Current progress in strategies to profile transcriptomic m6A modifications.

Various methods have been developed so far for detecting N 6-methyladenosine (m6A). The total m6A level or the m6A status at individual positions on mRNA can be detected and quantified through some sequencing-independent biochemical methods, such as LC/MS, SCARLET, SELECT, and m6A-ELISA. However, the m6A-detection techniques relying on high-throughput sequencing have more effectively advanced the understanding about biological significance of m6A-containing mRNA and m6A pathway at a transcriptomic level over the past decade. Various SGS-based (Second Generation Sequencing-based) methods with different detection principles have been widely employed for this purpose. These principles include m6A-enrichment using antibodies, discrimination of m6A from unmodified A-base by nucleases, a fusion protein strategy relying on RNA-editing enzymes, and marking m6A with chemical/biochemical reactions. Recently, TGS-based (Third Generation Sequencing-based) methods have brought a new trend by direct m6A-detection. This review first gives a brief introduction of current knowledge about m6A biogenesis and function, and then comprehensively describes m6A-profiling strategies including their principles, procedures, and features. This will guide users to pick appropriate methods according to research goals, give insights for developing novel techniques in varying areas, and continue to expand our boundary of knowledge on m6A.

Expression of 5-HT Relates to Stem Cell Marker LGR5 in Patients with Gastritis and Gastric Cancer.

BACKGROUND: 5-Hydroxytryptamine (5-HT) and stem cells marker G-protein-coupled receptor 5 (LGR5) are associate with gastrointestinal inflammation and tumorigenesis. But the relationship between 5-HT and LGR5 is unclear. OBJECTIVE: To explore the expression and correlation of 5-HT and LGR5 in gastric mucosa of patients with gastritis and gastric cancer (GC). METHODS: A total of 41 patients with GC and 98 patients with chronic gastritis were included in this study. The expression of TPH1 mRNA, LGR5 mRNA and ß-catenin mRNA in gastric mucosa were explored by Real-time Quantitative polymerase chain reaction (qPCR). 5-HT-positive cells and LGR5-positive cells in gastric mucosa were detected by immunohistochemistry stains. The co-localization of 5-HT and chromogranin A (CgA), 5-HT receptor4 (5-HTR4) and LGR5 were detected by multiplex immunofluorescence. RESULTS: The expression of 5-HT and LGR5 in patients with GC was significantly higher than patients with chronic gastritis (p < 0.05). The positive rate of 5-HT and LGR5 increased sequentially in the patients with non-atrophic gastritis, intestinal metaplasia and GC, which were 18.52%, 35.56% and 75.61% for 5-HT, and 27.78%, 40.91% and 95.12% for LGR5, respectively. The expression of 5-HT and LGR5 was positively correlated in gastritis and GC patients (p < 0.05). Moreover, the expression level of TPH1 mRNA and LGR5 mRNA was also positively correlated in gastritis patients (r = 0.7377, p < 0.001). Besides, 5-HT was partially co-localized with CgA, and 5-HTR4 was co-localized with LGR5 in gastric mucosa. CONCLUSION: The increase of 5-HT synthesis in gastric mucosa may have an impact on LGR5-positive gastric epithelial stem cells.

Preoperative plasma D-Dimer level is correlated with peritoneal cancer index of patients with pseudomyxoma peritonei.

PURPOSE: Accurate assessment of preoperative tumor burden contribute to formulate a scientific surgical plan for patients with pseudomyxoma peritonei (PMP). Present study aimed to assess whether the preoperative plasma D-Dimer level could reflect tumor burden for PMP patients. METHODS: A total of 253 PMP patients were included between June 1, 2013 and March 1, 2022. According to the peritoneal cancer index (PCI), all participants were divided into extensive (PCI ≥ 28) and none-extensive (PCI < 28) subgroups. The D-Dimer and tumor markers were compared between the two subgroups. The correlation between the abovementioned biomarkers and PCI will be calculated, and further compared with each other. Two-sided P value less than 0.05 is considered statistically significant. RESULTS: The level of D-Dimer (ng/ml) between extensive and none-extensive subgroup were 600 (328, 1268) vs. 339 (128, 598), Z = -5.425, p < 0.001. The Spearman correlation between D-Dimer, carcinoembryonic antigen (CEA), carbohydrate antigen 125 (CA 125), CA 19 - 9 and PCI were 0.487, 0.509, 0.469, and 0.499, respectively (all p < 0.001). The correlation coefficients were compared with each other according to Meng, Rosenthal and Rubin's method, however, there was no significant difference. CONCLUSION: Preoperative plasma D-Dimer could moderately reflect tumor burden for PMP. In the future, a multivariate prediction model will be developed to help surgeons to formulate a more precise surgical plan for the PMP patients.

Cell HE staining smears and paired cell paraffin sections in detection of epithelial growth factor receptor gene of pleural fluid specimens. / 细胞HEæŸ“è‰²æ¶‚ç‰‡ä¸Žç»†èƒžèœ¡å—æ£€æµ‹æ™šæœŸéžå°ç»†èƒžè‚ºç™Œèƒ¸è ”ç§¯æ¶²æ ‡æœ¬ä¸­è¡¨çš®ç”Ÿé•¿å› å­å—ä½“åŸºå› çªå˜.

OBJECTIVES: The advanced non-small cell lung cancer (NSCLC) patients with pleural effusion have no opportunity for surgery treatment. Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are the first-line drugs for these patients with EGFR-sensitive mutation. However, the disease progression and drug update during or after treatment of EGFR-TKIs bring more challenges and puzzles to clinical diagnosis and treatment, which inevitably requires archived pleural cell samples for EGFR re-examination or comparative study. Understanding the DNA quality of archived pleural fluid samples and effectively using archival data of pleural fluid cells are of great significance for tracing the origin of cases and basic medical research. This study aims to evaluate the consistency of EGFR mutant gene expression between the 2 methods, and to explore a reliable way for preserving cytological data and making full use of cytological archival data via cell HE staining smear and cell paraffin section. METHODS: A total of 57 pleural fluid cytology cases in the Department of Pathology of China Aerospace Center Hospital from October 2014 to April 2021 were selected. Tumor cells were detected by cell HE staining smears and immunohistochemical staining for TTF-1 and Napsin A in the paired cell paraffin sections. There were more than 200 tumor cells in cell HE staining smear and the proportion of tumor cells were ≥70% in matched cell paraffin sections. Patients with 2 cell smears (one for cell data retention and the other for DNA extraction) were selected as the research subjects, and 57 pleural fluid samples were enrolled. EGFR gene mutation was detected by amplification refractory mutation system-polymerase chain reaction in 57 paired cell HE staining smears and cell paraffin sections. DNA concentration was 2 ng/µL. Cell HE smear was amplified side-by-side with DNA samples from paired cell paraffin sections. Result determination was according to the requirements of the reagent instructions. The external control cycle threshold (Ct) value of the No. 8 well of the samples to be tested was between 13 and 21, which was considered as successful and reliable samples. When the Ct value of EGFR gene mutation was <26, it was considered as positive; when the Ct value was between 26 and 29, it was critical positive; when the Ct value was equal or more than 29, it was negative. ΔCt value was the difference between mutant Ct value and externally controlled Ct value. The smaller the ΔCt value was, the better the quality of DNA of the detected sample was. RESULTS: Among the 57 pleural effusion samples, 42 patients were hospitalized with pleural effusion as the first symptom, accounting for 73.7% (42/57). EGFR mutation was detected in 37 samples [64.9% (37/57)]. The mutation rate for 19del was 37.8% (14/37) while for L858R was 48.6% (18/37). Females were 56.7% (21/37) of mutation cases. The mutation consistency rate of cell HE staining smear and matched cell paraffin sections was 100%. The ΔCt values of cell HE staining smears were less than those of matched cell paraffin sections. The mutation Ct values of 37 cytological samples were statistically analyzed according to the preservation periods of the years of 2014-2015, 2016-2017, 2018-2019, and 2020-2021. There were significant differences in cell paraffin section in the years of 2014-2015 and 2016-2017 compared with the years of 2018-2019 and 2020-2021, while no significant differences were found in cell HE staining smear. Statistical analysis of externally controlled Ct values of 57 cytological samples showed that there were significant differences between cell HE staining smears and cell paraffin section in the years of 2014-2015 and 2016-2017, compared with the years of 2018-2019 and 2020-2021. The mutational Ct values of 37 paired cell blocks and smears were all <26, and the externally controlled Ct values of 57 paired cell paraffin sections and HE staining smears were all between 13 and 21. CONCLUSIONS: The DNA quality of cell HE smears and matched cell paraffin section met the qualified requirements. Two methods possess show an excellent consistency in detecting EGFR mutation in NSCLC pleural fluid samples. The DNA quality of cell HE staining smear is better than that of cell paraffin sections, so cell HE staining smear can be used as important supplement of the gene test source. It should be noted that the limitation of cell HE staining smears is non-reproducibility, so multiple smears of pleural fluid are recommended to be prepared for multiple tests.

Minimal change disease associated with gastrointestinal stromal tumor accompanied by significantly elevated serum IgE level: a case report.

BACKGROUND: Minimal change disease (MCD) is a common cause of the nephrotic syndrome. Several studies have shown an increased incidence of cancer in patients with MCD. However, there are no reports on the association between MCD and gastrointestinal stromal tumor (GIST). CASE PRESENTATION: We report a case of a 66-year-old female with severe nephrotic syndrome and concomitant duodenal GIST. Immunoglobulin test showed a significant increase of IgE levels. The diagnosis of renal histopathology was MCD with subacute tubulointerstitial injury. The combination of preoperative Imatinib mesylate chemotherapy and tumor excision was accompanied by significant remission of proteinuria, and IgE level decreasing, without immunosuppressivetherapy. CONCLUSIONS: It is the first case report that MCD was associated with GIST and elevated IgE level. Clinically, in patients with elevated IgE level associated with nephrotic syndrome, the possibility of tumor must be taken into account when allergic factors are excluded.

Differential diagnosis of appendiceal serrated lesions and polyps and low-grade appendiceal mucinous neoplasm: analysis of 88 cases.

PURPOSE: To identify clinicopathological features for the differential diagnosis of appendiceal serrated lesions and polyps (SPs) and low-grade appendiceal mucinous neoplasm (LAMN) for the purpose of avoiding over-diagnosis. METHODS: Clinical data and pathological features of 66 patients with SPs diagnosed at the Aerospace Center Hospital between January 2013 and January 2021 were collected and compared to 22 cases of LAMN. RESULTS: SPs, compared with LAMN, are likely to be associated with acute inflammation (SPs 53.0% vs. LAMN 18.2%), and may be located in the appendix partly, although with smaller diameter (average 9.6 vs. 27.2 mm); epithelial structures of serrated (100% vs. 22.7%) and filiform villous (47.0% vs. 18.2%) were often found in SPs. SPs occasionally show attenuated or flattened morphology (16.7% vs. 100%) and undulating or scalloped (7.6% vs. 40.9%) structures, and can also be accompanied by diverticulum (18.2% vs. 18.2%) and acellular mucin in the appendiceal wall (16.7% vs. 54.5%), which causes confusion with LAMN. The key point of the differential diagnosis is to observe whether the muscularis mucosa exists (loss, 0% vs. 100%) and fibrosis of the appendiceal wall (0% vs. 100%). SMA immunohistochemistry can assist in the diagnosis. Calcification is also indicative of LAMN. CONCLUSIONS: The epithelial structure of SPs can appear flattened and focally scalloped, and can be accompanied by mucin in the appendiceal wall, which may appear as complex lesions, easily over-diagnosed as LAMN. Key differential diagnostic features are identifying the structure of lamina propria, determining whether the muscularis mucosa exists, and whether the appendiceal wall is fibrotic.

[Clinical Features and Prognosis of Patients with Hematological Disease Complicated with Mucor Infection].

OBJECTIVE: To investigate the clinical features, treatment and prognosis of patients with hematological diseases complicated with mucor infection. METHODS: The risk factors, clinical features, treatment regimen and prognosis of 18 hematological disease patients with mucor infection diagnosed by histopathology in our center from April 2014 to June 2020 were retrospectively analyzed. RESULTS: Thirteen males and five females, with an average age of 30 (13－54) years old, were diagnosed as mucor infection by histopathological examination at the site of infection, including 16 cases of mucor infection alone and 2 cases of mucor + aspergillus mixed infection. There were 12 cases with malignant hematological disease and 6 cases with severe aplastic anemia, all of whom with long-term agranulocytosis, and their clinical manifestations and imaging findings were not specific. The common sites of infection were sinuses and lungs, and some patients showed multiple systemic manifestations. The remission status of hematological diseases and recovery of immune function showed an impact on the prognosis. All the patients were treated with amphotericin B liposome combined with posaconazole, and 15 patients were treated with surgery combined with antifungal drugs, 9 of whom were effective and 6 were ineffective, while intravenous administration in 3 cases was ineffective. CONCLUSION: It is difficult to diagnose hematological disease complicated with mucor infection. After early diagnosis, prognosis can be improved by amelioration of primary state and combination of drugs and surgery.

Clinicopathological Features of Low-Grade Appendiceal Mucinous Neoplasms Confined to the Appendix.

OBJECTIVE: To investigate the clinicopathological features and follow-up of low-grade appendiceal mucinous neoplasms (LAMNs) confined to the appendix. METHODS: The clinicopathological features, pathological primary tumor (pT) staging and follow-up of 22 patients with LAMNs confined to the appendix were analyzed retrospectively. RESULTS: Of 22 patients with LAMNs, 14 were pTis (eight pTism and six pTisf), six were pT3, and two were pT4a. The appendiceal diameter was significantly larger for pTisf than for pTism. The interval between first symptoms and surgery was longer for pTisf than for pTism, but not significantly different. No significant differences were found between the pT stages and appendiceal diameter or in the interval between the first symptoms and surgery. Pathomorphologically, the epithelial structures were mainly flat (100%), undulating or scalloped (82%); a few showed filiform villous hyperplasia (46%), and seven (32%) had serrated lesions in the background. Diverticula may be associated with LAMNs, and the location of acellular mucin caused by diverticula affected the pT stage of the LAMNs. The immunohistochemistry information showed the same pattern with cytokeratin 7 (CK7) negative, cytokeratin 20 (CK20) positive and caudal type homeobox 2 (CDX-2) positive. No lymph node metastasis was found. The lack of treatment guidelines for LAMNs confined to the appendix and different acceptances of patients of preventive intervention led to varied clinical treatments. However, we found no short-term benefits of prophylactic extended resection or hyperthermic intraperitoneal chemotherapy. CONCLUSION: LAMNs confined to the appendix are rare and must be differentiated from serrated lesions and diverticula. LAMNs with different pT stages have inert biological behavior. Determining the long-term effects of preventive treatment on survival and recurrence requires more data and a longer follow-up.

Significance of the Entire Appendiceal Evaluation in the Diagnosis of Serrated Lesions, Low-Grade Appendiceal Mucinous Neoplasm, and Appendiceal Diverticulosis Disease.

OBJECTIVE: This study was conducted in order to investigate the significance of the entire appendiceal evaluation in the pathological diagnosis of appendiceal serrated lesions, low-grade appendiceal mucinous neoplasm (LAMN), and appendiceal diverticulosis disease (ADD). METHODS: A total of 702 appendectomy specimens diagnosed from 2017 to 2020 were reviewed retrospectively. The specimens were divided into two groups according to the different sampling procedures. In group 1, the vast majority of 337 specimens were partially submitted by routine sampling within 18 months from October 2017 to March 2019. In group 2, 365 of specimens were entirely submitted and examined within 18 months from April 2019 to October 2020. The incidence and pathological features of serrated lesions, LAMN, and ADD in the two groups were compared and analyzed. The clinicopathological characteristics between different entities were also studied. RESULTS: Forty appendiceal serrated lesions, 8 LAMNs, and 21 diverticula were accidentally detected in 702 appendectomy specimens. As compared with group 1, the incidence of appendiceal serrated lesions in group 2 was significantly increased (9.3% vs. 1.8%, P < 0.01), especially for the serrated lesions without dysplasia (7.4% vs. 1.2%, P < 0.01). The entire sampling revealed that loss of lamina propria and replacement with dysplastic mucinous epithelium were statistically significantly associated with LAMN rather than serrated lesions and ADD (P < 0.01 and P < 0.01, respectively). Mural mucin deposition and fibrosis were useful features to distinguish LAMN from simple serrated lesions (P < 0.01 and P < 0.05, respectively), but mucin deposition was useless for the distinction between LAMN and ADD (P > 0.05) or serrated lesions combined with ADD. CONCLUSION: Our study highlights the importance and necessity of careful gross assessment and histologic examination of the entire appendectomy specimen, since the association with unexpected appendiceal lesions is significant and cannot be ignored. The entirely submitted appendix is more sensitive for the detection of appendiceal serrated lesions. In addition, thorough examination and evaluation are essential to distinguish the key pathological features between appendiceal serrated lesions, LAMN, and ADD.