans through antiangiogenic applications. Cartilage encompasses primarily a specialised extracellular matrix synthesised by chondrocytes that is both complex and unique as a result of the myriad molecules of which it is composed. Of these components, a few such as thrombospondin-1, chondromodulin-1, the type XVIII-derived endostatin, SPARC (secreted protein acidic and rich in cysteine) and the type II collagen-derived N-terminal propeptide (PIIBNP) have demonstrated antiangiogenic or antitumour properties in vitro and in vivo preclinical trials that involve several complicated mechanisms that are not completely understood. Thrombospondin-1, endostatin and the shark-cartilage-derived Neovastat preparation have also been investigated in human clinical trials to treat several different kinds of cancers, where, despite the tremendous success seen in preclinical trials, these molecules are yet to show success as anticancer agents. This review summarises the current state-of-the-art antiangiogenic characterisation of these molecules, highlights their most promising aspects and evaluates the future of these molecules in antiangiogenic applications.


Arthritis & Rheumatism | 2013

Transcriptome Analysis of Injured Human Meniscus Reveals a Distinct Phenotype of Meniscus Degeneration With Aging

Muhammad Farooq Rai; Debabrata Patra; Linda J. Sandell; Robert H. Brophy

OBJECTIVE Meniscus tears are associated with a heightened risk of osteoarthritis. This study aimed to advance our understanding of the metabolic state of injured human meniscus at the time of arthroscopic partial meniscectomy through transcriptome-wide analysis of gene expression in relation to the patients age and degree of cartilage chondrosis. METHODS The degree of chondrosis of knee cartilage was recorded at the time of meniscectomy in symptomatic patients without radiographic osteoarthritis. RNA preparations from resected menisci (n = 12) were subjected to transcriptome-wide microarray and QuantiGene Plex analyses. Variations in the relative changes in gene expression with age and chondrosis were analyzed, and integrated biologic processes were investigated computationally. RESULTS We identified a set of genes in torn menisci that were differentially expressed with age and chondrosis. There were 866 genes that were differentially regulated (≥1.5-fold difference and P < 0.05) with age and 49 with chondrosis. In older patients, genes associated with cartilage and skeletal development and extracellular matrix synthesis were repressed, while those involved in immune response, inflammation, cell cycle, and cellular proliferation were stimulated. With chondrosis, genes representing cell catabolism (cAMP catabolic process) and tissue and endothelial cell development were repressed, and those involved in T cell differentiation and apoptosis were elevated. CONCLUSION Differences in age-related gene expression suggest that in older adults, meniscal cells might dedifferentiate and initiate a proliferative phenotype. Conversely, meniscal cells in younger patients appear to respond to injury, but they maintain the differentiated phenotype. Definitive molecular signatures identified in damaged meniscus could be segregated largely with age and, to a lesser extent, with chondrosis.


Arthritis & Rheumatism | 2014

Relationship of gene expression in the injured human meniscus to body mass index: a biologic connection between obesity and osteoarthritis.

Muhammad Farooq Rai; Debabrata Patra; Linda J. Sandell; Robert H. Brophy

Higher body mass index (BMI) increases the risk of meniscus injury and knee osteoarthritis (OA). However, it is unknown if and how obesity affects meniscus biology. We analyzed transcriptome‐wide gene expression profiles of injured human menisci to test the hypothesis that meniscal gene expression signatures relate to patient BMI.


PLOS ONE | 2014

Cartilage-specific ablation of site-1 protease in mice results in the endoplasmic reticulum entrapment of type IIB procollagen and down-regulation of cholesterol and lipid homeostasis

Debabrata Patra; Elizabeth DeLassus; Guosheng Liang; Linda J. Sandell

The proprotein convertase site-1 protease (S1P) converts latent ER-membrane bound transcription factors SREBPs and ATF6 to their active forms. SREBPs are involved in cholesterol and fatty acid homeostasis whereas ATF6 is involved in unfolded protein response pathways (UPR). Cartilage-specific ablation of S1P in mice (S1Pcko) results in abnormal cartilage devoid of type II collagen protein (Col II). S1Pcko mice also lack endochondral bone development. To analyze S1Pcko cartilage we performed double-labeled immunofluorescence studies for matrix proteins that demonstrated that type IIB procollagen is trapped inside the ER in S1Pcko chondrocytes. This retention is specific to type IIB procollagen; other cartilage proteins such as type IIA procollagen, cartilage oligomeric matrix protein (COMP) and aggrecan are not affected. The S1Pcko cartilage thus exhibits COMP-, aggrecan-, and type IIA procollagen-derived matrices but is characterized by the absence of a type IIB procollagen-derived matrix. To understand the molecular reason behind S1Pcko phenotypes we performed genome-wide transcriptional profiling of cartilage isolated from S1Pcko and wild type littermates. While the UPR pathways are unaffected, the SREBPs-directed cholesterol and fatty acid pathways are significantly down-regulated in S1Pcko chondrocytes, with maximal down-regulation of the stearoyl-CoA desaturase-1 (Scd1) gene. However, mouse models that lack Scd1 or exhibit reduction in lipid homeostasis do not suffer from the ER retention of Col II or lack endochondral bone. These studies indicate an indispensable role for S1P in type IIB procollagen trafficking from the ER. This role appears not to be related to lipid pathways or other current known functions of S1P and is likely dependent on additional, yet unknown, S1P substrates in chondrocytes.


Matrix Biology | 2014

Characterization of a Murine Type IIB Procollagen-specific Antibody

Debabrata Patra; Elizabeth DeLassus; Audrey McAlinden; Linda J. Sandell

Type II collagen is the major collagenous component of the cartilage extracellular matrix; formation of a covalently cross-linked type II collagen network provides cartilage with important tensile properties. The Col2a1 gene is encoded by 54 exons, of which exon 2 is subject to alternative splicing, resulting in different isoforms named IIA, IIB, IIC and IID. The two major procollagen protein isoforms are type IIA and type IIB procollagen. Type IIA procollagen mRNA contains exon 2 and is generated predominantly by chondroprogenitor cells and other non-cartilaginous tissues. Differentiated chondrocytes generate type IIB procollagen, devoid of exon 2. Although type IIA procollagen is produced in certain non-collagenous tissues during development, this developmentally-regulated alternative splicing switch to type IIB procollagen is restricted to cartilage cells. Though a much studied and characterized molecule, the importance of the various type II collagen protein isoforms in cartilage development and homeostasis is still not completely understood. Effective antibodies against specific epitopes of these isoforms can be useful tools to decipher function. However, most type II collagen antibodies to date recognize either all isoforms or the IIA procollagen isoform. To specifically identify the murine type IIB procollagen, we have generated a rabbit antibody (termed IIBN) directed to a peptide sequence that spans the murine exon 1-3 peptide junction. Characterization of the affinity-purified antibody by western blotting of collagens extracted from wild type murine cartilage or cartilage from Col2a1(+ex2) knock-in mice (which generates predominantly the type IIA procollagen isoform) demonstrated that the IIBN antibody is specific to the type IIB procollagen isoform. IIBN antibody was also able to detect the native type IIB procollagen in the hypertrophic chondrocytes of the wild type growth plate, but not in those of the Col2a1(+ex2) homozygous knock-in mice, by both immunofluorescence and immunohistochemical studies. Thus the IIBN antibody will permit an in-depth characterization of the distribution of IIB procollagen isoform in mouse skeletal tissues. In addition, this antibody will be an important reagent for characterizing mutant type II collagen phenotypes and for monitoring type II procollagen processing and trafficking.


Journal of Orthopaedic Research | 2017

Early changes in the knee of healer and non-healer mice following non-invasive mechanical injury.

Xin Duan; Muhammad Farooq Rai; Nilsson Holguin; Matthew J. Silva; Debabrata Patra; Weiming Liao; Linda J. Sandell

In this study, we examined early time‐dependent changes in articular cartilage and synovium in response to tibial compression and sought the plausible origin of cells that respond to compression in the healer (LGXSM‐6) and non‐healer (LGXSM‐33) recombinant inbred mouse strains. The right knee of 13‐week old male mice was subjected to tibial compression using 9N axial loading. The contralateral left knee served as a control. Knees were harvested at 5, 9, and 14 days post‐injury. Histological changes in cartilage and synovium, immunofluorescence pattern of CD44, aggrecan, type‐II collagen, cartilage oligomeric matrix protein and the aggrecan neo‐epitope NITEGE, and cell apoptosis (by TUNEL) were examined. We used a double nucleoside analog cell‐labeling strategy to trace cells responsive to injury. We showed that tibial compression resulted in rupture of anterior cruciate ligament, cartilage matrix loss and chondrocyte apoptosis at the injury site. LGXSM‐33 showed higher synovitis and ectopic synovial chondrogenesis than LGXSM‐6 with no differences for articular cartilage lesions. With loading, an altered pattern of CD44 and NITEGE was observed: cells in the impacted area underwent apoptosis, cells closely surrounding the injured area expressed CD44, and cells in the intact area expressed NITEGE. Cells responding to injury were found in the synovium, subchondral bone marrow and the Groove of Ranvier. Taken together, we found no strain differences in chondrocytes in the early response to injury. However, the synovial response was greater in LGXSM‐33 indicating that, at early time points, there is a genetic difference in synovial cell reaction to injury.


Biology Open | 2018

Site-1 protease regulates skeletal stem cell population and osteogenic differentiation in mice

Debabrata Patra; Elizabeth DeLassus; Jennifer Mueller; Grazia Abou-Ezzi; Linda J. Sandell

ABSTRACT Site-1 protease (S1P) is a proprotein convertase with essential functions in the conversion of precursor proteins to their active form. In earlier studies, we demonstrated that S1P ablation in the chondrocyte lineage results in a drastic reduction in endochondral bone formation. To investigate the mechanistic contribution of S1P to bone development we ablated S1P in the osterix lineage in mice. S1P ablation in this lineage results in osteochondrodysplasia and variable degrees of early postnatal scoliosis. Embryonically, even though Runx2 and osterix expression are normal, S1P ablation results in a delay in vascular invasion and endochondral bone development. Mice appear normal when born, but by day 7 display pronounced dwarfism with fragile bones that exhibit significantly reduced mineral density, mineral apposition rate, bone formation rate and reduced osteoblasts indicating severe osteopenia. Mice suffer from a drastic reduction in bone marrow mesenchymal progenitors as analyzed by colony-forming unit-fibroblast assay. Fluorescence-activated cell sorting analysis of the skeletal mesenchyme harvested from bone marrow and collagenase-digested bone show a drastic reduction in hematopoietic lineage-negative, endothelial-negative, CD105+ skeletal stem cells. Bone marrow mesenchymal progenitors are unable to differentiate into osteoblasts in vitro, with no effect on adipogenic differentiation. Postnatal mice have smaller growth plates with reduced hypertrophic zone. Thus, S1P controls bone development directly by regulating the skeletal progenitor population and their differentiation into osteoblasts. This article has an associated First Person interview with the first author of the paper. Summary: S1P governs a fundamental aspect of skeletal development and homeostasis, mainly the maintenance and osteogenic differentiation of skeletogenic stem cells that are a source of osteoblast and chondrocyte lineages.


Osteoarthritis and Cartilage | 2010

183 CARTILAGE-SPECIFIC KNOCKOUT OF SITE-1 PROTEASE IN POSTNATAL MICE RESULTS IN AN ABNORMAL GROWTH PLATE WITH DISRUPTION OF HYPERTROPHIC CHONDROCYTE DIFFERENTIATION AND SUBSEQUENT CHONDRODYSPLASIA

Debabrata Patra; Elizabeth DeLassus; S. Hayashi; Linda J. Sandell

caused an upregulation of SOX9 and enhanced extracellular matrix protein production. Conclusions: Depletion of PHD2 resulted in greater HIF-2α levels, and therefore enhanced SOX9-induced cartilage matrix production compared to the levels normally found in hypoxia (1% oxygen) implying that PHD2 inhibition offers a novel means to promote the chondrocyte phenotype and enhance cartilage repair in vivo.


Genome Research | 2007

Computational identification and functional validation of regulatory motifs in cartilage-expressed genes.

Sherri R. Davies; Li Wei Chang; Debabrata Patra; Xiaoyun Xing; Karen L. Posey; Jacqueline T. Hecht; Gary D. Stormo; Linda J. Sandell

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Linda J. Sandell

Washington University in St. Louis

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Xiaoyun Xing

Washington University in St. Louis

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Elizabeth DeLassus

Washington University in St. Louis

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Jennifer Bryan

Washington University in St. Louis

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Carl J. Franz

Washington University in St. Louis

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Muhammad Farooq Rai

Washington University in St. Louis

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Robert H. Brophy

Washington University in St. Louis

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Sherri R. Davies

Washington University in St. Louis

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Guosheng Liang

University of Texas Southwestern Medical Center

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J. Mueller

Washington University in St. Louis

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