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1.
J Fungi (Basel) ; 10(6)2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38921409

ABSTRACT

This study aims to report three new species of Conoideocrella and Moelleriella from Yunnan Province, Southwestern China. Species of Conoideocrella and Moelleriella parasitize scale insects (Coccidae and Lecaniidae, Hemiptera) and whiteflies (Aleyrodidae, Hemiptera). Based on the phylogenetic analyses of the three-gene nrLSU, tef-1α, and rpb1, it showed one new record species (Conoideocrella tenuis) and one new species (Conoideocrella fenshuilingensis sp. nov.) in the genus Conoideocrella, and two new species, i.e., Moelleriella longzhuensis sp. nov. and Moelleriella jinuoana sp. nov. in the genus Moelleriella. The three new species were each clustered into separate clades that distinguished themselves from one another. All of them were distinguishable from their allied species based on their morphology. Morphological descriptions, illustrations, and comparisons of the allied taxa of the four species are provided in the present paper. In addition, calculations of intraspecific and interspecific genetic distances were performed for Moelleriella and Conoideocrella.

2.
Genes (Basel) ; 15(6)2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38927720

ABSTRACT

Many enzymes in the Raetz pathway for lipid A biosynthesis in Escherichia coli are essential. A homologous protein Pa1792|LpxH in Pseudomonas aeruginosa is known to complement the loss of LpxH in E. coli. Genome-wide transposon-insertion sequencing analysis indicates that lpxH is essential in P. aeruginosa. However, genetic analysis of lpxH in P. aeruginosa has not been carried out, partly because the conditional alleles of essential genes are not readily constructed. In this study, we first constructed a plasmid-based temperature-sensitive mutant ΔlpxH/pTS-lpxH or lpxH(Ts) in P. aeruginosa PAO1. Spot-plating assay indicated that lpxH(Ts) was lethal at a restrictive temperature, confirming its essentiality for growth. Microscopic analysis revealed that lpxH(Ts) exhibited an oval-shaped morphology, suggesting that lpxH was required for rod-shape formation. SDS-PAGE and Western blotting analysis showed that lpxH(Ts) failed to synthesize lipid A, consistent with its function in lipid A biosynthesis. Strong expression of lpxH but not the non-homologous isoenzyme lpxI or lpxG impeded growth and caused cell lysis, implying that lpxH-specific cofactors were required for this toxic effect in P. aeruginosa. Together, our results demonstrate that lpxH is essential for lipid A biosynthesis, rod-shaped growth, and viability in P. aeruginosa. We propose that this plasmid-based conditional allele is a useful tool for the genetic study of essential genes in P. aeruginosa.


Subject(s)
Bacterial Proteins , Plasmids , Pseudomonas aeruginosa , Pseudomonas aeruginosa/genetics , Plasmids/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Temperature , Mutation , Lipid A/genetics , Lipid A/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism
3.
Genes (Basel) ; 15(5)2024 05 07.
Article in English | MEDLINE | ID: mdl-38790219

ABSTRACT

Pa0665 in Pseudomonas aeruginosa shares homologous sequences with that of the essential A-type iron-sulfur (Fe-S) cluster insertion protein ErpA in Escherichia coli. However, its essentiality in P. aeruginosa and its complementation with E. coli erpA has not been experimentally examined. To fulfill this task, we constructed plasmid-based ts-mutant Δpa0665/pTS-pa0665 using a three-step protocol. The mutant displayed growth defects at 42 °C, which were complemented by expressing ec.erpA. Microscopic observations indicated a petite cell phenotype for Δpa0665/pTS-pa0665 at 42 °C, correlated with the downregulation of the oprG gene. RNA sequencing revealed significant transcriptional changes in genes associated with the oxidative phosphorylation (OXPHOS) system, aligning with reduced ATP levels in Δpa0665/pTS-pa0665 under 42 °C. Additionally, the ts-mutant showed heightened sensitivity to H2O2 at 42 °C. Overall, our study demonstrates the essential role of pa0665 for OXPHOS function and is complemented by ec.erpA. We propose that the plasmid-based ts-allele is useful for genetic analysis of essential genes of interest in P. aeruginosa.


Subject(s)
Bacterial Proteins , Oxidative Phosphorylation , Pseudomonas aeruginosa , Pseudomonas aeruginosa/genetics , Pseudomonas aeruginosa/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Mutation , Escherichia coli/genetics , Escherichia coli/metabolism , Iron-Sulfur Proteins/genetics , Iron-Sulfur Proteins/metabolism , Gene Expression Regulation, Bacterial
4.
Korean J Physiol Pharmacol ; 28(3): 265-273, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38682174

ABSTRACT

This study aims to explore possible effect of RNA polymerase I subunit D (POLR1D) on proliferation and angiogenesis ability of colorectal cancer (CRC) cells and mechanism herein. The correlation of POLR1D and Yin Yang 1 (YY1) expressions with prognosis of CRC patients in TCGA database was analyzed. Quantitative realtime polymerase chain reaction (qRT-PCR) and Western blot were applied to detect expression levels of POLR1D and YY1 in CRC cell lines and CRC tissues. SW480 and HT- 29 cells were transfected with si-POLR1D or pcDNA3.1-POLR1D to achieve POLR1D suppression or overexpression before cell migration, angiogenesis of human umbilical vein endothelial cells were assessed. Western blot was used to detect expressions of p38 MAPK signal pathway related proteins and interaction of YY1 with POLR1D was confirmed by dual luciferase reporter gene assay and chromatin immunoprecipitation (ChIP). TCGA data showed that both POLR1D and YY1 expressions were up-regulated in CRC patients. High expression of POLR1D was associated with poor prognosis of CRC patients. The results showed that POLR1D and YY1 were highly expressed in CRC cell lines. Inhibition or overexpression of POLR1D can respectively suppress or enhance proliferation and angiogenesis of CRC cells. YY1 inhibition can suppress CRC progression and deactivate p38 MAPK signal pathway, which can be counteracted by POLR1D overexpression. JASPAR predicted YY1 can bind with POLR1D promoter, which was confirmed by dual luciferase reporter gene assay and ChIP. YY1 transcription can up-regulate POLR1D expression to activate p38 MAPK signal pathway, thus promoting proliferation and angiogenesis ability of CRC cells.

5.
Biomolecules ; 14(4)2024 Mar 25.
Article in English | MEDLINE | ID: mdl-38672411

ABSTRACT

Intervertebral disc degeneration (IDD) is a major cause of lower back pain. The pathophysiological development of IDD is closely related to the stimulation of various stressors, including proinflammatory cytokines, abnormal mechanical stress, oxidative stress, metabolic abnormalities, and DNA damage, among others. These factors prevent normal intervertebral disc (IVD) development, reduce the number of IVD cells, and induce senescence and apoptosis. Stress-activated protein kinases (SAPKs), particularly, c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (p38 MAPK), control cell signaling in response to cellular stress. Previous studies have shown that these proteins are highly expressed in degenerated IVD tissues and are involved in complex biological signal-regulated processes. Therefore, we summarize the research reports on IDD related to JNK and p38 MAPK. Their structure, function, and signal regulation mechanisms are comprehensively and systematically described and potential therapeutic targets are proposed. This work could provide a reference for future research and help improve molecular therapeutic strategies for IDD.


Subject(s)
Intervertebral Disc Degeneration , JNK Mitogen-Activated Protein Kinases , p38 Mitogen-Activated Protein Kinases , Intervertebral Disc Degeneration/metabolism , Intervertebral Disc Degeneration/pathology , Humans , p38 Mitogen-Activated Protein Kinases/metabolism , JNK Mitogen-Activated Protein Kinases/metabolism , Animals , MAP Kinase Signaling System , Signal Transduction , Oxidative Stress , Intervertebral Disc/metabolism , Intervertebral Disc/pathology , Intervertebral Disc/enzymology
6.
Abdom Radiol (NY) ; 49(5): 1569-1583, 2024 05.
Article in English | MEDLINE | ID: mdl-38587628

ABSTRACT

OBJECTIVES: The purpose of this study was to explore and verify the value of various machine learning models in preoperative risk stratification of pheochromocytoma. METHODS: A total of 155 patients diagnosed with pheochromocytoma through surgical pathology were included in this research (training cohort: n = 105; test cohort: n = 50); the risk stratification scoring system classified a PASS score of < 4 as low risk and a PASS score of ≥ 4 as high risk. From CT images captured during the non-enhanced, arterial, and portal venous phase, radiomic features were extracted. After reducing dimensions and selecting features, Logistic Regression (LR), Extra Trees, and K-Nearest Neighbor (KNN) were utilized to construct the radiomics models. By adopting ROC curve analysis, the optimal radiomics model was selected. Univariate and multivariate logistic regression analyses of clinical radiological features were used to determine the variables and establish a clinical model. The integration of radiomics and clinical features resulted in the creation of a combined model. ROC curve analysis was used to evaluate the performance of the model, while decision curve analysis (DCA) was employed to assess its clinical value. RESULTS: 3591 radiomics features were extracted from the region of interest in unenhanced and dual-phase (arterial and portal venous phase) CT images. 13 radiomics features were deemed to be valuable. The LR model demonstrated the highest prediction efficiency and robustness among the tested radiomics models, with an AUC of 0.877 in the training cohort and 0.857 in the test cohort. Ultimately, the composite of clinical features was utilized to formulate the clinical model. The combined model demonstrated the best discriminative ability (AUC, training cohort: 0.887; test cohort: 0.874). The DCA of the combined model showed the best clinical efficacy. CONCLUSION: The combined model integrating radiomics and clinical features had an outstanding performance in differentiating the risk of pheochromocytoma and could offer a non-intrusive and effective approach for making clinical decisions.


Subject(s)
Adrenal Gland Neoplasms , Machine Learning , Pheochromocytoma , Tomography, X-Ray Computed , Humans , Pheochromocytoma/diagnostic imaging , Female , Male , Tomography, X-Ray Computed/methods , Adrenal Gland Neoplasms/diagnostic imaging , Middle Aged , Adult , Risk Assessment , Retrospective Studies , Aged , Radiographic Image Interpretation, Computer-Assisted/methods , Radiomics
7.
J Clin Ultrasound ; 52(5): 491-498, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38437597

ABSTRACT

OBJECTIVE: To investigate the value of ultrasonography in the diagnosis of heterotopic pregnancy and the follow-up. METHODS: A retrospective analysis of 50 cases of clinically diagnosed heterotopic pregnancy in our hospital was performed, the clinical characteristics and ultrasonographic manifestations of the patients were summarized, the reasons for initial ultrasound missed diagnosis and misdiagnosis were analyzed, and the pregnancy outcomes were followed up. RESULTS: Among the 50 cases, the initial ultrasound diagnoses of intrauterine pregnancy were all gestational sac type, 32 cases of ectopic pregnancy were located in the fallopian tube, and 10 cases were located in the uterine horn, 1 case at cervix, and 1 case at caesarean section scar. Forty-one cases were consistent with surgery and/or pathology, representing initial ultrasound diagnosis coincidence rate of about 82%. Six cases were missed in the initial ultrasound examination (12%), and three cases were misdiagnosed (6%). The maximum diameter of the intrauterine gestational sac was 9-48 mm, the average was about 24.90 ± 9.56 mm, the maximum diameter of the ectopic pregnancy gestational sac or mass was 11-63 mm, and the average was about 31.45 ± 13.82 mm (p < 0.05). Intrauterine pregnancy outcomes were followed up, 45 patients with complete data and 5 patients were lost to follow-up. The follow-up rate was about 90%. CONCLUSION: Combining the patient's medical history and clinical characteristics can reduce missed diagnosis and misdiagnosis of heterotopic pregnancy. Ultrasonography has important value in the assessment of intrauterine pregnancy growth and development, and the integrity of maternal uterus.


Subject(s)
Pregnancy, Heterotopic , Ultrasonography, Prenatal , Humans , Female , Pregnancy , Adult , Retrospective Studies , Ultrasonography, Prenatal/methods , Pregnancy, Heterotopic/diagnostic imaging , Young Adult , Pregnancy Outcome , Follow-Up Studies
8.
Cell Prolif ; 57(2): e13541, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37697480

ABSTRACT

Intervertebral disc degeneration (IDD) is a prevalent musculoskeletal degenerative disorder worldwide, and ~40% of chronic low back pain cases are associated with IDD. Although the pathogenesis of IDD remains unclear, the reduction in nucleus pulposus cells (NPCs) and degradation of the extracellular matrix (ECM) are critical factors contributing to IDD. Notochordal cells (NCs), derived from the notochord, which rapidly degrades after birth and is eventually replaced by NPCs, play a crucial role in maintaining ECM homeostasis and preventing NPCs apoptosis. Current treatments for IDD only provide symptomatic relief, while lacking the ability to inhibit or reverse its progression. However, NCs and their secretions possess anti-inflammatory properties and promote NPCs proliferation, leading to ECM formation. Therefore, in recent years, NCs therapy targeting the underlying cause of IDD has emerged as a novel treatment strategy. This article provides a comprehensive review of the latest research progress on NCs for IDD, covering their biological characteristics, specific markers, possible mechanisms involved in IDD and therapeutic effects. It also highlights significant future directions in this field to facilitate further exploration of the pathogenesis of IDD and the development of new therapies based on NCs strategies.


Subject(s)
Intervertebral Disc Degeneration , Intervertebral Disc , Nucleus Pulposus , Humans , Intervertebral Disc Degeneration/metabolism , Notochord/metabolism , Notochord/pathology , Nucleus Pulposus/metabolism , Cell Proliferation , Apoptosis , Intervertebral Disc/pathology
10.
Ann Surg Oncol ; 31(2): 1108-1115, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37925658

ABSTRACT

BACKGROUND: Stage IE primary thyroid lymphoma (PTL) has been diagnosed in approximately half of patients with PTL; however, the optimal treatment for stage IE PTL has not yet been established. METHODS: Stage IE PTL patients were identified from the Surveillance, Epidemiology, and End Results (SEER) database between 1998 and 2019. Thereafter, the disease-specific survival (DSS) and treatment modalities (surgery alone, surgery + radiotherapy (RT) and/or chemotherapy (CT), and RT and/or CT) of these patients were compared by Kaplan-Meier curves and log-rank test after propensity score matching (PSM). Additionally, patients with PTL from the Affiliated Sixth People's Hospital of the Shanghai Jiao Tong University and School of Medicine (Shanghai, China) between 2007 and 2022 were retrospectively analyzed as an external cohort. RESULTS: Among the 1596 patients with PTL from the SEER database, 842 were identified as patients with stage IE PTL, with an average follow-up period of 7.8 years. Pairwise analysis after PSM revealed no significant difference between the DSS of the three treatment groups. A total of 38 patients with PTL were identified in the external cohort, with an average follow-up period of 3.4 years. Compared with the RT and/or CT group, the surgery-alone group showed no significant difference in the incidence of hypothyroidism (p = 0.161) but had significantly fewer treatment-related complications (p = 0.021), shorter treatment duration (p < 0.001), and lower treatment costs (p = 0.025). CONCLUSIONS: The results of our study demonstrate that surgery is a viable treatment option for patients with stage IE PTL.


Subject(s)
Lymphoma , Thyroid Neoplasms , Humans , Retrospective Studies , China , Lymphoma/surgery , Thyroid Neoplasms/pathology
11.
Int J Mol Sci ; 24(17)2023 Aug 26.
Article in English | MEDLINE | ID: mdl-37686041

ABSTRACT

Lower back pain, a leading cause of disability worldwide, is associated with intervertebral disc degeneration (IDD) in approximately 40% of cases. Although nucleus pulposus (NP) cell senescence is a major contributor to IDD, the underlying mechanisms remain unclear. We collected NP samples from IDD patients who had undergone spinal surgery. Healthy and senescent NP tissues (n = 3) were screened using the Pfirrmann grading system combined with immunohistochemistry, as well as hematoxylin and eosin, Safranin O, Alcian blue, and Masson staining. Differentially expressed proteins (DEPs) were identified using quantitative TMT-based proteomics technology. Bioinformatics analyses included gene ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and protein-protein interaction (PPI) analyses. In addition, immunofluorescence was used to verify protein expression. In total, 301 DEPs were identified in senescent NP tissues, including 92 upregulated and 209 downregulated proteins. In GO, DEPs were primarily associated with NF-kappaB transcription factor, extracellular regions, cellular protein metabolic processes, and post-translational protein modification. The enriched KEGG pathways included TGF-ß, Wnt, RAP1, interleukin-17, extracellular matrix-receptor adhesion, and PI3K/Akt signaling pathways. PPI analysis demonstrated interactions between multiple proteins. Finally, immunofluorescence verified the expressions of MMP3, LUM, TIMP1, and CDC42 in senescent NP cells. Our study provides valuable insights into the mechanisms underlying senescent NP tissues in IDD patients. DEPs provide a basis for further investigation of the effects of senescent factors on IDD.


Subject(s)
Intervertebral Disc Degeneration , Nucleus Pulposus , Humans , Intervertebral Disc Degeneration/genetics , Phosphatidylinositol 3-Kinases , Proteomics , Genes, Regulator
12.
Microbiol Spectr ; 11(3): e0133823, 2023 06 15.
Article in English | MEDLINE | ID: mdl-37191499

ABSTRACT

It is uncertain whether PA1610|fabA is essential or dispensable for growth on LB-agar plates under aerobic conditions in Pseudomonas aeruginosa PAO1. To examine its essentiality, we disrupted fabA in the presence of a native promoter-controlled complementary copy on ts-plasmid. In this analysis, we showed that the plasmid-based ts-mutant ΔfabA/pTS-fabA failed to grow at a restrictive temperature, consistent with the observation by Hoang and Schweizer (T. T. Hoang, H. P. Schweizer, J Bacteriol 179:5326-5332, 1997, https://doi.org/10.1128/jb.179.17.5326-5332.1997), and expanded on this by showing that ΔfabA exhibited curved cell morphology. On the other hand, strong induction of fabA-OE or PA3645|fabZ-OE impeded the growth of cells displaying oval morphology. Suppressor analysis revealed a mutant sup gene that suppressed a growth defect but not cell morphology of ΔfabA. Genome resequencing and transcriptomic profiling of sup identified PA0286|desA, whose promoter carried a single-nucleotide polymorphism (SNP), and transcription was significantly upregulated (level increase of >2-fold, P < 0.05). By integration of the SNP-bearing promoter-controlled desA gene into the chromosome of ΔfabA/pTS-fabA, we showed that the SNP is sufficient for ΔfabA to phenocopy the sup mutant. Furthermore, mild induction of the araC-PBAD-controlled desA gene but not desB rescued ΔfabA. These results validated that mild overexpression of desA fully suppressed the lethality but not the curved cell morphology of ΔfabA. Similarly, Zhu et al. (Zhu K, Choi K-H, Schweizer HP, Rock CO, Zhang Y-M, Mol Microbiol 60:260-273, 2006, https://doi.org/10.1111/j.1365-2958.2006.05088.x) showed that multicopy desA partially alleviated the slow growth phenotype of ΔfabA, the difference in which was that ΔfabA was viable. Taken together, our results demonstrate that fabA is essential for aerobic growth. We propose that the plasmid-based ts-allele is useful for exploring the genetic suppression interaction of essential genes of interest in P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen whose multidrug resistance demands new drug development. Fatty acids are essential for viability, and essential genes are ideal drug targets. However, the growth defect of essential gene mutants can be suppressed. Suppressors tend to be accumulated during the construction of essential gene deletion mutants, hampering the genetic analysis. To circumvent this issue, we constructed a deletion allele of fabA in the presence of a native promoter-controlled complementary copy in the ts-plasmid. In this analysis, we showed that ΔfabA/pTS-fabA failed to grow at a restrictive temperature, supporting its essentiality. Suppressor analysis revealed desA, whose promoter carried a SNP and whose transcription was upregulated. We validated that both the SNP-bearing promoter-controlled and regulable PBAD promoter-controlled desA suppressed the lethality of ΔfabA. Together, our results demonstrate that fabA is essential for aerobic growth. We propose that plasmid-based ts-alleles are suitable for genetic analysis of essential genes of interest.


Subject(s)
Fatty Acids , Pseudomonas aeruginosa , Pseudomonas aeruginosa/genetics , Temperature , Promoter Regions, Genetic , Plasmids/genetics , Mutation , Bacterial Proteins/genetics
13.
J Cancer Res Clin Oncol ; 149(9): 6303-6313, 2023 Aug.
Article in English | MEDLINE | ID: mdl-36735028

ABSTRACT

PURPOSE: Locally advanced papillary thyroid cancer (LAPTC) has poor prognosis. Large-scale genomic testing has revealed multiple oncogenic drivers which may be essential for understanding tumor progression. However, the accurate identification of high recurrence risk and poor prognosis in thyroid carcinoma remains unclear. The objective of this study was to analyze genetic profile and clinicopathologic features of locally advanced papillary thyroid cancers. METHODS: An observational cohort study was performed to identify molecular characteristics of LAPTC and a prognosis comparison of LAPTC with different genetic mutations. ThyroSeq v2 next-generation sequencing (57-gene panel) was performed on fresh tumor tissue. Then, the clinicopathological features between tumors with different genetic mutations were compared. Additionally, correlations of tumor recurrence and disease free survival with different genetic alterations were analyzed. RESULTS: This study showed that the main mutation is common BRAFV600E (66.2%, 43/65) in LAPTC, followed by the TERT promoter mutations (38.5%, 25/65). Synergetic mutations of BRAFV600E and TERT promoters (B&T) were identified in 26.2% LAPTC (17/65), which is associated with tall-cell variant, extrathyroidal invasion and advanced tumor stage (III/IV). The synergetic mutations of B&T are also significantly associated with higher risk of recurrence (hazard ratio [HR], 6.0; 95% confidence interval, CI 1.26-28.55, P = 0.02) and mortality (17.6%, 3/17). CONCLUSIONS: Synergetic mutations of B&T are common in LAPTC, which is associated with the aggressive clinicopathologic features and an increased risk of recurrence and mortality. This finding may help to predict aggressive behavior of LAPTC and to assist in clinical decision-making.


Subject(s)
Carcinoma, Papillary , Telomerase , Thyroid Neoplasms , Humans , Thyroid Cancer, Papillary/genetics , Proto-Oncogene Proteins B-raf/genetics , Carcinoma, Papillary/genetics , Carcinoma, Papillary/pathology , Neoplasm Recurrence, Local/genetics , Thyroid Neoplasms/genetics , Thyroid Neoplasms/pathology , Prognosis , Mutation , Telomerase/genetics
14.
J Colloid Interface Sci ; 629(Pt A): 697-705, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36099839

ABSTRACT

Revealing the types of and interplays among multiple active-sites in iron-nitrogen-carbon (FeNC) materials is of great significance for developing high-performance, Fe-based non-precious metal catalysts for oxygen reduction reaction (ORR). In this paper, a single-atom FeNC catalyst is prepared through high-temperature pyrolyzing of melamine foam (MF), iron phthalocyanine (FePc), phthalocyanine (Pc), and zinc (Zn)-salts composite. The catalyst is found to contain a variety of active-sites, including carbon atom next to pyridinic-N (pyridinicNC), Fe-N4 and pore defect. It is shown that MF with high N-content is responsible for the formation of the main pyridinicNC sites and in the meantime acts as the self-sacrificed template for framework of the catalyst. The presence of Pc can facilitate the formation of the predominant Fe-N4 sites, since the interplay between Pc and FePc results in a confinement of Fe-N4. Zn-salts serve as the pore-forming additives to create sufficient pore defects which can also anchor pyridinicNC and Fe-N4 structures. The results of density functional theory (DFT) calculations suggest that the multiple active-sites function synergistically to enable high-efficiency ORR electrocatalysis. The optimal FeNC catalyst shows superior ORR activity with a half-wave potential of ∼0.88 V (vs. RHE), as well as high methanol tolerance and electrochemical stability compared to the commercial carbon-supported platinum (Pt/C) catalyst.

15.
Appl Environ Microbiol ; 88(14): e0048022, 2022 07 26.
Article in English | MEDLINE | ID: mdl-35762790

ABSTRACT

Over 300 essential genes are predicted using transposon sequencing in the genome of Pseudomonas aeruginosa. However, methods for reverse genetic analysis of essential genes are scarce. To address this issue, we developed a three-step protocol consisting of integration of deletion plasmid, introduction of temperature-sensitive rescue plasmid, and excision of integrated-deletion plasmid to construct the plasmid-based temperature-sensitive allele of essential genes. Using PA0006 as an example, we showed that PA0006(Ts) exhibited wild-type cell morphology at permissive temperature but filamentous form at restrictive temperatures. We further showed that the glycerol-mannoheptose-bisphosphate phosphatase GmhB in Escherichia coli shared 32.4% identity with that of PA0006p and functionally complemented the defect of PA0006(Ts) at 42°C. SDS-PAGE and Western blotting indicated the presence and absence of the complete core lipopolysaccharide (LPS) and B-band O-antigen in PA0006(Ts) at 30 and 42°C, respectively. An isolated suppressor sup displayed wild-type-like cell morphology but no complete core LPS or O-antigen. Genome resequencing together with comparative transcriptomic profiling identified a candidate suppressor fructose-bisphosphate phosphatase in which the promoter harbored a SNP and the transcription level was not downregulated at 42°C compared to 30°C in sup. It was further validated that fbp overexpression suppressed the lethality of PA0006(Ts) at 42°C. Taken together, our results demonstrate that PA0006 plays a role in regulation of cell morphology and biosynthesis of core LPS. This three-step protocol for construction of conditional lethal allele in P. aeruginosa should be widely applicable for genetic analysis of other essential genes of interest, including analysis of bypass suppressibility. IMPORTANCE Microbial essential genes encode nondispensable function for cell growth and therefore are ideal targets for the development of new drugs. Essential genes are readily identified using transposon-sequencing technology at the genome scale. However, genetic analysis of essential genes of interest was hampered by limited methodologies. To address this issue, we developed a three-step protocol for construction of conditional allele of essential genes in the opportunistic pathogen Pseudomonas aeruginosa. Using PA0006 as an example, we demonstrated that the plasmid-based PA0006(Ts) mutant exhibited defects in regulation of cell morphology, formation of intact core LPS, and attachment of the O-antigen at restrictive temperatures but not at permissive temperatures. A suppressor of PA0006(Ts) was isolated through spontaneous mutations and showed restored cell morphology but not core oligosaccharide or O-antigen. This method should be widely applicable for phenotype and suppressibility analyses of other essential genes of interest in P. aeruginosa.


Subject(s)
Lipopolysaccharides , Pseudomonas aeruginosa , Alleles , Escherichia coli/genetics , O Antigens , Phosphoric Monoester Hydrolases/genetics , Plasmids/genetics , Pseudomonas aeruginosa/genetics
16.
Oncotarget ; 13: 614, 2022.
Article in English | MEDLINE | ID: mdl-35419172

ABSTRACT

[This corrects the article DOI: 10.18632/oncotarget.9530.].

17.
J Clin Endocrinol Metab ; 107(6): 1589-1598, 2022 05 17.
Article in English | MEDLINE | ID: mdl-35213704

ABSTRACT

CONTEXT: A few papillary thyroid microcarcinomas (PTMCs) may have skip metastasis (SLNM), but the risk factors remain controversial and the prognosis is unclear. OBJECTIVES: To investigate the incidence, lymph node metastasis (LNM) patterns, risk factors, and prognosis of SLNM in PTMCs. METHODS: We reviewed the medical records of PTMC patients who underwent thyroid surgery in our institution. Analyses of risk factors were performed for SLNM. Recurrence-free survival (RFS) of SLNM, central lymph node metastasis (CLNM), and continuous metastasis (CLNM and lateral lymph node metastasis [CLNM + LLNM]) were compared after propensity score matching (PSM). RESULTS: SLNM was detected in 1.7% (50/3923) and frequently involved level III (66.7%). Compared with CLNM + LLNM, SLNM had more LNM at a single level (P < 0.01) and less LNM at 2 levels (P < 0.05). A tumor size of 0.5 to 1 cm (odds ratio [OR], 2.26; 95% CI, 1.27-4.00) and location in the upper pole (OR, 3.30; 95% CI, 2.02-5.40) were independent risk factors for SLNM. A total of 910 (23.2%) PTMCs with LNM were included in the prognostic analysis. At a median follow-up of 60 months, the RFS of SLNM did not differ from that of CLNM (P = 0.10) but was significantly higher than that of CLNM + LLNM (P < 0.01) after using PSM. CONCLUSIONS: When the tumor size is 0.5 to 1 cm or its location is in the upper pole, we must remain vigilant to SLNM in PTMC. Because its prognosis is comparable to that of only CLNM and better than that of CLNM + LLNM, less intensive treatment should be considered.


Subject(s)
Carcinoma, Papillary , Thyroid Neoplasms , Carcinoma, Papillary/pathology , Humans , Lymph Nodes/pathology , Lymphatic Metastasis/pathology , Prognosis , Retrospective Studies , Risk Factors , Thyroid Neoplasms/pathology
18.
Endocrine ; 75(2): 495-507, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34699028

ABSTRACT

PURPOSES: Distant metastasis from papillary thyroid microcarcinoma (PTMC) is extremely rare and the long-term outcomes and independent prognostic factors remain unclear. The present study aimed to investigate clinicopathological characteristics and evaluate the long-term outcomes and prognostic factors of PTMC patients with distant metastases (DM) who underwent surgery and radioactive iodine (131I) treatment. METHODS: We retrospectively reviewed the medical records of 13,441 patients with thyroid cancer (including 1697 cases with PTMC) who underwent 131I treatment at our institution between January 2008 and December 2019. PTMC patients with distant metastases with sufficient clinical follow-up data were enrolled in this cohort study. The overall survival (OS) and progression-free survival (PFS) were analyzed by the Kaplan-Meier method and the prognostic factors were assessed by Cox proportional hazards. RESULTS: Thirty-three PTMC patients with DM were enrolled in this study. The median follow-up was 75 months (range: 5-151 months). The 5-year and 10-year OS rates were 96.97 and 81.41%, respectively, and the 5-year and 10-year PFS rates were 90.46 and 69.68%, respectively. Multivariate analysis showed that male sex (P = 0.005), radioactive iodine refractory PTMC (P = 0.033), and symptomatic DM (P = 0.022) were significantly associated with worse 10-year PFS in PTMC patients with DM. No independent predictor related to poor 10-year OS was found in the present study. CONCLUSIONS: The prognosis of PTMC patients becomes worse after the development of DM. Male sex, radioactive iodine refractory PTMC, and symptomatic DM were identified as independent factors associated with PFS.


Subject(s)
Thyroid Neoplasms , Carcinoma, Papillary , Cohort Studies , Humans , Iodine Radioisotopes/therapeutic use , Male , Prognosis , Retrospective Studies , Thyroid Neoplasms/pathology , Thyroidectomy
19.
Front Endocrinol (Lausanne) ; 12: 729565, 2021.
Article in English | MEDLINE | ID: mdl-34790166

ABSTRACT

Background: Despite extensive research, the papillary thyroid carcinoma (PTC) ecosystem is poorly characterized and, in particular, locoregional progression. Available evidence supports that single-cell transcriptome sequencing (Sc-RNA seq) can dissect tumor ecosystems. Methods: Tissue samples from one PTC patient, including matched primary tumor (Ca), lymph node (LN) metastasis, and paracancerous tissue (PCa), were subjected to Sc-RNA seq with 10×Genomics. Dual-label immunofluorescence and immunohistochemistry were used to confirm the existence of cell subtypes in a separate cohort. Results: 11,805 cell transcriptomes were profiled, cell landscapes of PTC were composed of malignant follicular epithelial cells (MFECs), CD8+ and CD4+ T cells, B cells, vascular endothelial cells, fibroblasts and cancer-associated fibroblasts (CAFs). Between Ca and LN ecosystems, the proportions of MFEC and interstitial cells were similar, less than 1/25(229/6,694, 361/3,895), while the proportion of normal follicular epithelial cells (NFECs) and interstitial cells was > 2 in PCa (455/171). NFECs in PCa formed a separate cluster, while MFECs in Ca and LN exhibited a profound transcriptional overlap, and the interstitial cells among these samples had an overall concordance in their identity and representation, albeit with some distinctions in terms of the cell percentage per subset. A fraction of the B cell subpopulation in Ca expressed inhibitory receptors, while their respective ligand genes were clearly transcribed in T cell and malignant epithelial cell clusters, while some CD8+ T cells in both Ca and LN produced high levels of inhibitory receptors whose respective ligands were overexpressed in some CD4+ T cells. Three CAF subtypes in Ca and LN were identified, which may be due to mutual transitions. Conclusions: Our data provide new insights into the PTC ecosystem and highlight the differences in ecosystems in PTC progression, which updates our understanding of PTC biology and will improve individualized patient treatment.


Subject(s)
Biomarkers, Tumor/metabolism , Gene Expression Regulation, Neoplastic , Single-Cell Analysis/methods , Thyroid Cancer, Papillary/pathology , Thyroid Neoplasms/pathology , Transcriptome , Biomarkers, Tumor/genetics , CD8-Positive T-Lymphocytes/metabolism , CD8-Positive T-Lymphocytes/pathology , Cancer-Associated Fibroblasts/metabolism , Cancer-Associated Fibroblasts/pathology , Cohort Studies , Endothelial Cells/metabolism , Endothelial Cells/pathology , Female , Humans , Lymph Nodes/metabolism , Lymph Nodes/pathology , Middle Aged , Prognosis , Thyroid Cancer, Papillary/genetics , Thyroid Cancer, Papillary/metabolism , Thyroid Neoplasms/genetics , Thyroid Neoplasms/metabolism
20.
Clin Endocrinol (Oxf) ; 95(1): 209-216, 2021 07.
Article in English | MEDLINE | ID: mdl-33660317

ABSTRACT

CONTEXT: Multifocality and bilaterality are common in patients with papillary thyroid microcarcinoma (PTMC). However, their clinical behaviours and prognostic implications remain controversial. OBJECTIVE: To investigate the relationship between multifocality and classically aggressive characteristics and outcomes in patients with PTMC. METHODS: Clinical data of 3005 patients with PTMC were retrospectively reviewed at a tertiary medical centre. The role of unilateral and bilateral multifocality in aggressive characteristics and clinical outcomes of PTMC was evaluated using propensity score matching (PSM). RESULTS: A total of 573 patients had bilateral multifocal disease (B-MFD), 272 had unilateral multifocal disease (U-MFD), and 2160 had unifocal disease (UFD). Univariate analysis showed that patients in the multifocal disease (MFD) groups showed significantly different characteristics compared to patients in the UFD group in terms of age, chronic lymphocytic thyroiditis (CLT), follicular variant PTMC, tumour diameter, aggressive growth, including extrathyroidal extension (ETE), central lymph node metastasis (CLNM) and lateral lymph node metastasis (LLNM), and TNM stage, and underwent radioactive iodine (RAI) therapy. Further stratified analysis revealed that patients in the B-MFD group reflected the differences between the MFD and UFD groups. However, those in the U-MFD group showed slight differences only in sex, CLT and cell subtypes, compared to the UFD group. In addition, PSM indicated differences in ETE, CLNM and LLNM between the B-MFD and UFD groups (p < .001), while only ETE differed between the U-MFD and UFD groups (p < .001). After a median follow-up period of 60 months, no difference was observed in recurrence-free survival between the UFD and B-MFD (p = .294) or U-MFD (p = .603) groups using PSM. CONCLUSION: This propensity score matching analysis provides strong evidence that bilateral multifocality, rather than unilateral multifocality, should be considered as an aggressive marker at presentation, and neither is an independent prognostic factor for clinical outcome in PTMC.


Subject(s)
Thyroid Neoplasms , Carcinoma, Papillary , Humans , Iodine Radioisotopes , Prognosis , Propensity Score , Retrospective Studies , Risk Factors
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