bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevated Nuclease Activity Correlates With Clinical Spectrum Of Plasma Cell Dyscrasias
Authors: Patel Jaymin M. , Vahia Ankit V , Nanjappa Puru , Bajwa Ashun , Shah Sima , Yu-Tzu Tai , Anderson Kenneth C. , Shammas Masood , Munshi Nikhil C. 
Published: October 2019

Abstract
Over the last decade, there has been increasing interest in mechanisms that underlie genomic instability which is implicated in tumor progression, development of drug resistance and possibly even oncogenesis. We have observed that dysregulated homologous recombination (HR) is an important contributor to genomic instability. In this study, we aim to broaden our understanding of HR by exploring alternate pathways that may affect genomic instability such as nuclease activity.

Methods
We have developed an assay to measure total cellular nuclease activity and compare activity levels across a spectrum of plasma cell dyscrasias. Total nuclease activity in cell lines and patient samples was assessed using a novel plasmid degradation assay. Briefly, multiple myeloma (MM) cell lines and primary MM patient cells were lysed at equal cell concentration. The lysates were mixed with plasmid DNA in triplicate/quadruplicate and incubated at 37°C for fixed time points ranging from 0 to 30 minutes. Following forced cessation of enzymatic activity, samples were fractionated on agarose gel and resultant image analyzed for band intensity by Kodak 1D Image analysis software. The ratio of degraded plasmid over time was analyzed via nonlinear regression to calculate a half-life and k-constant.

Results
Non-linear regression analysis of data derived from assays involving 6 MM cell lines (RPMI, OPM1, H292, U266, INA6 & MM1S) with three pellets each of equal size taken from non-confluent cell culture with > 85% viability showed statistically significant reproducibility of best fit curve with an average R-squared of 0.93. Similar regression analysis could not be performed on data derived from normal PBMC pellets because they showed minimal degradation with linear regression slope of (-0.62). Lastly, non-linear regression analysis on 22 patient samples with a plasma cell dyscrasia diagnosis, revealed a broader range of activity by half-life. Further differentiation of plasma cell dyscrasia patients into 2 groups revealed a significantly higher half-life in MGUS & smouldering (9499.8 minutes) versus newly diagnosed and refractory or relapsed multiple myeloma patients (9.4,19.3 minutes respectively).

Conclusions
In conclusion, we show that nuclease activity, implicated in elevated recombination and genomic instability, can be measured in a statistically reproducible fashion by our in vitro assay and may be used to differentiate plasma cell dyscrasias across a clinical spectrum. Further analysis of nuclease activity in clinically annotated samples for correlation with clinical features, genomic data and survival outcomes is ongoing.

Disclosures:
Anderson: celgene: Consultancy; onyx: Consultancy; gilead: Consultancy; sanofi aventis: Consultancy; oncopep: Equity Ownership; acetylon: Equity Ownership.
KLF4 induces apoptosis in T-ALL through the BCL2/BCLXL pathway
Authors: Xu Bing , Wang Xiangmeng , Li Peng , Li Wei , Dong Huijuan , Zhou Yong , Li Yanyan 
Published: October 2019

Abstract
KLF4, also known as GKLF (gut KLF), is a member of the KLF zinc finger-containing transcription factor family. Klf4 together with Oct4, Sox2, and c-Mycare widely referred to as ‘Yamanaka factors’ because mouse somatic cells can be reprogrammed into pluripotent stem cells following their ectopic expression. The transcription factor Kruppel-like factor 4 (KLF4) may induce tumorigenesis or suppress tumor growth in a tissue-dependent manner. In T cell leukemia and pre-B cell lymphoma cells, KLF4 acts as a tumor suppressor. We found that over expression of KLF4 induced human acute T cell lymphoblastic leukemia (T-ALL) cell lines to undergo apoptosis through the BCL2/BCLXL pathway, and we confirmed KLF4-induced apoptosis in primary samples from T-ALL patients. We further characterized KLF4 function in human early and mature T cells. Our analysis uncovered that KLF4 suppressed the transcription of other T cell-associated genes in T-ALL.

Disclosures:
No relevant conflicts of interest to declare.
In Vitro Effect Of VPA Together With ATRA and Ara-C On Proliferation and Viability Of Pediatric AML Cell Line THP-1
Authors: Anak Sema , Kanbay Ayca Gul , Gulec Cagri 
Published: October 2019

Abstract
In addition to its HDAC inhibitory property, Valproic acid is also known as anticonvulsant agent and mood stabilizer in the treatment of bipolar disorders. Due to its HDAC inhibitory activity and its safety in long-term usage, VPA is presumed to be a good candidate for cancer treatment. It is known that VPA induces apoptosis in leukemic cells, while not in normal cells. VPA is reported as an effective agent in treatment of pediatric AML in clinical studies and is also well tolerated in children.
In this study, the in vitro effect of the combination of HDAC inhibitor VPA with Ara-C and ATRA which are used in AML therapy, is investigated on AML cells. For this purpose, the effect of VPA, Ara-C and ATRA on proliferation of AML cell line THP-1 is tested in cell culture condition. To assess the effect on cell proliferation, p21 expression was measured by RT-PCR method. The use of VPA alone, did not affect the cell viability, while increasing the expression of the p21 gene. VPA in combination with Ara-C, increased the expression of p21 gene more than the other combinations. Thus it is determined that the p21 gene expression is higher as a result of known cell cycle stops.
In this study, the understanding of how effective is VPA together with ATRA and/or Ara-C on AML cells, might be a good start for animal studies and clinical trials as a remarkable data for the development of new chemotherapeutic protocols.

Disclosures:
No relevant conflicts of interest to declare.
Reduction Of Immune Repertoire Diversity Through DNA Sequence Constraints At VDJ Junctions
Authors: Howie Bryan , Robins Harlan , Carlson Christopher S 
Published: October 2019

Abstract
B and T lymphocytes are effector cells of the adaptive immune system. These cells express surface receptors that bind a huge variety of antigens, and together they comprise a person’s immune repertoire. A diverse repertoire is essential for mounting robust immune responses against a wide range of pathogens, and repertoire diversity affects the probability that DNA sequencing can uniquely tag a clonally expanded population of cells for the detection of minimum residual disease (MRD) during cancer treatment.
Immune repertoire diversity arises partly through the combinatorial splicing of gene segments from the variable (V), diversity (D), and joining (J) regions of a B or T cell receptor locus. Much additional diversity is created through the stochastic insertion and deletion of nucleotides at the splice junctions, and by somatic hypermutation (SHM) in maturing lymphocytes. The generation of junctional diversity is an important part of this process, but it may be constrained by the underlying biological mechanisms.
To explore the landscape of junctional diversity among immune receptor loci, we developed a likelihood model that can annotate VDJ junctions in the presence of SHM and compute the probability that a given receptor sequence was generated only once in a person’s repertoire, which is essential for tracking MRD. Using high-throughput sequencing data from several individuals and a range of receptor loci, we identify mechanistic constraints that limit B and T cell receptor diversity. For example, we show that the usual variability in CDR3 length is reduced at the immunoglobulin kappa (IgK) locus, and we connect this finding to sequence motifs that constrain nucleotide deletion at the ends of IgK gene segments. Our findings will inform future genetic studies of the adaptive immune system, and they provide quantitative guidance for deciding which cancer clones can be tracked for reliable MRD detection.

Disclosures:
Howie: Adaptive Biotechnologies: Employment, Equity Ownership. Robins:Adaptive Biotechnologies: Consultancy, Equity Ownership, Patents & Royalties. Carlson:Adaptive Biotechnologies: Consultancy, Equity Ownership, Patents & Royalties.
Mutaome Profiling and Retrospective Mutaome Profiling Using Archived Bone Marrow Smear In AML
Authors: Liu Hongxing , Wang Fang , Teng Wen , Lin Yuehui , Yang Junfang , Zhang Xian , Yin Qing , Chen Xue , Zhu Ping , Tong Chunrong 
Published: October 2019

Abstract

Background
Acute myeloid leukemia (AML) is a heterogeneous disease with respect to presentation and clinical outcome. In recent years, more and more somatic mutations and their clinical significance were identified in AML. Most AML patients carry multiple gene mutations and the repertoire of mutations changing during the disease process, which determine the patient's unique clinical manifestations. Herein we recommend using the novel word ”mutaome¡± for representing the repertoire of somatic gene mutations in a specific tumor tissue, and aimed to establish a panel of mutation profiling protocol and retrospective profiling using archived bone marrow smear for clinical use in AML.

Methods and Cases
Mutation profiling protocol for CEBPA, DNMT3A, FLT3-ITD/TKD, IDH1, IDH2, KIT, NPM1, PHF6 and TET2 by PCR and Sanger sequencing was established, with the detection sensitivity about 15% to 20%. Bone Marrow (BM) or peripheral blood (PB) was collected form patients with newly diagnosed or relapsed. Archived BM smear on glass slides at the time of newly diagnosed were used for retrospective mutation analysis.

Results
1) Totally 61 archived smear, 106 fresh BM or PB and 2 paraffin-embedded pathological specimens from 157 patients were analyzed. Age ranged from 1 to 77 years old, with the median age of 27 years old.
2) 60.4% (102/169) samples carrying at least one mutation, 51.0% (53/102) of them carrying 2 or more mutations, 30.4% (31/102) carrying mutations within 2 or more different genes. The number of mutated sample for each gene is 33 for CEBPA¡¢9 DNMT3A¡¢35 FLT3¡¢6 IDH1¡¢7 IDH2¡¢7 KIT¡¢19 NPM1¡¢8 PHF6¡¢and 21 TET2.
3) Paired archived smear and relapsed samples were analyzed for 11 cases, 9 of them showing difference, detailed results shown in Table 1.
4) Totally 53 patients come to our hospital after certain treatment, with the tumor cells below 15% and without AML gene mutation results. For these patients, archived BM smear samples were used for retrospective mutation profiling and then to guide targeted therapy and stratified evaluation.

Conclusions
Panel testing for gene mutations is effective method for detection of AML molecular markers. For the patients came with partial remission and without gene mutation result, archived bone marrow smear sample can be used for retrospective mutation analysis and then help guiding targeted therapy and stratified evaluation.

Disclosures:
No relevant conflicts of interest to declare.
MicroRNA Dysregulation in Newly Diagnosed Chronic Myeloid Leukaemia Patients
Authors: Gordon Jane E. A. , Bailey Charles G , Rasko John , Ritchie William , Watkins Dale B. , White Deborah L. , Leclercq Tamara , Hughes Timothy P 
Published: October 2019

Abstract

Introduction
Heterogeneity within the CML patient population is evidenced by variable response dynamics and tolerability between patients treated with tyrosine kinase inhibitors (TKIs). Clinical risk scores have utility however do not inform upon the biology underpinning differential response. OCT1 activity has been established as a predictor of imatinib response but is not predictive for second generation TKIs nilotinib or dasatinib.
In CML, microRNAs (miRNAs) have been implicated in BCR-ABL mediated signalling pathways and alter rapidly after TKI treatment. Indeed, we have previously established that miR-142-3p decreases within 14 days of TKI initiation and correlates with the SOKAL score.

Method
We performed miRNA profiling on 75 newly diagnosed, clinical trial CML patients (56% male, 44% female, median age 51 years) with greater than 24 months follow-up. RNA was extracted from peripheral blood mononuclear cells. The expression of 800 mature miRNA was analysed using the nCounter Human v2 miRNA Expression Assay (NanoString Technologies). In addition, IC50 values for imatinib and nilotinib were determined on all samples as previously described.

Results
The miRNA expression levels obtained on this platform showed a wide dynamic range and substantial interpatient variation. This included miRNA previously reported in CML in vitro and patient studies: interquartile ranges were 52414 to 121632 for miR-142-3p, 3120 to 15599 for miR-451a, 2658 to 12023 for miR-150, 828 to 1461 for miR-181a-5p. In addition, we were able to identify miRNAs that were associated with nilotinib IC50 and imatinib IC50.

Discussion
The current study highlights the variability evident at the miRNA level between newly diagnosed CML patients. It provides a rationale to further examine the role of miRNA in CML pathogenesis, TKI response and define patient heterogeneity from diagnosis.

Disclosures:
White: Novartis: Research Funding; BMS: Research Funding, Speakers Bureau; Ariad: Research Funding; CSL: Research Funding. Hughes:Novartis: Honoraria, Research Funding; BMS: Honoraria, Research Funding; ARIAD: Honoraria, Research Funding.
Therapy Related Acute Lymphoblastic Leukemia: Pethema Experience
Authors: Kelleher Nicholas John , Gallardo David , Brunet Salut , Montesinos Pau , Ribera Josep-Maria , Barba Pere , Garcia Olga 
Published: October 2019

Abstract

Background
Therapy related acute lymphoblastic leukemia, a subset of secondary acute lymphoblastic leukemia has been estimated as accounting for between 1.2 and 6.9% of all adult acute lymphoblastic leukemia cases. It has been associated with an increased frequency of high risk cytogenetic alterations and with worse clinical outcomes. It has been suggested these patients should be included in high risk treatment protocols.

Method
In order to evaluate these characteristics in a group of similar patients we contacted centres working within the PETHEMA group to request data on patients diagnosed with ALL asking for clinical information including the presence or absence of previous neoplasia and of previous cytotoxic therapy along with treatment responses and survival data.

Results
We received information on 429 patients of whom 22 had received cytotoxic therapy for a prior neoplasm.Patients were divided into group 1 with prior cytotoxic therapy, group 2 with prior neoplasia without cytotoxic therapy and group 3 de novo ALL. We found patients in group 3 to be younger than the other two groups Group 1( 55 years) Group 2 (65 years) Group 3 (34 years) (p=0.001). No statistically significant difference was shown for white cell count, cytopenias, CNS involvement, LDH or for B versus T immunophenotype. Nor did our series show a significant difference in the frequencies of high risk cytogenetics between the groups. Figures for complete remission [Group 1- 13 (93%); Group 2- 6 (75%); Group 3-346 (85%) p=0.477] were higher in group 1 therapy related ALL compared with de novo patients without reaching clinical significance. Nor was a statistically significant difference shown for 3 year overall survival [Group 1 (80%); Group 2 (38%); Group 3 (47%) p=0.151] , 3 year event free survival [Group 1 (67%); Group 2 (38%); Group 3 (42%) p=0.24] or for complete remission duration [Group 1 (75%);Group 2 (50%); Group 3 (60%) p=0.462]

Conclusion
Apart from age, our series did not show an increase in poor risk clinical or cytogenetic features in therapy related ALL patients compared with de novo disease cases and nor was clinical outcome demonstrated to be worse. This would suggest that risk stratification should be carried out using currently recognized parameters without specifically taking into account the status of therapy related disease.

Disclosures:
No relevant conflicts of interest to declare.
Pathological Confirmation Of Apparent Metastatic Disease Is Essential: Incidentally Diagnosed Low Grade B Cell Lymphomas In Patients With Solid Tumors
Authors: Gaballa Sameh , Abdelmalek Cherif , Alpdogan Onder , Axelrod Rita S. , Campling Barbara , Kelly William kevin , Rodriguez Joanna , Gitelson Elena 
Published: October 2019

Abstract

Background
The detection of skeletal metastasis, enlarged lymph nodes or parenchymal lesions in patients (pts) with established solid tumors most commonly denotes advanced stage disease. If not confirmed histologically, a subset of pts might be over staged and mismanaged palliatively.

Methods
We report 7 cases of low-grade B cell lymphomas diagnosed in a bone, lymph node or lung biopsy during staging workup in patients with suspected metastatic solid tumors.

Results
All pts were men aged 41 to 80 yo diagnosed with: non-small cell lung (NSCL), prostate, lip squamous cell, bladder, renal cell cancer (CA) and nasal adenoid cystic carcinoma. Imaging studies done during initial workup or follow up after resection of the primary tumor revealed bone metastasis, lymphadenopathy or lung nodules suggesting advanced stage of the primary CA. Invasive workup of the lesions in question revealed incidental low-grade B cell lymphomas (2 low grade lymphomas of bone, 2 CLL/SLL, 1 BALT, 1 marginal zone and 1 nodular lymphocyte predominant Hodgkin lymphoma). In all cases, this led to down staging and changed the management of the solid CA. Surgical resection of the tumor was done after it was down staged from non-resectable to resectable in 2 pts with head/neck CA; 1 pt with NSCL was down staged from stage IV to IIIA and received chemo/radiotherapy; 1 pt with prostate CA was down staged from stage IV to I; 3 pts were down staged from stage IV and were in remission from previously resected solid tumors. Only 2 pts required therapy for the newly diagnosed lymphoma. Avidity of the lesions revealed SUV ranging from 1.28 to 14.11 in the bone and from 2.17 to 6.98 in the lymph nodes.

Conclusions
Accurate staging of pts with solid tumors is critical in defining optimal goals of therapy. The growing use of PET/CT scans results in a higher rate of incidentally detected bone lesions or lymphadenopathy. Whereas a number of solid tumors readily spread to bone and lymph nodes, a spectrum of indolent lymphoid disorders may coexist in pts with established solid tumors. These lymphomas may remain asymptomatic for years. This might be misinterpreted as advanced stage solid tumor unless confirmed histologically.

Disclosures:
No relevant conflicts of interest to declare.
Can Clinical Parameters Predict Bone Marrow Involvement In DLBCL?
Authors: Baillargeon Paul , Nistala Puja , Doll Donald 
Published: October 2019

Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma, accounting for about 1/3rd cases of NHL. At diagnosis, DLBCL involves the bone marrow in approximately 15-25% of cases. However, the bone marrow may reveal discordant morphology from the lymph node, usually an indolent lymphoma.
Bone marrow biopsy is routinely used in the staging evaluation of patients with DLBCL. The aim of this study was to determine if clinical variables could predict bone marrow involvement by DLBCL.

Methods
Retrospective chart review of all patients with a diagnosis of DLBCL at University of Missouri-Columbia/Ellis Fischel Cancer Center from 1993-2013. The following parameters were reviewed: bone marrow biopsy reports, anemia (Hb<10g/dl), leukopenia (wbc<4000), thrombocytopenia (<150,000), lactate dehydrogenase level and clinical stage. Statistical analysis was performed by Fischer Exact test and logistic regression analysis.

Results
80 charts were available for review and 7 patients had bone marrow involvement by DLBCL. Univariate analysis for cytopenias (p=0.459), elevated LDH (p=0.442), anemia (p=0.436), leukopenia (p=1.0) and thrombocytopenia (p=0.434) and bone marrow involvement by DLBCL showed no statistical significance (Fischer Exact test). Multivariate analysis comparing anemia, leukopenia, thrombocytopenia, elevated LDH and clinical stage with respect to bone marrow involvement revealed p=0.789, p=0.134, p=0.062, p=0.827 and p=0.521 respectively, and disclosed no statistical significance (logistic regression analysis). Univariate (Fisher exact tests and Cochran-Mantel-Haenszel statistics) and multivariate (logistic regression) analyses were used to test for the relationship of these parameters with bone marrow involvement.

Disclosures:
No relevant conflicts of interest to declare.
Breast Implant Related Anaplastic Large Cell Lymphoma ALK- (ALCL ALK-) – Case Report
Authors: Arbelaez Alejandro , Catley Laurence , Pool Louis 
Published: October 2019

Abstract

Case presentation
A 29 underwent bilateral cosmetic breast augmentation 10 years previously (McGhan Textured Round 400 mL implants). Six months before, she developed slowly progressive right breast pain and inflammatory signs associated with fluid collection around the right breast that was drained. A yellow cloudy fluid was examined and showed atypical large lymphoid cells. The cell block prepared in another institution showed numerous lymphoid cells including large atypical cells with lobated nuclei. PET CT scan was negative, same as bone marrow aspirate and trephine for lymphoma infiltration. Following bilateral removal of the breast implants, further histopathology studies showed no infiltration by lymphoma of the breast capsules or scar tissue. However, right breast peri prosthetic fluid microscopy showed a population of single malignant cells with scanty cytoplasm, numerous mitosis, and nuclei showing single and multiple nucleoli. Some cells showing horseshoe nuclei. The malignant cells were positive for CD30 and LCA and negative for CD20, CD68, AE1-3, and ALK 1. FISH for ALK was not possible (Fig 1)

Discussion
Primary breast lymphomas are very rare conditions; they represent less than 1% of all NHL and less than 0.7% of all breast malignancies. There have been some cases reported in the medical literature of ALCL ALK- associated with breast implants. All the cases have been described in patients with textured implants, such as in this case and the reason is unknown. There are two main types of ALCL of the breast based on published case reports: a mass and an effusion. Primary breast effusion associated ALCL portends a good prognosis despite the fact that they are ALK-. The development of ALCL proximal to breast implants suggests that they are the result of an immune reaction to the silicone. Whether they represent true malignancy or a localised reactive phenomenon is not entirely clear yet. In previous case series, the condition has been described as indolent. However, given the low incidence of this condition and the limited literature available; it is difficult to know what the best treatment approach is. Following confirmation of the diagnosis, treatment options were discussed with the patient and the preferred option was active treatment with local radiation after removal of breast implants.

Disclosures:
No relevant conflicts of interest to declare.