Fatty acid metabolism-related lncRNA prognostic signature for serous ovarian carcinoma.

Background: To explore the role of fatty acid metabolism (FAM)-related lncRNAs in the prognosis and antitumor immunity of serous ovarian cancer (SOC). Materials & methods: A SOC FAM-related lncRNA risk model was developed and evaluated by a series of analyses. Additional immune-related analyses were performed to further assess the associations between immune state, tumor microenvironment and the prognostic risk model. Results: Five lncRNAs associated with the FAM genes were found and used to create a predictive risk model. The patients with a low-risk profile exhibited favorable prognostic outcomes. Conclusion: The established prognostic risk model exhibits better predictive capabilities for the prognosis of patients with SOC and offers novel potential therapy targets for SOC.

Fluorescence detecting glycopeptide antibiotics via a dynamic molecular switch.

BACKGROUND: Glycopeptide antibiotics (GPAs) represented by vancomycin (VAN) are clinically used as a first-line treatment for serious infections caused by Gram-positive pathogens. The use and dosing methods of GPAs are rigorously managed for safety considerations, which calls for fast and accurate quantification approaches. RESULT: A new sort of fluorescent probes for GPAs has been proposed, each of which was integrated by a fluorescein-based reporter and a GPAs' recognition peptide D-alanyl-D-alanine (D-Ala-D-Ala). These probes work as dynamic molecular switches, which mainly exist as non-fluorescent spirolactam forms in the absence of GPAs. GPAs binding with the dipeptide regulates the dynamic balance between fluorescence OFF lactam form and fluorescence ON ring-opened form, rendering these probes capable of GPAs detecting. The most promising one P1 exhibits excellent sensitivity and selectivity towards GPAs detection. SIGNIFICANCE: Different to previous developments, P1 consists of a single fluorophore without the need of a fluorescence-quenching group or a secondary dye, which is the smallest fluorescent probe for GPAs up to now. P1 realizes direct VAN quantification from complex biological samples including real serums, dispensing with additional drug extraction. More interestingly, both P1 and P6 can distinguish GPAs with different peptide backbones, which has not been achieved previously.

Exploring Deep Learning for Estimating the Isoeffective Dose of FLASH Irradiation From Mouse Intestinal Histological Images.

PURPOSE: Ultrahigh-dose-rate (FLASH) irradiation has been reported to reduce normal tissue damage compared with conventional dose rate (CONV) irradiation without compromising tumor control. This proof-of-concept study aims to develop a deep learning (DL) approach to quantify the FLASH isoeffective dose (dose of CONV that would be required to produce the same effect as the given physical FLASH dose) with postirradiation mouse intestinal histology images. METHODS AND MATERIALS: Eighty-four healthy C57BL/6J female mice underwent 16 MeV electron CONV (0.12 Gy/s; n = 41) or FLASH (200 Gy/s; n = 43) single fraction whole abdominal irradiation. Physical dose ranged from 12 to 16 Gy for FLASH and 11 to 15 Gy for CONV in 1 Gy increments. Four days after irradiation, 9 jejunum cross-sections from each mouse were hematoxylin and eosin stained and digitized for histological analysis. CONV data set was randomly split into training (n = 33) and testing (n = 8) data sets. ResNet101-based DL models were retrained using the CONV training data set to estimate the dose based on histological features. The classical manual crypt counting (CC) approach was implemented for model comparison. Cross-section-wise mean squared error was computed to evaluate the dose estimation accuracy of both approaches. The validated DL model was applied to the FLASH data set to map the physical FLASH dose into the isoeffective dose. RESULTS: The DL model achieved a cross-section-wise mean squared error of 0.20 Gy2 on the CONV testing data set compared with 0.40 Gy2 of the CC approach. Isoeffective doses estimated by the DL model for FLASH doses of 12, 13, 14, 15, and 16 Gy were 12.19 ± 0.46, 12.54 ± 0.37, 12.69 ± 0.26, 12.84 ± 0.26, and 13.03 ± 0.28 Gy, respectively. CONCLUSIONS: Our proposed DL model achieved accurate CONV dose estimation. The DL model results indicate that in the physical dose range of 13 to 16 Gy, the biologic dose response of small intestinal tissue to FLASH irradiation is represented by a lower isoeffective dose compared with the physical dose. Our DL approach can be a tool for studying isoeffective doses of other radiation dose modifying interventions.

ART2Dose: A comprehensive dose verification platform for online adaptive radiotherapy.

BACKGROUND: Online adaptive radiotherapy (ART) involves the development of adaptable treatment plans that consider patient anatomical data obtained right prior to treatment administration, facilitated by cone-beam computed tomography guided adaptive radiotherapy (CTgART) and magnetic resonance image-guided adaptive radiotherapy (MRgART). To ensure accuracy of these adaptive plans, it is crucial to conduct calculation-based checks and independent verification of volumetric dose distribution, as measurement-based checks are not practical within online workflows. However, the absence of comprehensive, efficient, and highly integrated commercial software for secondary dose verification can impede the time-sensitive nature of online ART procedures. PURPOSE: The main aim of this study is to introduce an efficient online quality assurance (QA) platform for online ART, and subsequently evaluate it on Ethos and Unity treatment delivery systems in our clinic. METHODS: To enhance efficiency and ensure compliance with safety standards in online ART, ART2Dose, a secondary dose verification software, has been developed and integrated into our online QA workflow. This implementation spans all online ART treatments at our institution. The ART2Dose infrastructure comprises four key components: an SQLite database, a dose calculation server, a report generator, and a web portal. Through this infrastructure, file transfer, dose calculation, report generation, and report approval/archival are seamlessly managed, minimizing the need for user input when exporting RT DICOM files and approving the generated QA report. ART2Dose was compared with Mobius3D in pre-clinical evaluations on secondary dose verification for 40 adaptive plans. Additionally, a retrospective investigation was conducted utilizing 1302 CTgART fractions from ten treatment sites and 1278 MRgART fractions from seven treatment sites to evaluate the practical accuracy and efficiency of ART2Dose in routine clinical use. RESULTS: With dedicated infrastructure and an integrated workflow, ART2Dose achieved gamma passing rates that were comparable to or higher than those of Mobius3D. Additionally, it significantly reduced the time required to complete pre-treatment checks by 3-4 min for each plan. In the retrospective analysis of clinical CTgART and MRgART fractions, ART2Dose demonstrated average gamma passing rates of 99.61 ± 0.83% and 97.75 ± 2.54%, respectively, using the 3%/2 mm criteria for region greater than 10% of prescription dose. The average calculation times for CTgART and MRgART were approximately 1 and 2 min, respectively. CONCLUSION: Overall, the streamlined implementation of ART2Dose notably enhances the online ART workflow, offering reliable and efficient online QA while reducing time pressure in the clinic and minimizing labor-intensive work.

Invasive stratified mucin-producing carcinoma (ISMC) of the cervix: a clinicopathological and molecular analysis of 59 cases with special emphasis on histogenesis and potential therapeutic targets.

AIMS: This study aimed to better characterize the clinical and molecular features in invasive stratified mucin-producing carcinoma (ISMC), an uncommon aggressive subtype of endocervical adenocarcinoma (EAC). METHODS AND RESULTS: We recruited 59 ISMC for clinicopathological analysis, immunohistochemistry (n = 56), and targeted next-generation sequencing (n = 17). Our cases contained 29 pure and 30 mixed-type ISMC. Five patients developed local recurrence at 6-32 months (median: 13 months), and died of disease at 16-55 months (median: 16 months). Pure and mixed-type ISMC showed no significant difference in overall survival and tumour relapse (P > 0.05) except larger tumour size in the pure-type (P = 0.009). Compared to the usual-type EAC (n = 217), ISMsC were more frequently associated with large tumour size (P = 0.003), advanced FIGO stage (P = 0.017), lymph node metastasis (P = 0.022), Silva pattern C (P < 0.001), and poor overall survival and short tumour recurrence. SOX2 expression was observed in 82.1% (46/56) ISMC, substantially higher than p63 expression (P < 0.001), while positive SOX17 was present in 3.6% (2/56) cases. PD-L1 was positive in 41/56 ISMC (73.21%) (combined positive score: range: 1-92, median: 22). Three ISMC patients (17.65%) had PIK3CA mutations, while one each (5.88%) patient harboured an ERBB2, TP53, STK11, and PTEN mutation, respectively. CONCLUSION: We conclude that ISMC is clinically more aggressive than the usual-type EAC. ISMC may originate from cervical reserve cells with bidirectional differentiation. PD-L1 overexpression and the molecular profiles raise the possibility that a subset of ISMC patients may benefit from anti-PD-L1 immunotherapy and other targeted therapy, such as mTOR inhibitor and T-DM1.

Epidemiology Characteristics and Potential Clinical Value of Vulvar Human Papillomavirus in Chinese Women: A Multicenter Cross-Sectional Study.

CONTEXT.­: Noninvasive self-sampling is a convenient option that may be highly accepted by women for home-based detection, which could increase the screening rate for cervical cancer (CC) and reduce its incidence and mortality. OBJECTIVE.­: To compare the distribution of high-risk human papillomavirus (hr-HPV) between the vulva and cervix and to explore the clinical value of vulvar HPV detection in CC screening. DESIGN.­: The study was nested within a clinical trial on recombinant HPV 9-valent vaccine for women ages 20 to 45 years. Women with paired vulvar and cervical specimens were included and received cytology and HPV detection. The consistency of HPV detection between vulvar and cervical specimens was evaluated using Cohen κ statistics. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were used to evaluate the diagnostic accuracy of primary CC screening. The primary end points were cervical intraepithelial neoplasia (CIN) grade 2/3 or worse (CIN2+/3+). RESULTS.­: A total of 7999 women were enrolled, and 83/33 cases were diagnosed as CIN2+/CIN3+. The HPV-positive rate in vulvar specimens (1785 of 7999; 22.32%) was higher than that in cervical specimens (1390 of 7999; 17.38%), and there were no significant differences in the distribution of hr-HPV genotypes between the vulva and cervix in patients with CIN2+/CIN3+. Vulva-based HPV primary screening showed sensitivity, specificity, PPV, and NPV comparable to those for cervix-based HPV primary CC screening in the detection of CIN3+. CONCLUSIONS.­: The distribution of vulvar and cervical HPV was similar in patients with CIN2+/CIN3+. Vulva-based HPV primary CC screening had acceptable diagnostic efficacy and might be used as a modality for primary CC screening.

Comprehensive analysis of HDAC7 expression and its prognostic value in diffuse large B cell lymphoma: A review.

HDAC7 loss or dysregulation may lead to B cell-based hematological malignancies. This study aimed to explore the prognostic value of HDAC7 in patients with diffuse large B cell lymphoma (DLBCL). RNA sequencing data and clinical information for HDAC7 in DLBCL were collected from the cancer genome atlas database and analyzed using R software. Paired t and Mann-Whitney U tests were used to detect differences between DLBCL and adjacent normal tissues, and the pROC software package was used to generate receiver operator characteristic curves to detect cutoff values for HDAC7. Data from paraffin-embedded specimens from the 2 groups were used for validation of external immunohistochemical staining. The tumor immunity estimation resource and integrated repository portal for tumor immune system interactions databases were used to analyze the correlation between HDAC7 and DLBCL immune cell infiltration. Survival analysis of HDAC7 in patients with DLBCL was performed using the PrognoScan database. Compared with that in normal tissues, HDAC7 mRNA was overexpressed in DLBCL. The HDAC7 immunohistochemical staining scores of stage III and IV DLBCL patients were significantly lower than those of stage I and II DLBCL patients, which was associated with shorter overall survival and disease-specific survival. In addition, the higher expression of HDAC7 may play a role in the lower level of immune infiltration in DLBCL. Downregulation of HDAC7 expression was correlated with poor prognosis and immune infiltration in DLBCL patients.

PINK1-PTEN axis promotes metastasis and chemoresistance in ovarian cancer via non-canonical pathway.

BACKGROUND: Ovarian cancer is commonly associated with a poor prognosis due to metastasis and chemoresistance. PINK1 (PTEN-induced kinase 1) is a serine/threonine kinase that plays a crucial part in regulating various physiological and pathophysiological processes in cancer cells. METHODS: The ATdb database and "CuratedOvarianData" were used to evaluate the effect of kinases on ovarian cancer survival. The gene expression in ovarian cancer cells was detected by Western blot and quantitative real-time PCR. The effects of gene knockdown or overexpression in vitro were evaluated by wound healing assay, cell transwell assay, immunofluorescence staining, immunohistochemistry, and flow cytometry analysis. Mass spectrometry analysis, protein structure analysis, co-immunoprecipitation assay, nuclear-cytoplasmic separation, and in vitro kinase assay were applied to demonstrate the PINK1-PTEN (phosphatase and tensin homolog) interaction and the effect of this interaction. The metastasis experiments for ovarian cancer xenografts were performed in female BALB/c nude mice. RESULTS: PINK1 was strongly associated with a poor prognosis in ovarian cancer patients and promoted metastasis and chemoresistance in ovarian cancer cells. Although the canonical PINK1/PRKN (parkin RBR E3 ubiquitin protein ligase) pathway showed weak effects in ovarian cancer, PINK1 was identified to interact with PTEN and phosphorylate it at Serine179. Remarkably, the phosphorylation of PTEN resulted in the inactivation of the phosphatase activity, leading to an increase in AKT (AKT serine/threonine kinase) activity. Moreover, PINK1-mediated phosphorylation of PTEN impaired the nuclear import of PTEN, thereby enhancing the cancer cells' ability to resist chemotherapy and metastasize. CONCLUSIONS: PINK1 interacts with and phosphorylates PTEN at Serine179, resulting in the activation of AKT and the inhibition of PTEN nuclear import. PINK1 promotes ovarian cancer metastasis and chemotherapy resistance through the regulation of PTEN. These findings offer new potential therapeutic targets for ovarian cancer management.

Pan-cancer tRNA-derived fragment CAT1 coordinates RBPMS to stabilize NOTCH2 mRNA to promote tumorigenesis.

Transfer RNA-derived fragments (tRFs) are a class of small non-coding regulatory RNAs that are involved in the pathophysiology of many diseases. However, the role of tRFs in cancer progression remains largely elusive. Here, we demonstrate that a pan-cancer 3'-tRF, CAT1 (cancer associated tRF 1), is ubiquitously upregulated in tumors and associated with poor prognosis of a variety of cancers, including lung cancer. The upregulated CAT1 in cancer cells binds to RNA-binding protein with multiple splicing (RBPMS) and displaces NOTCH2 association from RBPMS, thereby inhibiting the subsequent CCR4-NOT deadenylation-complex-mediated NOTCH2 mRNA decay. The CAT1-enhanced NOTCH2 expression promotes lung cancer cell proliferation and metastasis in vitro and in vivo. In addition, plasma CAT1 levels are substantially increased in patients with lung cancer compared to non-cancer control subjects. Our findings reveal an intrinsic connection between cancer-specific upregulation of CAT1 and cancer progression, show the regulation of NOTCH signaling in cancer by a 3'-tRF, and highlight its great clinical potential.

Radical Hysterectomy with Preoperative Conization in Early-stage Cervical Cancer: A Systematic Review and Pairwise and Network Meta-analysis.

OBJECTIVE: The investigation of the role of preoperative conization in cervical cancer aiming to explore its potential clinical significance. DATA SOURCES: Cochrane Library, Embase, PubMed, and Web of Science, up to April 28, 2023. METHODS OF STUDY SELECTION: (1) Observational cohort studies, (2) studies comparing radical hysterectomy with preoperative conization (CO) vs radical hysterectomy without preoperative conization (NCO) in patients with early-stage cervical cancer, and (3) studies comparing disease-free survival outcomes. TABULATION, INTEGRATION, AND RESULTS: Two reviewers independently extracted the data and assessed the quality of the studies. The meta-analysis used combined hazard ratios along with their corresponding 95% confidence intervals to compare CO and NCO. We conducted a Bayesian network meta-analysis using Markov chain Monte Carlo methods to compare minimally invasive CO, open CO, minimally invasive NCO, and open NCO. Our study included 15 retrospective trials, 10 of which were used to traditional pairwise meta-analysis and 8 for network meta-analysis. The NCO group exhibited a notably higher probability of cancer recurrence than the CO group (hazard ratio, 0.52; 95% confidence interval, 0.41-0.65). In the network meta-analysis, minimally invasive NCO showed the worst survival outcome. CONCLUSION: Preoperative conization seems to be a protective factor in decreasing recurrence risk, assisting clinicians in predicting survival outcomes for patients with early-stage cervical cancer. It may potentially aid in selecting suitable candidates for minimally invasive surgery in clinical practice.

Second curettage versus conventional chemotherapy in avoiding unnecessary chemotherapy and reducing the number of chemotherapy courses for patients with gestational trophoblastic neoplasia: A systematic review and meta-analysis.

BACKGROUND: Chemotherapy is the recommended treatment for gestational trophoblastic neoplasia (GTN). Second curettage had been advocated to avoid unnecessary chemotherapy and to reduce the courses of chemotherapy; however, consensus has not been reached as there are arguments claiming its inability of inducing complete regression. OBJECTIVES: The present study was performed to clarify the effectiveness of second curettage for avoiding unnecessary chemotherapy and lowering the number of chemotherapy courses in patients with post-molar GTN. SEARCH STRATEGY: Seven predominant electronic databases were searched, including four English databases and three Chinese databases, from the inception of each database until January 31, 2023. SELECTION CRITERIA: Studies were included if they were: (1) human, (2) explicitly indicated exposure to second curettage, (3) explicitly indicated control to conventional chemotherapy, (4) explicitly indicated the participants were patients with gestational trophoblastic neoplasia (GTN), and (5) compared the outcome of interest as the number of the course of chemotherapy. DATA COLLECTION AND ANALYSIS: Two authors extracted and analyzed the data independently. Disagreements were reconciled by reviewing the full text by a third author. The data of study location, data collection, study design, number of participants, intervention strategy, control strategy, the follow-up period, outcome, adverse events were analyzed. MAIN RESULTS: With regard to avoiding unnecessary chemotherapy, the overall pooled effect size of the second curettage group had a significant advantage over the conventional chemotherapy group with an OR of 0.02 (95% CI: 0.00-0.06). Meanwhile, for reducing the number of chemotherapy courses, the overall pooled effect size of the second curettage group had significant advantage over the conventional chemotherapy group with a mean difference of -2.11 (95% CI: -3.72 to -0.51). CONCLUSION: The second curettage group had a significant advantage over the conventional chemotherapy group in avoiding unnecessary chemotherapy and reducing the number of chemotherapy courses. Further larger multi-center randomized controlled trials should be conducted to confirm our results and to clarify the optimal patients' group for second curettage in patients with post-molar GTN.

Leveraging global binary masks for structure segmentation in medical images.

Deep learning (DL) models for medical image segmentation are highly influenced by intensity variations of input images and lack generalization due to primarily utilizing pixels' intensity information for inference. Acquiring sufficient training data is another challenge limiting models' applications. Here, we proposed to leverage the consistency of organs' anatomical position and shape information in medical images. We introduced a framework leveraging recurring anatomical patterns through global binary masks for organ segmentation. Two scenarios were studied: (1) global binary masks were the only input for the U-Net based model, forcing exclusively encoding organs' position and shape information for rough segmentation or localization. (2) Global binary masks were incorporated as an additional channel providing position/shape clues to mitigate training data scarcity. Two datasets of the brain and heart computed tomography (CT) images with their ground-truth were split into (26:10:10) and (12:3:5) for training, validation, and test respectively. The two scenarios were evaluated using full training split as well as reduced subsets of training data. In scenario (1), training exclusively on global binary masks led to Dice scores of 0.77 ± 0.06 and 0.85 ± 0.04 for the brain and heart structures respectively. Average Euclidian distance of 3.12 ± 1.43 mm and 2.5 ± 0.93 mm were obtained relative to the center of mass of the ground truth for the brain and heart structures respectively. The outcomes indicated encoding a surprising degree of position and shape information through global binary masks. In scenario (2), incorporating global binary masks led to significantly higher accuracy relative to the model trained on only CT images in small subsets of training data; the performance improved by 4.3%-125.3% and 1.3%-48.1% for 1-8 training cases of the brain and heart datasets respectively. The findings imply the advantages of utilizing global binary masks for building models that are robust to image intensity variations as well as an effective approach to boost performance when access to labeled training data is highly limited.

WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean.

BACKGROUND: Soybean is one of the most important oil crops in the world. The domestication of wild soybean has resulted in significant changes in the seed oil content and seed size of cultivated soybeans. To better understand the molecular mechanisms of seed formation and oil content accumulation, WDD01514 (E1), ZYD00463 (E2), and two extreme progenies (E23 and E171) derived from RILs were used for weighted gene coexpression network analysis (WGCNA) combined with transcriptome analysis. RESULTS: In this study, both seed weight and oil content in E1 and E171 were significantly higher than those in E2 and E23, and 20 DAF and 30 DAF may be key stages of soybean seed oil content accumulation and weight increase. Pathways such as "Photosynthesis", "Carbon metabolism", and "Fatty acid metabolism", were involved in oil content accumulation and grain formation between wild and cultivated soybeans at 20 and 30 DAF according to RNA-seq analysis. A total of 121 oil content accumulation and 189 seed formation candidate genes were screened from differentially expressed genes. WGCNA identified six modules related to seed oil content and seed weight, and 76 candidate genes were screened from modules and network. Among them, 16 genes were used for qRT-PCR and tissue specific expression pattern analysis, and their expression-levels in 33-wild and 23-cultivated soybean varieties were subjected to correlation analysis; some key genes were verified as likely to be involved in oil content accumulation and grain formation. CONCLUSIONS: Overall, these results contribute to an understanding of seed lipid metabolism and seed size during seed development, and identify potential functional genes for improving soybean yield and seed oil quantity.

Prevalence of Helicobacter pylori Antibiotic Resistance in Patients Enrolled in Guangzhou, China.

Purpose: Helicobacter pylori (H. pylori) infection is a high-risk factor for the occurrence of gastric cancer. The quadruple therapy has been widely used as the first-line treatment for H. pylori in China. However, the increasing resistance rate to antibiotics has become a major challenge in the treatment of H. pylori. Therefore, there is an urgent need for rapid and cost-effective detection of antibiotic resistance to different antibiotics. To evaluate the prevalence of H. pylori antibiotic resistance in Guangzhou and the diagnostic performance of DOB value of 13C UBT in predicting antibiotic resistance. Patients and Methods: In this retrospective study, we collected data from 193 H. pylori culture-positive patients in Guangzhou on their DOB values and resistance to antibiotics. We analyzed the antibiotic resistance rate of commonly used antibiotics in quadruple therapy, and the diagnostic efficacy of DOB value was evaluated. Results: The resistance rates of clarithromycin (CLA) and levofloxacin (LEV) were 46.1% and 44.0%, respectively. In the age group under 40, the resistance rate of LEV was lower than that of CLA. However, the diagnostic efficacy of DOB value was found to be low and it could not serve as an independent indicator for diagnosing resistance to CLA and LEV. Conclusion: The high resistance rates of CLA and LEV in H. pylori patients in Guangzhou indicate the urgent need for effective detection methods. The DOB value is not a direct indicator of antibiotic resistance to CLA and LEV. Therefore, it is important to use a combination of diagnostic methods to accurately assess antibiotic resistance in H. pylori infection.

CircSLC39A8 attenuates paclitaxel resistance in ovarian cancer by regulating the miR­185­5p/BMF axis.

Chemoresistance to paclitaxel (PTX) is one of the main reasons for treatment failure and poor prognosis in patients with advanced ovarian cancer. Therefore, it is imperative to explore the mechanisms related to chemotherapy resistance in ovarian cancer to find potential therapeutic targets. Circular RNAs (circRNAs) play important roles in cancer development and progression. However, their biological functions and clinical significance in ovarian cancer have not been fully elucidated. Therefore, in this study, we aimed to investigate the function and underlying mechanism of hsa_circ_0002782 (circSLC39A8), identified by circRNA sequencing, in regulating PTX resistance. The effects of circSLC39A8 on PTX resistance was assessed by cell viability, colony formation, flow cytometry assays and an in vivo subcutaneous xenografted tumor mouse model. RNA immunoprecipitation and dual-luciferase reporter assays were performed to verify the interaction between circSLC39A8 and the miR-185-5p/BMF signal axis. We found that circSLC39A8 was downregulated in PTX-resistant ovarian cancer cells and tissues, and its low expression was associated with poor prognosis. Biologically, circSLC39A8 knockdown promoted PTX resistance in vitro and in vivo, while circSLC39A8 overexpression showed the opposite effect. Mechanistically, circSLC39A8, acting as an endogenous sponge for miR-185-5p, could relieve the inhibition of miR-185-5p on the expression of its downstream target, BMF; thus enhancing the sensitivity of ovarian cancer to PTX. Our findings demonstrate that circSLC39A8 can promote PTX sensitivity by regulating the miR-185-5p/BMF axis. This may be a valuable prognostic biomarker and a promising therapeutic target for patients with ovarian cancer.

Treatment With Niraparib Maintenance Therapy in Patients With Newly Diagnosed Advanced Ovarian Cancer: A Phase 3 Randomized Clinical Trial.

Importance: The efficacy of niraparib maintenance therapy with an individualized starting dose (ISD) warrants further investigation in a broad population with newly diagnosed advanced ovarian cancer (aOC), including patients without postoperative residual disease. Objective: To evaluate the efficacy and safety of niraparib with an ISD in a broad population with newly diagnosed aOC (R0 resection permitted). Design, Setting, and Participants: This multicenter, randomized, double-blind, placebo-controlled, phase 3 study was conducted in China and enrolled 384 patients with newly diagnosed aOC who received primary or interval debulking surgery and responded to treatment with first-line platinum-based chemotherapy. By data cutoff (September 30, 2021), median follow-up for progression-free survival (PFS) was 27.5 (IQR, 24.7-30.4) months. Interventions: Patients were randomized 2:1 to receive niraparib or placebo with ISD (200 mg/d for those with a body weight of <77 kg and/or platelet count of <150 ×103/µL [to convert to ×109/µL, multiply by 1] at baseline; 300 mg/d otherwise) stratified by germline BRCA variant status, tumor homologous recombination deficiency status, neoadjuvant chemotherapy, and response to first-line platinum-based chemotherapy. Main Outcomes and Measurements: The primary end point was blinded, independent central review-assessed PFS in the intention-to-treat population. Results: A total of 384 patients were randomized (255 niraparib [66.4%]; median [range] age, 53 [32-77] years; 129 placebo [33.6%]; median [range] age, 54 [33-77] years), and 375 (247 niraparib [65.9%], 128 placebo [34.1%]) received treatment at a dose of 200 mg per day. Median PFS with niraparib vs placebo was 24.8 vs 8.3 months (hazard ratio [HR], 0.45; 95% CI, 0.34-0.60; P < .001) in the intention-to-treat population; not reached vs 10.8 months (HR, 0.40; 95% CI, 0.23-0.68) and 19.3 vs 8.3 months (HR, 0.48; 95% CI, 0.34-0.67) in patients with and without germline BRCA variants, respectively; not reached vs 11.0 months (HR, 0.48; 95% CI, 0.34-0.68) and 16.6 vs 5.5 months (HR, 0.41; 95% CI, 0.22-0.75) in homologous recombination deficient and proficient patients, respectively; and 24.8 vs 8.3 months (HR, 0.44; 95% CI, 0.32-0.61) and 16.5 vs 8.3 months (HR, 0.27; 95% CI, 0.10-0.72) in those with optimal and suboptimal debulking, respectively. Similar proportions of niraparib-treated and placebo-treated patients (6.7% vs 5.4%) discontinued treatment due to treatment-emergent adverse events. Conclusion and Relevance: This randomized clinical trial found that niraparib maintenance therapy prolonged PFS in patients with newly diagnosed aOC regardless of postoperative residual disease or biomarker status. The ISD was effective and safe in the first-line maintenance setting. Trial Registration: ClinicalTrials.gov Identifier: NCT03709316.

Comprehensive analysis and establishment of a prognostic model based on non-genetic predictors in multiple myeloma.

BACKGROUND: Multiple myeloma (MM) is a systemic hematological malignancy usually incurable. The value of some important prognostic factors may gradually decrease. OBJECTIVE: We aimed to explore the non-genetic indexes, prognostic models, and significance of clinical staging systems of MM. METHODS: A retrospective analysis was conducted on clinical data from 110 patients with MM who first visit the First Affiliated Hospital of Guangzhou Medical University between September 2005 to December 2018. RESULTS: Bone marrow plasma cell percentage (BMPC%), cystatin C (CysC), and ß2 microglobulin (ß2-MG) were positively correlated with Durie-Salmon (D-S) and international staging system (ISS) stages, while red blood cell count (RBC) and hemoglobin volume (HGB) were negatively correlated (P< 0.05). Univariate analysis showed that ISS stage, treatment protocol, immunofixation electrophoresis (IFE), ratio of red cell distribution width to platelet count (RPR), monocyte count (MONO), lactate dehydrogenase, and immunoglobulin G were significantly associated with the three-year overall survival (OS). IFE, treatment protocol, and ß2-MG significantly affected progression-free survival (P< 0.05). Multivariate analysis showed that the treatment protocol, ISS stage, RPR, MONO, and IFE were independent prognostic factors for three-year OS (P< 0.05). CONCLUSIONS: BMPC%, CysC, and ß2-MG were positively correlated with both clinical staging systems and RBC and HGB were negatively correlated. RPR and MONO affect MM prognosis and the established prognostic model can guide patient prognosis.

A genome-wide association study and genomic prediction for Phakopsora pachyrhizi resistance in soybean.

Soybean brown rust (SBR), caused by Phakopsora pachyrhizi, is a devastating fungal disease that threatens global soybean production. This study conducted a genome-wide association study (GWAS) with seven models on a panel of 3,082 soybean accessions to identify the markers associated with SBR resistance by 30,314 high quality single nucleotide polymorphism (SNPs). Then five genomic selection (GS) models, including Ridge regression best linear unbiased predictor (rrBLUP), Genomic best linear unbiased predictor (gBLUP), Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), Random Forest (RF), and Support vector machines (SVM), were used to predict breeding values of SBR resistance using whole genome SNP sets and GWAS-based marker sets. Four SNPs, namely Gm18_57,223,391 (LOD = 2.69), Gm16_29,491,946 (LOD = 3.86), Gm06_45,035,185 (LOD = 4.74), and Gm18_51,994,200 (LOD = 3.60), were located near the reported P. pachyrhizi R genes, Rpp1, Rpp2, Rpp3, and Rpp4, respectively. Other significant SNPs, including Gm02_7,235,181 (LOD = 7.91), Gm02_7234594 (LOD = 7.61), Gm03_38,913,029 (LOD = 6.85), Gm04_46,003,059 (LOD = 6.03), Gm09_1,951,644 (LOD = 10.07), Gm10_39,142,024 (LOD = 7.12), Gm12_28,136,735 (LOD = 7.03), Gm13_16,350,701(LOD = 5.63), Gm14_6,185,611 (LOD = 5.51), and Gm19_44,734,953 (LOD = 6.02), were associated with abundant disease resistance genes, such as Glyma.02G084100, Glyma.03G175300, Glyma.04g189500, Glyma.09G023800, Glyma.12G160400, Glyma.13G064500, Glyma.14g073300, and Glyma.19G190200. The annotations of these genes included but not limited to: LRR class gene, cytochrome 450, cell wall structure, RCC1, NAC, ABC transporter, F-box domain, etc. The GWAS based markers showed more accuracies in genomic prediction than the whole genome SNPs, and Bayesian LASSO model was the ideal model in SBR resistance prediction with 44.5% ~ 60.4% accuracies. This study aids breeders in predicting selection accuracy of complex traits such as disease resistance and can shorten the soybean breeding cycle by the identified markers.

NKAP acts with HDAC3 to prevent R-loop associated genome instability.

Persistent R-loop accumulation can cause DNA damage and lead to genome instability, which contributes to various human diseases. Identification of molecules and signaling pathways in controlling R-loop homeostasis provide important clues about their physiological and pathological roles in cells. Here, we show that NKAP (NF-κB activating protein) is essential for preventing R-loop accumulation and maintaining genome integrity through forming a protein complex with HDAC3. NKAP depletion causes DNA damage and genome instability. Aberrant accumulation of R-loops is present in NKAP-deficient cells and leads to DNA damage and DNA replication fork progression defects. Moreover, NKAP depletion induced R-loops and DNA damage are dependent on transcription. Consistently, the NKAP interacting protein HDAC3 exhibits a similar role in suppressing R-loop associated DNA damage and replication stress. Further analysis uncovers that HDAC3 functions to stabilize NKAP protein, independent of its deacetylase activity. In addition, NKAP prevents R-loop formation by maintaining RNA polymerase II pausing. Importantly, R-loops induced by NKAP or HDAC3 depletion are processed into DNA double-strand breaks by XPF and XPG endonucleases. These findings indicate that both NKAP and HDAC3 are novel key regulators of R-loop homeostasis, and their dysregulation might drive tumorigenesis by causing R-loop associated genome instability.