Claudin18.2 expression and its clinicopathological feature in adenocarcinoma from various parts.

AIMS: To clarify claudin18.2 expression and its clinicopathological features in various cancers, especially in lung adenocarcinoma. METHODS: Immunohistochemistry staining and fluorescence in situ hybridisation (FISH) were performed to detect claudin18.2 expression and CLDN18 gene rearrangement in adenocarcinoma from different organs. RESULTS: The results showed that claudin18.2 expression was found in 68% (27 of 40) of lung mucinous adenocarcinoma, 52% (16 of 31) of cholangiocarcinoma, 2% (10 of 423) of colorectal adenocarcinoma tissue microarray, 27% (6 of 22) of colorectal mucinous adenocarcinoma and 30% (3 of 10) of cervical adenocarcinoma, but not in all 39 cases of invasive breast adenocarcinoma by immunohistochemistry staining. There was significantly positive correlation between ratio of claudin18.2-positive carcinoma cells and staining intensity in lung mucinous adenocarcinoma and cholangiocarcinoma. Claudin18.2 expression was much more in female patients than male patients with lung mucinous adenocarcinoma. In addition, cholangiocarcinoma with claudin18.2 expression was more aggressive and had perineural invasion. Intraductal papillary neoplasm of the bile duct and epithelial dysplasia of the adjacent bile in cholangiocarcinoma also showed claudin18.2 expression. All three cases of cervical adenocarcinoma with claudin18.2 expression were moderately differentiated adenocarcinoma including one human papillomavirus (HPV)-associated carcinoma, two non-HPV-associated and gastric-type carcinoma. CLDN18 gene rearrangement was not found in all 22 cases with high claudin18.2 expression by FISH. CONCLUSIONS: Our results suggest claudin18.2 might be a potential biomarker for targeted therapy on lung mucinous adenocarcinoma, cholangiocarcinoma, colorectal mucinous adenocarcinoma and gastric-type cervical adenocarcinoma.

Whole-Mount Fluorescence In Situ Hybridization to Study Spermatogenesis in the Anopheles Mosquito.

Spermatogenesis is a complex biological process during which diploid cells undergo successive mitotic and meiotic division followed by large structural changes to form haploid spermatozoa. Besides the biological aspect, studying spermatogenesis is of paramount importance for understanding and developing genetic technologies such as gene drive and synthetic sex ratio distorters, which, by altering Mendelian inheritance and the sperm sex ratio, respectively, could be used to control pest insect populations. These technologies have proven to be very promising in lab settings and could potentially be used to control wild populations of Anopheles mosquitoes, which are vectors of malaria. Due to the simplicity of the testis anatomy and their medical importance, Anopheles gambiae, a major malaria vector in sub-Saharan Africa, represents a good cytological model for studying spermatogenesis. This protocol describes how whole-mount fluorescence in situ hybridization (WFISH) can be used to study the dramatic changes in cell nuclear structure through spermatogenesis using fluorescent probes that specifically stain the X and Y chromosomes. FISH usually requires the disruption of the reproductive organs to expose mitotic or meiotic chromosomes and allow the staining of specific genomic regions with fluorescent probes. WFISH enables the preservation of the native cytological structure of the testis, coupled with a good level of signal detection from fluorescent probes targeting repetitive DNA sequences. This allows researchers to follow changes in the chromosomal behavior of cells undergoing meiosis along the structure of the organ, where each phase of the process can clearly be distinguished. This technique could be particularly useful for studying chromosome meiotic pairing and investigating the cytological phenotypes associated with, for example, synthetic sex ratio distorters, hybrid male sterility, and the knock-out of genes involved in spermatogenesis.

Phase separation of DDX21 promotes colorectal cancer metastasis via MCM5-dependent EMT pathway.

RNA binding proteins (RBPs) contributes to cancer progression, but the underlying mechanism reminds unclear. Here, we find that DDX21, a representative RBP, is highly expressed in colorectal cancer (CRC), which leads to CRC cell migration and invasion in vitro, and CRC to liver metastasis and lung metastasis in vivo. This effect of DDX21 on CRC metastasis is correlated to the activation of Epithelial-mesenchymal transition (EMT) pathway. Moreover, we reveal that DDX21 protein is phase separated in vitro and in CRC cells, which controls CRC metastasis. Phase-separated DDX21 highly binds on MCM5 gene locus, which is markedly reduced when phase separation is disrupted by mutations on its intrinsically disordered region (IDR). The impaired metastatic ability of CRC upon DDX21 loss is restored by ectopic expression of MCM5, indicating MCM5 is a key downstream target of DDX21 for CRC metastasis. Furthermore, co-higher expressions of DDX21 and MCM5 is significantly correlated with poor survival outcomes of stage III and IV CRC patients, indicating the importance of this mechanism in CRC late and metastatic stage. Altogether, our results elucidate a new model of DDX21 in regulating CRC metastasis via phase separation.

Molecular characterization and genetic authentication assay for Anopheles 'hemocyte-like' cell lines 4a-3A and 4a-3B.

BACKGROUND: Anopheles cell lines are used in a variety of ways to better understand the major vectors of malaria in sub-Saharan Africa. Despite this, commonly used cell lines are not well characterized, and no tools are available for cell line identification and authentication. METHODS: Utilizing whole genome sequencing, genomes of 4a-3A and 4a-3B 'hemocyte-like' cell lines were characterized for insertions and deletions (indels) and SNP variation. Genomic locations of distinguishing sequence variation and species origin of the cell lines were also examined. Unique indels were targeted to develop a PCR-based cell line authentication assay. Mitotic chromosomes were examined to survey the cytogenetic landscape for chromosome structure and copy number in the cell lines. RESULTS: The 4a-3A and 4a-3B cell lines are female in origin and primarily of Anopheles coluzzii ancestry. Cytogenetic analysis indicates that the two cell lines are essentially diploid, with some relatively minor chromosome structural rearrangements. Whole-genome sequence was generated, and analysis indicated that SNPs and indels which differentiate the cell lines are clustered on the 2R chromosome in the regions of the 2Rb, 2Rc and 2Ru chromosomal inversions. A PCR-based authentication assay was developed to fingerprint three indels unique to each cell line. The assay distinguishes between 4a-3A and 4a-3B cells and also uniquely identifies two additional An. coluzzii cell lines tested, Ag55 and Sua4.0. The assay has the specificity to distinguish four cell lines and also has the sensitivity to detect cellular contamination within a sample of cultured cells. CONCLUSIONS: Genomic characterization of the 4a-3A and 4a-3B Anopheles cell lines was used to develop a simple diagnostic assay that can distinguish these cell lines within and across research laboratories. A cytogenetic survey indicated that the 4a-3A and Sua4.0 cell lines carry essentially normal diploid chromosomes, which makes them amenable to CRISPR/Cas9 genome editing. The presented simple authentication assay, coupled with screening for mycoplasma, will allow validation of the integrity of experimental resources and will promote greater experimental reproducibility of results.

A clinicopathologic study of 13 cases of primary lymphoma in soft tissue and review of literature.

Primary lymphoma in soft tissue is very rare. In order to understand the clinicopathological features of primary lymphoma in soft tissue, we found 13 cases (0.3%) of primary lymphoma in soft tissue by reviewing 4303 lymphomas diagnosed in our institution from 2010 to 2019. Tumors were found in the following sites: 8 in lower extremity (2 in leg, 1 in calf, 1 in knee and 4 in buttock), 1 in upper extremity (left shoulder) and 4 in the trunk (3 in waist and 1 in thoracolumbar). The most common histologic type was DLBCL (7/13, 54.8%). 6 cases of which had follow-up information. 25 patients were also selected by screening the English literature search (from Jan 2010 to December 2019) including 1102 studies. Compared to the results of literature review, our results are similar with them. The tumor sites were as follows: 10 in lower extremity, 4 in upper extremity, 9 in the trunk and 2 in masticatory muscle. The most common histological type was also DLBCL (n=11/25, 44%). Overall survival analysis of all 31 patients including our 6 cases with primary lymphoma in soft tissue showed no significant difference between different histological type (Log Rank P=0.120, Breslow P=0.157). The differential diagnosis includes malignant melanoma, rhabdomyosarcoma and metastatic carcinoma in soft tissue.

The value of combined PET/MRI, CT and clinical metabolic parameters in differentiating lung adenocarcinoma from squamous cell carcinoma.

Objective: This study aimed to study the diagnostic efficacy of positron emission tomography (PET)/magnetic resonance imaging (MRI), computed tomography (CT) and clinical metabolic parameters in predicting the histological classification of lung adenocarcinoma (ADC) and squamous cell carcinoma (SCC). Methods: PET/MRI, CT and clinical metabolic data of 80 patients with lung ADC or SCC were retrospectively collected. According to the pathological results from surgery or fiberscopy, the patients were diagnosed with lung ADC (47 cases) or SCC (33 cases). All 80 patients were divided into a training group (64 cases), an internal testing group (8 cases) and an external testing group (8 cases) in the ratio of 8:1:1. Nine models were constructed by integrating features from different modalities. The Gaussian classifier was used to differentiate ADC and SCC. The prediction ability was evaluated using the receiver operating characteristic curve. The area under the curve (AUC) of the models was compared using Delong's test. Based on the best composite model, a nomogram was established and evaluated with a calibration curve, decision curve and clinical impact curve. Results: The composite model (PET/MRI + CT + Clinical) owned the highest AUC values in the training, internal testing and external testing sets, respectively. In the training set, significant differences in the AUC were found between the composite model and other models except for the PET/MRI + CT model. The calibration curves showed good consistency between the predicted output and actual disease. The decision curve analysis and clinical impact curves demonstrated that the composite model increased the clinical net benefit for predicting lung cancer subtypes. Conclusion: The composite prediction model of PET/MRI + CT + Clinical better distinguished ADC from SCC pathological subtypes preoperatively and achieved clinical benefits, thus providing an accurate clinical diagnosis.

Obtaining Polytene, Meiotic, and Mitotic Chromosomes from Mosquitoes for Cytogenetic Analysis.

Chromosome visualization is a key step for developing cytogenetic maps and idiograms, analyzing inversion polymorphisms, and identifying mosquito species. Three types of chromosomes-polytene, mitotic, and meiotic-are used in cytogenetic studies of mosquitoes. Here, we describe a detailed method for obtaining high-quality polytene chromosome preparations from the salivary glands of larvae and the ovaries of females for Anopheles mosquitoes. We also describe how to obtain mitotic chromosomes from imaginal discs of fourth-instar larvae and meiotic chromosomes from the testes of male pupae for all mosquitoes. These chromosomes can be used for fluorescence in situ hybridization (FISH), a fundamental technique in cytogenetic research that is used for physical genome mapping, detecting chromosomal rearrangements, and studying chromosome organization.

Visualization of Polytene Chromatin in Mosquito Cell Nuclei Using Three-Dimensional Fluorescence In Situ Hybridization.

Chromosomes are intricately folded within the cell nucleus and interact with peripheral nuclear proteins. The chromatin architecture has a profound effect on how the genome is organized. 3D-FISH is a powerful technique that can reveal the structural and functional organization of chromosomes in the nuclear space. Here, we present a protocol for visualizing specific genomic regions in whole-mount paraformaldehyde-fixed cell nuclei of Anopheles mosquitoes. This protocol was tested in our laboratories and has been showed to be effective and reliable for visualizing genomic regions of various lengths-from 1-kb gene-scale fragments to chromosome-scale segments of DNA.

Visualization of the Linear and Spatial Organization of Chromosomes in Mosquitoes.

Mosquitoes are vectors of dangerous human diseases such as malaria, dengue, Zika, West Nile fever, and lymphatic filariasis. Visualization of the linear and spatial organization of mosquito chromosomes is important for understanding genome structure and function. Utilization of chromosomal inversions as markers for population genetics studies yields insights into mosquito adaptation and evolution. Cytogenetic approaches assist with the development of chromosome-scale genome assemblies that are useful tools for studying mosquito biology and for designing novel vector control strategies. Fluorescence in situ hybridization is a powerful technique for localizing specific DNA sequences within the linear chromosome structure and within the spatial organization of the cell nucleus. Here, we introduce protocols used in our laboratories for chromosome visualization and their application in mosquitoes.

A diagnosis model in nasopharyngeal carcinoma based on PET/MRI radiomics and semiquantitative parameters.

BACKGROUND: The staging of nasopharyngeal carcinoma (NPC) is of great value in treatment and prognosis. We explored whether a positron emission tomography/ magnetic resonance imaging (PET/MRI) based comprehensive model of radiomics features and semiquantitative parameters was useful for clinical evaluation of NPC staging. MATERIALS AND METHODS: A total of 100 NPC patients diagnosed with non-keratinized undifferentiated carcinoma were divided into early-stage group (I-II) and advanced-stage group (III-IV) and divided into the training set (n = 70) and the testing set (n = 30). Radiomics features (n = 396 × 2) of the primary site of NPC were extracted from MRI and PET images, respectively. Three major semiquantitative parameters of primary sites including maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), and total lesion glycolysis (TLG) in all NPC patients were measured. After feature selection, three diagnostic models including the radiomics model, the metabolic parameter model, and the combined model were established using logistic regression model. Finally, internal validation was performed, and a nomogram for NPC comprehensive diagnosis has been made. RESULTS: The radiomics model and metabolic parameter model showed an area under the curve (AUC) of 0.83 and 0.80 in the testing set, respectively. The combined model based on radiomics and semiquantitative parameters showed an AUC of 0.90 in the testing set, with the best performance among the three models. CONCLUSION: The combined model based on PET/MRI radiomics and semiquantitative parameters is of great value in the evaluation of clinical stage (early-stage group and advanced-stage group) of NPC.

Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes.

Genes that originate during evolution are an important source of novel biological functions. Retrogenes are functional copies of genes produced by retroduplication and as such are located in different genomic positions. To investigate retroposition patterns and retrogene expression, we computationally identified interchromosomal retroduplication events in nine portions of the phylogenetic history of malaria mosquitoes, making use of species that do or do not have classical sex chromosomes to test the roles of sex-linkage. We found 40 interchromosomal events and a significant excess of retroduplications from the X chromosome to autosomes among a set of young retrogenes. These young retroposition events occurred within the last 100 million years in lineages where all species possessed differentiated sex chromosomes. An analysis of available microarray and RNA-seq expression data for Anopheles gambiae showed that many of the young retrogenes evolved male-biased expression in the reproductive organs. Young autosomal retrogenes with increased meiotic or postmeiotic expression in the testes tend to be male biased. In contrast, older retrogenes, i.e., in lineages with undifferentiated sex chromosomes, do not show this particular chromosomal bias and are enriched for female-biased expression in reproductive organs. Our reverse-transcription PCR data indicates that most of the youngest retrogenes, which originated within the last 47.6 million years in the subgenus Cellia, evolved non-uniform expression patterns across body parts in the males and females of An. coluzzii. Finally, gene annotation revealed that mitochondrial function is a prominent feature of the young autosomal retrogenes. We conclude that mRNA-mediated gene duplication has produced a set of genes that contribute to mosquito reproductive functions and that different biases are revealed after the sex chromosomes evolve. Overall, these results suggest potential roles for the evolution of meiotic sex chromosome inactivation in males and of sexually antagonistic conflict related to mitochondrial energy function as the main selective pressures for X-to-autosome gene reduplication and testis-biased expression in these mosquito lineages.

Clinicopathologic and molecular features of vascular tumors in a series of 118 cases.

AIMS: Vascular tumors are composed of benign, intermediate, and malignant lesions. The diagnosis is challenging because some entities demonstrate overlapping morphologies and harbor the same genetic alterations. We describe herein a cohort of vascular tumors with clinicopathologic, immunohistochemical, and molecular features. METHODS AND RESULTS: 118 vascular tumors including 56 angiosarcomas, 18 epithelioid haemangioendotheliomas (EHE), 25 epithelioid haemangiomas (EH), 8 pseudomyogenic haemangioendotheliomas (PHE), 1 papillary intralymphatic angioendothelioma (PILA), 2 kaposiform haemangioendotheliomas (KHE), 3 Kaposi sarcomas, 2 retiform haemangioendotheliomas (RHE), and 3 anastomosing haemangiomas were assessed. FOSB, c-Fos, CAMTA1, and TFE3 expression and gene rearrangements were analyzed by immunohistochemical staining and FISH, respectively. Our results showed that FOSB expression was diffusely positive in all 8 PHEs, focally or sparsely in 12 EHs, and in 2 angiosarcomas. C-FOS expression was sparsely to diffusely positive in 15 EHs, focally or sparsely in 17 angiosarcomas, 1 EHE, 1 Kaposi sarcoma, and 1 PHE. CAMTA1 expression was positive in only 12 EHEs. TFE3 expression was focally or sparsely positive in all 8 PHEs, 22 angiosarcomas, 6 EHEs, 3 EHs, 2 Kaposi sarcomas, and 2 AHs. FOSB rearrangement was found in 5 PHEs, FOS rearrangement only in 1 EH, CAMTA1 rearrangement in 4 EHEs. CONCLUSIONS: FOSB and CAMTA1 are useful diagnostic markers for PHE and EHE, respectively. FOSB and FOS fusion represent a subset of epithelioid haemangioma. TFE3 is not a diagnostically meaningful marker in a majority of vascular tumors. The combined utility of these markers will facilitate the differential diagnosis in vascular tumors with morphologic overlap.

Anopheles mosquitoes reveal new principles of 3D genome organization in insects.

Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profile genome organizations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. Evolutionary analysis reveals conservation of chromatin architecture within synteny blocks for tens of millions of years and enrichment of synteny breakpoints in regions with increased genomic insulation. However, in-depth analysis shows a confounding effect of gene density on both insulation and distribution of synteny breakpoints, suggesting limited causal relationship between breakpoints and regions with increased genomic insulation. At the level of individual loci, we identify specific, extremely long-ranged looping interactions, conserved for ~100 million years. We demonstrate that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin.

Pan-cancer analysis of oncogenic role of Programmed Cell Death 2 Like (PDCD2L) and validation in colorectal cancer.

BACKGROUND: Programmed Cell Death 2 Like (PDCD2L) correlates with cell proliferation, apoptosis and mouse embryonic development. However, the role of PDCD2L in human cancers is unclear. METHODS: Multiple bioinformatic methods, in vitro function experiments and validation were performed to clarify the oncogenic role of PDCD2L in human cancers. RESULTS: Our study found that PDCD2L was aberrantly expressed in multiple types of human cancers, and associated with clinical stage and molecular subtype. Furthermore, overexpression of PDCD2L predicted poor overall survival in adrenocortical carcinoma(ACC), kidney chromophobe(KICH), acute myeloid leukemia(LAML), brain lower grade glioma(LGG),liver hepatocellular carcinoma(LIHC), mesothelioma(MESO), uveal melanoma(UVM) and poor diseases free survival in ACC, bladder urothelial carcinoma(BLCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), kidney renal clear cell carcinoma(KIRC), kidney renal papillary cell carcinoma(KIRP), LGG, LIHC, and UVM. PDCD2L expression was negatively associated with cancer associated fibroblast in breast invasive carcinoma (BRCA), lung squamous cell carcinoma (LUSC), sarcoma (SARC), stomach adenocarcinoma (STAD) and testicular germ cell tumors (TGCT). Mechanically, we found that PDCD2L expression was associated with apoptosis, invasion and cell cycle by investigating single cell sequencing data. For further validation, PDCD2Lwas highly expressed in colorectal cancer (CRC) cell lines and tissue samples compared with the normal colon cell line and non-tumor adjacent colorectal mucosa tissues. PDCD2L knockdown induced the apoptosis and proliferation of CRC cells. CONCLUSIONS: Our study shows that the oncogenic role of PDCD2L in various cancers and PDCD2L could be served as a biomarker of CRC.

Positron Emission Tomography/Magnetic Resonance Imaging Radiomics in Predicting Lung Adenocarcinoma and Squamous Cell Carcinoma.

OBJECTIVE: To investigate the diagnostic value of positron emission tomography (PET)/magnetic resonance imaging (MRI) radiomics in predicting the histological classification of lung adenocarcinoma and lung squamous cell carcinoma. METHODS: PET/MRI radiomics and clinical data were retrospectively collected from 61 patients with lung cancer. According to the pathological results of surgery or fiberscope, patients were divided into two groups, lung adenocarcinoma and squamous cell carcinoma group, which were set as positive for adenocarcinoma (40 cases) and negative for squamous cell carcinoma (21 cases). The radiomics characteristics most related to lung cancer classification were calculated and selected using radiomics software, and the two lung cancer groups were randomly assigned into a training set (70%) and a test set (30%). Maximum relevance and minimum redundancy (mRMR) and least absolute shrinkage and selection operator (LASSO) methods in the uAI Research Portal software (United Imaging Intelligence, China) were used to select the desired characteristics from 2600 features extracted from MRI and PET. Eight optimal features were finally retained through 5-fold cross-validation, and a PET/MRI fusion model was constructed. The predictive ability of this model was evaluated by the difference in area under the curve (AUC) obtained from the receiver operating characteristic (ROC) curve. RESULTS: AUC of PET/MRI model for the training group and test group were 0.886 (0.787-0.985) and 0.847 (0.648-1.000), respectively. PET/MRI radiomics features revealed different degrees of correlation with the classification of lung adenocarcinoma and squamous cell carcinoma, with significant differences. CONCLUSION: The prediction model constructed based on PET/MRI radiomics features can predict the preoperative histological classification of lung adenocarcinoma and squamous cell carcinoma without seminality and repeatability. It can also provide an objective basis for accurate clinical diagnosis and individualized treatment, thus having important guiding significance for clinical treatment.

18F-FDG PET/MR Assessment of Pediatric Langerhans Cell Histiocytosis.

INTRODUCTION: Langerhans cell histiocytosis (LCH) is a histiocytic proliferative disease without a well-understood etiology. The aim of our study is to summarize the imaging features of PET/MR in children with LCH and to explore its diagnostic role in LCH. METHODS: Retrospective analysis was performed of the pretreatment PET/MR imaging data of 15 children with LCH. Comparison of ADC values was done between lesions and normal tissues. RESULTS: Of the fifteen patients enrolled, five had single-organ or single-system involvement, and ten had multiple-system involvement. Nine patients had varying degrees of bone destruction and increased FDG uptake, whereas thickening and deviation of the pituitary stalk and disappearance of the normal high-signal intensity of T1WI in the neurohypophysis were observed in the pituitary gland in six of them. Splenomegaly with diffuse increased FDG uptake or a normal spleen with increased FDG uptake was found in four cases, liver in three, multiple lymph node enlargement in three, pulmonary lesions in three, and increased metabolism in medullary cavity in two cases. Additionally, two cases involved the skin. Hypermetabolic nodules were detected in muscle in one case, thyroid involvement in one case, and a mediastinal lesion in one case. CONCLUSION: PET/MR can show well the distribution of the organs, systems, and lesions involved in LCH and is of considerable significance in the systemic evaluation of LCH.

Estimation of Nuclear Medicine Exposure Measures Based on Intelligent Computer Processing.

This paper provides an in-depth discussion and analysis of the estimation of nuclear medicine exposure measurements using computerized intelligent processing. The focus is on the study of energy extraction algorithms to obtain a high energy resolution with the lowest possible ADC sampling rate and thus reduce the amount of data. This paper focuses on the direct pulse peak extraction algorithm, polynomial curve fitting algorithm, double exponential function curve fitting algorithm, and pulse area calculation algorithm. The detector output waveforms are obtained with an oscilloscope, and the analysis module is designed in MATLAB. Based on these algorithms, the data obtained from six different lower sampling rates are analyzed and compared with the results of the high sampling rate direct pulse peak extraction algorithm and the pulse area calculation algorithm, respectively. The correctness of the compartment model was checked, and the results were found to be realistic and reliable, which can be used for the analysis of internal exposure data in radiation occupational health management, estimation of internal exposure dose for nuclear emergency groups, and estimation of accidental internal exposure dose. The results of the compartment model of the respiratory tract and the compartment model of the digestive tract can be used to calculate the distribution and retention patterns of radionuclides and their compounds in the body, which can be used to assess the damage of radionuclide internal contamination and guide the implementation of medical treatment.

A Prognosis Marker SLC2A3 Correlates With EMT and Immune Signature in Colorectal Cancer.

SLC2A3 is a membrane transporter that belongs to the solute carrier family, whose function includes transmembrane transport and glucose transmembrane transport activity. To clarify the expression and role of SLC2A3 in colorectal cancer (CRC), we analyzed the TCGA and GEO databases and found that SLC2A3 mRNA levels were significantly higher in CRC tissues than that in adjacent non-tumor tissues. Furthermore, high expression of SLC2A3 predicted poor overall survival and disease free survival for CRC patients. For validation, we collected 174 CRC samples and found that SLC2A3 expression was higher in CRC tissues than that in adjacent non-tumor colorectal mucosa tissues by immunohistochemistry staining. Further study showed that high expression of SLC2A3 was enriched in epithelial-mesenchymal transition (EMT) classical pathway, interferon-γ pathway by GSEA analysis enrichment, indicating that SLC2A3 may play a key role in the progression of CRC through EMT and immune response, which also has been validated by the global gene expression profiling of human CRC cell lines. The expression of SLC2A3 was positively correlated with CD4 and CD8+T cells by using TIMER and EPIC algorithm, respectively. SLC2A3 knockdown suppressed migration and inhibited the expression of Vimentin and MMP9 in CRC cell line SW480 and RKO. Meanwhile, PD-L1 expression was also significantly attenuated in SW480 and RKO cells transfected with SLC2A3 siRNA. The result suggests that SLC2A3 may be involved in the immune response of CRC by regulating PD-L1 immune checkpoint. In our series, SLC2A3 and PD-L1 positive expression was 74% (128/174) and 22% (39/174) of CRC, respectively. SLC2A3 expression was significantly associated with perineural invasion in CRC patients. In conclusion, SLC2A3 may play an important role in progression of CRC by regulating EMT and PD-L1 mediated immune responses.

Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis.

BACKGROUND: Anopheles coluzzii and Anopheles arabiensis belong to the Anopheles gambiae complex and are among the major malaria vectors in sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species. FINDINGS: In this study, we produced de novo chromosome-level genome assemblies for A. coluzzii and A. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 and 256.8 Mb of the total assemblies for A. coluzzii and A. arabiensis, respectively. Each assembly consists of 3 chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in A. coluzzii and A. arabiensis. CONCLUSION: The new chromosome-level assemblies will facilitate functional and population genomic studies in A. coluzzii and A. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.

Radiomics Analysis and Correlation With Metabolic Parameters in Nasopharyngeal Carcinoma Based on PET/MR Imaging.

Objective: Accurate staging is of great importance in treatment selection for patients with nasopharyngeal carcinoma (NPC). The aims of this study were to construct radiomic models of NPC staging based on positron emission tomography (PET) and magnetic resonance (MR) images and to investigate the correlation between metabolic parameters and radiomic features. Methods: A total of 100 consecutive cases of NPC (70 in training and 30 in the testing cohort) with undifferentiated carcinoma confirmed pathologically were recruited. Metabolic parameters of the local lesions of NPC were measured. A total of 396 radiomic features based on PET and MRI images were calculated [including histogram, Haralick, shape factor, gray level co-occurrence matrix (GLCM), and run length matrix (RLM)] and selected [using maximum relevance and minimum redundancy (mRMR) and least shrinkage and selection operator (LASSO)], respectively. The logistic regression models were established according to these features. Finally, the relationship between the metabolic parameters and radiomic features was analyzed. Results: We selected the nine most relevant radiomic features (six from MR images and three from PET images) from local NPC lesions. In the PET model, the area under the receiver operating characteristic (ROC) curve (AUC), accuracy, sensitivity, and the specificity of the training group were 0.84, 0.75, 0.90, and 0.69, respectively. In the MR model, those metrics were 0.85, 0.83, 0.75, and 0.86, respectively. Pearson's correlation analysis showed that the metabolic parameters had different degrees of correlation with the selected radiomic features. Conclusion: The PET and MR radiomic models were helpful in the diagnosis of NPC staging. There were correlations between the metabolic parameters and radiomic features of primary NPC based on PET/MR. In the future, PET/MR-based radiomic models, with further improvement and validation, can be a more useful and economical tool for predicting local invasion and distant metastasis of NPC.