scholarly journals Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with thePax5promoter in a chicken B cell line

2016 ◽  
Author(s):  
Toshitsugu Fujita ◽  
Fusako Kitaura ◽  
Miyuki Yuno ◽  
Yutaka Suzuki ◽  
Sumio Sugano ◽  
...  

AbstractChromosomal interactions regulate genome functions, such as transcription, via dynamic chromosomal organization in the nucleus. In this study, we identified genomic regions that physically bind to the promoter region of thePax5gene in the chicken B-cell line DT40, with the goal of obtaining mechanistic insight into transcriptional regulation through chromosomal interaction. Using insertional chromatin immunoprecipitation (iChIP) in combination with next-generation sequencing (NGS) (iChIP-Seq), we found that thePax5promoter bound to multiple genomic regions. The identified chromosomal interactions were independently confirmed byin vitroengineered DNA-binding molecule-mediated ChIP (in vitroenChIP) in combination with NGS (in vitroenChIP-Seq). Comparing chromosomal interactions in wild-type DT40 with those in a macrophage-like counterpart, we found that some of the identified chromosomal interactions were organized in a B cell–specific manner. In addition, deletion of a B cell–specific interacting genomic region in chromosome 11, which was marked by active enhancer histone modifications, resulted in moderate but significant down-regulation ofPax5transcription. Together, these results suggested thatPax5transcription in DT40 cells is regulated by inter-chromosomal interactions. Moreover, these analyses showed that iChIP-Seq andin vitroenChIP-Seq are useful for non-biased identification of functional genomic regions that physically interact with a locus of interest.

2002 ◽  
Vol 365 (1) ◽  
pp. 69-77 ◽  
Author(s):  
Amanda C. FENSOME ◽  
Michelle JOSEPHS ◽  
Matilda KATAN ◽  
Fernando RODRIGUES-LIMA

DT40 cells have approx. 10-fold higher Mg2+-dependent neutral sphingomyelinase (NSM) activity in comparison with other B-cell lines and contain very low acidic sphingomyelinase activity. Purification of this activity from DT40 cell membranes suggested the presence of one major NSM isoform. Although complete purification of this isoform could not be achieved, partially purified fractions were examined further with regard to the known characteristics of previously partially purified NSMs and the two cloned enzymes exhibiting in vitro NSM activity (NSM1 and NSM2). For a direct comparative study, highly purified brain preparations, purified NSM1 protein and Bacillus cereus enzyme were used. Analysis of the enzymic properties of the partially purified DT40 NSM, such as cation dependence, substrate specificity, redox regulation and stimulation by phosphatidylserine, together with the localization of this enzyme to the endoplasmic reticulum (ER), suggested that this NSM from DT40 cells corresponds to NSM1. Further studies aimed to correlate presence of the high levels of this NSM1-like activity in DT40 cells with the ability of these cells to accumulate ceramide and undergo apoptosis. When DT40 cells were stimulated to apoptose by a variety of agents, including the ER stress, an increase in endogenous ceramide levels was observed. However, these responses were not enhanced compared with another B-cell line (Nalm-6), characterized by low sphingomyelinase activity. In addition, DT40 cells were not more susceptible to ceramide accumulation and apoptosis when exposed to the ER stress compared with other apoptotic agents. Inhibition of de novo synthesis of ceramide partially inhibited its accumulation, indicating that the ceramide production in DT40 cells could be complex and, under some conditions, could involve both sphingomyelin hydrolysis and ceramide synthesis.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 28-29
Author(s):  
Jie Wang ◽  
Katarzyna Urbanska ◽  
Prannda Sharma ◽  
Mathilde Poussin ◽  
Reza Nejati ◽  
...  

Background: Peripheral T-cell lymphomas (PTCL) encompass a highly heterogeneous group of T-cell malignancies and are generally associated with a poor prognosis. Combination chemotherapy results in consistently poorer outcomes for T-cell lymphomas compared with B-cell lymphomas.1 There is an urgent clinical need to develop novel approaches to treatment of PTCL. While CD19- and CD20-directed immunotherapies have been successful in the treatment of B-cell malignancies, T-cell malignancies lack suitable immunotherapeutic targets. Brentuximab Vedotin, a CD30 antibody-drug conjugate, is not applicable to PTCL subtypes which do not express CD30.2 Broadly targeting pan-T cell markers is predicted to result in extensive T-cell depletion and clinically significant immune deficiency; therefore, a more tumor-specific antigen that primarily targets the malignant T-cell clone is needed. We reasoned that since malignant T cells are clonal and express the same T-cell receptor (TCR) in a given patient, and since the TCR β chain in human α/β TCRs can be grouped into 24 functional Vβ families targetable by monoclonal antibodies, immunotherapeutic targeting of TCR Vβ families would be an attractive strategy for the treatment of T-cell malignancies. Methods: We developed a flexible approach for targeting TCR Vβ families by engineering T cells to express a CD64 chimeric immune receptor (CD64-CIR), comprising a CD3ζ T cell signaling endodomain, CD28 costimulatory domain, and the high-affinity Fc gamma receptor I, CD64. T cells expressing CD64-CIR are predicted to be directed to tumor cells by Vβ-specific monoclonal antibodies that target tumor cell TCR, leading to T cell activation and induction of tumor cell death by T cell-mediated cytotoxicity. Results: This concept was first evaluated in vitro using cell lines. SupT1 T-cell lymphoblasts, which do not express a native functioning TCR, were stably transduced to express a Vβ12+ MART-1 specific TCR, resulting in a Vβ12 TCR expressing target T cell line.3 Vβ family specific cytolysis was confirmed by chromium release assays using co-culture of CD64 CIR transduced T cells with the engineered SupT1-Vβ12 cell line in the presence of Vβ12 monoclonal antibody. Percent specific lysis was calculated as (experimental - spontaneous lysis / maximal - spontaneous lysis) x 100. Controls using no antibody, Vβ8 antibody, and untransduced T cells did not show significant cytolysis (figure A). Next, the Jurkat T cell leukemic cell line, which expresses a native Vβ8 TCR, was used as targets in co-culture. Again, Vβ family target specific cytolysis was achieved in the presence of CD64 CIR T cells and Vβ8, but not Vβ12 control antibody. Having demonstrated Vβ family specific cytolysis in vitro using target T cell lines, we next evaluated TCR Vβ family targeting in vivo. Immunodeficient mice were injected with SupT1-Vβ12 or Jurkat T cells with the appropriate targeting Vβ antibody, and either CD64 CIR T cells or control untransduced T cells. The cell lines were transfected with firefly luciferase and tumor growth was measured by bioluminescence. The CD64 CIR T cells, but not untransduced T cells, in conjunction with the appropriate Vβ antibody, successfully controlled tumor growth (figure B). Our results provide proof-of-concept that TCR Vβ family specific T cell-mediated cytolysis is feasible, and informs the development of novel immunotherapies that target TCR Vβ families in T-cell malignancies. Unlike approaches that target pan-T cell antigens, this approach is not expected to cause substantial immune deficiency and could lead to a significant advance in the treatment of T-cell malignancies including PTCL. References 1. Coiffier B, Brousse N, Peuchmaur M, et al. Peripheral T-cell lymphomas have a worse prognosis than B-cell lymphomas: a prospective study of 361 immunophenotyped patients treated with the LNH-84 regimen. The GELA (Groupe d'Etude des Lymphomes Agressives). Ann Oncol Off J Eur Soc Med Oncol. 1990;1(1):45-50. 2. Horwitz SM, Advani RH, Bartlett NL, et al. Objective responses in relapsed T-cell lymphomas with single agent brentuximab vedotin. Blood. 2014;123(20):3095-3100. 3. Hughes MS, Yu YYL, Dudley ME, et al. Transfer of a TCR Gene Derived from a Patient with a Marked Antitumor Response Conveys Highly Active T-Cell Effector Functions. Hum Gene Ther. 2005;16(4):457-472. Figure Disclosures Schuster: Novartis, Genentech, Inc./ F. Hoffmann-La Roche: Research Funding; AlloGene, AstraZeneca, BeiGene, Genentech, Inc./ F. Hoffmann-La Roche, Juno/Celgene, Loxo Oncology, Nordic Nanovector, Novartis, Tessa Therapeutics: Consultancy, Honoraria.


Blood ◽  
2000 ◽  
Vol 95 (11) ◽  
pp. 3548-3554 ◽  
Author(s):  
Antonio Condino-Neto ◽  
Peter E. Newburger

Abstract X-linked chronic granulomatous disease (CGD) derives from defects in the CYBB gene, which encodes the gp91-phox component of NADPH oxidase. We studied the molecular basis of the disease in a kindred with variant CGD, due to a single base substitution at the sixth position of CYBB first intron. The patients' phagocytes have been shown previously to greatly increase superoxide release in response to interferon-gamma (IFN-γ) in vitro and in vivo. We examined CYBB gene expression in an Epstein-Barr virus (EBV)-transformed B-cell line from 1 patient in this kindred. These cells showed markedly decreased levels of CYBB transcripts in total RNA (5% of normal) and nuclear RNA (1.4% of normal), despite equal CYBB transcription rates in the CGD and control cells. Incubation with IFN-γ produced a 3-fold increase in CYBBtotal messenger RNA (mRNA) levels in the patient's cells, and decreased nuclear transcripts to undetectable levels. Reverse transcriptase–polymerase chain reaction analysis of RNA splicing revealed a preponderance of unspliced CYBB transcripts in the patient's nuclear RNA. In vitro incubation with IFN-γ increased by 40% the ratio of spliced relative to unspliced CYBB mRNA in nuclei from the CGD B-cell line. Total RNA harvested from the same patient's monocytes, on and off therapy with IFN-γ, showed a similar improvement in splicing. We conclude that IFN-γ partially corrects a nuclear processing defect due to the intronic mutation in theCYBB gene in this kindred, most likely by augmentation of nuclear export of normal transcripts, and improvement in the fidelity of splicing at the first intron.


2010 ◽  
Vol 150 ◽  
pp. 440-441
Author(s):  
Hitoshi Ohmori ◽  
Masaki Magari ◽  
Naoki Kanayama ◽  
Shuichi Matsuda ◽  
Yuichi Kanehiro
Keyword(s):  
B Cell ◽  

2003 ◽  
Vol 77 (3) ◽  
pp. 2134-2146 ◽  
Author(s):  
Vicky M.-H. Sung ◽  
Shigetaka Shimodaira ◽  
Alison L. Doughty ◽  
Gaston R. Picchio ◽  
Huong Can ◽  
...  

ABSTRACT Hepatitis C virus (HCV) is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Studies of HCV replication and pathogenesis have so far been hampered by the lack of an efficient tissue culture system for propagating HCV in vitro. Although HCV is primarily a hepatotropic virus, an increasing body of evidence suggests that HCV also replicates in extrahepatic tissues in natural infection. In this study, we established a B-cell line (SB) from an HCV-infected non-Hodgkin's B-cell lymphoma. HCV RNA and proteins were detectable by RNase protection assay and immunoblotting. The cell line continuously produces infectious HCV virions in culture. The virus particles produced from the culture had a buoyant density of 1.13 to 1.15 g/ml in sucrose and could infect primary human hepatocytes, peripheral blood mononuclear cells (PBMCs), and an established B-cell line (Raji cells) in vitro. The virus from SB cells belongs to genotype 2b. Single-stranded conformational polymorphism and sequence analysis of the viral RNA quasispecies indicated that the virus present in SB cells most likely originated from the patient's spleen and had an HCV RNA quasispecies pattern distinct from that in the serum. The virus production from the infected primary hepatocytes showed cyclic variations. In addition, we have succeeded in establishing several Epstein-Barr virus-immortalized B-cell lines from PBMCs of HCV-positive patients. Two of these cell lines are positive for HCV RNA as detected by reverse transcriptase PCR and for the nonstructural protein NS3 by immunofluorescence staining. These observations unequivocally establish that HCV infects B cells in vivo and in vitro. HCV-infected cell lines show significantly enhanced apoptosis. These B-cell lines provide a reproducible cell culture system for studying the complete replication cycle and biology of HCV infections.


Blood ◽  
1994 ◽  
Vol 83 (1) ◽  
pp. 26-32 ◽  
Author(s):  
T Miki ◽  
N Kawamata ◽  
S Hirosawa ◽  
N Aoki

Abstract Chromosomal translocations involving band 3q27 are the recently described nonrandom cytogenetic abnormalities in B-cell malignancies. We have previously cloned the breakpoint region of 3q27, designated as the BCL5 locus, from the B-cell line carrying the t(3;22). The cDNA for the BCL5 gene was cloned from the human liver cDNA library. The nucleotide sequencing analysis showed that the BCL5 gene encodes a potential transcription factor containing six repeats of the Cys2-His2 zinc-finger motif resembling the Drosophila segmentation gene Kruppel. The calculated molecular weight was 78.8 kD, which was supported by an in vitro transcription and translation experiment. A part of the sequence was essentially identical to that of a genomic fragment, ZNF51, previously reported to be located at 3qter. The translocation occurred in the 5′ region of the BCL5 gene, and the protein-coding exons were fused to the Ig-lambda gene in a head-to-head configuration in the cell line carrying t(3;22). The BCL5 cDNA probe detected a major transcript of 3.8 kb in Burkitt's lymphoma cell lines and an aberrant transcript in the t(3;22) cell line, whereas no transcript was detected in myeloid, monocytoid, erythroid, T-lymphoid, and Epstein-Barr virus- immortalized B-lymphoblastoid cell lines.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 283-283
Author(s):  
Randall M Rossi ◽  
Valerie Grose ◽  
Polly Pine ◽  
Richard I Fisher ◽  
Craig T. Jordan ◽  
...  

Abstract Abstract 283 Certain malignant B-cells rely upon B-cell receptor-mediated survival signals. Spleen tyrosine kinase (Syk) initiates and amplifies the B-cell receptor-mediated signal. We and others have demonstrated that fostamatinib disodium (FosD: a prodrug of R406, a potent and specific inhibitor of Syk) induces apoptosis in lymphoma cell lines and primary tumors. A recent clinical trial has demonstrated significant clinical activity of FosD in relapsed/refractory B-cell non-Hodgkin lymphoma (NHL) and chronic lymphocytic leukemia, and minimal overlap in toxicities with conventional agents. Given this background, future development in B-cell NHL will include rational combinations of FosD and currently available therapies. Therefore, we conducted in vitro and in vivo studies of rational combinations including FosD, in anticipation of clinical trial development. First, using a human DLBCL cell line of GCB genotype, (OCI-Ly19), we analyzed in vitro the combination of R406 with the following agents: fludarabine, rapamycin, rituximab, bendamustine and bortezomib. Increased cytotoxicity was observed using in vitro culture assays with the addition of fludarabine, rapamycin, or rituximab to R406. Cell viability at 72 hours was 25% with R406 alone, 27% for fludarabine alone, and only 9% for the fludarabine/R406. At 48 hours, cell viability was 49% using R406 alone, 31% using rituximab alone, and 21% for rituximab/R406. At 120 hours using primary lymphoma cells (DLCL27), there were no viable cells treated with the rapamycin/FosD combination, compared with rapamycin alone (7%) or FosD alone (25%) The addition of bortezomib or bendamustine to FosD resulted in only a minimal additive increase in cytotoxicity. Results with all combinations were similar with the OCI-Ly10 human DLBCL line of ABC genotype. We then performed in vivo studies by subcutaneous transplantation of the DLBCL cell line OCI-Ly19, (engineered to express luciferase allowing for real time in vivo imaging) into immune deficient NOD/SCID mice which reproducibly formed tumors. Recipient animals were separated into uniform cohorts when the tumors were less than or equal to 500 mm3 in size. The animals were then simultaneously treated with FosD (n=7; 3 gm/kg ad. lib.; translates into 2-5 micromolar R406 systemically throughout the 24h period) and either bortezomib, (n=6; 0.4 mg/kg weekly IP), or rituximab, (n=13; 3 mg/kg, 2x weekly IP). Analysis of the OCI-Ly19 tumor volumes at day 46 showed a median of 2364 mm3 with bortezomib alone compared with 1823 mm3 with bortezomib and FosD. When FosD was combined with rituximab the most significant cytotoxicity was observed: (p=0.01; median tumor volume of 497 mm3 following the combination) in comparison to either FosD alone (3150 mm3) or rituximab alone (1764 mm3). We conclude that the addition of FosD appears to increase activity against NHL of several drugs, including fludarabine and rapamycin. These agents have significant activity in indolent and mantle cell NHL as well as CLL. Moreover, there is no evidence that FosD impedes rituximab responses in vitro or in vivo; in fact we have suggested possible synergy with the combination of rituximab and FosD. Based upon the documented single agent activity of FosD in humans, and this data, clinical trials are now indicated using these promising combinations in NHL and CLL. Disclosures: Pine: Rigel: Employment. Friedberg:Rigel: Research Funding.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 118-118
Author(s):  
Danielle C Bongero ◽  
Luca Paoluzzi ◽  
Enrica Marchi ◽  
Neisa Roberto ◽  
Rafael Escandon ◽  
...  

Abstract Abstract 118 A mitotic spindle target that has emerged as unique and potentially restricted to the mitotic spindle is Eg5, also known as the kinesin spindle protein (KSP). SB-743921 induces mitotic spindle dysfunction and cell cycle arrest by inhibiting Eg5. Preliminary Phase 1 studies of SB-743921 have demonstrated that this compound is not associated with any neuropathy like other anti-mitotic agents. These studies have also demonstrated a potential signal in patients with relapsed and refractory lymphoma. We investigated the efficacy of SB-743921 in aggressive B-cell lymphomas to evaluate effectiveness and tolerability in germinal center (GCB) and post germinal center (ABC) diffuse large B-cell lymphomas (DLBCL). For cytotoxicity assays, luminescent cell viability was performed using CellTiter-Glo™ followed by acquisition with Biotek Synergy HT. The IC50s were calculated using the Calcusyn software (Biosoft). Cell Cycle was assessed by staining with Vybrant DyeCycle Green (Invitrogen) followed by FACSCalibur acquisition. Whole cell lysate proteins were extracted and quantified according to Bradford assay. After electrophoresis on a gradient 4–20% SDS-PAGE gels the proteins were transferred to nitrocellulose membrane. After blocking and incubation with the primary and the secondary antibodies, the chemiluminescent agent was added and the x-ray films were exposed to the membranes. In vivo experiments were performed with five to 7-week-old severe combined immunodeficiency (SCID) beige mice (Taconic Laboratories, Germantown, NY) injected with 1 × 107 Ly1-DLBCL cells on the flank via a subcutaneous (SQ) route. When tumor volumes approached 80 mm3, mice were separated into cohorts of ten mice each. Tumors were assessed using the two largest perpendicular axes (l, length; w, width) as measured with standard calipers. Tumor volume was calculated using the formula 4/3 r3, where r=(l + w) / 4. Tumor-bearing mice were assessed for weight loss and tumor volume at least twice weekly. The IC50 values for SB-743921 across a panel of different DLBCL lines are listed in table 1. Cell cycle analysis showed that compared to the untreated group, after treatment with 100nM of SB 743921 the percentage of GCB cells in G2/M phase increased from 17.6% to 40.3% (+129%) in Ly7, 23.9% to 40.7 % (+70%) in Sudhl6 and from 17.55% to 32.4% (+85%) in Ly1. In comparison, the percent increase of cells in G2/M for the ABC lines was statistically less (p-value 0.001). For example, Ly10 increased from 15% to 27.6% (+45%), Riva from 29.3% to 36.95% (+26%) and Sudhl2 from 22.6% to 27.6% (+22%). Immunoblot analysis of DLBCL cells treated with SB-743921 probed for Eg5, CyclinB1, and phosphorylated BubR1 revealed that although all cells demonstrated a measurable increase in Eg5, the total Eg5 present varied from cell line to cell line. The In vivo xenograft experiment was conducted with the GCB Ly1 cell line and consisted of 4 cohorts; one control and 3 treatments with doses of 2.5 mg/kg, 5 mg/kg and 10 mg/kg. SB-743921 was administered by the intraperitoneal route on days 1, 5, and 9 on a 23 day cycle for 2 cycles. The graph below displays the inhibition of tumor growth in the cohorts after treatment with SB-74321. All 3 cohorts had a p-value of <0.001 relative to the control. In conclusion, SB-743921 is promising as a single agent for treatment of DLBCL. Future studies exploring the specific cell cycle features of different cell lines with respect to their check-point control will afford new opportunities to better understand the mechanisms of increased resistance in ABC compared to GCB. The data suggests SB 743921 overall is effective in the treatment of DLBCL both in vitro and in vivo. Further studies exploring potential synergistic interactions with conventional chemotherapeutic agents as well as establishing the most effective treatment schedules for the agent may provide a new approach to treating these diseases. Disclosures: Escandon: Cytokinetics: Employment. Wood:Cytokinetics: Employment. O'Connor:Millennium Pharmaceuticals, Inc.: Membership on an entity's Board of Directors or advisory committees, Research Funding.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 4606-4606
Author(s):  
Shabirul Haque ◽  
Bukhtawar Waqas ◽  
Hyunjoo Lee ◽  
Piers EM Patten ◽  
Jonathan E Kolitz ◽  
...  

Abstract Abstract 4606 Curcumin is a natural phenolic compound within the spice, Curcuma longa. It has noted anti-inflammatory effects, in large part due to its potent suppressive effect on the NF-kB signaling pathway. AID is a NF-kB-regulated enzyme, essential for B cell Ig class switch recombination and somatic hypermutation and recently shown to promote oncogenic transformation within both B cell and non-B cell lineages. This study has examined the effect of curcumin on the division-linked upregulation of AID protein and mRNA within several human B cell populations: in vitro-activated normal and CLL B lymphocytes and the AID-positive, pre-germinal center B cell line, CL-01. CFSE-labeled, IgM+ human B2 cells isolated from spleen/tonsil were pre-activated for 4–5 days with stimuli likely encountered in sites of inflammation, i.e. limiting surrogate C3dg-coated antigen (anti-IgM: anti-CD21: dextran) + IL-4 + BAFF. Peripheral blood B-CLL cells were activated with TLR-9 ligand, ODN-2006, + IL-15. Curcumin at doses from 6 to 50 μ M, and parallel DMSO vehicle controls, were pulsed into dividing B cell cultures (day 3, 4, or 5 of activation), and AID mRNA and protein assessed after 1 to 2 days. In experiments with CL-01 B cells, the kinetics of curcumin-induced AID suppression was further analyzed. Messenger RNA was monitored by both quantitative and qualitative RT-PCR; AID protein was assessed by two-color flow cytometry of CFSE-labeled cells and immunoblotting. The above experiments revealed that curcumin can significantly down-regulate AID mRNA and protein, in dose dependent fashion within each of the above B cell populations. Following a 16h pulse of curcumin (25 μ M), AID mRNA within CL-01 cells was inhibited by 60% (p=0.001), and accompanied by ~ 60% decrease in AID protein. Within cultures of replicating normal human B lymphocytes, a similar pulse of curcumin reduced total culture AID mRNA by an average of 70% in 3 experiments. AID protein in blasts representing 3–4 divisions was reduced by 79%, and in those representing 1–2 divisions by 58%, within a representative experiment. AID mRNA was evident within all in vitro-activated B-CLL clones tested (total = 6 clones at the time of submission). This was significantly reduced by a 15–24 hr pulse with curcumin (20-25 μ M): 42% inhibition (p=0.02)). The inhibitory effects of curcumin were evident in both IgHV mutated and unmutated clones. Within stimulated B-CLL assessed for AID protein (4 total clones, of which 2 were positive), a 20 hr pulse of curcumin at 40 μ M and 20 μ M reduced AID expression in one clone by 80% and 40%, respectively. In the other clone, a maximal tested dose of 20 μ M curcumin reduced AID protein by only 12%. Suppression of AID mRNA in the CL-01 cell line was noted as soon as 3 hours following exposure to curcumin and was preceded by inhibition of NF-kB activation, both baseline and BAFF-induced. The latter was determined through monitoring intracellular levels of phospho-p65-Ser(529) – an active phosphorylated form of NF-kB RelA. Taken together, these findings suggest that NF-kB- and AID-suppressing curcumin may be useful in reducing the risk of malignant transformation and B-CLL progression into more malignant subclones, as well as treating B cell autoimmune diseases driven by pathogenic, somatically-mutated IgG autoantibodies. Disclosures: No relevant conflicts of interest to declare.


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