Liquid biopsy using cell-free DNA in the early diagnosis of hepatocellular carcinoma.

Hepatocellular carcinoma ranks fourth in cancer-related causes of death worldwide and second in China. Patients with hepatocellular carcinoma (HCC) at the early stage have a better prognosis compared to HCC patients at the late stage. Therefore, early screening for HCC is critical for clinical treatment decisions and improving the prognosis of patients. Ultrasound (US), computed tomography (CT), and serum alpha fetoprotein (AFP) have been used to screen HCC, but HCC is still difficult to be diagnosed in the early stage due to the low sensitivity of the above methods. It is urgent to find a method with high sensitivity and specificity for the early diagnosis of HCC. Liquid biopsy is a noninvasive detection method using blood or other bodily fluids. Cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) are important biomarkers for liquid biopsy. Recently, HCC screening methods using the application of cfDNA and ctDNA have become the hot spot of early HCC diagnostics. In this mini review, we summarize the latest research progress of liquid biopsy based on blood cfDNA in early screening of HCC.

Gastrointestinal signet ring cell malignancy: current advancement and future prospects.

Globally, gastrointestinal cancer is the most widespread neoplastic disease and the primary contributor to cancer-associated fatalities. Gastrointestinal signet ring cell carcinoma (SRCC) exhibits unique distinguishing features in several aspects when compared to adenocarcinomas (ACs). The scarcity of signet ring cell carcinoma has resulted in a heightened significance of related clinical and molecular investigations. However, a comprehensive and systematic review of the clinical, molecular, therapeutic, and research aspects of this disease is currently absent. This review provides an overview of the latest developments in our understanding of the clinical and molecular features of gastrointestinal signet ring cell carcinoma (SRCC). Additionally, we have compiled a list of potential therapeutic targets or biomarkers, as well as an examination of the current treatment options and the possible mechanisms of formation.

Rufibacter roseolus sp. nov. and Rufibacter aurantiacus sp. nov., isolated from desert soil.

Two novel bacterial strains, designated as SYSU D00344T and SYSU D00433T, were isolated from soil of Gurbantunggut Desert in Xinjiang, north-west PR China. Cells of both strains were Gram-stain-negative, aerobic, short-rod-shaped, catalase-positive and non-motile. Oxidase activities of SYSU D00344T and SYSU D00433T were negative and positive, respectively. Optimal growth occurred at 30 °C, with 0-0.5 % (w/v) NaCl and at pH 7.0. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that they represented members of the genus Rufibacter and were closely related to Rufibacter hautae NBS58-1T. The results of phylogenomic analysis indicated that the two strains formed two independent and robust branches distinct from all reference type strains. The analyses of average nucleotide identity (ANI), digital DNA-DNA hybridisation (dDDH) values and 16S rRNA gene similarities between the two strains and their relatives further demonstrated that SYSU D00344T and SYSU D00433T represented two different novel genospecies. The polar lipids consisted of phosphatidylethanolamine, one unidentified glycolipid, two unidentified aminophospholipids, and two or four unidentified lipids. MK-7 was the only respiratory quinone. The major fatty acids (>10 %) for both strains were identified as iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), as well as summed feature 4 (anteiso-C17 : 1B and/or iso-C17 : 1I) for SYSU D00344T and C16 : 1ω5c for SYSU D00433T. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, we propose Rufibacter roseolus sp. nov. and Rufibacter aurantiacus sp. nov. as two novel species in the genus Rufibacter. The type strains are SYSU D00344T (=CGMCC 1.8625T=MCCC 1K04971T=KCTC 82274T) and SYSU D00433T (=CGMCC 1.8617T=MCCC 1K04982T=KCTC 82277T), respectively.

Sintilimab plus fluorouracil, leucovorin, oxaliplatin and docetaxel regimen as neoadjuvant therapy for resectable gastric cancer and biomarker exploration.

At present, preoperative chemotherapy is the standard of care for the neoadjuvant treatment of potentially resectable gastric cancer (GC). However, because the efficacy and prognosis are not ideal, curative effects for this population are unsatisfactory. With the development of immune checkpoint inhibitors, the results of a few encouraging early trials of immunotherapeutic agents as neoadjuvant therapies for resectable GC have been reported. However, markers of the efficacy of immune checkpoint inhibitors remain unclear. This prospective single-center, single-arm observational study was designed to evaluate the efficacy of sintilimab plus the fluorouracil, leucovorin, oxaliplatin and docetaxel regimen as a neoadjuvant treatment for localized GC. More importantly, this work assesses multiple dimensions and include ctDNA, the immune microenvironment and intestinal microbiome to explore correlations between biomarkers and neoadjuvant therapeutic efficacy. Clinical trial registration: ChiCTR2200061629 (www.chictr.org.cn/index.aspx).

Sphingomonas arenae sp. nov., isolated from desert soil.

Two bacterial strains, designated as SYSU D00720T and SYSU D00722, were isolated from a desert sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped, oxidase-positive and catalase-negative. Colonies were circular, opaque, convex, smooth, orange on Reasoner's 2A (R2A) agar. The isolates were found to grow at 4-45 °C (optimum, 28-30 °C), at pH 6.0-7.0 (optimum, 7.0) and with 0-1.5 % (w/v) NaCl (optimum, 0%). Growth was observed on R2A agar, Luria-Bertani agar and nutrient agar, but not on trypticase soy agar. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified aminolipids, one unidentified glycolipid, one unidentified aminoglycolipid, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified lipids. The main fatty acids (>10%) were C17 : 1 ω6c, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major respiratory quinone was ubiquinone-10 and the major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.0 mol%. Strains SYSU D00720T and SYSU D00722 were nearly identical with a 16S rRNA gene sequence similarity of 99.6 %, and 100.0 % average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values. Phylogenetic analyses clearly demonstrated that these two strains belonged to the same species of the genus Sphingomonas, and had highest sequence similarity to Sphingomonas lutea KCTC 23642T (97.3 %). The ANI, AAI and dDDH values of strains SYSU D00720T and SYSU D00722 to S. lutea KCTC 23642T were both 73.2, 69.9 and 19.2 %, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strains SYSU D00720T and SYSU D00722 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas arenae sp. nov. is proposed. The type strain is SYSU D00720T (=MCCC 1K05154T=NBRC 115061T).

Successful treatment of an adult patient with diffuse midline glioma employing olaparib combined with bevacizumab.

Diffuse midline gliomas (DMGs), which are malignant, fast-growing and entail a poor prognosis, are a rare subtype of glial tumor. DMGs harboring H3 K27-mutation are a novel entity with a poorer prognosis than the H3 wildtype and are categorized as a grade IV glioma. Histone-mutated DMGs characterized by a midline location occur more commonly in children and less frequently in adults. Considering the DMG treatment is limited, there is an urgent need for effective therapeutic strategies. Olaparib is a poly-adenosine diphosphate-ribose polymerase inhibitor, which has been reported to inhibit glioma in preclinical and clinical trials. Olaparib plus bevacizumab has been successfully used in ovarian cancer. However, the application of olaparib in DMGs has not been reported yet. Herein, we firstly reported that an adult DMG patient benefited from olaparib combined with bevacizumab and achieved complete remission. The duration of response and overall survival was 8 months and 16 months respectively. This report provides a promising treatment option for patients with DMG.

Temperature and oxygen level determine N2 O respiration activities of heterotrophic N2 O-reducing bacteria: Biokinetic study.

Nitrous oxide (N2 O), a potent greenhouse gas, is reduced to N2 gas by N2 O-reducing bacteria (N2 ORB), a process which represents an N2 O sink in natural and engineered ecosystems. The N2 O sink activity by N2 ORB depends on temperature and O2 exposure, yet the specifics are not yet understood. This study explores the effects of temperature and oxygen exposure on biokinetics of pure culture N2 ORB. Four N2 ORB, representing either clade I type nosZ (Pseudomonas stutzeri JCM5965 and Paracoccus denitrificans NBRC102528) or clade II type nosZ (Azospira sp. strains I09 and I13), were individually tested. The higher activation energy for N2 O by Azospira sp. strain I13 (114.0 ± 22.6 kJ mol-1 ) compared with the other tested N2 ORB (38.3-60.1 kJ mol-1 ) indicates that N2 ORB can adapt to different temperatures. The O2 inhibition constants (KI ) of Azospira sp. strain I09 and Ps. stutzeri JCM5965 increased from 0.06 ± 0.05 and 0.05 ± 0.02 µmol L-1 to 0.92 ± 0.24 and 0.84 ± 0.31 µmol L-1 , respectively, as the temperature increased from 15°C to 35°C, while that of Azospira sp. strain I13 was temperature-independent (p = 0.106). Within the range of temperatures examined, Azospira sp. strain I13 had a faster recovery after O2 exposure compared with Azospira sp. strain I09 and Ps. stutzeri JCM5965 (p < 0.05). These results suggest that temperature and O2 exposure result in the growth of ecophysiologically distinct N2 ORB as N2 O sinks. This knowledge can help develop a suitable N2 O mitigation strategy according to the physiologies of the predominant N2 ORB.

Sabulicella rubraurantiaca gen. nov., sp. nov., a new member of the family Acetobacteraceae, isolated from desert soil.

Strain SYSU D01096T was isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, PR China. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence revealed that strain SYSU D01096T belonged to the family Acetobacteraceae and was closest to Rubritepida flocculans DSM 14296T (96.0% similarity). Cells of strain SYSU D01096T were observed to be non-motile, short rod-shaped and Gram-staining negative. The colonies were observed to be translucent, reddish orange, circular, convex and smooth. Growth occurred at 15-37 °C (optimum, 28-30 °C), pH 4.0-8.0 (optimum, pH 7.0) and 0-0.5% NaCl (w/v; optimum, 0%) on Reasoner's 2A medium. The predominant ubiquinone was identified as ubiquinone 9 and the major fatty acids were Summed Feature 8 (C18:1 ω7c and/or C18:1 ω6c) and C16:0. The polar lipids consisted of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), one unidentified phospholipid (PL), three unidentified aminolipids (AL1-3) and one unidentified aminophospholipid (APL). The genomic DNA G + C content was 69.1%. Phylogenetic tree based on 16S rRNA gene sequences indicated strain SYSU D01096T represented an individual lineage in the family Acetobacteraceae, which was supported by 30 core gene-based phylogenomic tree. Based on the multi-analysis including physiological, chemotaxonomic and phylogenetic comparison, strain SYSU D01096T was proposed to represent a novel species of a novel genus, named Sabulicella rubraurantiaca gen. nov., sp. nov., within the family Acetobacteraceae. The type strain is SYSU D01096T (= CGMCC 1.8619T = KCTC 82268T = MCCC 1K04998T).

Arenibaculum pallidiluteum gen. nov., sp. nov., a novel bacterium in the family Azospirillaceae, isolated from desert soil, and reclassification of Skermanella xinjiangensis to a new genus Deserticella as Deserticella xinjiangensis comb. nov., and transfer of the genera Indioceanicola and Oleisolibacter from the family Rhodospirillaceae to the family Azospirillaceae.

A novel pale orange-coloured bacterium, designated strain SYSU D00532T, was isolated from sandy soil collected from the Gurbantunggut desert in Xinjiang, PR China. Cells of strain SYSU D00532T were found to be aerobic, Gram-stain-negative, oxidase-positive, catalase-positive, motile and rod-shaped with a single polar or subpolar flagellum. Growth occurred at 15-45 °C (optimum, 28-37 °C, pH 5.0-8.0 (optimum, pH 6.0-7.0) and with 0-1.5% NaCl (w/v; optimum, 0.5 %). The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. Unidentified aminolipids, unidentified polar lipids, an unidentified aminophospholipid and an unidentified phospholipid were also detected. The major respiratory quinone was ubiquinone-10 and the major fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0 and C19:0 cyclo ω8c. The genomic DNA G+C content was 69.8 mol%. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D00532T belonged to the family Azospirillaceae and showed 93.4% (Desertibacter roseus 2622T), 93.2% (Skermanella xinjiangensis 10-1-101T), 93.2% ('Skermanella rubra' YIM 93097T) and 92.4% (Desertibacter xinjiangensis M71T) similarities. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain SYSU D00532T is proposed to represent a new species of a new genus, named Arenibaculum pallidiluteum gen. nov., sp. nov., within the family Azospirillaceae. The type strain is SYSU D00532T (=KCTC 82269T=CGMCC 1.18631T=MCCC 1K04984T). We also propose the reclassification of Skermanella xinjiangensis to a new genus Deserticella as Deserticella xinjiangensis comb. nov., and the transfer of the genera Indioceanicola and Oleisolibacter from the family Rhodospirillaceae to the family Azospirillaceaewe based on the phylogenetic results.

Se-Methylselenocysteine Alleviates Liver Injury in Diethylnitrosamine (DEN)-Induced Hepatocellular Carcinoma Rat Model by Reducing Liver Enzymes, Inhibiting Angiogenesis, and Suppressing Nitric Oxide (NO)/Nitric Oxide Synthase (NOS) Signaling Pathway.

BACKGROUND Hepatocellular carcinoma is the third leading cause of cancer-associated mortality. This study aimed to investigate the effects of se-methylselenocysteine (MSC) on oncogenesis of diethylnitrosamine (DEN)-induced hepatocellular carcinoma. MATERIAL AND METHODS A hepatocellular carcinoma rat model was established by administering DEN. Rat models were divided into Model (0.1 mg/kg MSC), Model+0.3 mg/kg MSC, Model+1 mg/kg MSC, and Model+3 mg/kg MSC groups. A Normal control group consisted of mice not administered MSC. Hematoxylin and eosin staining was used to determine liver injury. Immunohistochemical analysis was conducted to identify CD34 and vascular endothelial growth factor (VEGF) expression. VEGF gene transcription was detected with RT-PCR. Biochemical analyses were performed to determine alanine aminotransferase, aspartate aminotransferase, total bilirubin, γ-glutamyl transpeptidase, alkaline phosphatase, and albumin levels in serum, and nitric oxide (NO)/nitric oxide synthase (NOS) levels in liver tissues. Transmission electron microscopy was used to observe the ultra-microstructures of hepatocytes. RESULTS MSC treatment markedly alleviated liver injury and nuclear lesions in the treatment groups compared to the Model group. MSC treatment significantly improved liver functions in the treatment groups compared to the Model group (P<0.05). MSC treatment significantly decreased CD34 expression and NO and NOS levels in liver tissues and suppressed VEGF expression compared to the Model group (all P<0.05). CONCLUSIONS MSC administration alleviated liver injury in a DEN-induced hepatocellular carcinoma rat model through reducing liver enzymes, inhibiting angiogenesis, and suppressing the NO/NOS signaling pathway.

Characterization of LRL5 as a key regulator of root hair growth in maize.

Root hair, a special type of tubular-shaped cell, outgrows from the root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stresses. Studies in the model plant Arabidopsis have revealed that root-hair initiation and elongation are hierarchically regulated by a group of basic helix-loop-helix (bHLH) transcription factors (TFs). However, knowledge regarding the regulatory pathways of these bHLH TFs in controlling root hair growth remains limited. In this study, RNA-seq analysis was conducted to profile the transcriptome in the elongating maize root hair and >1000 genes with preferential expression in root hair were identified. A consensus cis-element previously featured as the potential bHLH-TF binding sites was present in the regulatory regions for the majority of the root hair-preferentially expressed genes. In addition, an individual change in ZmLRL5, the highest-expressed bHLH-TF in maize root hair resulted in a dramatic reduction in the elongation of root hair, and rendered the growth of root hair hypersensitive to translational inhibition. Moreover, RNA-seq, yeast-one-hybrid and ribosome profile analysis suggested that ZmLRL5 may function as a key player in orchestrating the translational process by directly regulating the expression of translational processes/ribosomal genes during maize root hair growth.

ABAT and ALDH6A1, regulated by transcription factor HNF4A, suppress tumorigenic capability in clear cell renal cell carcinoma.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is a malignancy characterized by metabolic reprogramming. ABAT and ALDH6A1 are metabolic enzymes. In this study, we aim to investigate the associations of ABAT and ALDH6A1 with the malignancy of ccRCC cells. METHODS: The gene expression levels of ABAT and ALDH6A1 in ccRCC were analyzed from gene expression microarray datasets and RNA sequencing data. Clinical information was analyzed from The Cancer Genome Atlas (TCGA) data. The distributions of ABAT and ALDH6A1 in ccRCC clinical tissues were screened by reverse transcription-quantitative polymerase chain reaction (RT-QPCR) and immunohistochemical assays. The effect of overexpression of ABAT or ALDH6A1 was measured by detecting the cell viability, migration ability, and the ratio of lactate and nicotinamide adenine dinucleotide phosphate (NADPH). Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were carried out to investigate the transcript regulation of HNF4A in ABAT and ALDH6A1. RESULTS: Remarkable downregulated ABAT and ALDH6A1 expression levels were observed in ccRCC patients and low expression of ABAT and ALDH6A1 was correlated with poor survival. Overexpression of ABAT or ALDH6A1 significantly attenuated cell proliferation and migration, and impaired lactate production. In ABAT increased ccRCC cells, the ratio of NADPH/NADP+ was reduced. Finally, we demonstrated that ABAT and ALDH6A1 were directly regulated by a tumor suppressor, HNF4A. CONCLUSIONS: These observations identified HNF4A-regulated low-expressed ABAT and ALDH6A1 as promising diagnostic and prognostic biomarkers for ccRCC.

Decrease in DNA methylation 1 (DDM1) is required for the formation of m CHH islands in maize.

DNA methylation plays a crucial role in suppressing mobilization of transposable elements and regulation of gene expression. A number of studies have indicated that DNA methylation pathways and patterns exhibit distinct properties in different species, including Arabidopsis, rice, and maize. Here, we characterized the function of DDM1 in regulating genome-wide DNA methylation in maize. Two homologs of ZmDDM1 are abundantly expressed in the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development. We establish that ZmDDM1 is critical for DNA methylation, at CHG sites, and to a lesser extent at CG sites, in heterochromatic regions, and unexpectedly, it is required for the formation of m CHH islands. In addition, ZmDDM1 is indispensable for the presence of 24-nt siRNA, suggesting its involvement in the RdDM pathway. Our results provide novel insight into the role of ZmDDM1 in regulating the formation of m CHH islands, via the RdDM pathway maize, suggesting that, in comparison to Arabidopsis, maize may have adopted distinct mechanisms for regulating m CHH.

The novel circ_0004674/miR-139-5p/ZBTB2 regulatory cascade inhibits the development of oral squamous cell carcinoma.

BACKGROUND: Circular RNAs (circRNAs) are an intriguing family of RNA molecules due to their crucial roles in the pathogenesis of oral squamous cell carcinoma (OSCC). Here, we sought to define the action of human circ_0004674 in OSCC progression. METHODS: The functional role of circ_0004674 was validated by determining its effect on cell growth, apoptosis, and tube formation ability of OSCC cells. For protein quantification, a western blot or immunohistochemistry method was applied. The interaction between miR-139-5p and circ_0004674 or zinc finger and BTB domain containing 2 (ZBTB2) was predicted by online algorithms, and their relationships were confirmed by dual-luciferase reporter and RIP assays. Xenograft models were established to uncover circ_0004674's role in tumor growth. RESULTS: Circ_0004674 expression was upregulated in OSCC. Functionally, knocking down circ_0004674 led to suppressed OSCC cell progression in vitro and delayed tumor growth in vivo. Mechanistically, circ_0004674 post-transcriptionally controlled ZBTB2 expression by competitively pairing to miR-139-5p. Furthermore, the deficiency of miR-139-5p abated circ_0004674 silencing-mediated OSCC cell progression repression, and augmentation of ZBTB2 reversed the anticancer effect of miR-139-5p on OSCC. CONCLUSION: Our findings uncover a novel regulatory cascade, the circ_0004674/miR-139-5p/ZBTB2 axis, with the ability to affect OSCC development in vitro and in vivo, providing a potential opportunity for development of OSCC therapy.

Pd-Catalyzed Enantioselective Desymmetrizing 1,7-Enyne Cycloisomerization of Alkyne-Tethered Cyclopentenes.

An enantioselective Pd-catalyzed intramolecular desymmetrizing cycloisomerization of N-(cyclopent-3-en-1-yl)propiolamides has been developed by employing a new chiral phosphoramidite ligand. A series of structurally unique bridged azabicycles are achieved in moderate to excellent yields with good E/Z selectivity and high enantioselectivity. Synthetic transformations are conducted to demonstrate the practical utility of this reaction.