Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.

Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation. However, we currently lack a detailed understanding of how chromatin and gene expression patterns are coordinated during developmental transitions in the cardiac lineage. Here, we interrogated the transcriptome and several histone modifications across the genome during defined stages of cardiac differentiation. We find distinct chromatin patterns that are coordinated with stage-specific expression of functionally related genes, including many human disease-associated genes. Moreover, we discover a novel preactivation chromatin pattern at the promoters of genes associated with heart development and cardiac function. We further identify stage-specific distal enhancer elements and find enriched DNA binding motifs within these regions that predict sets of transcription factors that orchestrate cardiac differentiation. Together, these findings form a basis for understanding developmentally regulated chromatin transitions during lineage commitment and the molecular etiology of congenital heart disease.

A novel technique for NO.253 lymph node dissection and left colic artery preservation to avoid potential postoperative internal hernia in laparoscopic radical resection for rectal cancer.

BACKGROUND: The preservation of the left colic artery (LCA) has emerged as a preferred approach in laparoscopic radical resection for rectal cancer. However, preserving the LCA while simultaneously dissecting the NO.253 lymph node can create a mesenteric defect between the inferior mesenteric artery (IMA), the LCA, and the inferior mesenteric vein (IMV). This defect could act as a potential "hernia ring," increasing the risk of developing an internal hernia after surgery. The objective of this study was to introduce a novel technique designed to mitigate the risk of internal hernia by filling mesenteric defects with autologous tissue. METHODS: This new technique was performed on eighteen patients with rectal cancer between January 2022 and June 2022. First of all, dissected the lymphatic fatty tissue on the main trunk of IMA from its origin until the LCA and sigmoid artery (SA) or superior rectal artery (SRA) were exposed and then NO.253 lymph node was dissected between the IMA, LCA and IMV. Next, the SRA or SRA and IMV were sequentially ligated and cut off at an appropriate location away from the "hernia ring" to preserve the connective tissue between the "hernia ring" and retroperitoneum. Finally, after mobilization of distal sigmoid, on the lateral side of IMV, the descending colon was mobilized cephalad. Patients'preoperative baseline characteristics and intraoperative, postoperative complications were examined. RESULTS: All patients' potential "hernia rings" were closed successfully with our new technique. The median operative time was 195 min, and the median intraoperative blood loss was 55 ml (interquartile range 30-90). The total harvested lymph nodes was 13.0(range12-19). The median times to first flatus and liquid diet intake were both 3.0 days. The median number of postoperative hospital days was 8.0 days. One patient had an injury to marginal arterial arch, and after mobolization of splenic region, tension-free anastomosis was achieved. No other severe postoperative complications such as abdominal infection, anastomotic leakage, or bleeding were observed. CONCLUSIONS: This technique is both safe and effective for filling the mesenteric defect, potentially reducing the risk of internal hernia following laparoscopic NO.253 lymph node dissection and preservation of the left colic artery in rectal cancer surgeries.

Laparoscopic Complete Mesocolic Excision with Central Vascular Ligation (CME + CVL) for Right-Sided Colon Cancer: A New "Superior Mesenteric Artery First" Approach.

PURPOSE: It remains a technical challenge to perform "superior mesenteric artery (SMA) first" approach for laparoscopic right hemicolectomy with complete mesocolon excision (CME) as the vascular anatomy of the right colon varies a lot, which may cause difficulty in early location of SMA and the risk of vascular damage during central vascular ligation (CVL). The purpose of this study was to describe a new "SMA first" approach for laparoscopic CME with CVL in right hemicolectomy with Treitz's ligament and ileocolic vascular pedicle as the anatomical landmarks for early identification of and exposure of SMA. METHODS: This procedure was performed on 21 patients with right colon cancer between March 2020 and August 2021. To start, the transverse mesocolon was retracted to expose the ligament of Treitz, and the pedicle of ileocolic vessels was anteriorly grasped. Next, the peritoneum near the right border of the ligament of Treitz was divided along the left side of SMA until the peritoneum below the ileocolic vessels. Next, the mesenteric lymphatic adipose tissue outside of the sheath of SMA was dissected from medial to lateral. Then, laparoscopic right hemicolectomy with complete mesocolic excision (CME) was performed. Patients' preoperative baseline characteristics and intraoperative and postoperative complications were examined. RESULTS: The median operative time was 180 min, and the median intraoperative blood loss was 50 ml (interquartile range 40-90). Chylous leakage occurred in four patients, and all the patients resolved with percutaneous drainage. The total harvested lymph nodes was 21.0 (range 16-27). The median times to first flatus and liquid diet intake were both 3.0 days. The median number of postoperative hospital days was 10.0 days. No severe postoperative complications, such as abdominal infection, anastomotic leakage, or bleeding, were observed. CONCLUSIONS: This new "SMA first" approach is safe and technically feasible for laparoscopic CME with CVL in right hemicolectomy.

A Novel Technique With Ileal Mesentery to Reconstruct the Pelvic Peritoneum After Pelvic Dissection With End Colostomy for Rectal Cancer.

BACKGROUND: After abdominoperineal resection, low anterior resection, and end colostomy for lower rectal cancer, it is necessary to reconstruct the pelvic peritoneum to avoid small bowel obstruction, perineal hernia, and radiation enteritis in patients for whom postoperative radiotherapy is planned. However, pelvic peritoneal closure is technically difficult in patients who lack enough peritoneum to cover the defect or have received neoadjuvant radiation and have a rigid pelvis. IMPACT OF INNOVATION: The impact of this innovation is to reconstruct the pelvic peritoneum with the distal ileal mesentery laparoscopically. TECHNOLOGY, MATERIALS AND METHODS: After removal of the tumor, the distal ileal mesentery was selected to completely cover the defect. Subsequently, suturing of the ileal mesentery to the posterior wall of the urinary bladder and all sides of the pelvic cavity was performed. Finally, the patients were returned to the headfirst supine position to ensure that there was no small bowel falling into the pelvic dead space. PRELIMINARY RESULTS: All surgical procedures were successfully performed laparoscopically from January 2019 to April 2021. No perineal complications or intestinal obstructions occurred during the follow-up period. CONCLUSIONS AND FUTURE DIRECTIONS: This novel technique was found to be safe and effective. Moreover, it provided an economical method for the reconstruction of the pelvic peritoneum using autologous material, which could preserve the small intestine in the abdomen to avoid related complications. Additional larger series of patients with longer follow-up are needed to validate the safety and feasibility of this method.

Identification and evaluation of circulating small extracellular vesicle microRNAs as diagnostic biomarkers for patients with indeterminate pulmonary nodules.

BACKGROUND: The identification of indeterminate pulmonary nodules (IPNs) following a low-dose computed tomography (LDCT) is a major challenge for early diagnosis of lung cancer. The inadequate assessment of IPNs' malignancy risk results in a large number of unnecessary surgeries or an increased risk of cancer metastases. However, limited studies on non-invasive diagnosis of IPNs have been reported. METHODS: In this study, we identified and evaluated the diagnostic value of circulating small extracellular vesicle (sEV) microRNAs (miRNAs) in patients with IPNs that had been newly detected using LDCT scanning and were scheduled for surgery. Out of 459 recruited patients, 109 eligible patients with IPNs were enrolled in the training cohort (n = 47) and the test cohort (n = 62). An external cohort (n = 99) was used for validation. MiRNAs were extracted from plasma sEVs, and assessed using Small RNA sequencing. 490 lung adenocarcinoma samples and follow-up data were used to investigate the role of miRNAs in overall survival. RESULTS: A circulating sEV miRNA (CirsEV-miR) model was constructed from five differentially expressed miRNAs (DEMs), showing 0.920 AUC in the training cohort (n = 47), and further identified in the test cohort (n = 62) and in an external validation cohort (n = 99). Among five DEMs of the CirsEV-miR model, miR-101-3p and miR-150-5p were significantly associated with better overall survival (p = 0.0001 and p = 0.0069). The CirsEV-miR scores were calculated, which significantly correlated with IPNs diameters (p < 0.05), and were able to discriminate between benign and malignant PNs (diameter ≤ 1 cm). The expression patterns of sEV miRNAs in the benign, adenocarcinoma in situ/minimally invasive adenocarcinoma, and invasive adenocarcinoma subgroups were found to gradually change with the increase in aggressiveness for the first time. Among all DEMs of the three subgroups, five miRNAs (miR-30c-5p, miR-30e-5p, miR-500a-3p, miR-125a-5p, and miR-99a-5p) were also significantly associated with overall survival of lung adenocarcinoma patients. CONCLUSIONS: Our results indicate that the CirsEV-miR model could help distinguish between benign and malignant PNs, providing insights into the feasibility of circulating sEV miRNAs in diagnostic biomarker development. TRIAL REGISTRATION: Chinese Clinical Trials: ChiCTR1800019877. Registered 05 December 2018, https://www.chictr.org.cn/showproj.aspx?proj=31346 .

A New Medial-to-Lateral Approach for Laparoscopic D3 Lymphadenectomy plus Complete Mesocolic Excision (D3 + CME) for Right-Sided Colon Cancer.

BACKGROUND: D3 lymphadenectomy is important for accurate staging and provides long-term benefits, especially for T3-4/N + tumors.1,2 Both D3 lymphadenectomy as well as complete mesocolic excision (CME) require central ligation of vessels at their origins to ensure radical resection.3 Currently, superior mesentery vein (SMV) is navigated by ileocolic vessels while its sheath is dissected stepwise from caudal to cranial.4-6 This report describes a new medial-to-lateral approach for laparoscopic right hemicolectomy with D3 + CME. METHODS: The patient was a 47-year-old man with diagnosis of hepatic flexure cancer (cT4N1M0). First, the pedicle of the middle colic vessels and ileocolic vessels were both grasped, then the sheath of SMV was dissected at its left side as there are fewer blood vessels entering here compared with its right side. Second, after identification of middle colic artery (MCA), SMV was skeletonized from medial to lateral and no. 213 and no. 203 lymph nodes were dissected. Third, MCA and ileocolic vein and artery (ICV and ICA) were ligated at their roots. After separating the transverse mesocolon from the duodenum, the branches of the Henle trunk were exposed and no. 223 lymph nodes were dissected. Accessory right colic vein, right colic vein, and middle colic vein were ligated respectively. Fourth, the ascending mesocolon was separated from the retroperitoneal tissues through the front side of Toldt's fascia, the mesocolon was mobilized completely, and the tumor was removed en bloc. RESULTS: The operation time was 175 min, with estimated blood loss of 50 ml. The patient recovered well without bleeding complications and was discharged on postoperative day 7. Histology revealed moderately differentiated adenocarcinoma with 5 of 24 lymph nodes involved (pT3N2M0). CONCLUSIONS: The medial-to-lateral approach presented in the video might be helpful for standardization of laparoscopic D3 + CME for right-sided colon cancer.

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity.

Cells differentiate when transcription factors bind accessible cis-regulatory elements to establish specific gene expression programs. In differentiating embryonic stem cells, chromatin at lineage-restricted genes becomes sequentially accessible, probably by means of 'pioneer' transcription factor activity, but tissues may use other strategies in vivo. Lateral inhibition is a pervasive process in which one cell forces a different identity on its neighbours, and it is unclear how chromatin in equipotent progenitors undergoing lateral inhibition quickly enables distinct, transiently reversible cell fates. Here we report the chromatin and transcriptional underpinnings of differentiation in mouse small intestine crypts, where notch signalling mediates lateral inhibition to assign progenitor cells into absorptive or secretory lineages. Transcript profiles in isolated LGR5(+) intestinal stem cells and secretory and absorptive progenitors indicated that each cell population was distinct and the progenitors specified. Nevertheless, secretory and absorptive progenitors showed comparable levels of H3K4me2 and H3K27ac histone marks and DNase I hypersensitivity--signifying accessible, permissive chromatin-at most of the same cis-elements. Enhancers acting uniquely in progenitors were well demarcated in LGR5(+) intestinal stem cells, revealing early priming of chromatin for divergent transcriptional programs, and retained active marks well after lineages were specified. On this chromatin background, ATOH1, a secretory-specific transcription factor, controls lateral inhibition through delta-like notch ligand genes and also drives the expression of numerous secretory lineage genes. Depletion of ATOH1 from specified secretory cells converted them into functional enterocytes, indicating prolonged responsiveness of marked enhancers to the presence or absence of a key transcription factor. Thus, lateral inhibition and intestinal crypt lineage plasticity involve interaction of a lineage-restricted transcription factor with broadly permissive chromatin established in multipotent stem cells.

Embryonic transcription factor SOX9 drives breast cancer endocrine resistance.

The estrogen receptor (ER) drives the growth of most luminal breast cancers and is the primary target of endocrine therapy. Although ER blockade with drugs such as tamoxifen is very effective, a major clinical limitation is the development of endocrine resistance especially in the setting of metastatic disease. Preclinical and clinical observations suggest that even following the development of endocrine resistance, ER signaling continues to exert a pivotal role in tumor progression in the majority of cases. Through the analysis of the ER cistrome in tamoxifen-resistant breast cancer cells, we have uncovered a role for an RUNX2-ER complex that stimulates the transcription of a set of genes, including most notably the stem cell factor SOX9, that promote proliferation and a metastatic phenotype. We show that up-regulation of SOX9 is sufficient to cause relative endocrine resistance. The gain of SOX9 as an ER-regulated gene associated with tamoxifen resistance was validated in a unique set of clinical samples supporting the need for the development of improved ER antagonists.

A Modified Side-to-Side Anastomosis Using a Circular Stapler Reduces Anastomotic Leakage in Colonic Surgery.

Background. Anastomotic leakage (AL) remains one of the serious complications after colonic surgery. Method. A prospective interventional study to assess a modified technique of creating the ileocolic, colic-colic, and colorectal side-to-side anastomoses using a circular stapler. The primary endpoint was to evaluate the safety and efficacy of this technique in the reduction of AL. Computed tomography scan was performed when AL was clinically suspected. Result. One hundred and forty-five patients who underwent colonic resection between January 2015 and August 2018 were included. One patient underwent surgery for severe inflammatory bowel disease, and the others underwent surgery for colonic cancer. The procedures were open surgeries, including right hemicolectomy (n = 79 [54.5%]), left hemicolectomy (n = 29 [20%]), sigmoidectomy (n = 30 [20.7%]), and transverse colectomy (n = 7 [4.8%]). In 23 patients with ascending colonic obstruction, emergency right colectomy with primary anastomosis was performed. Two surgeons performed the operations (52.4% and 47.6%, respectively), and intraoperative blood loss was 50 to 100 mL. The operative time was 160 to 240 minutes. There was no mortality postoperatively, and 26 (17.9%) patients developed complications. One patient who underwent transverse colonic cancer resection developed a clinical AL (0.7%). After ileostomy, the patient was discharged with no other serious complication. The median of postoperative hospital stay was 8 days (range = 5-18 days). Conclusion. This modified technique is a safe and efficient method for anastomotic configuration in colonic surgery.

FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer.

Forkhead box protein A1 (FOXA1) is a pioneer factor of estrogen receptor α (ER)-chromatin binding and function, yet its aberration in endocrine-resistant (Endo-R) breast cancer is unknown. Here, we report preclinical evidence for a role of FOXA1 in Endo-R breast cancer as well as evidence for its clinical significance. FOXA1 is gene-amplified and/or overexpressed in Endo-R derivatives of several breast cancer cell line models. Induced FOXA1 triggers oncogenic gene signatures and proteomic profiles highly associated with endocrine resistance. Integrated omics data reveal IL8 as one of the most perturbed genes regulated by FOXA1 and ER transcriptional reprogramming in Endo-R cells. IL-8 knockdown inhibits tamoxifen-resistant cell growth and invasion and partially attenuates the effect of overexpressed FOXA1. Our study highlights a role of FOXA1 via IL-8 signaling as a potential therapeutic target in FOXA1-overexpressing ER-positive tumors.

The characteristics of ctDNA reveal the high complexity in matching the corresponding tumor tissues.

BACKGROUND: Next-generation sequencing (NGS) is an efficient and sensitive method to detect mutations from ctDNA. Many features and clinical conditions could significantly affect the concordance between ctDNA and corresponding tumor tissues. Our goal was to systematically investigate the critical factors contributing to different concordance between ctDNA and corresponding tumor tissues. METHODS: We recruited two groups of IIIB or IV lung cancer patients: The standard group to evaluate the accuracy of our method and the concordance between ctDNA and tumor tissues, and the study group with various clinical conditions. We applied our unique identification (UID) indexed capturing-based sequencing (UC-Seq) to ctDNA samples, and confirm the results by Droplet digital PCR (ddPCR). RESULTS: Considering mutations detected from NGS of tumor tissues as golden standard, UC-Seq achieved overall 93.6% sensitivity for SNVs and Indels, and 0.8 Pearson correlation between tumor TMB and bTMB. Efficacious treatments, long sampling date (more than 2 weeks) between tumor tissues and ctDNA and low concentrations of cfDNA (less than 9 ng/ml) could significantly decrease the concordance between ctDNA and tumor tissues. About 84% mutations showed shorter mutant fragment length than that of wild-type fragments, and the AFs of mutations could be significantly enriched in small-size ctDNA. CONCLUSIONS: In late-stage lung cancer patients, ctDNA generally has high concordance with tumor tissues. However it could be significantly affected by three clinical conditions which could dynamically change the content of ctDNA. Moreover, the detection limit could be further extended by enriching small-size ctDNA in the preparation of samples.

Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions.

Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation.

Enhanced synergistic anti-Lewis lung carcinoma effect of a DNA vaccine harboring a MUC1-VEGFR2 fusion gene used with GM-CSF as an adjuvant.

In order to achieve a synergistic effect on anti-tumour and anti-angiogenesis activity, we designed and constructed a DNA vaccine that expresses MUC1and VEGFR2 in the same reading frame. The aim of this study was to investigate the anti-tumour activity of this DNA vaccine. Furthermore, we also investigated the enhanced synergistic anti-Lewis lung carcinoma effect of this DNA vaccine by using GM-CSF as an adjuvant. A series of DNA plasmids encoding MUC1, VEGFR2, GM-CSF, and their conjugates were constructed and injected into mice intramuscularly (i.m.) followed by an electric pulse. The humoral and cellular immune responses after immunization were detected by enzyme-linked immunosorbent assay (ELISA) and enzyme-linked immunospot (ELISPOT), respectively. To evaluate the anti-tumour efficacy of these plasmids, murine models with MUC1-expressing tumours were generated. After injection into the tumour-bearing mouse model, the plasmid carrying the fusion gene of MUC1 and VEGFR2 showed stronger inhibition of tumour growth than the plasmid expressing MUC1 or VEGFR2 alone, which indicated that MUC1 and VEGFR2 could exert a synergistic anti-tumour effect. Furthermore, mice vaccinated with the combination of the GM-CSF expressing plasmid and the plasmid carrying the fusion gene of MUC1 and VEGFR2 showed an increased inhibition in the growth of MUC1-expressing tumours and prolonged mouse survival. These observations emphasize the potential of the synergistic anti-tumour and anti-angiogenesis strategy used in DNA vaccines, and the potential of the GM-CSF gene as an adjuvant for DNA vaccines, which could represent a promising approach for tumour immunotherapy.

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.

BACKGROUND: Transcription factor binding, histone modification, and chromatin accessibility studies are important approaches to understanding the biology of gene regulation. ChIP-seq and DNase-seq have become the standard techniques for studying protein-DNA interactions and chromatin accessibility respectively, and comprehensive quality control (QC) and analysis tools are critical to extracting the most value from these assay types. Although many analysis and QC tools have been reported, few combine ChIP-seq and DNase-seq data analysis and quality control in a unified framework with a comprehensive and unbiased reference of data quality metrics. RESULTS: ChiLin is a computational pipeline that automates the quality control and data analyses of ChIP-seq and DNase-seq data. It is developed using a flexible and modular software framework that can be easily extended and modified. ChiLin is ideal for batch processing of many datasets and is well suited for large collaborative projects involving ChIP-seq and DNase-seq from different designs. ChiLin generates comprehensive quality control reports that include comparisons with historical data derived from over 23,677 public ChIP-seq and DNase-seq samples (11,265 datasets) from eight literature-based classified categories. To the best of our knowledge, this atlas represents the most comprehensive ChIP-seq and DNase-seq related quality metric resource currently available. These historical metrics provide useful heuristic quality references for experiment across all commonly used assay types. Using representative datasets, we demonstrate the versatility of the pipeline by applying it to different assay types of ChIP-seq data. The pipeline software is available open source at https://github.com/cfce/chilin . CONCLUSION: ChiLin is a scalable and powerful tool to process large batches of ChIP-seq and DNase-seq datasets. The analysis output and quality metrics have been structured into user-friendly directories and reports. We have successfully compiled 23,677 profiles into a comprehensive quality atlas with fine classification for users.

Analysis of Cytokine Levers in Pleural Effusions of Tuberculous Pleurisy and Tuberculous Empyema.

The aim is to examine whether the interleukin-1ß (IL-1ß), IL-2, IL-6, tumor necrosis factor-α (TNF-α), plasminogen activator inhibitor type-1 (PAI-1), and tissue plasminogen activator (t-PA) levels were different in pleural effusions of tuberculous pleurisy and tuberculous empyema. IL-1ß, IL-2, IL-6, TNF-α, PAI-1, and t-PA levels in pleural fluids of 40 patients with tuberculous pleurisy and 38 patients with tuberculous empyema were measured. The levels of IL-1ß, PAI-1, and t-PA in the pleural effusions were different between tuberculous pleurisy and tuberculous empyema; it could be helpful to differentiate the two diseases. The levels of PAI-1, IL-1ß were higher and t-PA, IL-6 were lower in pleural effusions of the patients with tuberculous empyema and who must undergo operation than the patients who could be treated with closed drainage and anti-TB chemotheraphy. These indications may be helpful to evaluate whether the patient needs the operation.

Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes.

Cells respond to stress by controlling gene expression at several levels, with little known about the role of translation. Here, we demonstrate a coordinated translational stress response system involving stress-specific reprogramming of tRNA wobble modifications that leads to selective translation of codon-biased mRNAs representing different classes of critical response proteins. In budding yeast exposed to four oxidants and five alkylating agents, tRNA modification patterns accurately distinguished among chemically similar stressors, with 14 modified ribonucleosides forming the basis for a data-driven model that predicts toxicant chemistry with >80% sensitivity and specificity. tRNA modification subpatterns also distinguish SN1 from SN2 alkylating agents, with SN2-induced increases in m(3)C in tRNA mechanistically linked to selective translation of threonine-rich membrane proteins from genes enriched with ACC and ACT degenerate codons for threonine. These results establish tRNA modifications as predictive biomarkers of exposure and illustrate a novel regulatory mechanism for translational control of cell stress response.

Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity.

Toxoplasma gondii is a highly successful protozoan parasite that infects all warm-blooded animals and causes severe disease in immunocompromised and immune-naïve humans. It has an unusual global population structure: In North America and Europe, isolated strains fall predominantly into four largely clonal lineages, but in South America there is great genetic diversity and the North American clonal lineages are rarely found. Genetic variation between Toxoplasma strains determines differences in virulence, modulation of host-signaling pathways, growth, dissemination, and disease severity in mice and likely in humans. Most studies on Toxoplasma genetic variation have focused on either a few loci in many strains or low-resolution genome analysis of three clonal lineages. We use whole-genome sequencing to identify a large number of SNPs between 10 Toxoplasma strains from Europe and North and South America. These were used to identify haplotype blocks (genomic regions) shared between strains and construct a Toxoplasma haplotype map. Additional SNP analysis of RNA-sequencing data of 26 Toxoplasma strains, representing global diversity, allowed us to construct a comprehensive genealogy for Toxoplasma gondii that incorporates sexual recombination. These data show that most current isolates are recent recombinants and cannot be easily grouped into a limited number of haplogroups. A complex picture emerges in which some genomic regions have not been recently exchanged between any strains, and others recently spread from one strain to many others.

A pooled analysis of clinical outcome in driver-gene negative non-small cell lung cancer patients with MET overexpression treated with gumarontinib.

Background: MET overexpression represents the most MET aberration in advanced non-small-cell lung cancer (NSCLC). However, except MET exon 14 (METex14) skipping mutation was recognized as a clinical biomarker, the role of MET overexpression as a predictive factor to MET inhibitor is not clear. Objectives: The purpose of the pooled analysis is to explore the safety and efficiency of gumarontinib, a highly selective oral MET inhibitor, in drive-gene negative NSCLC patients with MET overexpression. Design and methods: NSCLC patients with MET overexpression [immunohistochemistry (IHC) ⩾3+ as determined by central laboratory] not carrying epidermal growth factor receptor mutation, METex14 skipping mutation or other known drive gene alternations who received Gumarontinib 300 mg QD from two single arm studies were selected and pooled for the analysis. The efficacy [objective response rate (ORR), disease control rate (DCR), duration of response, progression-free survival (PFS) and overall survival (OS)] and safety [treatment emergent adverse event (TEAE), treatment related AE (TRAE) and serious AE (SAE) were assessed. Results: A total of 32 patients with MET overexpression were included in the analysis, including 12 treatment naïve patients who refused or were unsuitable for chemotherapy, and 20 pre-treated patients who received ⩾1 lines of prior systemic anti-tumour therapies. Overall, the ORR was 37.5% [95% confidence interval (CI): 21.1-56.3%], the DCR was 81.3% (95% CI: 63.6-92.8%), median PFS (mPFS) and median OS (mOS) were 6.9 month (95% CI: 3.6-9.7) and 17.0 month (95% CI: 10.3-not evaluable), respectively. The most common AEs were oedema (59.4%), hypoalbuminaemia (40.6%), alanine aminotransferase increased (31.3%). Conclusion: Gumarontinib showed promising antitumour activity in driver-gene negative locally advanced or metastatic NSCLC patients with MET overexpression, which warranted a further clinical trial. Trial registration: ClinicalTrials.gov identifier: NCT03457532; NCT04270591.

Residues and dietary risk assessment of fluazinam in root mustard after field experiments.

The residue levels of fluazinam in root mustard were investigated by using a quick, easy, cheap, effective, rugged, and safe (QuEChERS) technique with ultra-performance liquid chromatography tandem mass spectrometry. Samples of leaf and root mustard were analyzed. The recoveries of fluazinam were 85.2-110.8% for leaf mustard with the coefficient of variation of 1.0-7.2%, and 88.8-93.3% for root mustard with the coefficient of variation of 1.9-12.4%. The suspension concentrate formulation of fluazinam was applied on root mustard at 262.5 g a.i. ha-1 in accordance with good agricultural practice (GAP), respectively. After the final application, the root mustard samples were collected at 3, 7, and 14 days. Fluazinam residues in root mustard were less than 0.01-0.493 mg kg-1. The dietary risk of fluazinam was predicted by comparing intake amounts with the toxicological data, namely acceptable daily intake (ADI) and acute reference dose (ARfD). The risk quotient (RQ) was 72.2-74.3%, for ordinary consumers, which showed negligible risk. According to the maximum residue limit (MRL) and dietary risk assessment, it is suggested that the pre-harvest interval (PHI) of 3 days; meanwhile, the MRL of 2 mg kg-1 was suggested for fluazinam in root mustard, which indicates that the dietary risk of fluazinam 500 g L-1 suspension concentrate (SC) with the recommended usage on root mustard is negligible. This study provided basic data on the use and safety of fluazinam in root mustard to help the Chinese government formulate a maximum residue level for fluazinam in root mustard.

Gumarontinib in patients with non-small-cell lung cancer harbouring MET exon 14 skipping mutations: a multicentre, single-arm, open-label, phase 1b/2 trial.

Background: Approximately 3-4% of patients with non-small-cell lung cancer (NSCLC) have MET exon 14 (METex14) skipping mutations. We report primary results from the phase 2 stage of a phase 1b/2 study of gumarontinib, a selective, potent, oral MET inhibitor, in patients with METex14 skipping mutation-positive (METex14-positive) NSCLC. Methods: The single-arm, multicentre, open-label, phase 2 stage of the GLORY study was conducted at 42 centres across China and Japan. Adults with locally advanced or metastatic METex14-positive NSCLC received oral gumarontinib 300 mg once daily in continuous 21-day cycles until disease progression, intolerable toxicity, or withdrawal of consent. Eligible patients had failed one or two prior lines of therapy (not including a MET inhibitor), were ineligible for/refused chemotherapy, and had no genetic alterations targetable with standard therapies. The primary endpoint was objective response rate in patients with a valid baseline tumour assessment, by blinded independent review. The study was registered at ClinicalTrials.gov (NCT04270591). Findings: Between Aug 2, 2019 and Apr 28, 2021, 84 patients were enrolled and received gumarontinib (median follow-up 13.5 months [IQR 8.7-17.1]), at data cut-off (Apr 28, 2022) five patients whose METex14 status could not be confirmed by a central laboratory were excluded from the efficacy analysis. The objective response rate was 66% (95% CI 54-76) overall (n = 79), 71% (95% CI 55-83) in treatment-naïve patients (n = 44), and 60% (95% CI 42-76) in previously-treated patients (n = 35). The most common treatment-related adverse events (any grade) were oedema (67/84 patients, 80%) and hypoalbuminuria (32/84, 38%). Grade ≥3 treatment-emergent adverse events occurred in 45 (54%) patients. Treatment-related adverse events leading to permanent discontinuation occurred in 8% (7/84) of patients. Interpretation: Gumarontinib monotherapy had durable antitumour activity with manageable toxicity in patients with locally advanced or metastatic METex14-positive NSCLC when used in first line or later. Funding: Haihe Biopharma Co., Ltd. Supported in part by grants from the National Science and Technology Major Project of China for "Clinical Research of Gumarontinib, a highly selective MET inhibitor" (2018ZX09711002-011-003); the National Natural Science Foundation of China (82030045 to S.L. and 82172633 to YF.Y); Shanghai Municipal Science & Technology Commission Research Project (19411950500 to S.L.); Shanghai Shenkang Action Plan (16CR3005A to S.L.) and Shanghai Chest Hospital Project of Collaborative Innovation (YJXT20190105 to S.L.).