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Journal For Immunotherapy of Cancer May 2024The incidence of papillary thyroid cancer (PTC) continues to rise all over the world, 10-15% of the patients have a poor prognosis. Although immunotherapy has been...
BACKGROUND
The incidence of papillary thyroid cancer (PTC) continues to rise all over the world, 10-15% of the patients have a poor prognosis. Although immunotherapy has been applied in clinical practice, its therapeutic efficacy remains far from satisfactory, necessitating further investigation of the mechanism of PTC immune remodeling and exploration of novel treatment targets.
METHODS
This study conducted a single-cell RNA sequencing (scRNA-seq) analysis using 18 surgical tissue specimens procured from 14 patients diagnosed with adjacent tissues, non-progressive PTC or progressive PTC. Key findings were authenticated through spatial transcriptomics RNA sequencing, immunohistochemistry, multiplex immunohistochemistry, and an independent bulk RNA-seq data set containing 502 samples.
RESULTS
A total of 151,238 individual cells derived from 18 adjacent tissues, non-progressive PTC and progressive PTC specimens underwent scRNA-seq analysis. We found that progressive PTC exhibits the following characteristics: a significant decrease in overall immune cells, enhanced immune evasion of tumor cells, and disrupted antigen presentation function. Moreover, we identified a subpopulation of lysosomal associated membrane protein 3 (LAMP3) dendritic cells (DCs) exhibiting heightened infiltration in progressive PTC and associated with advanced T stage and poor prognosis of PTC. LAMP3 DCs promote CD8 T cells exhaustion (mediated by NECTIN2-TIGIT) and increase infiltration abundance of regulatory T cells (mediated by chemokine (C-C motif) ligand 17 (CCL17)-chemokine (C-C motif) receptor 4 (CCR4)) establishing an immune-suppressive microenvironment. Ultimately, we unveiled that progressive PTC tumor cells facilitate the retention of LAMP3 DCs within the tumor microenvironment through NECTIN3-NECTIN2 interactions, thereby rendering tumor cells more susceptible to immune evasion.
CONCLUSION
Our findings expound valuable insights into the role of the interaction between LAMP3 DCs and T-cell subpopulations and offer new and effective ideas and strategies for immunotherapy in patients with progressive PTC.
Topics: Humans; Dendritic Cells; Thyroid Cancer, Papillary; Lysosomal-Associated Membrane Protein 3; Thyroid Neoplasms; Male; Female; Tumor Microenvironment; Middle Aged; Tumor Escape; T-Lymphocyte Subsets; Neoplasm Proteins
PubMed: 38816233
DOI: 10.1136/jitc-2024-008983 -
PLoS Genetics May 2024Whether single-cell RNA-sequencing (scRNA-seq) captures the same biological information as single-nucleus RNA-sequencing (snRNA-seq) remains uncertain and likely to be...
Whether single-cell RNA-sequencing (scRNA-seq) captures the same biological information as single-nucleus RNA-sequencing (snRNA-seq) remains uncertain and likely to be context-dependent. Herein, a head-to-head comparison was performed in matched normal-adenocarcinoma human lung samples to assess biological insights derived from scRNA-seq versus snRNA-seq and better understand the cellular transition that occurs from normal to tumoral tissue. Here, the transcriptome of 160,621 cells/nuclei was obtained. In non-tumor lung, cell type proportions varied widely between scRNA-seq and snRNA-seq with a predominance of immune cells in the former (81.5%) and epithelial cells (69.9%) in the later. Similar results were observed in adenocarcinomas, in addition to an overall increase in cell type heterogeneity and a greater prevalence of copy number variants in cells of epithelial origin, which suggests malignant assignment. The cell type transition that occurs from normal lung tissue to adenocarcinoma was not always concordant whether cells or nuclei were examined. As expected, large differential expression of the whole-cell and nuclear transcriptome was observed, but cell-type specific changes of paired normal and tumor lung samples revealed a set of common genes in the cells and nuclei involved in cancer-related pathways. In addition, we showed that the ligand-receptor interactome landscape of lung adenocarcinoma was largely different whether cells or nuclei were evaluated. Immune cell depletion in fresh specimens partly mitigated the difference in cell type composition observed between cells and nuclei. However, the extra manipulations affected cell viability and amplified the transcriptional signatures associated with stress responses. In conclusion, research applications focussing on mapping the immune landscape of lung adenocarcinoma benefit from scRNA-seq in fresh samples, whereas snRNA-seq of frozen samples provide a low-cost alternative to profile more epithelial and cancer cells, and yield cell type proportions that more closely match tissue content.
PubMed: 38814983
DOI: 10.1371/journal.pgen.1011301 -
PloS One 2024DNA barcoding is used to identify cryptic species, survey environmental samples, and estimate phyletic and genetic diversity. Armored scale insects are phytophagous...
DNA barcoding is used to identify cryptic species, survey environmental samples, and estimate phyletic and genetic diversity. Armored scale insects are phytophagous insects and are the most species-rich taxa in the Coccoidea superfamily. This study developed a DNA barcode library for armored scale insect species collected from southern China during 2021-2022. We sequenced a total of 239 specimens, recognized as 50 morphological species, representing two subfamilies and 21 genera. Sequencing analysis revealed that the average G + C content of the cytochrome oxidase subunit I (COI) gene sequence was very low (~18.06%) and that the average interspecific divergence was 10.07% while intraspecific divergence was 3.20%. The intraspecific divergence value was inflated by the high intraspecific divergence in ten taxa, which may indicate novel species overlooked by current taxonomic treatments. All the Automated Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Taxon DNA analysis and Bayesian Poisson Tree Process methods yielded largely consistent results, indicating a robust and credible species delimitation. Based on these results, an intergeneric distance threshold of ≤ 5% was deemed appropriate for the differentiation of armored scale insect species in China. This study establishes a comprehensive barcode library for the identification of armored scale insects, future research, and application.
Topics: Animals; DNA Barcoding, Taxonomic; China; Hemiptera; Phylogeny; Electron Transport Complex IV; Genetic Variation; Gene Library; Bayes Theorem
PubMed: 38814962
DOI: 10.1371/journal.pone.0301499 -
Infection and Drug Resistance 2024Aspiration pneumonia (AP) challenges public health globally. The primary aim of this study was to ascertain the microbiological profile characteristics of patients with...
PURPOSE
Aspiration pneumonia (AP) challenges public health globally. The primary aim of this study was to ascertain the microbiological profile characteristics of patients with AP evaluated by combined detection methods, including conventional microbiological tests (CMTs), chips for complicated infection detection (CCID), and metagenomic next-generation sequencing (mNGS).
PATIENTS AND METHODS
From June 2021 to March 2022, a total of thirty-nine patients with AP or community-acquired pneumonia with aspiration risk factors (AspRF-CAP) from 3 hospitals were included. Respiratory specimens, including bronchoalveolar lavage fluid (BALF), sputum, and tracheal aspirate, were collected for microorganism detection.
RESULTS
Patients with AP were more inclined to be older, to have a shorter duration from illness onset to admission, to have a higher prevalence of different underlying diseases, particularly diabetes mellitus, chronic heart disease, and cerebrovascular disease, and to have a higher CURB-65 score (all < 0.05). A total of 213 and 31 strains of microorganisms were detected in patients with AP and AspRF-CAP, respectively. The most common pathogens in AP were (17/213, 7.98%), (15/213, 7.04%), (15/213, 7.04%), and (14/213, 6.57%). Besides, the most common pathogens in AspRF-CAP were (5/31, 16.13%), (3/31, 9.68%) and (3/31, 9.68%). Moreover, (7/67, 10.45%) and (5/67, 7.46%) were the most common pathogens among the 9 non-survived patients with AP.
CONCLUSION
The prevalent pathogens detected in cases of AP were , and . Early combined detection methods for patients with AP enhance the positive detection rate of pathogens and potentially expedites the initiation of appropriate antibiotic therapeutic strategies.
PubMed: 38813526
DOI: 10.2147/IDR.S461935 -
Turkish Journal of Medical Sciences 2023To investigate the effects of acetylsalicylic acid (ASA) and the use of ultrasound elastography on testicular torsion.
BACKGROUND/AIM
To investigate the effects of acetylsalicylic acid (ASA) and the use of ultrasound elastography on testicular torsion.
MATERIALS AND METHODS
Herein, 6 equal groups of rats were formed (n: 48): control group, sham group, torsion/detorsion (T/D)-1 h group, T/D-1 h + ASA group, T/D-8 h group, and T/D-8 h + ASA group. Testicular torsion was created by rotating the left testis 720° clockwise. At 30 min before torsion, 100 mg/kg of ASA was injected intraperitoneally. Elastography was performed at 8 and 24 h. After orchiectomy, specimens were collected for histopathological evaluation.
RESULTS
When comparing the left testicular volume (LV) parameters obtained from the elastography applied at 8 h, significant differences were observed between the following group pairs: the sham and T/D-8 h groups, T/D-1 h and T/D-8 h groups, and T/D-1 h + ASA and T/D-8 h groups (p = 0.004, p = 0.023, and p = 0.026, respectively). The mean LVS (velocity) (stiffness assessment) of the groups was similar at 8 h. When comparing the LV parameters at 24 h, significant differences were found between the T/D-1 h and T/D-8 h groups and between the T/D-8 h and T/D-8 h + ASA groups (p = 0.008 and p = 0.004, respectively). For the LVS mean values at 24 h, significant differences were found between the control and sham groups, sham and T/D-1 h groups, sham and T/D-8 h groups, and sham and T/D-8 h + ASA groups (p = 0.009, p = 0.021, p = 0.027, and p = 0.009, respectively).Histopathological evaluation showed a decrease in the morphological grades and an increase in the mean testicular injury scores in the T/D-1 h + ASA group compared to the T/D-1 h group. The T/D-8 h + ASA group had a higher morphological grade than the T/D-8 h group, whereas their mean testicular injury scores were similar.
CONCLUSION
ASA treatment for testicular torsion was shown to be ineffective. Elastography can be a complementary method to Doppler ultrasonography in the diagnosis of testicular torsion and can guide surgeons in their approach to surgery.
Topics: Male; Spermatic Cord Torsion; Animals; Aspirin; Elasticity Imaging Techniques; Rats; Testis; Disease Models, Animal; Anti-Inflammatory Agents, Non-Steroidal
PubMed: 38813515
DOI: 10.55730/1300-0144.5729 -
Data in Brief Jun 2024This research introduces an extensive dataset of unprocessed aerial RGB images and orthomosaics of Brassica oleracea crops, captured via a DJI Phantom 4. The dataset,...
This research introduces an extensive dataset of unprocessed aerial RGB images and orthomosaics of Brassica oleracea crops, captured via a DJI Phantom 4. The dataset, publicly accessible, comprises 244 raw RGB images, acquired over six distinct dates in October and November of 2020 as well as 6 orthomosaics from an experimental farm located in Portici, Italy. The images, uniformly distributed across crop spaces, have undergone both manual and automatic annotations, to facilitate the detection, segmentation, and growth modelling of crops. Manual annotations were performed using bounding boxes via the Visual Geometry Group Image Annotator (VIA) and exported in the Common Objects in Context (COCO) segmentation format. The automated annotations were generated using a framework of Grounding DINO + Segment Anything Model (SAM) facilitated by YOLOv8x-seg pretrained weights obtained after training manually annotated images dated 8 October, 21 October, and 29 October 2020. The automated annotations were archived in Pascal Visual Object Classes (PASCAL VOC) format. Seven classes, designated as Row 1 through Row 7, have been identified for crop labelling. Additional attributes such as individual crop ID and the repetitiveness of individual crop specimens are delineated in the Comma Separated Values (CSV) version of the manual annotation. This dataset not only furnishes annotation information but also assists in the refinement of various machine learning models, thereby contributing significantly to the field of smart agriculture. The transparency and reproducibility of the processes are ensured by making the utilized codes accessible. This research marks a significant stride in leveraging technology for vision-based crop growth monitoring.
PubMed: 38813239
DOI: 10.1016/j.dib.2024.110506 -
Journal of Medical Education and... 2024To better construct teaching resources, enhance real-time interaction and feedback between teachers and students in and out of class, and improve the teaching quality of...
OBJECTIVE
To better construct teaching resources, enhance real-time interaction and feedback between teachers and students in and out of class, and improve the teaching quality of parasitology, our team set up a WeChat public account .
METHODS
The data sources were mainly from original pictures and multimedia materials of different parasites collected and produced by our team, as well as related materials collected from traditional publications and digital media. With the instant interactive platform, course schedules and corresponding teaching contents were sent by push notifications, case-based learning was carried out, and 2-way communication between students and teachers was achieved. Teaching effectiveness was assessed using a self-evaluation questionnaire.
RESULTS
A WeChat public account suitable for our daily teaching of parasitology was established. The second recursion and implementation of the learning resources allowed students to conduct in-depth reading and get unrestricted access to high-quality resources through the public account. In addition, all contents were in digital forms and made the original resources reborn, which would make up for our current and future shortage of physical teaching specimens. Moreover, the results from the questionnaire indicated that all these actions encouraged students to master theoretical knowledge, improved their abilities of case analysis and communication, and increased their knowledge of academic progress.
CONCLUSION
Our WeChat public account can provide excellent learning materials for students and is a good supplement to the routine education of human parasitology.
PubMed: 38813087
DOI: 10.1177/23821205241255224 -
Journal of Taibah University Medical... Jun 2024Lymphoma ranks fifth in prevalence among common cancer types worldwide. This lymphatic system cancer arises from T or B cells. Diffuse large B cell lymphomas (DLBCLs)...
BACKGROUND
Lymphoma ranks fifth in prevalence among common cancer types worldwide. This lymphatic system cancer arises from T or B cells. Diffuse large B cell lymphomas (DLBCLs) are associated with most non-Hodgkin lymphomas. Non-coding microRNAs (miRNAs) greatly affect gene expression. A single miRNA can target numerous genes, thus largely influencing gene expression networks. MiRNAs can act as oncogenes or tumor suppressors in controlling DLBCL progression. This study investigated the roles of miRNAs in patients with DLBCL through next-generation sequencing, which was found to be sensitive, accurate, and robust.
METHODS
The study involved seven patients with DLBCLs and three controls at a hematology-oncology clinic. MiRNA was extracted from existing formalin-fixed, paraffin-embedded (FFPE) tissue specimens. Illumina next-generation sequencing was used to sequence samples for miRNA profiling.
RESULTS
Samples from patients showed expression of various hsa-mir miRNAs (1248, 3607, 21, 142, 1244, 182, 6516, 766, 1291, 4449, and 181a), whereas those from healthy individuals showed expression of hsa-mir 1248, 3607, 21, 142, and 877. Hsa-mir-877-3p is known to target multiple genes, and miRNAs such as hsa-mir-877-3p, hsa-mir-1291, and hsa-mir-181a-5p interact primarily with target genes.
CONCLUSIONS
MiRNA profiling in FFPE tissues from patients with DLBCL suggested that miRNA levels can distinguish patients with DLBCL from controls, and therefore may provide prognostic or diagnostic biomarkers for DLBCL. Altered genes and miRNAs may also be potential therapeutic targets.
PubMed: 38812724
DOI: 10.1016/j.jtumed.2024.04.010 -
Turkish Journal of Medical Sciences 2024Intestinal neomucosa formation is a technique defined for the treatment of short bowel syndrome. This study evaluates the effect of glutamine and omega-3 fatty acids on...
BACKGROUND/AIM
Intestinal neomucosa formation is a technique defined for the treatment of short bowel syndrome. This study evaluates the effect of glutamine and omega-3 fatty acids on the growth of intestinal neomucosa on the colonic serosal surface has been evaluated.
MATERIALS AND METHODS
Thirty-two adult male Sprague-Dawley rats were randomly divided into 4 groups: sham, control, glutamine, and omega-3. Laparotomy was performed on all groups. For rats other than the sham group, a 1-cm full-thickness incision was made 4 cm proximal to the ileocecal valve, and colonic serosal surface was sutured as a serosal patch over these openings. By using the oral gavage technique, the glutamine group was ingested with 200 mg/kg/day of glutamine, and the omega-3 group was ingested with 100 mg/kg/day of omega-3 fatty acids. At the end of 14 days, the rats were euthanized, blood specimens were collected, and intestinal segments, including serosal patches, were excised.
RESULTS
Transforming growth factor-beta was significantly lower in the glutamine group compared to the control group. Similarly, fibroblast growth factor-2 was significantly lower in the glutamine group compared to the sham group. Intestinal neomucosa formation was observed in 100% of rats in the glutamine group. In the control and omega-3 groups, intestinal neomucosa formation was observed in 57.1% and 60% of rats, respectively. The inflammatory response, granulation tissue formation, and fibroblastic activity were more severe in the rats of the glutamine and omega-3 groups.
CONCLUSION
The intestinal neomucosa formation is an experimental technique, and both glutamine and omega-3 fatty acids have the potential to positively affect inflammatory response, granulation tissue formation, and fibroblastic activity. Specifically, glutamine has a favorable effect on intestinal neomucosa formation.
Topics: Animals; Glutamine; Fatty Acids, Omega-3; Rats, Sprague-Dawley; Male; Rats; Colon; Short Bowel Syndrome; Serous Membrane; Intestinal Mucosa
PubMed: 38812652
DOI: 10.55730/1300-0144.5766 -
Radiology Case Reports Aug 2024Uterine adenomyomas of endocervical type are rare benign tumors of the uterine cervix commonly presented as cyst-like, dilated glandular structures within polypoid...
Uterine adenomyomas of endocervical type are rare benign tumors of the uterine cervix commonly presented as cyst-like, dilated glandular structures within polypoid masses. A premenopausal woman in her 50s was referred to our hospital because of an increasing watery vaginal discharge. A multifocal cyst measuring 5 × 4.5 cm in size projecting into the endocervical canal was revealed on a contrast-enhanced MRI. The fluid within the tumor showed a hypointense signal on T1-weighted imaging (T1WI) and a hyperintense signal on T2-weighted imaging (T2WI). On T2WI, most of the septa within the tumor showed a slightly hyperintense to hypointense signal, whereas some areas revealed a strong hypointense signal; the contrast effect on the septum was satisfactory. On the T2WI taken 2 years previously, the tumor was a 4.5 × 3.5 cm polypoid mass protruding from the posterior endocervical wall. Contrastingly, the current T2WI showed that the stem was no longer identifiable because of tumor growth. Because previous imaging showed that the tumor was a stalked tumor protruding from the posterior endocervical wall, the imaging diagnosis was uterine adenomyoma of the endocervical type. A biopsy suggested the possibility of a minimal deviation adenocarcinoma (MDA). Hence, a total hysterectomy was performed. The final diagnosis confirmed the uterine adenomyoma of endocervical type. Uterine adenomyoma of the endocervical type might be difficult to differentiate from MDA in small biopsy specimens; therefore, evaluation of morphology by MRI is considered important in preoperative diagnosis.
PubMed: 38812595
DOI: 10.1016/j.radcr.2024.04.084