bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binding of FANCD2 to SRSF1 Splicing Factor Prevents Genomic Instability through R Loop Regulation
Authors: Olazabal-Herrero Anne , Green Allison M. , Chen Xiaoyong , Sung Patrick , Pillai Manoj M , Kupfer Gary M. 
Published: November 2020

BACKGROUND. Fanconi Anemia (FA) is a rare disease characterized by congenital abnormalities, bone marrow failure and cancer susceptibility. The pivotal role of the FA pathway is DNA interstrand crosslink (ICL) repair, where FANCD2-FANCI complex monoubiquitination is the key regulatory step. Recent studies have linked defects in the FA pathway to R-loop metabolism and implicated R-loops as an endogenous source of genomic instability that contributes to the FA phenotype, although the mechanism remains elusive. Splicing factors, such as SRSF1 (ASF/SF2), have also been linked to R loops, cancer, and myelodysplastic syndrome (MDS), so we hypothesized a link between SRSF1 and FA.
METHODS. Cells: FA-D2 mutant (PD20) and corrected (D2), HeLa. siRNA transfections were used to reduce SRSF1 and FANCD2 protein levels. Survival assays were performed to determine cell sensitivity to DNA damaging agents. In vitro immunoprecipitation was performed using SRSF1 purified from bacteria and FANCD2-FANCI purified from insect cells. R-loops were studied using the Damage At RNA Transcription (DART) assay and S9.6 immunofluorescence.
RESULTS. In order to study the involvement of splicing factors in the FA pathway, we knocked down SRSF1 by using siRNA. SRSF1 knockdown lead to impaired FANCD2 monoubiquitination after DNA damage as well as diminished cell survival, thus creating a FA-like phenotype (A). In addition, immunoprecipitation in cells (B) and in vitro showed direct interaction between FANCD2 and SRSF1. We found that double FANCD2+SRSF1 knockdown led to increased R-loops compared to FANCD2/SRSF1 single knockdown visualized by S9.6 immunofluorescence. In addition, DART assay revealed colocalization of SRSF1 and FANCD2 with R-loops in highly transcribed genomic sites, known to be R-loop hotspots (C). Finally, we found that SRSF1 interacts with the mRNA export factor NFX1 in a FANCD2-dependent fashion (D) through RNA, suggesting that they could cooperate in the prevention of R-loop formation by exporting accumulated RNA in the nucleus.
CONCLUSION. Our findings suggest a novel non-canonical mechanism of FANCD2 via regulation of SRSF1 in R-loop prevention via facilitation of mRNA export, thus preventing genomic instability (E).
CLINICAL APPLICABILITY. These results will reveal a novel mechanism for a non-canonical role of the FA pathway in prevention of genomic instability and will shed light upon the most basic cellular processes of the FA pathway, which is germane for delineating more generalized mechanisms of oncogenesis and genome maintenance. As accumulation of R-loops is associated with FA, we propose that R-loops and R-loop processing proteins (such as SRSF1) offer new avenues as relevant therapeutic targets not only for FA but also for multiple cancers.

Disclosures
No relevant conflicts of interest to declare.
Lyophilized Human Platelets Restore Hemostasis in the Presence of the P2Y12 Inhibitors Cangrelor, Ticagrelor and Clopidogrel
Authors: Dickerson Matthew , Lee Amber , Hale Anne , Moskowitz Keith A. 
Published: November 2020

• Background: P2Y12 inhibitors block platelet ADP receptors thereby reducing clotting capacity. In an emergency, these agents must be reversed or therapeutically overcome to stop bleeding. Additionally, prior to and during elective procedures these inhibitors must be withdrawn, thereby increasing thrombotic risk. Lyophilized human platelets (Thrombosomes®) are stabilized platelet derived hemostatic agents currently under Phase 2 clinical development for thrombocytopenia and have potential as antiplatelet reversal agents.
• Aims: The aim of this study was to determine if lyophilized human platelets are resistant to the antiplatelet effect of P2Y12 inhibitors and therefore restore hemostasis in the presence of P2Y12 inhibitors.
• Methods: Fresh drawn platelet rich plasma (PRP) was treated with pharmacological concentrations of P2Y12 inhibitors cangrelor or ticagrelor and confirmed to inhibit ADP-stimulated aggregation on the PAP-8E Platelet Aggregometer. Changes in hemostatic properties of the P2Y12 inhibitor treated PRP were also tested under shear force on the Total Thrombus formation Analysis System (T-TAS®). P2Y12 inhibitor treated PRP samples were dosed with lyophilized platelets and tested for return of hemostatic properties by T-TAS. NOD SCID mice were used in a tail snip model to determine hemostatic efficacy of Thrombosomes® after super pharmacological doses of clopidogrel treatment.
• Results: Fresh PRP derived platelet aggregation response to ADP was inhibited by cangrelor or ticagrelor whereas lyophilized platelets did not respond to either inhibitor. Normal thrombus formation of PRP as measured by T-TAS occurred at 19.5± 1.5 minutes (n=4) but increases to 28.0±3.0 minutes with cangrelor (n=4) or 28.0±3.0 minutes with ticagrelor (n=5) treatment. The addition of 150k/µL lyophilized platelets to P2Y12-inhibited PRP reduced time to thrombus formation to lower than PRP alone; 15.5 ±0.5 minutes in the presence of cangrelor (n=3) versus 17.5 ±1.5 minutes in the presence of ticagrelor (n=5). In the in vivo tail snip mouse model animals treated with super pharmacological dose of clopidogrel bled for 18.0±10.0 minutes (n=5) unlike those not treated that only bleed for 9.5±2.5 minutes (n=6). Lyophilized platelet treated clopidogrel animals stopped bleeding at 12.5 ±4.5 minutes (n=5) after tail snip.
• Conclusion: Lyophilized human platelets, unlike normal platelets were resistant to the antiplatelet effects of P2Y12 inhibitors. In vitro and in vivo studies reveal that lyophilized human platelets can be used to recover the anti-thrombotic effect of P2Y12 antagonists, potentially allowing continued drug compliance prior to elective procedures and as a possible treatment for emergent acute bleeding while on P2Y12 antagonist therapy.

Disclosures
Dickerson: Cellphire Inc.: Current Employment. Lee:Cellphire, Inc.: Current Employment. Hale:Cellphire: Current Employment. Moskowitz:Cellphire Inc.: Current Employment.
NCOR2 Mutations Are Associated with IMiD Resistance in Human Myeloma Cells
Authors: Mori Tomoaki , Panaroni Cristina , Onyewadume Chukwuamaka , Raje Noopur S. 
Published: November 2020

The immunomodulatory drug thalidomide, and its analogs, lenalidomide, and pomalidomide (IMiDs) have significantly changed the treatment paradigm of multiple myeloma (MM). Despite this progress, IMiD resistance develops in the majority of patients resulting in the development of refractory disease. Cereblon (CRBN), a direct target, has been implicated in IMiD resistance. However, alternate mechanisms of IMiD resistance independent of CRBN remain largely unknown.
To understand and study the mechanisms responsible for the development of IMiD resistance, we created lenalidomide-resistant (Len-R) and pomalidomide-resistant (Pom-R) human myeloma MM.1s cell lines, by continuous culture in the presence of lenalidomide or pomalidomide for 3 months. Whole genome sequencing of these 2 resistant cell lines compared with parental MM.1s revealed 172 genes with exonic mutations in both Len-R and Pom-R myeloma cells. Furthermore, a protein-protein interaction (PPI) network was constructed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The PPI network demonstrated 8 genes that scored a high degree of protein-protein interaction. Among these genes, we identified NCOR2, a corepressor that negatively regulates gene expression, as a downregulated gene in resistant cell lines.
To study this further, we created NCOR2 knock out MM.1s cell lines using CRISPR/cas9 gene modification. Our data demonstrates that depletion of NCOR2 confers IMiD resistance independent to CRBN. Interestingly, Len-R, Pom-R and NCOR2 knock out MM.1s showed increased MYC protein expression, which is essential for myeloma cell survival and proliferation. A BET inhibitor, known to disrupt the binding of BRD4 to chromatin, inhibited the proliferation of Len-R and Pom-R and NCOR2 knock out MM.1s by completely suppressing MYC expression. These results indicate that NCOR2 down regulation in IMiD resistant cells induces MYC upregulation which may in part result in IMiD resistance. Our findings reveal a novel molecular mechanism associated with IMiD resistance, independent of CRBN and suggest that NCOR2-MYC pathway may be a new target for IMiD refractory patients.

Disclosures
Raje: Celgene: Consultancy.
Defining the Super Massive Transfusion in US and Coalition Forces during Combat Operations in Afghanistan and Iraq
Authors: Schauer Steven Gremel , Fisher Andrew , Bynum James , Cap Andrew P. 
Published: November 2020

Introduction: Hemorrhage is the leading cause of potentially preventable death on the battlefield. After hemorrhage control, the resuscitation with blood products is essential to restore circulating volume and prevent coagulopathy. While massive transfusion (MT) occurs frequently after major trauma, it remains unclear who the subset of casualties is that define a super massive transfusion which would require mobilization of additional resources. We seek to determine what defines a super MT as this would help allocate resources.
Methods: This is a secondary analysis of a previously described dataset from the Department of Defense Trauma Registry. In this analysis, we isolated US and Coalition casualties that received at least 1 unit of packed red cells or whole blood. To describe the super MT, we sought the top quartile of total products administered within the first 24 hours.
Results: Out of the 28222 casualties within our dataset, we identified 2204 US military and 498 Coalition that met inclusion for this analysis. The median number of total products administered within the first 24 hours was 16 with 39 total product units at the 75th percentile, which included 691 casualties. Of those in the super MT group, their median injury severity score was higher (29 versus 18, p&lt;0.001), they were most frequently injured by explosive (84% versus 69%, p&lt;0.001), they had a higher mean emergency department pulse (116 versus 103, p&lt;0.001), lower mean systolic 109 versus 122, p&lt;0.001), and higher mean international normalized ratio (1.53 versus 1.28, p&lt;0.001). They more frequently had serious injuries to the thorax (29% versus 22%, p&lt;0.001), abdomen (32% versus 17%, p&lt;0.001), and extremities (85% versus 64%, p&lt;0.001). Super MT was associated with worse survival (86% versus 92%, p&lt;0.001).
Conclusions: In our dataset, we identified the top 25th percentile of total product administration within the first 24 hours at 39 total product units. More data is needed to define this population early in their clinical course to better mobile resources early when needed.

Disclosures
No relevant conflicts of interest to declare.
Rare Case Report of Adult T-Cell Leukemia / Lymphoma (ATLL), in the City of Macau- Rio Grande Do Norte; Brazil
Authors: Ferreira Hugo Henrique de Freitas , Silva Alessandra Suelen Jardim , Júnior Lenilton Silva DA Silva , Oliveira Gustavo Henrique de Medeiros , Araujo Maria das Graças Pereira , Soares Victor lima , Bahia Frank , Oliveira Taissa Moura , Silva Dany GKC , Sales Valéria SF , Paiva Aldair Sousa , Cavalcanti Geraldo Barroso 
Published: November 2020

Introduction:Adult T-cell leukemia / lymphoma (ATLL) is a rare type of malignant haemopathy with the Human T-Cell Lymphotropic Virus type I (HTLV-1) as its etiologic agent. The clinical picture includes skin lesions, hypercalcemia, elevated lactate dehydrogenase (LDH), adenomegaly, myelopathy and leukocytosis with atypical TCD4 lymphocytes.Objective:To report a case of a patient from the city of Macau-RN, with ATLL, presenting skin lesions, weight loss (&gt; 13%), leukocytosis and supraclavicular lymph node enlargement. Case Description: Male patient, bricklayer, 67-year-old, hypertensive, was admitted to a hospital in Natal-RN, with severe itching, diffuse exanthematic skin lesions for 13 days, adynamia, associated with progressive, weight loss (P: 73Kg, 63Kg -13.6%), hyporexia, feverish (37.8 ° C), insidious and progressive drowsiness. Physical examination showed palpable lymphadenomegaly in the right supraclavicular chain, 1 cm, mobile and painless. Painful abdomen on deep palpation in the right hypochondrium and left iliac fossa, moderate hepatosplenomegaly. The blood count showed leukocytosis with the presence of atypical lymphocytes with convoluted nucleus (Flow-Cell), Creatinine (6.81), urea 349, hyperuricemia (14.9 mg / dL), hypercalcemia (12.8), LDH (723), Alkaline phosphatase (1388) GGT (183). Abdominal, kidney and urinary tract ultrasound revealed acute pancreatitis with signs of saponification (steatonecrosis of peripancreatic fat) and bilateral acute parenchymal nephropathy, respectively. The transthoracic echocardiogram identified aortic and mitral valve sclerosis. Immunophenotyping by flow cytometry found lymphoproliferative disease of mature TCD4 + cells, and the diagnosis of ATLL was confirmed by the serological reagent for HTLV-1. From then on, adequate treatment for ATLL was started with reversion of the clinical period, currently being followed up on an outpatient basis.Conclusions:The multiprofessional performance with accurate clinical investigation associated and specific laboratory exams such as immunophenotyping by flow cytometry and serological tests are essential for the early diagnosis and treatment of ATLL, a rare entity in the state of Rio Grande do Norte., Brazil and that high mortality when not diagnosed and treated early.

Disclosures
No relevant conflicts of interest to declare.
CD200 expression marks leukemia stem cells in human AML
Authors: Ho Jenny M. , Dobson Stephanie M. , Voisin Veronique , McLeod Jessica , Kennedy James A. , Mitchell Amanda , Jin Liqing , Eppert Kolja , Bader Gary , Minden Mark D. , Dick John E. , Wang Jean C. Y. 
Published: November 2020

Abstract
The leukemia stem cell (LSC) populations of acute myeloid leukemia (AML) exhibit phenotypic, genetic, and functional heterogeneity that contribute to therapy failure and relapse. Progress toward understanding the mechanistic basis for therapy resistance in LSCs has been hampered by difficulties in isolating cell fractions that enrich for the entire heterogeneous population of LSCs within individual AML samples. We previously reported that CD200 gene expression is upregulated in LSC-containing AML fractions. Here, we show that CD200 is present on a greater proportion of CD45dim blasts compared with more differentiated CD45high cells in AML patient samples. In 75% (49 of 65) of AML cases we examined, CD200 was expressed on ≥10% of CD45dim blasts; of these, CD200 identified LSCs within the blast population in 9 of 10 (90%) samples tested in xenotransplantation assays. CD200+ LSCs could be isolated from CD200+ normal HSCs with the use of additional markers. Notably, CD200 expression captured both CD34– and CD34+ LSCs within individual AML samples. Analysis of highly purified CD200+ LSC-containing fractions from NPM1-mutated AMLs, which are commonly CD34–, exhibited an enrichment of primitive gene expression signatures compared with unfractionated cells. Overall, our findings support CD200 as a novel LSC marker that is able to capture the entire LSC compartment from AML patient samples, including those with NPM1 mutation.
Real-world evidence of tisagenlecleucel for pediatric acute lymphoblastic leukemia and non-Hodgkin lymphoma
Authors: Pasquini Marcelo C. , Hu Zhen-Huan , Curran Kevin , Laetsch Theodore , Locke Frederick , Rouce Rayne , Pulsipher Michael A. , Phillips Christine L. , Keating Amy , Frigault Matthew J. , Salzberg Dana , Jaglowski Samantha , Sasine Joshua P. , Rosenthal Joseph , Ghosh Monalisa , Landsburg Daniel , Margossian Steven , Martin Paul L. , Kamdar Manali K. , Hematti Peiman , Nikiforow Sarah , Turtle Cameron , Perales Miguel-Angel , Steinert Patricia , Horowitz Mary M. , Moskop Amy , Pacaud Lida , Yi Lan , Chawla Raghav , Bleickardt Eric , Grupp Stephan 
Published: November 2020

Abstract
Tisagenlecleucel is a CD19 chimeric antigen receptor (CAR) T-cell therapy approved for treatment of pediatric and young adult patients with relapsed/refractory acute lymphoblastic leukemia (ALL) and adults with non-Hodgkin lymphoma (NHL). The initial experience with tisagenlecleucel in a real-world setting from a cellular therapy registry is presented here. As of January 2020, 511 patients were enrolled from 73 centers, and 410 patients had follow-up data reported (ALL, n = 255; NHL, n = 155), with a median follow-up of 13.4 and 11.9 months for ALL and NHL, respectively. Among patients with ALL, the initial complete remission (CR) rate was 85.5%. Twelve-month duration of response (DOR), event-free survival, and overall survival (OS) rates were 60.9%, 52.4%, and 77.2%, respectively. Among adults with NHL, the best overall response rate was 61.8%, including an initial CR rate of 39.5%. Six-month DOR, progression-free survival, and OS rates were 55.3%, 38.7%, and 70.7%, respectively. Grade ≥3 cytokine release syndrome and neurotoxicity were reported in 11.6% and 7.5% of all patients, respectively. Similar outcomes were observed in patients with in-specification and out-of-specification products as a result of viability &lt;80% (range, 61% to 79%). This first report of tisagenlecleucel in the real-world setting demonstrates outcomes with similar efficacy and improved safety compared with those seen in the pivotal trials.
Household air pollution and under-five mortality in sub-Saharan Africa: an analysis of 14 demographic and health surveys
Authors: Bickton Fanuel Meckson , Ndeketa Latif , Sibande Grace Thandekire , Nkeramahame Juvenal , Payesa Chipiliro , Milanzi Edith B. 
Published: November 2020

Abstract

Background
Globally, over four million deaths are attributed to exposure to household air pollution (HAP) annually. Evidence of the association between exposure to HAP and under-five mortality in sub-Saharan Africa (SSA) is insufficient. We assessed the association between exposure to HAP and under-five mortality risk in 14 SSA countries.

Methods
We pooled Demographic and Health Survey (DHS) data from 14 SSA countries (N = 164376) collected between 2015 and 2018. We defined exposure to HAP as the use of biomass fuel for cooking in the household. Under-five mortality was defined as deaths before age five. Data were analyzed using mixed effects logistic regression models.

Results
Of the study population, 73% were exposed to HAP and under-five mortality was observed in 5%. HAP exposure was associated with under-five mortality, adjusted odds ratio (OR) 1.33 (95% confidence interval (CI) [1.03–1.71]). Children from households who cooked inside the home had higher risk of under-five mortality compared to households that cooked in separate buildings [0.85 (0.73–0.98)] or outside [0.75 (0.64–0.87)]. Lower risk of under-five mortality was also observed in breastfed children [0.09 (0.05-0.18)] compared to non-breastfed children.

Conclusions
HAP exposure may be associated with an increased risk of under-five mortality in sub-Saharan Africa. More carefully designed longitudinal studies are required to contribute to these findings. In addition, awareness campaigns on the effects of HAP exposure and interventions to reduce the use of biomass fuels are required in SSA.
SAlign–a structure aware method for global PPI network alignment
Authors: Ayub Umair , Haider Imran , Naveed Hammad 
Published: November 2020

Abstract

Background
High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks. Studying complete protein networks can reveal more insight about healthy/disease states than studying proteins in isolation. Similarly, a comparative study of protein–protein interaction (PPI) networks of different species reveals important insights which may help in disease analysis and drug design. The study of PPI network alignment can also helps in understanding the different biological systems of different species. It can also be used in transfer of knowledge across different species. Different aligners have been introduced in the last decade but developing an accurate and scalable global alignment algorithm that can ensures the biological significance alignment is still challenging.

Results
This paper presents a novel global pairwise network alignment algorithm, SAlign, which uses topological and biological information in the alignment process. The proposed algorithm incorporates sequence and structural information for computing biological scores, whereas previous algorithms only use sequence information. The alignment based on the proposed technique shows that the combined effect of structure and sequence results in significantly better pairwise alignments. We have compared SAlign with state-of-art algorithms on the basis of semantic similarity of alignment and the number of aligned nodes on multiple PPI network pairs. The results of SAlign on the network pairs which have high percentage of proteins with available structure are 3–63% semantically better than all existing techniques. Furthermore, it also aligns 5–14% more nodes of these network pairs as compared to existing aligners. The results of SAlign on other PPI network pairs are comparable or better than all existing techniques. We also introduce $$\hbox {SAlign}^{\mathrm{mc}}$$

SAlign
mc

, a Monte Carlo based alignment algorithm, that produces multiple network alignments with similar semantic similarity. This helps the user to pick biologically meaningful alignments.

Conclusion
The proposed algorithm has the ability to find the alignments that are more biologically significant/relevant as compared to the alignments of existing aligners. Furthermore, the proposed method is able to generate alternate alignments that help in studying different genes/proteins of the specie.
LncRNA IMFlnc1 promotes porcine intramuscular adipocyte adipogenesis by sponging miR-199a-5p to up-regulate CAV-1
Authors: Wang Jing , Chen Ming-yue , Chen Jun-feng , Ren Qiao-ling , Zhang Jia-qing , Cao Hai , Xing Bao-song , Pan Chuan-ying 
Published: November 2020

Abstract

Background
Local Chinese local pig breeds have thinner muscle fiber and higher intramuscular-fat (IMF) content. But its regulation mechanism has not been discussed in-depth. Studies indicated that long non coding RNAs (lncRNAs) play important role in muscle and fat development.

Results
The lncRNAs expressional differences in the longissimus dorsi (LD) muscle were identified between Huainan pigs (local Chinese pigs, fat-type, HN) and Large White pigs (lean-type, LW) at 38, 58, and 78 days post conception (dpc). In total, 2131 novel lncRNAs were identified in 18 samples, and 291, 305, and 683 differentially expressed lncRNAs (DELs) were found between these two breeds at three stages, respectively. The mRNAs that co-expressed with these DELs were used for GO and KEGG analysis, and the results showed that muscle development and energy metabolism were more active at 58 dpc in HN, but at 78 dpc in LW pigs. Muscle cell differentiation and myofibril assembly might associated with earlier myogenesis and primary-muscle-fiber assembly in HN, and cell proliferation, insulin, and the MAPK pathway might be contribute to longer proliferation and elevated energy metabolism in LW pigs at 78 dpc. The PI3K/Akt and cAMP pathways were associated with higher IMF deposition in HN. Intramuscular fat deposition-associated long noncoding RNA 1 (IMFlnc1) was selected for functional verification, and results indicated that it regulated the expressional level of caveolin-1 (CAV-1) by acting as competing endogenous RNA (ceRNA) to sponge miR-199a-5p.

Conclusions
Our data contributed to understanding the role of lncRNAs in porcine-muscle development and IMF deposition, and provided valuable information for improving pig-meat quality.