SpRY-mediated screens facilitate functional dissection of non-coding sequences at single-base resolution.

CRISPR mutagenesis screens conducted with SpCas9 and other nucleases have identified certain cis-regulatory elements and genetic variants but at a limited resolution due to the absence of protospacer adjacent motif (PAM) sequences. Here, leveraging the broad targeting scope of the near-PAMless SpRY variant, we have demonstrated that saturated SpRY mutagenesis and base editing screens can faithfully identify functional regulatory elements and essential genetic variants for target gene expression at single-base resolution. We further extended this methodology to investigate a genome-wide association study (GWAS) locus at 10q22.1 associated with a red blood cell trait, where we identified potential enhancers regulating HK1 gene expression, despite not all of these enhancers exhibiting typical chromatin signatures. More importantly, our saturated base editing screens pinpoint multiple causal variants within this locus that would otherwise be missed by Bayesian statistical fine-mapping. Our approach is generally applicable to functional interrogation of all non-coding genomic elements while complementing other high-coverage CRISPR screens.

The epigenetic regulators EP300/CREBBP represent promising therapeutic targets in MLL-rearranged acute myeloid leukemia.

Acute myeloid leukemia (AML) with mixed-lineage leukemia (MLL) gene rearrangements (MLL-r) is an aggressive subtype of blood cancer with dismal prognosis, underscoring the urgent need for novel therapeutic strategies. E1A-binding protein (EP300) and CREB-binding protein (CREBBP) function as essential transcriptional coactivators and acetyltransferases, governing leukemogenesis through diverse mechanisms. Targeting EP300/CREBBP holds great promise for treating leukemia with some certain cytogenetic abnormalities. Here, we demonstrated that EP300 and CREBBP are core epigenetic regulators in the pathogenesis of MLL-r AML through assaying the transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Knocking-out EP300/CREBBP and inhibitor (A-485) treatment depressed the MLL-r cells proliferation, while the MLL wild-type cells remained uninfluenced. We found that the CDK4/RB/E2F axis was downregulated specifically in MLL-r AML cell after A-485 treatment by RNA-seq, western blot and cut-tag analyses. EP300/CREBBP inhibitor selectively exerted potent anti-leukemia activity through blocking the MLL-r-BET complex binding to H3K27Ac modification on critical genes loci, distinct from global histone acetylation. Collectively, our study identified EP300/CREBBP as a critical epigenetic driver of MLL-r leukemia and validated their therapeutic potential through targeting inhibition, offering a promising avenue for improving clinical outcomes in this aggressive leukemia.

Comparison of blinatumomab and CAR T-cell therapy in relapsed/refractory acute lymphoblastic leukemia: a systematic review and meta-analysis.

OBJECTIVES: This study evaluated the benefits and risks of patients with refractory or relapsed acute lymphocytic leukemia (R/R ALL) treated with anti-CD19 chimeric antigen receptor (CAR) T-cell therapy and blinatumomab. METHODS: PubMed, Web of Science, Embase, and the Cochrane Library were searched for relevant studies. RESULTS: The pooled complete remission (CR) rate and minimal residual disease (MRD) negative rate were 48%, 31% for blinatumomab, and 86% and 80% for CAR T-cell therapy. CONCLUSIONS: The CAR T-cell therapy group exhibited a higher likelihood of CR rate than the blinatumomab group in every analysis regardless of adjustment subgroups. CAR T-cell therapy was associated with a significantly prolonged overall survival (OS) and relapse-free survival (RFS) compared with blinatumomab (2-year OS 55% vs 25%; 2-year RFS 40% vs 22%). CAR T-cell therapy was more effective for achieving CR and bridging to allogeneic hematopoietic stem cell transplantation (allo-SCT) than blinatumomab (2-year OS 75% vs. 57%). An emerging role for blinatumomab is as a bridging agent pre-SCT, and for patients who achieve an MRD-negative state pre-SCT, post-SCT outcomes are expected to be the same as CAR-T. For adverse effects (AEs), blinatumomab was associated with a lower rate of grade ≥3 hematological toxicity, CRS, and neurological events.

Corrigendum: Identification of microtube-associated biomarkers in diffuse large B-cell lymphoma and prognosis prediction.

[This corrects the article DOI: 10.3389/fgene.2022.1092678.].

Prognostic Significance of Ribosome-related Genes Signature in Diffuse Large B Cell Lymphoma.

Background: The diffuse large B-cell lymphoma (DLBCL) is a heterogeneous lymphoma with a dismal outcome, due to approximately 40% patients will be relapsed or refractory to the standard therapy of rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP). Therefore, we need urgently to explore the approach to classify the risk of DLBCL patients accurately and accurately targeting therapy. The ribosome is a vital cellular organelle that is mainly responsible for translation mRNA into protein, moreover, more and more reports revealed that ribosome was associated with cellular proliferation and tumorigenesis. Therefore, our study aimed to construct a prognostic model of DLBCL patients using ribosome-related genes (RibGs). Method: We screened differentially expressed RibGs between healthy donors' B cells and DLBCL patients' malignant B cells in GSE56315 dataset. Next, we performed analyses of univariate Cox regression, the least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analyses to establish the prognostic model consisting of 15 RibGs in GSE10846 training set. Then, we validated the model by a range of analyses including Cox regression, Kaplan-Meier survival, ROC curve, and nomogram in training and validation cohorts. Results: The RibGs model showed a reliably predictive capability. We found the upregulated pathways in high-risk group most associated with innate immune reaction such as interferon response, complement and inflammatory responses. In addition, a nomogram including age, gender, IPI score and risk score was constructed to help explain the prognostic model. We also discovered the high-risk patients were more sensitive to some certain drugs. Finally, knocking out the NLE1 could inhibit the proliferation of DLBCL cell lines. Conclusion: As far as we know, it is the first time to predict the prognosis of DLBCL using the RibGs and give a new sight for DLBCL treatment. Importantly, the RibGs model could be acted as a supplementary to the IPI in classifying the risk of DLBCL patients.

Room temperature fabrication of magnetic covalent organic frameworks for efficient enrichment of parabens in water.

A novel 4 + 2 covalent magnetic organic framework (COF) with core-shell structure was synthesized for the first time with N, N, N', N'-Tetrakis (4-aminophenyl)-1, 4- benzenediamine (TPDA) and 2, 6-Pyridinedicarboxaldehyde (PCBA) at room temperature. The synthesized magnetic TPDA-PCBA-COF has a large specific surface area and superparamagnetism, which makes it an ideal sorbent for trace analytes enrichment. To this end, we combined it with magnetic solid phase extraction (MSPE) to enrich trace parabens in environmental water. The parameters affecting the enrichment efficiency of magnetic solid phase extraction, such as the amount of Fe3O4@TPDA-PCBA-COF, extraction time, pH of samples, salt concentration, desorption solvent volume and desorption time, were optimized. A simple method for extraction and determination of parabens in water samples by MSPE combined with high performance liquid chromatography (HPLC) was established under optimized conditions. The validation results revealed that the linear ranges were at 1.0-5.0 × 102 ng mL-1 with R value between 0.9915 and 0.9999, the spiked recoveries were in the range of 82.8% to 99.9% and RSDs were lower than 10%. The method was further applied to the determination of parabens in water samples, with recoveries in the range of 82.2% to 110.0% and RSDs ≤ 7.7%. These results suggest that the magnetic TPDA-PCBA-COF could be used as a promising adsorbent for efficient extraction and quantitation of parabens in environmental water samples.

Fabrication of a core-shell porphyrin-based magnetic covalent organic framework for effective extraction of PCPs in a wide polarity range.

A novel porphyrin-based magnetic covalent organic framework (PCOF) was first reported by using a facile synthetic procedure. The Fe3O4@NH2@PCOF nanospheres were utilized to effectively extract personal care products in a wide polarity range (log Kow values from 1.96 to 7.60). The successful magnetic solid-phase extraction (MSPE) of target analytes could be ascribed to the sufficient oxygen-, nitrogen- and phenyl-containing functional groups of the COF layer, which are demonstrated to be of good compatibility with pollutants exhibiting different polarities by using molecular dynamics simulations, independent gradient model analysis and various characterizations. The MSPE extraction efficiency was enhanced by optimizing key parameters. The findings indicated that the method had a wide linearity range (1-500 ng mL-1 for parabens and UV filters) and low detection limits (0.4-0.9 ng mL-1 for parabens and 0.2-0.6 ng mL-1 for UV filters). The accuracy was reflected by recoveries ranging from 74% to 114%. Satisfactory intra- and inter-day precisions from 3.0% to 9.8% and 0.5%-9.1% were obtained. Overall, the proposed MSPE-HPLC method is accurate and reliable for identifying parabens as well as UV filters in wastewater and swimming pool water. The potential of the method for evaluating human exposure risk was unfolded.

Evolutionary Characteristics and Immunologic Divergence of Lung and Brain Metastasis Lesions in NSCLC.

Brain metastases (BM) is one of the main reasons for lung cancer-related deaths but lack prediction methods. Many patients with BMs do not benefit from immunotherapy. A comprehensive genomic analysis of matched primary tumors (PT) and their BM lesions may provide new insight into the evolutionary and immune characteristics. To describe evolutionary features and immune characteristic differences, we analyzed whole-exome sequencing data for 28 paired PT and BM samples from 14 patients with non-small cell lung cancer. In addition, we used another 26 matched PT and BM samples as a validation cohort. We found that total mutational signatures were relatively consistent between paired primary and brain metastatic tumors. Nevertheless, the shared mutations of the two lesions were fewer than the mutations present in each of the lesions alone. In the process of BM, driver genes undergo evolutionary branches. Typical driver genes, including EGFR and TP53, appear relatively conserved throughout evolution; however, specific signals are enriched in BM lesions. We found several main characteristics of lung cancer BMs that were different from primary lung cancer, such as genomic instability, novel driver genes, tumor mutation burden, and BM lesion private neoantigens. In addition, the estimated timing of dissemination showed that BMs might occur early in lung cancer. IMPLICATIONS: Mechanistic insight from this study provides new insight into the biology of the metastatic brain process and a new beneficial approach for preventing and treating lung cancer BMs.

[Analysis of parabens in environmental water samples by covalent organic framework-based magnetic solid-phase extraction-high performance liquid chromatography].

Parabens are a class of antimicrobial preservatives that are widely used in cosmetics, pharmaceuticals, and food products because of their ease of production, antimicrobial effect, and low price. The widespread use of these parabens, poses potential risks to human health. Therefore, it is necessary to establish a simple and rapid method for the detection of parabens. The large number of substrate interferences in complex samples is an important factor affecting the sensitivity of analytical methods. Magnetic solid-phase extraction (MSPE) has received much attention because of its advantages of easy operation, short extraction time, small sample amount, low cost, and environmental friendliness. Covalent organic frameworks (COFs) with high crystallinity, high specific surface area, adjustable pore size, regular porosity, as well as high chemical and thermal stability are now widely used in separation and analysis. Therefore, a sample pretreatment method combining MSPE and COF for the analysis of parabens in complex matrices is very promising. A magnetic covalent organic framework, Fe3O4@TbBd, was successfully synthesized by the Schiff base reaction of 1,3,5-triformylbenzene (Tb) and benzidine (Bd) at room temperature using Fe3O4 nanoparticles as magnetic cores. Characterization by scanning electron microscopy (SEM), thermogravimetric analysis (TGA), X-ray diffraction (XRD), vibrating sample magnetometer (VSM) measurements, etc. revealed that the magnetic COF has high magnetic responsiveness, as well as good thermal and chemical stability, which make it an ideal adsorbent for the MSPE of parabens. Some factors related to the extraction efficiency, including the amount of adsorbent, extraction time, pH, desorption solvent, desorption time, and number of desorption were systematically investigated. A method involving MSPE and high performance liquid chromatography-ultraviolet detection (HPLC-UV) based on the Fe3O4@TbBd was developed for the determination of four parabens (ethylparaben, propylparaben, butylparaben, and benzylparaben) in environmental water samples. Under the optimal extraction conditions, the method showed good linearities. The limits of detection and limits of quantification were 0.2-0.4 µg/L and 0.7-1.4 µg/L for the four analytes, respectively. The recoveries at three spiked levels were in the range of 86.1%-110.8% with intra-day and inter-day RSDs of less than 5.5% and 4.9%, respectively. The method was successfully applied to the determination of parabens in East Lake water, Yangtze water, and domestic wastewater. Ethyl paraben and propyl paraben were detected in domestic wastewater at the levels of 1.8 µg/L and 0.4 µg/L, respectively. The recoveries of the parabens at different spiked levels ranged from 80.7% to 117.5%, with RSDs of 0.2%-8.8%. The method has good potential for the determination of parabens in environmental water samples because of its operational simplicity, short extraction time, high sensitivity, and environmental friendliness.

A Novel Defined Super-Enhancer Associated Gene Signature to Predict Prognosis in Patients With Diffuse Large B-Cell Lymphoma.

Background: Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous disease that can have profound differences in survival outcomes. A variety of powerful prognostic factors and models have been constructed; however, the development of more accurate prognosis prediction and targeted treatment for DLBCL still faces challenges. An explosion of research on super-enhancer (SE)-associated genes provide the possibility to use in prognostication for cancer patients. Here, we aimed to establish a novel effective prognostic model using SE-associated genes from DLBCL. Methods: A total of 1,105 DLBCL patients from the Gene Expression Omnibus database were included in this study and were divided into a training set and a validation set. A total of 11 SE-associated genes (BCL2, SPAG16, PXK, BTG1, LRRC37A2, EXT1, TGFBR2, ANKRD12, MYCBP2, PAX5, and MYC) were initially screened and identified by the least absolute shrinkage and selection operator (Lasso) penalized Cox regression, univariate and multivariate Cox regression analysis. Finally, a risk score model based on these 11 genes was constructed. Results: Kaplan-Meier (K-M) curves showed that the low-risk group appeared to have better clinical survival outcomes. The excellent performance of the model was determined via time-dependent receiver operating characteristic (ROC) curves. A nomogram based on the polygenic risk score was further established to promote reliable prognostic prediction. This study proposed that the SE-associated-gene risk signature can effectively predict the response to chemotherapy in DLBCL patients. Conclusion: A novel and reliable SE-associated-gene signature that can effectively classify DLBCL patients into high-risk and low-risk groups in terms of overall survival was developed, which may assist clinicians in the treatment of DLBCL.

Immunophenotypic Landscape and Prognosis-Related mRNA Signature in Diffuse Large B Cell Lymphoma.

Diffuse large B cell lymphoma (DLBCL) exhibits a tightly complexity immune landscape. In this study, we intended to identify different immune phenotype and to examine the immune related mRNA signature for clinical characteristic, therapeutic responsiveness as well as risk stratification and survival prediction in DLBCL. We identified two immune infiltration subtypes of DLBCL patients based on 28 immune cell types. GSEA analysis uncovered the concordant classification of two robust significant subtypes of DLBCL. Considering the convenient application of the immune infiltration subtypes for prognostic prediction, we developed a risk score based on the differentially expressed genes between the Immunity-H and Immunity-L groups. By a least absolute shrinkage and selection operator (LASSO)-Cox regression model, a sixteen-gene risk signature, comprising ANTXR1, CD3D, TIMP1, FPR3, NID2, CTLA4, LPAR6, GPR183, LYZ, PTGDS, ITK, FBN1, FRMD6, PLAU, MICAL2, C1S, was established. The comprehensive results showed that the high-risk group was correlated with lower immune infiltration, more aggressive phenotypes, lower overall survival and more sensitive to lenalidomide. In contrast, a low-risk group score was associated with higher immune infiltration, less aggressive phenotypes, better overall survival and more likely to benefit from PD-1/PD-L1 inhibitors. Finally, a nomogram comprised of the risk score and IPI score was verified to more accurately predict the overall survival of DLBCL than traditional clinical prediction models. Altogether, our data demonstrate the heterogeneity of immune patterns within DLBCL and deepen our molecular understanding of this tumor entity.

Efficient activation of peroxymonosulfate mediated by Co(II)-CeO2 as a novel heterogeneous catalyst for the degradation of refractory organic contaminants: Degradation pathway, mechanism and toxicity assessment.

A series of Co(II)-CeO2 mixed metal oxides were synthesized by a facile hydrothermal-calcination procedure for activating peroxymonosulfate (PMS) and degrading toxic and difficult biodegradable organics. Co(II)-CeO2 showed excellent degradation performance toward rhodamine B (RhB), toluidine blue, methylene blue and diclofenac. RhB is a refractory organic contaminant, and ecotoxicological evaluation unraveled its harmfulness to the biosphere. RhB was selected as the model pollutant to investigate catalytic mechanisms. Parameters affecting degradation performance were profoundly investigated, including Co:Ce feed ratio, initial pH, PMS dosage, catalyst dosage, RhB concentration, coexisting ions and reaction temperature. Reaction mechanisms were proposed based on density functional theory calculations and identifications of reactive oxygen species. Improvements have been achieved in seven aspects compared to previous studies, including 100% degradation ratio in both real water samples and each reuse of the catalyst, ultrafast degradation rate, cost-effectiveness of the catalyst, toxicity-attenuation provided by the developed degradation method, high degree of mineralization for the model pollutant, negligible leaching of active sites, and the enhancement of catalytic performance by utilizing trace leached cobalt, endowing the technique with broad applicability and prospect.

The efficiency of autologous stem cell transplantation as the first-line treatment for nodal peripheral T-cell lymphoma: results of a systematic review and meta-analysis.

BACKGROUND: Nodal peripheral T cell lymphoma (PTCL) confers a dismal prognosis when treated with conventional chemotherapy. Autologous stem cell transplantation (ASCT) seems a reasonable alternative in eligible patients. Nevertheless, a consensus on the role of ASCT as the first-line consolidation therapy for nodal PTCL patients has not been reached so far. METHODS: A quantitative meta-analysis was performed via a systematic search in PubMed, Web of Science, Embase, and The Cochrane Library. The overall survival (OS), progression-free survival (PFS), hazard ratio (HR), and 95% confidence intervals (CIs) were compared and calculated from database inception to September 2021. RESULTS: Twelve articles were eligible. The results showed that ASCT could improve the survival of patients compared with chemotherapy alone. In terms of subtype analysis, results showed that angioimmunoblastic T cell lymphoma (AITL) patients could benefit more from chemotherapy followed by ASCT. Statistical differences were also confirmed for OS and PFS in different remission status, clinical stage, performance status (PS), chemotherapy regimen, and gender. CONCLUSION: ASCT could serve as the first-line consolidation treatment strategy for nodal PTCL patients, especially AITL patients. Early clinical stage, good PS status, CR before transplantation, CHOEP regimen, and female patients may indicate a better outcome.

Efficacy of chimeric antigen receptor T cell therapy and autologous stem cell transplant in relapsed or refractory diffuse large B-cell lymphoma: A systematic review.

Background: We aimed to compare the efficacy of chimeric antigen receptor T (CAR-T) cell therapy with that of autologous stem cell transplantation (auto-HSCT) in relapsed/refractory diffuse large B cell lymphoma (R/R DLBCL). Research design and methods: We searched eligible publications up to January 31st, 2022, in PubMed, Cochrane Library, Springer, and Scopus. A total of 16 publications with 3484 patients were independently evaluated and analyzed using STATA SE software. Results: Patients who underwent CAR-T cell therapy showed a better overall response rate (ORR) and partial response (PR) than those treated with auto-HSCT (CAR-T vs. auto-HSCT, ORR: 80% vs. 73%, HR:0.90,95%CI:0.76-1.07,P = 0.001; PR: 20% vs. 14%, HR:0.65,95%CI:0.62-0.68,P = 0.034). No significant difference was observed in 6-month overall survival (OS) (CAR-T vs. auto-HSCT, six-month OS: 81% vs. 84%, HR:1.23,95%CI:0.63-2.38, P = 0.299), while auto-HSCT showed a favorable 1 and 2-year OS (CAR-T vs. auto-HSCT, one-year OS: 64% vs. 73%, HR:2.42,95%CI:2.27-2.79, P < 0.001; two-year OS: 54% vs. 68%, HR:1.81,95%CI:1.78-1.97, P < 0.001). Auto-HSCT also had advantages in progression-free survival (PFS) (CAR-T vs. auto-HSCT, six-month PFS: 53% vs. 76%, HR:2.81,95%CI:2.53-3.11,P < 0.001; one-year PFS: 46% vs. 61%, HR:1.84,95%CI:1.72-1.97,P < 0.001; two-year PFS: 42% vs. 54%, HR:1.62,95%CI:1.53-1.71, P < 0.001). Subgroup analysis by age, prior lines of therapy, and ECOG scores was performed to compare the efficacy of both treatment modalities. Conclusion: Although CAR-T cell therapy showed a beneficial ORR, auto-HSCT exhibited a better long-term treatment superiority in R/R DLBCL patients. Survival outcomes were consistent across different subgroups.

Identification of microtubule-associated biomarkers in diffuse large B-cell lymphoma and prognosis prediction.

Background: Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous disease with a complicated prognosis. Even though various prognostic evaluations have been applied currently, they usually only use the clinical factors that overlook the molecular underlying DLBCL progression. Therefore, more accurate prognostic assessment needs further exploration. In the present study, we constructed a novel prognostic model based on microtubule associated genes (MAGs). Methods: A total of 33 normal controls and 1360 DLBCL samples containing gene-expression from the Gene Expression Omnibus (GEO) database were included. Subsequently, the univariate Cox, the least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analysis were used to select the best prognosis related genes into the MAGs model. To validate the model, Kaplan-Meier curve, and nomogram were analyzed. Results: A risk score model based on fourteen candidate MAGs (CCDC78, CD300LG, CTAG2, DYNLL2, MAPKAPK2, MREG, NME8, PGK2, RALBP1, SIGLEC1, SLC1A1, SLC39A12, TMEM63A, and WRAP73) was established. The K-M curve presented that the high-risk patients had a significantly inferior overall survival (OS) time compared to low-risk patients in training and validation datasets. Furthermore, knocking-out TMEM63A, a key gene belonging to the MAGs model, inhibited cell proliferation noticeably. Conclusion: The novel MAGs prognostic model has a well predictive capability, which may as a supplement for the current assessments. Furthermore, candidate TMEM63A gene has therapeutic target potentially in DLBCL.