bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Successful Use of Archived Formalin-Fixed Paraffin-Embedded (FFPE) Material for Gene Expression Studies.
Authors: Lilakos Konstantinos , Angelopoulou Maria K. , Georgiou George , Salpeas Vassilios , Korkolopoulou Penelope , Panayiotidis Panayiotis , Pangalis Gerassimos A. 
Published: April 2020

Abstract
BACKGROUND: FFPE tissues are widely used as a source of genomic DNA (gDNA), as well as for immunohistochemistry. RNA amplification and its usage for gene expression studies from archived FFPE material has been hampered due to RNA degradation.
AIM: The description of a protocol for RNA extraction from archived FFPE tissues followed by reverse transcription (RT) and real time PCR and its implementation in the study of reference genes.
METHODS: RNA was extracted from single 15μm sections from 18 samples 30 months old and 6 samples 10 years old from patients with diffuse large B-cell lymphoma (DLBCL). The FFPE RNA Extraction kit (Roche) was used, followed by DNA digestion and run on an Agilent2100 Bioanalyzer. RT was performed using the Transcriptor System (Roche) with modified temperatures followed by real time PCR for the c-abl and Survivin genes using the Universal Library probes and primers (Roche). In addition for the 10-year old samples, beta2 microglobulin (b2m) and G6PDH were also amplified.
RESULTS: RNA that was yielded, was around 250 bp. c-abl was successfully amplified in all 18 samples up to 30 months old with a median cycle (Ct) number of 33.74. All 3 control genes were successfully amplified from the 10-year old samples with a median Ct number of 30.3 for G6PDH, 23.4 for b2m and 28.6 for c-abl. To further evaluate the amplification potency we successfully amplified Survivin transcripts with a median Ct number of 35.2. Survivin/abl ratio was calculated at a median of 0.5 for all DLBCL samples. gDNA interferenence was excluded, since no amplification signal was observed when gDNA was used as a template. The special RNA extraction methods, elevated temperatures for RT, as well as the use of the Universal Library probes, which are specifically designed to be short (8–9bp) and hybridize to a short amplicon (72bp for c-abl and 97bp for Survivin) were the major novelties of this method.
Conclusions: Specialized RNA extraction methods and the use of Universal Library Probes can succesfully lead to several target gene amplification from archived FFPE material and potentially provide templates for gene expression studies.
CCL2 Chemokine Gene Expression in Lymph Nodes May Have Prognostic Value in Non-Hodgkin’s Lymphoma.
Authors: Mazur Grzegorz , Kryczek Ilona , Wrobel Tomasz , Dlubek Dorota , Klimczak Aleksandra , Jaskula Emilia , Jelen Michal , Lange Andrzej , Kuliczkowski Kazimierz 
Published: April 2020

Abstract
Background: Non-Hodgkin’s lymphomas (nHL) constitute complex group of lymphoproliferative disorders in which clinical outcome is difficult to predict at the moment of diagnosis. Formation of International Prognostic Index has provided criteria dividing patients into groups of risk, but still new prognostic factors are being searched. There are several reports that some chemokines including CCL2 play a role in progression of solid tumours (bladder, ovarian, non-small cell lung cancer) and increased level of CCL2 has been found in myeloma multiple. CCL2 is the chemokine produced by tumour cells and some stromal cells, such as: fibroblasts, endothelial cells and monocytes. CCL2 is chemoattractant for monocytes, T, NK and dendritic cells and basophlis. CCL2 has also angiogenic activity and is necessary for tumour growth and metastatic process.
Aim: The purpose of this study was to evaluate gene expression of CCL2 chemokine in lymphoma and reactive lymph nodes.
Material and methods: CCL2 gene expression was determined in 37 lymph nodes of lymphoma patients (26 B-cell lymphoma: 12 females and 14 males aged 26–73 years; 4 T-cell lymphoma: males aged 41–81 years; 7 Hodgkin’s lymphoma: 4 females and 3 males aged 21–58 years) and 25 reactive lymph nodes (15 females, 10 males, aged 18–59 years, median age 32 years). Gene expression was determined by the reverse transcription (RT)-polymerase chain reaction method. Scale of expression was 0–3 AU. Statistical analysis was performed using Kruskall-Wallis and Mann-Witney tests (p&lt;0,05).
Results: In lymphoma lymph nodes CCL2 expression was significantly higher (2–3 AU) than in reactive lymph nodes (p=0,0008). Increased CCL2 expression was detected in 19/26 (73%) B-cell lymphoma lymph nodes and all (4/4, 100%) T-cell lymphomas. In reactive lymph nodes 2 AU expression was observed in 7/25 cases (28%). Particularly high expression characterized diffuse large B-cell lymphomas and Burkitt lymphomas. Patients with high CCL2 expression had significantly shorter survival than those with low expression (p=0,004). There was positive correlation between CCL2 expression and Ki-67 proliferation marker (p&lt;0,05; coefficient 0,39).
Conclusions: CCL2 expression is higher in B-cell lymphoma lymph nodes than in reactive lymph nodes. Multivariate analysis has proved CCL2 as independent prognostic factor in nHL.
B-Chronic Lymphoproliferative Disorders (BCLD) Presenting with Splenomegaly: Differential Diagnosis and Outcome.
Authors: Angelopoulou Maria K. , Papakonstantinou Maria , Kontopidou Flora N. , Dimopoulou Maria N. , Siakantaris Marina P. , Vassilakopoulos Theodoros P. , Kalpadakis Christina , Kokoris Styliani , Dimitriadou Evangelia M. , Galani Zacharoula , Sachanas Sotirios , Tsirkinidis Padelis , Kyrtsonis Marie-Christine , Korkolopoulou Penelope , Panayiotidis Panayiotis , Pangalis Gerassimos A. 
Published: April 2020

Abstract
BACKGROUND: The differential diagnosis of BCLD in patients (pts) presenting with splenomegaly as the sole clinical finding is extremely difficult, due to the lack of lymph node histology. The diagnosis is based on morphology and immunophenotype (IF) from the blood and/or bone marrow. However, the reproducibility of morphology is limited and there is considerable overlap in IF findings. AIMS: The comparative analysis of pts with BCLD presenting with sole splenomegaly.
METHODS: All pts presented to our Unit with a probable BCLD and splenomegaly as the sole clinical finding, between 1980 and 2005 were retrospectively analyzed. Pts were classified into 4 groups according to their IF: Group A: CD5+/CD23+ [B-CLL phenotype], Group B: CD5+/CD23− [Mantle cell lymphoma phenotype], Group C: CD5−/CD23+, and Group D: CD5−/CD23− [Groups C and D: Splenic marginal zone lymphoma phenotype]. Hairy cell leukemia cases were excluded from the analysis. Pts’ characteristics, first line treatment, disease specific survival (DSS), freedom from 1st treatment (FF1T)and freedom from 2nd treatment (FF2T) were analyzed.
RESULTS: 71 pts (41 males) with a median age of 63 years (range: 39–83 y) were recorded. The 4 groups differed significantly in all their main characteristics, except of age, platelet count and frequency of lymphocytosis as shown in the table. 6 pts have not received any treatment, 27 were splenectomized, 16 received chlorambucil, 11 Rituximab and the remaining 11 other first-line treatments. The median follow up of the currently alive pts is 44.7 months (3–303). 34 pts have not required 2nd therapeutic intervention. The 10-year DSS of all 71 pts was 71±7%. The 10-year DSS and 5-year FF2T did not differ significantly between the 4 groups. However group B had a worse DSS (p=0.05) and FF2T (p=0.0036) compared to all other groups together. Cases who were CD38+ (p=0.055), CD11c− (p=0.001) and had Hb ≤12g/dL (p=0.03) had a worse prognosis.
CONCLUSIONS: Pts with BCLD and splenomegaly can be classified into different clinicopathologic entities according to basic IF characteristics. CD5+/CD23− splenomegalic BCLDS seem to have a worse outcome. CD38+, CD11c− and anemia are poor prognostic features. The best therapeutic strategy remains to be established.
Characteristics of the 4 Splenomegalic Groups Group A Group B Group C Group D p N 19 16 20 16 Spleen (cm) 14 (6–20) 16 (9–34) 10 (5–30) 10 (4–20) 0.03 Hb (g/dL) 12.0 11.0 10.0 12.4 0.02 WBC (×10 ^9/L) 30 10.8 10.1 10.8 0.02 CD38+ 28% 75% 5% 6% &lt;0.001 CD25+ 63% 38% 19% 0% 0.002 CD11c+ 56% 27% 47% 80% 0.03
Mutational Analysis of NOTCH1 Gene in Mature T-Cell Leukemia/Lymphoma.
Authors: Shimizu Daisuke , Taki Tomohiko , Utsunomiya Atae , Nakagawa Hitoshi , Nomura Kenichi , Matsumoto Yosuke , Nishida Kazuhiro , Horiike Shigeo , Taniwaki Masafumi 
Published: April 2020

Abstract
A somatic mutation of the NOTCH1 gene is frequently observed in T-cell acute lymphoblastic leukemia (T-ALL) of immature T-cell leukemia, but its prevalence in mature T-cell leukemia/lymphoma remains unknown. T-cell non-Hodgkin lymphomas (T-NHL) are relatively uncommon malignancies that represent approximately 12% of all lymphomas. The current WHO/EORTC classification recognizes 9 distinct clinicopathologic peripheral T-NHLs. The identification of genetic abnormalities and chromosomal rearrangements has been helpful in recognizing and defining lymphoma entities according to the WHO classification. However, the molecular changes that could play a role in leukemogenesis and progression remain unknown. NOTCH1 gene mutation was analyzed in 53 mature T-cell leukemia/lymphoma in adults, comprising 21 with adult T-cell leukemia (ATL), 25 with T-cell non-Hodgkin lymphoma (T-NHL), seven with T-cell prolymphocytic leukemia (T-PLL). We analyzed the hotspots of the NOTCH1 activating mutation in T-ALL cases located in exons 26 and 27, which encodes the N-terminal and C-terminal region of the heterodimerization (HD-N, HD-C) domain, and in exon 34, which encodes the PEST domain and terminal activation domain (TAD). Mutation detection in these two locations was performed by means of PCR-based denaturing high-performance liquid chromatography (dHPLC) using a WAVE DNA fragment analysis system followed by sequencing. We detected a nonsense mutation, C7249T, resulting in Q2417X, in an ATL patient, and a missense mutation, A6955G, resulting in M2319V, as well as a 3-bp deletion between 7234 and 7236 that resulted in deletion of the proline at codon 2412 in the same allele in a T-NHL, peripheral T-cell lymphoma, unspecified (PTCL-u), patient. NOTCH1 mutation was infrequent in mature T-cell leukemia/lymphoma, but NOTCH1 may be involved in leukemogenesis associated with a variety of T-cell leukemia/lymphoma rather than only with T-ALL.
Figure 1. (A) ATL case No.9, (B) T-NHL case No.38, (C) T-NHL case No.38 Figure 1. (A) ATL case No.9, (B) T-NHL case No.38, (C) T-NHL case No.38
Outcome of Diffuse Large B Cell Lymphoma in the VA Health System: Do We Need To Do Better?.
Authors: Komrokji Rami S. , Maraboyina Sanjay , Safa Malek M. , Nahleh Zeina A. , Haddad Rami Y. 
Published: April 2020

Abstract
Background: Diffuse Large B cell lymphoma (DLBCL) is the commonest subtype of non-Hodgkin Lymphoma (NHL). Data on outcome of DLBCL in large cohorts of patients or community practices outside clinical trials are lacking. Treatment and outcomes of DLBCL among the VA patients have not been reported previously. We utilized the VA Central Cancer Registry to study cases of DLBCL in the VA system.
Methods: This was a retrospective analysis. The VA Central Cancer Registry (VACCR) database was used to identify patients with DLBCL diagnosed between 1995 and 2005. There are approximately 120 VA medical centers diagnosing and/or treating patients with cancer. The VACCR aggregates the data collected by the medical centers’ cancer registries. Data were extrapolated and analyzed using bio-statistical software SPSS. Variables included age, sex, stage of disease, histology subtype, date of diagnosis, date of last contact, date of relapse, vital status, whether patients received chemotherapy and or radiation.
Results: There were 2792 patients with DLBCL at the VACCR between 1995 and 2005, 2402 were white, 323 black patients, and 67 patients from other racial groups. The mean age at diagnosis was to 65. Majority were males (2721 patients). More patients were diagnosed at advanced stage (stage III and IV) (40%), in 34% of cases stage was not known or missing. IPI score data were not available. Most patients received multi-agent chemotherapy 70%, and 20% of patients received radiation (31 % in early stage and 12% in late stage). The 5-year overall survival was 28%. 5 year OS was 41% for stage I, 32% for stage II, 25% for stage III and 17% for stage IV. Using Cox regression multivariable analysis age and use of mutli-agent chemotherapy were the only statistically significant independent variables affecting survival.
Conclusions: Outcome of DLBCL in VA patients seems inferior to what is reported in clinical studies. The age of patients treated in the VA as well as sex could be factors affecting the outcome. There are no data available on outcome of DLBCL in such large cohort of patients outside context of clinical trials to make meaningful comparisons.
Fludarabine and Mitoxantrone for the Refractory Relapse Treatment of B-Cell Low-Grade Non-Hodgkin Lymphoma (NHL): LACOHG First Interim Report (Latin American Cooperative Oncology Hematology Group).
Authors: Baltazar-Arellano Severiano , Pimentel Patricia , Vera Luis , Bezares Fernando , Málaga Jose , Huamani-Z Julia , Montante Antonio , Rivas-Vera Silvia , Carrasco-Yalan Antonio A. , Beltran-Garate Brady E. 
Published: April 2020

Abstract
Background: fludarabine (F) is licensed for the management of indolent non Hodgkin’s lymphoma in countries such as Canada and Switzerland. Clinical evidence suggests that fludarabine monotherapy is as least as effective, than conventional therapies such as cyclophosphamide, vincristine, prednisone (CVP) for the first and second line treatment of B-cell low grade NHL achieving objective response rates. Better response rates can be achieved combining F with Mitoxantrone (M) in low grade NHL even in refractory relapsed (RR) patients (pts). The Latin American Cooperative Oncology Hematology Group (LACOHG) proposed a multicenter study in Latin American countries in 2002 to use FM in RR B-cell low grade NHL.
Aims: to assess the response rate, safety, disease free survival (DFS) and overall survival (OS) of FM in RR B-cell low grade NHL during (2003–2006).
Methods: Forty-eight patients in the period of January 2003 to February 2006 were evaluated. Forty-four pts. had follicular lymphoma and 4 small lymphocytic lymphoma. Median age 63.5 years old (range: 24–83). Gender: female 56% and male 44%. Inclusion criteria for low grade NHL-LG was: any previous treatment excluding autologous transplantation, Ann Arbor stage II to IV, age &gt; 18 years old, ECOG performance status 0–2 and written informed consent. ECOG performance status 0: 2%, 1: 71% and 2: 27%. Ann Arbor staging: II: 2%, III: 29% and IV: 69%. International Prognostic Index (IPI): 0–1: 19%, 2–3: 71% and 4–5: 10%. Median previous treatment was 1 (range: 1–3). FM treatment consisted of F 25 mg/m2 i.v. (day 1–3) and M 10 mg/m m2 i.v. (day 1) each 28 days for 6–8 cycles.
Results: on this low grade NHL cohort the overall response rate (ORR was 81%; progressive disease and non-response 19%. With a median follow up of 17 months, OS at 24 months was 86% (DE 5.2%) and DFS at 24 months 57.1% (DE 11.3%). LDH in serum was not an adverse prognostic factor for DFS and OS.
Safety: on the 286 cycles in 48 pts, the toxicity was: 18 episodes of grade 3-4 neutropenias, 15 episodes of grade 3-4 thrombocytopenia, 7 episodes of grade 1–2 nausea/vomiting, grade 1–2 diarrhea in 4 pts, 8 pts were admitted to the clinic, 11 fever episodes, 2 allopecia, 4 pts developed grade 1–2 peripheral neuropathy and infections 7%: one case herpes zoster.
Mortality rate: 12,5% (6/48 patients), 5 of them because progressive disease. No cardiac toxicity was reported.
Conclusions: FM is an effective and safe treatment for RR low grade NHL. A longer follow up and a larger trial, might be needed to confirm these results in a multicenter, randomized study.
DFS with FM in RR low grade NHL : LACOHG DFS with FM in RR low grade NHL : LACOHG
High Expression and Persistent Activation of STAT1, 3 and 5 Predicts Vorinostat (Suberoylanilide Hydroxamic Acid, SAHA) Resistance in Cutaneous T-Cell Lymphoma Cells.
Authors: Fantin Valeria R. , Loboda Andrey , Roth Jennifer A. , Paweletz Cloud , Randolph Sophia , Pierce Jacqueline W. , Harrington Elizabeth A. , Hendrickson Ronald C. , Reilly John F. , Ware Christopher , Kadin Marshall E. , Duvic Madeleine , Frankel Stanley R. , Richon Victoria M. 
Published: April 2020

Abstract
The hydroxamic acid vorinostat (SAHA) is an HDAC inhibitor that induces differentiation, growth arrest and/or apoptosis of malignant cells both in vitro and in vivo, and is currently being tested in the clinic for a variety of indications. In particular, vorinostat has demonstrated an overall response rate of approximately 30% in advanced cutaneous T-cell lymphoma (CTCL). The purpose of this study was to identify biomarkers that predict response to vorinostat in CTCL using preclinical model systems based upon gene expression profiling and pathogenesis of lymphoma. Herein we report the results of our evaluation of the STAT (signal transducer and activator of transcription) signaling pathway. The relative level of mRNA and protein expression as well as activation status of several members of this family have been evaluated in lymphoid cell lines with diverse vorinostat sensitivity (proliferation/viability IC50 range: 0.3–14 mM). Among them, the more responsive CTCL cells lines HH and HUT102 exhibited an IC50 ≃ 0.8 mM. These cells underwent apoptosis in response to vorinostat as assessed by TUNEL assay, in contrast to Hut78 and MJ cells (IC50 &gt; 2 mM) that did not show signs of DNA fragmentation upon incubation in vorinostat-containing media for 48 h. Our results indicate that in lymphoma cell lines elevated protein levels and persistent activation of STAT1, 3 and 5 correlate with resistance to vorinostat. Immunofluorescence microscopy studies revealed that STAT proteins preferentially localize to the nuclear compartment in cells with impaired vorinostat response, consistent with the expected distribution for this group of transcription factors in the active state. Simultaneous treatment with a pan-JAK inhibitor (JAK inhibitor I; Calbiochem) resulted in an additive antiproliferative effect consistent with a survival, antiapoptotic role for STAT proteins in the response to vorinostat treatment. Immunohistochemical analysis of STAT1 in skin biopsies isolated from CTCL patients (N = 49) enrolled in the vorinostat Phase IIb clinical trial showed that malignant T cells were positively stained in approximately half of the samples (21 positively stained; 25 negatively stained; 3 poor quality specimens), and in those cases a relationship between nuclear accumulation of STAT1 and lack of response to treatment exists (p=0.007&lt;0.05; Fisher’s exact test). In conclusion, our results suggest that deregulation of STAT signaling plays a role in resistance to vorinostat in CTCL and strategies that block this pathway may improve response to vorinostat.
Activity of Bortezomib in Mantle Cell Lymphoma, Diffuse Large B Cell, and Small Lymphocytic Lymphoma.
Authors: Fauble Veena S. , Lobocki Catherine , Eapen Amy , Terebelo Howard R. 
Published: April 2020

Abstract
Bortezomib (PS341, Velcade) is a selective, reversible proteosome inhibitor. It is a unique inhibitor of the ubiquitin-proteosome pathway leading to arrest in tumor growth, induction of apoptosis, inhibition of tumor metastasis and angiogenesis. It plays an important role in the activation of NF Kappa B, which is responsible for transcription of inhibitors in apoptosis. It is a novel therapeutic agent that has demonstrated in vitro and in vivo activity in mantle cell lymphoma (MCL). In one phase II study, O’Conner et al reported that bortezomib demonstrated a response rate of 50% in refractory cases of mantle cell lymphoma, where as in small lymphocytic lymphoma there was a 0% response rate. Why certain types of non-Hodgkins lymphoma (NHL) are sensitive to this agent and others resistant is currently not well understood. It is believed that disregulation has been shown to play a role in the development of drug resistance in NHL Our objective was to determine the efficacy of bortezomib in vitro using three subtypes of NHL. Three lymphocytic cell lines were used: Granta-519 (mantle cell lymphoma), Toledo (diffuse large cell lymphoma) and EHEB (chronic B cell leukemia). The cytotoxic effects were determined by the colorimetric MTT assay after 24 hours of treatment with bortezomib (1 – 20 nM). Apoptosis was assessed by measuring Caspase-3 activity after 6 and 16 hours of treatment with bortezomib (4 or 20 nM). Bortezomib demonstrated a dose-dependent cytotoxic effect for all three cell lines, with an IC50 of 3.5 nM, 4.1 nM, and 18.5 nM for Toledo, Granta-519 and EHEB, respectively. Apoptotic studies showed that bortezomib (20 nM) induced a 1.4 to 5.6-fold increase (after 6 hrs) and 5.8 to 16.6-fold increase (after 16 hrs) in apoptosis. The EHEB cell line was most resistant, showing no increase in Caspase-3 activity at the lower dose (4 nM) at either time-point. Granta-519 was most sensitive showing a 5.2-fold increase in apoptosis with the lower dose after 16 hours of treatment. This in vitro study demonstrated a dose and time dependent response of bortezomib in both the mantle cell lymphoma (Granta-519) and the diffuse large cell lymphoma (Toledo) cell lines. The resistance to bortezomib in the chronic B cell leukemia (EHEB) cell line was confirmed in this study as evidenced by the lack of Caspase-3 activity at the 4 nM dose at both 6 and 16 hours. Our future studies will attempt to unmask the reason for this resistance. Perhaps manipulation of the apoptotic pathway through the use of combinations of various biologic response modifiers may be an attractive option in overcoming resistance in certain subtypes of NHL.