bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymorphisms in One-Carbon Metabolism Genes and Overall Survival in Diffuse Large B-Cell Lymphoma (DLBCL).
Authors: Cerhan James R. , Maurer Matthew J. , Hartge Patricia , Chanock Stephen J. , Habermann Thomas M. , Cozen Wendy , Davis Scott , Lynch Charles F. , Severson Richard K. , Rothman Nathaniel , Morton Lindsay M. , Wang Sophia S. 
Published: April 2020

Abstract
Background. Intracellular one-carbon transfer reactions are essential for nucleotide synthesis and methylation of biologic compounds including DNA. Previous studies have linked genetic variants in one-carbon metabolism genes with risk of developing NHL, but little is known regarding the impact of these variants on disease outcome. We evaluated the hypothesis that inherited genetic variation in genes involved in one-carbon metabolism is associated with overall survival in DLBCL.
Methods. We genotyped 30 single nucleotide polymorphisms (SNPs) from 18 candidate one-carbon metabolism genes in 215 DLBCL patients who participated in a population-based case-control study conducted from 1998–2000 using the SEER (Surveillance, Epidemiology and End Results) cancer registries in the Detroit, Iowa, Los Angeles and Seattle. Stage, B-symptoms, first course of therapy, date of last follow-up and vital status through early 2005 were obtained from cancer registry files. Cox proportional hazards analysis was used to estimate hazard ratios (HR) and corresponding 95% confidence intervals for the association between individual SNPs and overall survival, adjusting for age, demographic and clinical factors. We also used parallel modeling strategies to identify the best summary multi-SNP risk score to predict survival.
Results. The median age at diagnosis was 57 years (range, 20–74), and 50 (23%) of the patients died during follow-up, with a median follow-up of 57 months (range, 31–78 months) for surviving patients. After adjusting for demographic and clinical variables, SNPs in SHMT1 (rs1979276; HRCT/TT=2.47, 1.31–4.67), BHMT (rs585800; HRAT/TT=2.02, 1.16–3.54), and TCN1 (rs526934; HRTT=1.86, 1.04–3.33) were the strongest and most robust predictors of survival. A summary score of the number of deleterious genotypes (0–3) from these three genes was strongly associated with survival (p=7.9 x 10−5) after accounting for demographic and clinical variables (HR=2.58 per deleterious genotype, 95% CI 1.75–3.80). A risk score combining the three SNPs with clinical and demographic variables (score of 0 to 5) was even more strongly associated with survival (p=1.4 x 10−13); the Kaplan Meier survival curves are shown in the Figure. In a time-dependent ROC analysis, the combined risk score had a concordance index of 0.75 at 5 years of follow-up (95% CI 0.69–0.81).
Conclusion: Host genetic variation in the one-carbon metabolism genes SHMT1, BHMT, and TCN1, individually and particularly in combination, was associated with overall DLBCL survival after accounting for clinical and demographic factors, supporting a role for this pathway in disease progression. Future work should evaluate interactions of genes from this pathway with dietary nutrients and therapeutic agents in DLBCL prognosis.
Figure Figure
Inhibition of Ubiquitin-Proteasome Pathway Causes Growth Suppression and Induces Apoptosis in Diffuse Large B Cell Lymphoma.
Authors: Uddin Shahab , Hussain Azhar , Khan Asma , Bavi Prashant , Al-Kuraya Khawla 
Published: April 2020

Abstract
SKP2, an F-box protein targets cell cycle regulators including cycle-dependent kinase inhibitor p27KIP1 via ubiquitin-mediated degradation. SKP2 is frequently overexpressed in variety of cancer cells and has been implicated in oncogenesis, however its role in diffuse large B-cell lymphoma (DLBCL) has not been elucidated. Therefore, we investigated the role of SKP2 and its ubiquitin-proteasome pathway in DLBL using a panel of cell lines and clinical samples. MG132, a reversible and specific inhibitor of ubiquitin-proteasome pathway that acts through blocking ubiquitin-mediated proteolysis via binding to 20S and 26S proteasomes. Our study showed that treatment of DLBCL cell lines (SUDHL4, SUDHL5, SUDHL8 and OCILY19) with MG132 suppressed growth and induced apoptosis. Treatment of DLBCL cells with MG132 caused downregulation of SKP2, accumulation and stabilization of p27KIP1 leading to the apoptosis. Further downstream, MG132 induced activation of caspase-8 and cleavage of Bid subsequently leading to loss of mitochondrial membrane potential and release of cytochrome c from mitochondria into cytosol, resulting in activation of caspase-3 and cleavage of PARP. zVAD-fmk, a universal inhibitor of caspases prevented caspase-3 activation and abrogated apoptosis induced by MG132 treatment. Finally, using immunohistochemistry, SKP2 was detected in 94 (32.9%) of 286 DLBCL tumors. Furthermore, patients with high SKP2 expression were associated with high expression of Ki67, a proliferative marker. Altogether, these results suggest that SKP2 and ubiquitin-proteasome pathway may be a potential target for therapeutic intervention in diffuse large B-cell lymphoma.
Expression of Phosphorylated mTOR (p-mTOR) Correlates with Advanced Stage in Diffuse Large B-Cell Lymphomas.
Authors: Patel Raina A. , Ahmad Imran , Sheehan Christine E. , Ross Jeffrey S. , Wilner George D. , Hayner-Buchan Alida , Nazeer Tipu 
Published: April 2020

Abstract
Background: The mammalian target of rapamycin (mTOR), plays a major role in regulating cell growth. The activated form of mTOR (phosphorylated mTOR) mediates its effects through mitogen and nutrient dependant signal transduction that regulates mRNA translation. Levels of phosphorylated mTOR (p-mTOR) have been shown to correlate with cell proliferation and inhibition of the mTOR pathway has shown therapeutic promise in some tumors. Information on the role of p-mTOR in hematopoietic malignancies is limited. The aim of the current study is to evaluate the expression of p-mTOR in diffuse large B-cell lymphomas.
Design: Formalin-fixed paraffin-embedded tissue sections from 45 DLBCLs were immunostained by an automated method (Ventana Medical Systems, Inc., Tucson, AZ) using p-mTOR rabbit monoclonal antibody (IHC specific Ser2448/49F9; Cell Signaling Technology, Inc., Danvers, MA). Immunoreactivity (cytoplasmic with membranous accentuation) was semiquantitatively assessed based on p-mTOR stain intensity (none, weak, moderate, intense) and distribution (none, focal&lt;10%, regional 11–50%, diffuse&gt;50%). Staining was correlated with histologic and prognostic factors.
Results: Membranous/cytoplasmic p-mTOR immunoreactivity was present in 88% of DLBCLs and correlated with advanced tumor stage, with 100% advanced stage versus 73% low stage tumors expressing membranous/cytoplasmic p-mTOR protein (p=0.002). One hundred percent of cases with complete absence of p-mTOR immunoreactivity were low stage DLBCLs.
Conclusion: Membranous/cytoplasmic protein expression of p-mTOR correlates with advanced stage in DLBCL. Activated mTOR may play an important role in disease progression and provide a target for therapy in DLBCL. Further studies of the m-TOR pathway in hematopoietic malignancies appear warranted.
CXCL12 and CXCL13 Levels in Cerebrospinal Fluid (CSF) of Patients with CNS Lymphoma.
Authors: Fischer Lars , Kiewe Philipp , Pfeiffer Sebastian , Cakiroglu Hüsniye , Thiel Eckhard 
Published: April 2020

Abstract
Background: The mechanisms leading to development of CNS lymphoma (CNSL) are still poorly understood. Homing of malignant lymphocytes to the CNS may play an important role in the pathogenesis of CNSL. Expression of chemokine receptors CXCR4 and CXCR5 has been shown on tumor cells of primary CNSL. In this study we examined the level of chemokines CXCL12 and CXCL13 which are ligands of CXCR4 and CXCR5 respectively in the CSF of CNSL patients and compared it to non-CNSL controls.
Methods: Lumbar CSF and peripheral blood from 16 patients with primary and one with secondary CNSL, as well as control CSF from 8 patients with hydrocephalus, glioblastoma, peripheral lymphoma without CNS involvement or unspecific neurological symptoms were collected, and after centrifugation supernatant and serum were cryopreserved at −80°C until analysis. Chemokine concentrations were measured using commercially available ELISA kits (CXCL13/BCA-1 and CXCL12/SDF-1α Quantikine Immunoassay, R&D Systems, Minneapolis) according to the manufacturer’s instructions. Results were confirmed by duplicate measurements.
Results: 22 CSF samples and 11 serum samples from CNSL patients and nine CSF samples from controls were evaluated (see table). There was no correlation between serum and CSF chemokine levels in CNSL patients. Median concentrations of both CXCL12 and CXCR13 were higher in patients with CNS lymphoma compared to controls, CXCL13 being significantly raised (p=0.0019). In one CNSL patient three serial CSF samples could be analysed and a ten-fold decrease of CXCL12 during succesfull chemotherapy was found whilst concentration of CXCL13 remained stable.
Conclusion: CXCL12 and CXCL13 can be measured in the CSF of CNS lymphoma patients at higher concentration as compared to non-CNSL patients. Analysis of a larger population is warranted in order to define the role of these chemokines in CNSL and to establish their value for diagnosis and follow up.
Serum CSF CNSL patients CNSL patients controls p range median (range) median (range) CXCL12 1788–2933 pg/ml 481 (55–2079) pg/ml 115 (0–2442) pg/ml 0.067 CXCL13 36–657 pg/ml 457 (18–657) pg/ml 16.9 (0.6–187) pg/ml 0.00019
Clonal Heavy and Light Chain Immunoglobulin DNA in Plasma/Serum of AIDS Lymphoma Patients.
Authors: Wagner-Johnston Nina D. , Nurmemet Dilber , Gocke Christopher , Lin Lan , Lemas Victor M. , Martinez-Maza Otoniel , Ambinder Richard F. 
Published: April 2020

Abstract
Background DNA tumor markers in plasma and serum such as point mutations, hypermethylation of tumor suppressor genes, and viral sequences have attracted much interest. We investigated clonal Ig DNA rearrangements in the plasma of AIDS-related lymphoma (ARL) patients (pts).
Methods We evaluated specimens for Ig rearrangements from pts with ARL using fluorescently-labeled multiplex primers targeting IgH and IgK. PCR products were analyzed by capillary electrophoresis. Re-amplified PCR products from plasma and tumor were cloned and sequenced.
Results Clonal IgH DNA spikes were seen in plasma at baseline in 5 of 10 pts. Clonal DNA was detected in plasma in pts with either early or advanced stage disease, with or without marrow involvement. Presence of a plasma clone was associated with high LDH. Serial specimens were available from 4 pts. In 2 pts who died with primary refractory disease, clonal peaks remained present after the administration of chemotherapy. In a pt with disease that initially responded and then relapsed, clonal DNA disappeared with chemotherapy, then reappeared presaging relapse and death. In 4 pts, matching serum specimens were available. Results were similar in both types of specimens with identical sized rearrangements amplified from matched specimens. Furthermore in 2 pts, the IgH amplification products from plasma and tumor were sequenced and confirmed to be identical. Two pts with positive IgH amplification products were also screened for light chains in the plasma and in both, clonal IgK rearrangements were detected. For purposes of comparison, plasma from healthy donors (n=20) and AIDS pts with Kaposi’s sarcoma (KS) (n=10) were also surveyed. Clonal Ig DNA rearrangements were not detected in any of these.
Conclusions These results are consistent with observations suggesting that free tumor DNA can often be detected in plasma or serum of cancer pts. The absence of clonal Ig DNA in plasma from healthy donors and pts with AIDS KS suggests that detection of such DNA may be highly specific. Identification of the same Ig rearrangement and sequence in plasma and tumor is consistent with this interpretation. Serial monitoring of circulating clonal DNA appears to track—and perhaps anticipate—clinical evidence of disease. These approaches may be especially valuable in ARL where FDG uptake reflective of inflammatory disease or benign lymphoproliferation detected by PET scan often renders interpretation of imaging ambiguous. Similarly, elevated LDH in this population is relatively non-specific.
Host Genetic Variation in the Cell Cycle and NF-κB Pathways and Overall Survival in Mantle Cell Lymphoma.
Authors: Habermann Thomas M. , Maurer Matthew J. , Wang Sophia S. , Morton Lindsay M. , Lynch Charles F. , Hartge Patricia , Cozen Wendy , Severson Richard K. , Scott Davis , Watson David A. , Chanock Stephen J. , Rothman Nathanial , Cerhan James R. 
Published: April 2020

Abstract
Background: Mantle cell lymphoma (MCL) is an incurable non-Hodgkin lymphoma. MCL is characterized by the chromosomal translocation t(11;14) leading to overexpression of cyclin D1 (CCND1), a regulator of the cell cycle. NF-κB plays a central role in key cellular processes, including cell cycle regulation and apoptosis, and it has been shown to be constitutively activated in MCL cell lines and in patient biopsy samples and to play a key role in the growth and survival of MCL cells. In an exploratory study, we evaluated the hypothesis that germline variation in candidate genes from the cell cycle and NF-κB pathways predict overall survival in MCL.
Methods: We genotyped 235 SNPs from 29 cell cycle genes and 447 SNPs from 55 NF-κB genes in 39 MCL patients aged 38–64 years who participated in a population-based study conducted from 1998–2000 through the Surveillance, Epidemiology, and End Results (SEER) cancer registries in Detroit, Seattle, Iowa, and Los Angeles county. Tagging single nucleotide polymorphisms (SNPs) were selected from HapMap. Stage, presence of B-symptoms, first course of therapy, date of last follow-up, and vital status were derived from linkage to registry databases at each study site. To assess the statistical significance of a gene, we first used principal components analysis to capture the genetic variation of the SNPs within a gene. Cox proportional hazards analysis was then used to assess the association between the top principal components from a gene with overall survival.
Results: Through early 2005, there were 22 deaths in 39 patients (56%). The median follow-up of the 17 surviving patients was 56 months (range 36–70). Eleven of the 55 genes (TNFSF14 p=0.0007, NF-κBIA p=0.003, IL1R2 p=0.01, TNFRSF25 p=0.02, TNFSF13B p=0.02, FAS p=0.03, TLR2 p=0.04, TNFSF10D p=0.04, TNFSF10 p=0.06, MAP3K2 p=0.06) in the NF-κB pathway were associated with overall survival. In the cell cycle pathway, only 3 of the 29 genes (CASP5 p=0.06, CASP9 p=0.09, BCL2 p=0.09) were associated with overall survival, and a previously reported SNP in CCND1 (rs603965) showed no association (p=0.5). Permutation p-values for observing at least this number of associated tests in each pathway due to chance (from multiple testing) was p=0.8 for the cell cycle pathway and p=0.03 for NF-κB pathway. The small sample size precluded multi-gene modeling.
Conclusion: In a population series of MCL patients, we found suggestive evidence that host genetic variation in candidate NF-κB pathway genes affects overall survival. These results complement tumor expression data implicating this pathway in the pathogenesis of MCL. In addition, such findings further support the value of developing therapeutic targets from this pathway.
Pifithrin α, a Selective Inhibitor of p53-Mediated Transcription, Augments Apoptotic Killing of Chronic Lymphocytic Leukemia Cells by Nutlin 3a and Cytotoxic Drugs.
Authors: Steele Andrew J. , Prentice Archie , Cwynarski Kate , Hoffbrand A. Victor , Wickremasinghe R. Gitendra 
Published: April 2020

Abstract
The p53 protein plays a key role in triggering DNA damage-induced apoptosis. The classical pathway of p53-mediated apoptosis involves transcriptional upregulation of pro-apoptotic proteins Puma and Noxa. However, recent studies identified a non-transcriptional mechanism, involving direct association of p53 with mitochondrial anti-apoptotic proteins Bcl-2 or Bcl-XL. We studied the relative contributions of transcription-dependent and -independent mechanisms of p53-mediated apoptosis in CLL cells in vitro. The cytotoxic drugs chlorambucil (chl) and fludarabine (flu) were used to induce p53, as was nutlin 3a, which augments p53 levels by inhibiting interaction with its negative regulator MDM2. Using differential detergent fractionation to isolate cytosolic (cyt), mitochondrial (mt) and nuclear (nuc) fractions, we found that a significant proportion (&gt;50%) of the induced p53 was stably associated with mitochondria in cells treated with nutlin 3a (Fig 1), chl or flu. Co-immunoprecipitation studies established that p53 bound to Bcl-2. PFTα, an inhibitor of p53-mediated transcription, blocked upregulation of the known p53 targets p21CIP1, MDM2 and Puma. Surprisingly, apoptosis induction by nutlin 3a (Figure 2), chl or flu, quantified by western blot analysis of cleavage of poly(ADP ribose) polymerase (PARP), was augmented by PFTα. This observation was confirmed by morphological analysis of apoptosis. Cytochrome c release from mitochondria following p53 induction was also enhanced by PFTα. PFTα did not augment nutlin-, chl- or flu-induced killing of CLL cells lacking functional p53. Furthermore, PFTα did not augment killing by the p53-independent drug parthenolide and failed to increase apoptosis of normal T lymphocytes treated with chl or nutlin 3a. Our observations suggest that p53 induces apoptosis of CLL cells principally via its transcription-independent function, involving direct association with mitochondrial Bcl-2. p53’s transcriptional function apparently blocks apoptosis at a point between p53 association with Bcl-2 and subsequent release of cytochrome c. Therefore, therapeutic strategies aimed at blocking p53-mediated transcription may be of value in enhancing the action of agents which induce apoptosis of CLL cells via p53 upregulation.
Figure 1 Figure 1. Figure 2 Figure 2.
The Novel HSP90 Inhibitor IPI-504 Synergizes with Bortezomib in Mantle Cell Lymphoma Cells by Targeting Both NF-kappaB Signaling and Unfolded Protein Response and Leading to Increased Mitochondrial Apoptosis.
Authors: Roue Gael , Perez-Galan Patricia , Lopez-Guerra Monica , Villamor Neus , Campo Elias , Colomer Dolors 
Published: April 2020

Abstract
Mantle cell lymphoma (MCL) is an aggressive B lymphoid neoplasm with a mature B-cell phenotype and genetically characterized by the t(11;14)(q13;q32) leading to cyclin D1 overexpression with the consequent deregulation of cell cycle at the G1-S checkpoint. MCL cells present a constitutive activation of the NF-kappaB pathway which leads to the overexpression of several anti-apoptotic regulators. Recently, MCL cells have been shown to express high levels of the chaperone heat shock protein of 90 kDa (HSP90) and to respond well to the ansamycin derivative 17-AAG, an HSP90 inhibitor. We have analyzed the sensitivity to the novel, highly soluble, 17-AAG derivative IPI-504 (Infinity Pharmaceuticals) on a panel of eleven human MCL cell lines and primary cells from MCL patients, which differ in their p53-dependent pathway status, growth characteristics and sensitivity to cytotoxic drugs. We observed that IPI-504 heterogeneously exerted cytostatic effect among MCL samples, with IC50 ranging from 0.06 to 15.4 μM, irrespective of the mutational status of the client protein p53 and/or expression levels of other client proteins such as cyclin D1 and BCL-2. IPI-504 activity involved the downregulation of the client proteins IKKb and phospho-AKT, and consequent inhibition of NF-kappaB signaling. In the most sensitive samples, these events led to the induction of cell death characterized by loss of mitochondrial membrane potential, activation of caspases and phophatidylserine exposure. IPI-504 cytotoxic activity was increased by cotreatment with pharmacological inhibitors of IKK and AKT. Noteworthy, IPI-504 showed remarkable synergistic interaction with the proteasome inhibitor bortezomib, reaching combination indexes (CIs) between 0.53 and 1.094. Efficiency of this latest combination was found to be correlated with the ratio between HSP90 and the co-chaperone HSP70 (P&lt;0.05), whose levels were increased following treatment with both IPI-504 and bortezomib, thus limiting the cytotoxicity. Accordingly, pharmacological inhibition of HSP70 sensitized MCL cells primarily resistant to IPI-504. We compared the modulation of some components of the physiologic unfolded protein response (UPR) among samples harboring different sensitivity to IPI-504 and bortezomib. We observed, in the most sensitive cells, a complete inhibition of the spliced isoform of XBP-1 and phospho-eIF2a after a long time exposure to the combination, a fact that was associated to increased upregulation of the proapoptotic BH3-only protein NOXA and induction of apoptosis. Considering that both bortezomib and IPI-504 have already demonstrated selective cytotoxicity against malignant B cells, combining these two drugs may represent an attractive model for the design of a new and rational combination therapy for MCL.
Targeting Histone Deacetylase 6 and the Aggresome Pathway in Acute Lymphoblastic Leukemia Cells.
Authors: Rodriguez-Gonzalez Augustin , Ch’ng James , Ikeda Alan K. , Lin Tara , Bahrami Bita , Mazitschek Ralph , Bradner James E. , Fu Cecilia , Sakamoto Kathleen M. 
Published: April 2020

Abstract
Acute lymphoblastic leukemia (ALL) is the most common form of childhood cancer. Despite effective chemotherapy, 20% of patients will relapse. Therefore, it is critical that we identify novel therapies to treat ALL. We are studying a new small molecule compound known as tubacin (tubulin acetylation inducer) that selectively inhibits histone deacetylase 6 (HDAC6). HDAC6 binds to polyubiquitinated misfolded proteins and to dynein motor proteins, including alpha-tubulin, thereby recruiting misfolded or unwanted proteins to aggresomes and subsequent degradation by the lysosome. Tubacin was discovered through a chemical genetic screen of a 7,392 small molecule library and was found to induce acetylation of alpha-tubulin by inhibiting one of the two catalytic domains of HDAC6. This inhibition disrupts the interaction of HDAC6 with dynein resulting in marked accumulation of ubiquitinated proteins. Previous work demonstrated that treatment of multiple myeloma cells with tubacin inhibited growth at low micromolar concentrations. Tubacin does not appear to affect global histone acetylation, gene expression, or cell cycle regulation. To determine the effects of tubacin in human ALL cells, we treated both B- and T-cell ALL cell lines with varying concentrations of the drug and performed MTT assays. In T-ALL cells (Jurkat, Loucy), the IC50 of tubacin was found to be 1 to 3 uM, while in B-cell ALL cells (REH, Nalm-6), the IC50 was 2 to 5uM. Tubacin induced apoptosis of Jurkat and Loucy cells stained with Annexin V and propidium iodide. Within 12 hours, we observed increased protein polyubiquitination and PARP cleavage, but no difference in Rb phosphorylation in cells treated with tubacin. Furthermore, tubacin treatment increased acetylation of alpha-tubulin in Loucy and Jurkat cells within 3 hours. To study whether tubacin was toxic to normal hematopoietic cells, we treated human bone marrow cells cultured in methylcellulose containing IL-3, IL-6, and Stem Cell Factor with varying concentrations of tubacin. The IC50 of 20uM was determined from numbers of colonies plated in triplicate. Similarly, treatment of normal human lymphocytes cultured in IL-2, demonstrated an IC50 of 16uM. Finally, we examined the effects of tubacin on growth of primary ALL cells. Bone marrow cells from three patients with B-cell ALL at diagnosis were cultured in tubacin at varying concentrations and MTT assays were performed. In two of the three ALL samples, the IC50 was less than 5uM. Experiments to study the effects of tubacin in mouse models of leukemia are in progress. Our results suggest that inhibition of HDAC6 and the aggresome pathway provides a novel approach to treat ALL.