bluuebunny/crossref_metadata_2025_split huggingface dataset:
Humoral immune reconstitution after anti-BCMA CAR T-cell therapy in relapsed/refractory multiple myeloma
Authors: Wang Ying , Li Chunrui , Xia Jieyun , Li Ping , Cao Jiang , Pan Bin , Tan Xu , Li Hujun , Qi Kunming , Wang Xiangmin , Shi Ming , Jing Guangjun , Yan Zhiling , Cheng Hai , Zhu Feng , Sun Haiying , Sang Wei , Li Depeng , Zhang Xi , Li Zhenyu , Zheng Junnian , Liang Aibin , Zhou Jianfeng , Xu Kailin 
Published: September 2021

Abstract
Systematic and dynamic humoral immune reconstitution is little-known for patients with relapsed/refractory (R/R) multiple myeloma (MM) who received anti–B-cell maturation antigen (BCMA) chimeric antigen receptor (CAR) T-cell therapy. We investigated the kinetics of B-cell, normal plasma cell, and immunoglobulin recovery in 40 patients who achieved ongoing response after anti-BCMA CAR T-cell therapy. All patients developed B-cell aplasia and the median duration of B-cell aplasia was 70 days (range, 23-270). The B-cell count reached its nadir on median day 7 and returned to baseline level on median day 97. BCMA+ cells in bone marrow turned undetectable on median day 28 (13-159) in 94.87% (37 of 39) of patients. Normal plasma cells in bone marrow were first redetected on median day 212. All patients developed a significant decrease in serum IgG, IgA, and IgM on median day 60. At year 1, recovery of serum IgG, IgM, and IgA was observed in 53.33% (8 of 15; non-IgG MM), 73.08% (19 of 26; non-IgM MM), and 23.81% (5 of 21;non-IgA MM) of the patients, respectively. Median time to IgG, IgM, and IgA recovery were days 386, 254, and not reached during follow-up, respectively. Virus-specific IgG levels decreased with loss of protection. Twenty-three of 40 (57.5%) patients had a total of 44 infection events. There were no infection-related deaths. These results reveal a 7-month aplasia of bone marrow normal plasma cells and longer period of hypogammaglobulinemia, suggesting a profound and lasting humoral immune deficiency after anti-BCMA CAR T-cell therapy, especially for IgA.
Rational biomarker development for the early and minimally invasive monitoring of AML
Authors: Abdelhamed Sherif , Butler John T. , Jung Seul , Chen Ding-Wen , Jenkins Gaye , Gao Lina , Lim Jeong Y. , Klco Jeffery M. , Horton Terzah M. , Kurre Peter 
Published: September 2021

AbstractRecurrent disease remains the principal cause for treatment failure in acute myeloid leukemia (AML) across age groups. Reliable biomarkers of AML relapse risk and disease burden have been problematic, as symptoms appear late and current monitoring relies on invasive and cost-ineffective serial bone marrow (BM) surveillance. In this report, we discover a set of unique microRNA (miRNA) that circulates in AML-derived vesicles in the peripheral blood ahead of the general dissemination of leukemic blasts and symptomatic BM failure. Next-generation sequencing of extracellular vesicle-contained small RNA in 12 AML patients and 12 controls allowed us to identify a panel of differentially incorporated miRNA. Proof-of-concept studies using a murine model and patient-derived xenografts demonstrate the feasibility of developing miR-1246, as a potential minimally invasive AML biomarker.
FlowCT for the analysis of large immunophenotypic data sets and biomarker discovery in cancer immunology
Authors: Botta Cirino , Maia Catarina , Garcés Juan-José , Termini Rosalinda , Perez Cristina , Manrique Irene , Burgos Leire , Zabaleta Aintzane , Alignani Diego , Sarvide Sarai , Merino Juana , Puig Noemi , Cedena María-Teresa , Rossi Marco , Tassone Pierfrancesco , Gentile Massimo , Correale Pierpaolo , Borrello Ivan , Terpos Evangelos , Jelinek Tomas , Paiva Artur , Roccaro Aldo , Goldschmidt Hartmut , Avet-Loiseau Hervé , Rosinol Laura , Mateos Maria-Victoria , Martinez-Lopez Joaquin , Lahuerta Juan-José , Bladé Joan , San-Miguel Jesús F. , Paiva, Bruno 
Published: September 2021

Abstract
Large-scale immune monitoring is becoming routinely used in clinical trials to identify determinants of treatment responsiveness, particularly to immunotherapies. Flow cytometry remains one of the most versatile and high throughput approaches for single-cell analysis; however, manual interpretation of multidimensional data poses a challenge when attempting to capture full cellular diversity and provide reproducible results. We present FlowCT, a semi-automated workspace empowered to analyze large data sets. It includes pre-processing, normalization, multiple dimensionality reduction techniques, automated clustering, and predictive modeling tools. As a proof of concept, we used FlowCT to compare the T-cell compartment in bone marrow (BM) with peripheral blood (PB) from patients with smoldering multiple myeloma (SMM), identify minimally invasive immune biomarkers of progression from smoldering to active MM, define prognostic T-cell subsets in the BM of patients with active MM after treatment intensification, and assess the longitudinal effect of maintenance therapy in BM T cells. A total of 354 samples were analyzed and immune signatures predictive of malignant transformation were identified in 150 patients with SMM (hazard ratio [HR], 1.7; P &lt; .001). We also determined progression-free survival (HR, 4.09; P &lt; .0001) and overall survival (HR, 3.12; P = .047) in 100 patients with active MM. New data also emerged about stem cell memory T cells, the concordance between immune profiles in BM and PB, and the immunomodulatory effect of maintenance therapy. FlowCT is a new open-source computational approach that can be readily implemented by research laboratories to perform quality control, analyze high-dimensional data, unveil cellular diversity, and objectively identify biomarkers in large immune monitoring studies. These trials were registered at www.clinicaltrials.gov as #NCT01916252 and #NCT02406144.
t(4;12)(q12;p13) ETV6-rearranged AML without eosinophilia does not involve PDGFRA: relevance for imatinib insensitivity
Authors: Mueller Sarah B. , Dal Cin Paola , Le Long P. , Dias-Santagata Dora , Lennerz Jochen K. , Iafrate A. John , Marble Hetal Desai , Brunner Andrew M. , Weinstock Matthew J. , Luskin Marlise R. , De Angelo Daniel J. , Stone Richard M. , Nardi Valentina 
Published: September 2021

Abstract
Acute myeloid leukemia (AML) with t(4;12)(q12;p13) translocation is rare and often associated with an aggressive clinical course and poor prognosis. Previous reports based on fluorescence in situ hybridization (FISH) analysis have suggested that ETV6::PDGFRA fusions are present in these patients, despite the absence of eosinophilia, which is typically found in other hematopoietic malignancies with PDGFRA-containing fusions. We first detected an ETV6-SCFD2 fusion by targeted RNA sequencing in a patient with t(4;12)(q12;p13) who had been diagnosed with an ETV6-PDGFRA fusion by FISH analysis but failed to respond to imatinib. We then retrospectively identified 4 additional patients with AML and t(4;12)(q12;p13) with apparent ETV6-PDGFRA fusions using chromosome and FISH analysis and applied targeted RNA sequencing to archival material. We again detected rearrangements between ETV6 and non-PDGFRA 4q12 genes, including SCFD2, CHIC2, and GSX2. None of the 3 patients who received imatinib based on the incorrect assumption of an ETV6-PDGFRA fusion responded. Our findings highlight the importance of using a sequencing-based assay to confirm the presence of targetable gene fusions, particularly in genomic regions, such as 4q12, with many clinically relevant genes that are too close to resolve by chromosome or FISH analysis. Finally, combining our data and review of the literature, we show that sequence-confirmed ETV6-PDGFRA fusions are typically found in eosinophilic disorders (3/3 cases), and patients with t(4;12)(q12;p13) without eosinophilia are found to have other 4q12 partners on sequencing (17/17 cases).
VITT following Ad26.COV2.S vaccination presenting without radiographically demonstrable thrombosis
Authors: Kennedy Vanessa E. , Wong Chelsea C. , Hong Jessica M. , Peng Theodore , Brondfield Sam , Reilly Linda M. , Cornett Patricia , Leavitt Andrew D. 
Published: September 2021

Abstract
We report a case of vaccine-induced immune thrombotic thrombocytopenia (VITT) in a young man diagnosed 13 days after Ad26.COV2.S COVID-19 (Johnson & Johnson/Janssen) vaccination. He presented to us with 5 days of progressive left leg pain, thrombocytopenia, hypofibrinogenemia, and markedly elevated d-dimers, but without radiographically demonstrable thrombosis. Despite negative imaging, we initiated treatment of presumptive VITT given the striking clinical picture that included the timing of his recent adenovirus-based COVID-19 vaccine, leg symptoms, marked thrombocytopenia, and consumptive coagulopathy. He received intravenous immune globulin, prednisone, and argatroban and was discharged 7 days later much improved. His positive platelet factor 4 enzyme-linked immunosorbent assay antibody test returned after treatment was initiated. To our knowledge, this is the first reported case of VITT following Ad26.COV2.S vaccination presenting without radiographically demonstrable thrombosis. Our patient highlights the importance of knowing vaccine status and initiating treatment as soon as possible in the right clinical setting, even in the absence of radiographic evidence of thrombus. Early VITT recognition and treatment provide an opportunity to prevent serious thrombotic complications.
Association of early-life factors with prematurity-associated lung disease: prospective cohort study
Authors: Hart Kylie , Cousins Michael , Watkins W. John , Kotecha Sarah J. , Henderson A. John , Kotecha Sailesh 
Published: September 2021

BackgroundAlthough bronchopulmonary dysplasia (BPD) is associated with lung function deficits in childhood, many who develop BPD have normal lung function in childhood and many without BPD, including those born at 33–34 weeks of gestation, have lung dysfunction in childhood. Since the predictability of BPD for future lung deficits is increasingly doubted, we prospectively recruited preterm-born children to identify early-life factors associated with lung function deficits after preterm birth.MethodsFrom 767 children aged 7–12 years who had their respiratory symptoms assessed, and had spirometry before and after a bronchodilator in our Respiratory Health Outcomes in Neonates (RHiNO) study, 739 (544 preterm-born at ≤34 weeks of gestation and 195 term-born) had satisfactory lung function. Data were analysed using multivariable logistic regression and mediation.ResultsWhen preterm-born children were classified according to their lung function, low lung function (prematurity-associated lung disease (PLD)) was associated with BPD, gestation and intra-uterine growth restriction (IUGR) on univariable logistic regression analyses. However, on multivariable logistic regression analyses, gestation (β= –0.153,se0.051; p=0.003) and IUGR (OR 1.783, 95% CI 1.06–3.00; p=0.029) remained significantly associated with later deficits of lung function, but BPD (OR 0.99, 95% CI 0.52–1.89; p=0.974) did not. Mediation analyses confirmed these results.ConclusionsAlthough traditionally BPD has been associated with low lung function in later life, the data show that gestation and IUGR are significantly associated with PLD in childhood, but BPD is not. By identifying children with PLD, we can better understand the underlying mechanisms and develop optimal therapies.
Mendelian randomisation and experimental medicine approaches to interleukin-6 as a drug target in pulmonary arterial hypertension
Authors: Toshner Mark , Church Colin , Harbaum Lars , Rhodes Christopher , Villar Moreschi Sofia S. , Liley James , Jones Rowena , Arora Amit , Batai Ken , Desai Ankit A. , Coghlan John G. , Gibbs J. Simon R. , Gor Dee , Gräf Stefan , Harlow Louise , Hernandez-Sanchez Jules , Howard Luke S. , Humbert Marc , Karnes Jason , Kiely David G. , Kittles Rick , Knightbridge Emily , Lam Brian , Lutz Katie A. , Nichols William C. , Pauciulo Michael W. , Pepke-Zaba Joanna , Suntharalingam Jay , Soubrier Florent , Trembath Richard C. , Schwantes-An Tae-Hwi L. , Wort S. John , Wilkins Martin R. , Gaine Sean , Morrell Nicholas W. , Corris Paul A. 
Published: September 2021

BackgroundInflammation and dysregulated immunity are important in the development of pulmonary arterial hypertension (PAH). Compelling preclinical data supports the therapeutic blockade of interleukin-6 (IL-6) signalling.MethodsWe conducted a phase 2 open-label study of intravenous tocilizumab (8 mg·kg−1) over 6 months in patients with group 1 PAH. Co-primary end-points were safety, defined by incidence and severity of adverse events, and change in pulmonary vascular resistance. Separately, a mendelian randomisation study was undertaken on 11 744 individuals with European ancestry including 2085 patients with idiopathic/heritable disease for the IL-6 receptor (IL6R) variant (rs7529229), known to associate with circulating IL-6R levels.ResultsWe recruited 29 patients (male/female 10/19; mean±sdage 54.9±11.4 years). Of these, 19 had heritable/idiopathic PAH and 10 had connective tissue disease-associated PAH. Six were withdrawn prior to drug administration; 23 patients received at least one dose of tocilizumab. Tocilizumab was discontinued in four patients owing to serious adverse events. There were no deaths. Despite evidence of target engagement in plasma IL-6 and C-reactive protein levels, both intention-to-treat and modified intention-to-treat analyses demonstrated no change in pulmonary vascular resistance. Inflammatory markers did not predict treatment response. Mendelian randomisation did not support an effect of the leadIL6Rvariant on risk of PAH (OR 0.99, p=0.88).ConclusionAdverse events were consistent with the known safety profile of tocilizumab. Tocilizumab did not show any consistent treatment effect.
ROSE: radiology, obstruction, symptoms and exposure – a Delphi consensus definition of the association of COPD and bronchiectasis by the EMBARC Airways Working Group
Authors: Traversi Letizia , Miravitlles Marc , Martinez-Garcia Miguel Angel , Shteinberg Michal , Bossios Apostolos , Dimakou Katerina , Jacob Joseph , Hurst John R. , Paggiaro Pier Luigi , Ferri Sebastian , Hillas Georgios , Vogel-Claussen Jens , Dettmer Sabine , Aliberti Stefano , Chalmers James D. , Polverino Eva 
Published: September 2021

IntroductionThe coexistence of COPD and bronchiectasis seems to be common and associated with a worse prognosis than for either disease individually. However, no definition of this association exists to guide researchers and clinicians.MethodsWe conducted a Delphi survey involving expert pulmonologists and radiologists from Europe, Turkey and Israel in order to define the “COPD– [bronchiectasis] BE association”.A panel of 16 experts from EMBARC selected 35 statements for the survey after reviewing scientific literature. Invited participants, selected on the basis of expertise, geographical and sex distribution, were asked to express agreement on the statements. Consensus was defined as a score of ≥6 points (scale 0 to 9) in ≥70% of answers across two scoring rounds.Results102 (72.3%) out of 141 invited experts participated in the first round. Their response rate in the second round was 81%. The final consensus definition of “COPD–BE association” was: “The coexistence of (1) specific radiological findings (abnormal bronchial dilatation, airways visible within 1 cm of pleura and/or lack of tapering signin ≥1 pulmonary segment and in >1 lobe) with (2) an obstructive pattern on spirometry ([forced expiratory volume in 1 s] FEV1/[forced vital capacity] FVC <0.7), (3) at least two characteristic symptoms (cough, expectoration, dyspnoea, fatigue, frequent infections) and (4) current or past exposure to smoke(≥10 pack-years) or other toxic agents (biomass, etc.)”. These criteria form the acronym “ROSE” (Radiology, Obstruction, Symptoms, Exposure).ConclusionsThe Delphi process formulated a European consensus definition of “COPD–BE association”. We hope this definition will have broad applicability across clinical practice and research in the future.
Natural toxins: environmental contaminants calling for attention
Authors: Hansen Hans Christian Bruun , Hilscherova Klara , Bucheli Thomas D. 
Published: September 2021

AbstractBiosynthetic toxic compounds from plants and cyanobacteria constitute a chemically diverse family of at least 20,000 compounds. Recent work with natural toxin databases and toxin characterization shows that the majority of natural toxins are polar and mobile, with toxicity ranging from low to very high, while persistence is highly variable. Natural toxins may be produced in high quantities—some exceeding 10 g/m2/year—resulting in high environmental loads. Recent phytotoxin monitoring indicates that one or more natural toxin is always present in a surface water sample, but that concentrations are highly variable often with pulses during rain events. Phytotoxins belong to many classes, but often with flavonoids and alkaloids dominating. Likewise, advanced monitoring discovers a wide spectrum of cyanobacterial metabolites that are released directly into surface waters during water blooms. Except of the few known cyanobacterial toxins, we have very limited info regarding their environmental fate and toxicity.The 16 papers in this article collection present examples of natural toxin occurrence, properties, fate and toxicity. The overarching conclusion is that natural toxins should be monitored and characterized regarding their risk potential, and that natural toxins of greatest expected risk should be evaluated as thoroughly as industrial xenobiotics. Cyanotoxins are well known water contaminants that should be removed for producing drinking water, while for phytotoxins the current knowledge base is very limited. We advocate to intensify research on natural toxins, and to address the evident knowledge gaps on natural toxin analysis/monitoring, physical–chemical properties and degradation/pathways, transport modelling, and toxicity. The complex and dynamic interplays between biotic and site conditions such as vegetation, toxic plant densities, climate, soil types, nutrients and radiation, play decisive roles for both biotoxin formation and fate. Environmental and toxicological research in biosynthesized compounds extends beyond natural toxins, with important perspectives for risk assessment of biopesticides, growth regulators and biomedicine (or biologicals collectively) produced by plants and microorganisms.
Detecting selection in low-coverage high-throughput sequencing data using principal component analysis
Authors: Meisner Jonas , Albrechtsen Anders , Hanghøj Kristian 
Published: September 2021

Abstract
Background
Identification of selection signatures between populations is often an important part of a population genetic study. Leveraging high-throughput DNA sequencing larger sample sizes of populations with similar ancestries has become increasingly common. This has led to the need of methods capable of identifying signals of selection in populations with a continuous cline of genetic differentiation. Individuals from continuous populations are inherently challenging to group into meaningful units which is why existing methods rely on principal components analysis for inference of the selection signals. These existing methods require called genotypes as input which is problematic for studies based on low-coverage sequencing data.

Materials and methods
We have extended two principal component analysis based selection statistics to genotype likelihood data and applied them to low-coverage sequencing data from the 1000 Genomes Project for populations with European and East Asian ancestry to detect signals of selection in samples with continuous population structure.

Results
Here, we present two selections statistics which we have implemented in the framework. These methods account for genotype uncertainty, opening for the opportunity to conduct selection scans in continuous populations from low and/or variable coverage sequencing data. To illustrate their use, we applied the methods to low-coverage sequencing data from human populations of East Asian and European ancestries and show that the implemented selection statistics can control the false positive rate and that they identify the same signatures of selection from low-coverage sequencing data as state-of-the-art software using high quality called genotypes.

Conclusion
We show that selection scans of low-coverage sequencing data of populations with similar ancestry perform on par with that obtained from high quality genotype data. Moreover, we demonstrate that outperform selection statistics obtained from called genotypes from low-coverage sequencing data without the need for ad-hoc filtering.
The expression landscape of JAK1 and its potential as a biomarker for prognosis and immune infiltrates in NSCLC
Authors: Shen Kaikai , Wei Yuqing , Lv Tangfeng , Song Yong , Jiang Xiaogan , Lu Zhiwei , Zhan Ping , Wang Xianghai , Fan Meng , Lu Weihua 
Published: September 2021

Abstract
Background
Janus-activated kinase-1 (JAK1) plays a crucial role in many aspects of cell proliferation, differentiation, apoptosis and immune regulation. However, correlations of JAK1 with prognosis and immune infiltration in NSCLC have not been documented.

Methods
We analyzed the relationship between JAK1 expression and NSCLC prognosis and immune infiltration using multiple public databases.

Results
JAK1 expression was significantly decreased in NSCLC compared with that in paired normal tissues. JAK1 overexpression indicated a favourable prognosis in NSCLC. In subgroup analysis, high JAK1 expression was associated with a preferable prognosis in lung adenocarcinoma (OS: HR, 0.74, 95% CI from 0.58 to 0.95, log-rank P = 0.017), not squamous cell carcinoma. In addition, data from Kaplan–Meier plotter revealed that JAK1 overexpression was associated with a preferable prognosis in male and stage N2 patients and patients without distant metastasis. Notably, increased levels of JAK1 expression were associated with an undesirable prognosis in patients with stage 1 (OS: HR, 1.46, 95% CI from 1.06 to 2.00, P = 0.02) and without lymph node metastasis (PFS: HR, 2.18, 95% CI from 1.06 to 4.46, P = 0.029), which suggests that early-stage NSCLC patients with JAK1 overexpression may have a bleak prognosis. Moreover, multiple immune infiltration cells, including NK cells, CD8 + T and CD4 + T cells, B cells, macrophages, neutrophils, and dendritic cells (DCs), in NSCLC were positively correlated with JAK1 expression. Furthermore, diverse immune markers are associated with JAK1 expression.

Conclusions
JAK1 overexpression exhibited superior prognosis and immune infiltration in NSCLC.