Engineering Gene-Specific DNAzymes for Accessible and Multiplexed Nucleic Acid Testing.

The accurate and timely detection of disease biomarkers at the point-of-care is essential to ensuring effective treatment and epidemiological surveillance. Here, we report the selection and engineering of RNA-cleaving DNAzymes that respond to specific genetic markers and amplify detection signals. Because the target-specific activation of gene-specific DNAzymes (gDz) is like the trans-cleavage activity of clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated (Cas) machinery, we further developed a CRISPR-like assay using RNA-cleaving DNAzyme coupled with isothermal sequence and signal amplification (CLARISSA) for nucleic acid detection in clinical samples. Building on the high sequence specificity and orthogonality of gDzs, CLARISSA is highly versatile and expandable for multiplex testing. Upon integration with an isothermal recombinase polymerase amplification, CLARISSA enabled the detection of human papillomavirus (HPV) 16 in 189 cervical samples collected from cervical cancer screening participants (n = 189) with 100% sensitivity and 97.4% specificity, respectively. A multiplexed CLARISSA further allowed the simultaneous analyses of HPV16 and HPV18 in 46 cervical samples, which returned clinical sensitivity of 96.3% for HPV16 and 83.3% for HPV18, respectively. No false positives were found throughout our tests. Besides the fluorescence readout using fluorogenic reporter probes, CLARISSA is also demonstrated to be fully compatible with a visual lateral flow readout. Because of the high sensitivity, accessibility, and multiplexity, we believe CLARISSA is an ideal CRISPR-Dx alternative for clinical diagnosis in field-based and point-of-care applications.

A comprehensive pan-cancer analysis identifies a novel glycolysis score and its hub genes as prognostic and immunological biomarkers.

Background: Glycolysis plays significant roles in tumor progression and immune response. However, the exact role of glycolysis in prognosis and immune regulation has not been explored in all cancer types. This study first calculated a novel glycolysis score and screened out 12 glycolytic hub genes, and comprehensively analyzed molecular expression, clinical implications, and immune features of glycolysis among pan-cancer. Methods: The glycolysis score was derived by the single sample gene set enrichment analysis (ssGSEA) algorithm. The correlations of glycolysis with clinical parameters were analyzed using "limma" package. Downstream pathways of glycolysis were identified by Gene Set Enrichment Analysis (GSEA). The immune cell infiltration was explored and validated by three databases. The association between glycolysis and some immunotherapy biomarkers was explored by Pearson correlation analysis. Single-nucleotide variation (SNV), copy number variation (CNV), DNA methylation, and drug sensitivity analyses of 12 glycolytic hub genes were investigated. IMvigor210 and GSE91061 immunotherapeutic cohorts were retrieved to assess the ability of glycolysis score to predict immunotherapy efficacy. The expression of glycolysis key genes was detected in normal and endometrial cancer cell lines. Results: We found that glycolysis score was generally higher in tumor tissues compared to normal tissues and a high glycolysis score predominated as a risk prognostic factor. A high glycolysis score was associated with decreased immunostimulatory natural killer (NK) cells and CD8+ T cells infiltration, well increased immunosuppressive M2-tumor-associated macrophages (M2-TAM) cells infiltration. Tumor mutational burden (TMB), microsatellite instability (MSI), and immune checkpoints (ICPs) all closely interacted with glycolysis score and the frequency of gene mutation was confirmed to be higher in colon adenocarcinoma (COAD) patients with higher glycolysis score. The SNV, CNV, and DNA methylation of 12 glycolysis key genes occurred at different frequencies and showed different impacts on survival outcomes. The predictive and prognostic value of glycolysis score for immunotherapy outcomes was validated in two immunotherapy cohorts. The expression levels of key genes differ in normal endometrial and three endometrial cancer cell lines. Conclusions: This work indicated that glycolysis score and 12 glycolytic hub genes were correlated with an immunosuppressive microenvironment. They could be served as promising biomarkers aiding diagnosis, predicting prognosis and immunotherapy response for some tumor patients.

Risk of cervical intraepithelial neoplasia grade 3 or more diagnoses for human papillomavirus16/18-positive women by cytology and co-infection status.

BACKGROUND: Human papillomavirus (HPV) 16 and 18 cause approximately 70% of cervical cancer cases. The aim of this study was to evaluate whether co-infected with other HPV genotypes will affect the risk of cervical carcinogenesis in HPV16/18 positive-women. METHODS: In this cross-sectional study, cervical cytology and histological classifications from women who tested positive for HPV 16/18 and underwent colposcopy within 6 months, between January 2010 and May 2021 were obtained from West China Second University Hospital of Sichuan University. MAIN OUTCOMES AND MEASURES: Immediate risk of cervical intraepithelial neoplasia grade 3 or more diagnoses (CIN 3+). RESULTS: A total of 7940 HPV 16/18-positive women were included, with a median age of 40 years (range 25-84 years). Among them, 2710 (34.1%) were infected with multiple genotypes, 6533 (82.28%) had cytology results and 2116 (26.65%) women were diagnosed with CIN 3+. The effects of HPV 16/18 coinfecting with other HPV on CIN3 + risk varied with specific HPV genotypes. After adjusting for cofactors, compared to single HPV 16 infection, the CIN 3 + risk was significantly reduced in women infected with HPV 16 + other high-risk HPV (hrHPV) [odds ratio (OR) = 0.621, 95% confidence interval (CI) 0.511-0.755], HPV 16 + low-risk HPV (lrHPV) (OR = 0.620, 95% CI 0.436-0.883), and HPV 16 + lrHPVs + other hrHPVs (OR = 0.248, 95% CI 0.157-0.391). The prevalence of CIN 3 + was associated with increased severity of cytologic abnormalities in HPV 16/18-positive women and peaked at cytology HSIL + (89.9% and 82.3%), which held a substantially greater risk than that of NILM (OR = 65.466, 95% CI 50.234-85.316). CONCLUSIONS: In this cross-sectional study of HPV 16/18-positive women, the effects of multiple infection were likely complicated and varied with specific HPV genotypes. The coinfection of HPV 16 and other genotypes of HPV except HPV 18 was associated with decreased CIN 3 + risk. Cytologic results were informative when HPV 16/18 was positive. It might be reasonable to recommend expedited treatment for patients with HPV 16/18 positive and HSIL + cytology in the Chinese population.

SULF1 Activates the VEGFR2/PI3K/AKT Pathway to Promote the Development of Cervical Cancer.

BACKGROUND AND PURPOSE: Sulfatase 1 (SULF1) can regulate the binding of numerous signaling molecules by removing 6-O-sulfate from heparan sulfate proteoglycans (HSPGs) to affect numerous physiological and pathological processes. Our research aimed to investigate the effect of the SULF1-mediated VEGFR2/PI3K/AKT signaling pathway on tumorigenesis and development of cervical cancer (CC). METHODS: The expression and prognostic values of SULF1 in patients with CC were analyzed through bioinformatics analysis, RT-PCR, immunohistochemistry, and western blot assays. The function and regulatory mechanism of SULF1 in proliferation, migration, and invasion of cervical cancer cells were examined through lentivirus transduction, CCK8, flow cytometry analysis, plate colony formation assay, scratch assay, transwell assay, western blot, VEGFR2 inhibitor (Ki8751), and mouse models. RESULTS: SULF1 expression was significantly upregulated in CC tissues, which was significantly associated with poor prognosis of patients with CC. In vitro, the upregulation of SULF1 expression in cervical cancer HeLa cells promoted cell proliferation, colony formation, migration, and invasion while inhibiting apoptosis. Conversely, the downregulation of SULF1 expression had the opposite effect. In vivo, the upregulation of SULF1 expression resulted in a significant increase in both tumor growth and angiogenesis, while its downregulation had the opposite effect. Furthermore, western blot detection and cell function rescue assay confirmed that the upregulation of SULF1 in HeLa cells promoted the tumorigenic behaviors of cancer cells by activating the VEGFR2/PI3K/AKT signaling pathway. CONCLUSION: SULF1 plays an oncogenic role in the tumorigenesis and development of CC, indicating its potential as a novel molecular target for gene-targeted therapy in patients with CC.

Identification of TRPM2 as a Potential Therapeutic Target Associated with Immune Infiltration: A Comprehensive Pan-Cancer Analysis and Experimental Verification in Ovarian Cancer.

The exact role of Transient receptor potential melastatin 2 (TRPM2) in tumor progression and immunomodulation remains elusive. We comprehensively investigated the expression pattern, diagnostic value, prognostic impact, genetic and epigenetic alterations of TRPM2 in pan-cancer. Then, we explored underlying pathways associated with TRPM2 and immune-related signatures. Ovarian cancer (OV) specimens were enrolled to test the expression of TRPM2 by immunohistochemistry and RT-qPCR. OV cell A2780 transfected with shRNA targeting TRPM2 was used in subsequent experiments. TRPM2 was aberrantly expressed and associated with unfavorable prognosis across various cancers. It possesses significant diagnostic values with AUC > 0.90. TRPM2 participated in pathways mediating immunoregulation and tumorigenesis. The expression of TRPM2 was significantly correlated with tumor microenvironment scores, tumor-stemness index, macrophages infiltration, immune checkpoints, and immune-related genes. OV single-cell datasets also indicated that TRPM2 was predominantly distributed on macrophages and malignancies. The overexpressed TRPM2 in OV tissues was validated at both the mRNA and protein levels. TRPM2 expression was significantly correlated with type2 macrophage marker CD206. Knockdown of TRPM2 inhibited OV cell proliferation and promoted apoptosis. Overall, TRPM2 has relevance to an immunosuppressive tumor microenvironment by modulating macrophage. It could serve as a powerful biomarker for tumor screening and prognosis, and a potential therapeutic target for tumor treatment, especially for OV.

Loss of RBPMS in ovarian cancer compromises the efficacy of EGFR inhibitor gefitinib through activating HER2/AKT/mTOR/P70S6K signaling.

RBPMS may be a tumor suppressor in cancer, but its impact in modulation of drug sensitivity is unclear. This study aimed to investigate the regulatory role of RBPMS in cellular response to EGFR inhibitor gefitinib in ovarian cancer (OC). By western blotting assay, we revealed RBPMS was down-regulated in epithelial ovarian cancer tissues compared to normal control ovarian epithelial tissues. Overexpression of RBPMS inhibited cell viability and proliferation, and conferred gefitinib sensitivity, accompanied by reduced expression of p-EGFR, and vice versa. Proteomic analysis and flow cytometry experiments showed that RBPMS induced S-stage cell cycle arrest in gefitinib-treated OC cells. Co-IP assay suggested that HER2 was a downstream target of RBPMS, and RBPMS negatively regulated HER2 expression. HER2 counteracted the stimulation of RBPMS to cell growth blocking, gefitinib sensitivity and cell cycle arrest. We further demonstrated that RBPMS overexpression suppressed the activation of p-AKT, p-mTOR and p-P70S6K, which was rescued by up-regulation of HER2. The combination of AKT inhibitor MK2206 and gefitinib had a synergistic effect on OC cells with high level of RBPMS. In conclusion, through the direct inhibition of HER2/AKT/mTOR/P70S6K pathway, RBPMS may be a potential therapeutic target for improving gefitinib sensitivity in OC.

Prognostic significance of Naples prognostic score in operable renal cell carcinoma.

Background: Naples prognostic score (NPS), a novel scoring system based on nutritional and inflammatory status, is associated with prognosis in several cancers. This study aimed to evaluate the prognostic significance of preoperative NPS in patients undergoing nephrectomy. Patients and Methods: This study retrospectively analyzed patients with renal cell carcinoma (RCC) who underwent radical or partial nephrectomy between 2010 and 2013. The clinicopathological characteristics of patients stratified by preoperative NPS were compared. Survival analysis was performed using the Kaplan-Meier method and log-rank test. Univariate and multivariate Cox proportional hazards models were used to identify independent prognostic factors. Receiver operating characteristic curves were used to evaluate prediction efficiency. Results: A total of 638 patients with operable RCC were included. The high-NPS group (NPS group 2) was significantly associated with older age (P < 0.001), larger tumor size (P < 0.001), worse pathological T stage (P < 0.001), positive lymph node pathology (P = 0.002), higher tumor grade (P < 0.001), and greater tumor necrosis (P < 0.001). Multivariable analysis demonstrated that the high-NPS subgroup had significantly worse overall survival (OS) [hazard ratio (HR): 2.25, 95% confidence interval (CI): 1.45-3.50, P < 0.001] and progression-free survival (PFS) (HR: 2.26, 95% CI: 1.48-3.44, P < 0.001). Among several preoperative scoring systems, NPS had the strongest discriminatory power for predicting OS and PFS. Conclusion: Preoperative NPS can serve as a simple novel risk stratification tool to optimize the prognosis of patients with operable RCC. Further prospective and large-scale studies are needed to validate our findings.

A retrospective study of cytology and HPV genotypes results of 3229 vaginal intraepithelial neoplasia patients.

To analyze the distribution of human papillomavirus (HPV) genotype, cytology, and the clinical characteristics of vaginal intraepithelial neoplasia (VaIN). All patients with histological-proven VaIN at West China Second University Hospital, between January 1, 2014, and October 1, 2020, were retrospectively identified. The demographics, medical history, HPV genotype, viral load, and cytology results were retrieved. Standard statistical analyses were conducted. Of 3229 patients included, 42.3% were diagnosed with VaIN 1, 30.3% with VaIN 2% and 27.4% with VaIN 3. Patients with VaIN 3 were the oldest (p < 0.001). The leading HPV genotypes were HPV 16, 52, 58, 53, 56 and 81. The positive rate of HPV 16 was positively correlated with the grade of VaIN and infected most VaIN 3 patients (76.0%). The sensitivities of cytology for VaIN only, concomitant VaIN, and VaIN after hysterectomy were 75.6%, 78.8%, and 82.9%, respectively (p = 0.013), and the sensitivities of HPV were 91.1%, 93.5%, and 91.7%, respectively (p = 0.205). Cotesting improved the sensitivities, up to 96.9%, 97.1%, and 98.1%, respectively. VaIN can occur alone or be concomitant with cervical or vulvar intraepithelial neoplasia. Most of those with VaIN 2/3 are infected with HPV 16. The sensitivity of cytology and HPV testing is non-inferior to that of cervical intraepithelial neoplasia 2+. Therefore, these testings might be helpful in the early detection of VaIN.

Risk factors analysis of persistence, progression and recurrence in vaginal intraepithelial neoplasia.

OBJECTIVE: to profile patients with vaginal intraepithelial neoplasia (VAIN), to evaluate natural history and to identify risk factors for persistence, progression and recurrence. METHODS: At West China Second University Hospital, all patients with histologically confirmed VAIN over a five-year period with minimum follow-up of 6 months were retrospectively identified. Demographics, medical history and clinical information related to the diagnosis and treatment were extracted. Clinical outcomes included normalization, persistence, progression and recurrence. We evaluated risk factors by univariate and multivariate analyses. RESULTS: A total of 1478 patients fulfilled the inclusion criteria with a median follow-up of 14 months (range, 6-60 months). In 86.6% of patients, VAIN went into normalization, 6.4% persisted, 3.5% progressed and 3.5% recurred. Besides, 24 (7.1%) VAIN 3 patients and 4 (0.8%) progressed to cancer, accounting for 85.7% and 14.3% of cancer cases, respectively. VAIN 3 patients treated with excision yielded superior outcomes. Risk factors for persistence were HPV 16, 56, 59 and 43 infections, for progression were prior hysterectomy for cervical lesions and HPV 56 infection, for recurrence were HPV 61 infection. CONCLUSION: Although VAIN will regress in most patients, there are still risks of persistence, recurrence and progression, even malignancy. Therefore, a long-term follow-up is recommended. Patients with VAIN 3 are at higher risk of progressing to cancer and excision is preferred. HPV 16, 56, 59 and 43 infections might associate with an increased risk of persistence and patients with prior hysterectomy for cervical lesions tend to progress.

Adjuvant chemotherapy-associated lipid changes in breast cancer patients: A real-word retrospective analysis.

Adjuvant chemotherapy may cause alterations in serum lipids in postoperative breast cancer (BC) patients, but the specific alterations caused by different chemotherapy regimens remain unclear. The aim of this study was to investigate the status of serum lipids pre- and post-chemotherapy and to compare the side effects of different chemotherapy regimens on serum lipid.We retrospectively analysed the lipid profiles of 1934 consecutive postoperative BC patients who received one of the following chemotherapy regimens:The levels of triglycerides (TG), total cholesterols (TC), and low-density lipoprotein (LDL-C) were significantly elevated in patients who received chemotherapy regimens above (P < .001). With respect to different chemotherapy regimens, FEC had less side effects on lipid profiles (TG (P = .006), high-density lipoprotein (HDL-C) (P < .001), and LDL-C (P < .001)) than TC regimen and AC-T and EC-T regimen. Also, the incidence of newly diagnosed dyslipidemia after chemotherapy was lower in FEC group than TC group and AC-T and EC-T group (P < .001). Additionally, the magnitude of the alterations in lipid profiles (TG, TC, HDL-C, and LDL-C) was greater in premenopausal patients than that of the postmenopausal patients (P = .004; P < .001; P = .002; P = .003, respectively). Moreover, after adjusting for multiple baseline covariates, anthracycline-plus-taxane-based regimens (AC-T and EC-T) were still statistically associated with a high level of TG (P = .004) and a low level of HDL-C (P = .033) after chemotherapy compared with FEC regimen. Also, body mass index (BMI) > 24 was associated with abnormal lipid profiles (TG, TC, HDL-C, LDL-C) post-chemotherapy compared with BMI ≤ 24 (P < .001; P = .036; P = .012; P = .048, respectively).BC patients receiving chemotherapy may have elevated lipid profiles, and anthracycline-based regimen had less side effects on lipid profiles compared with regimens containing taxane. Therefore, it is necessary to take lipid metabolism into consideration when making chemotherapy decisions and dyslipidemia prevention and corresponding interventions are indispensable during the whole chemotherapy period.

Efficacy of Raman spectroscopy in the diagnosis of bladder cancer: A systematic review and meta-analysis.

BACKGROUND: Bladder cancer is one of the severest human malignancies which are hardly detected at an early stage. Raman spectroscopy is reported to maintain a high diagnostic accuracy, sensitivity and specificity in some tumors. METHODS: We carried out a complete systematic review based on articles from PubMed/Medline, EMBASE, Web of Science, Ovid, Web of Knowledge, Cochrane Library and CNKI. We identified 2341 spectra with strict criteria in 9 individual studies between 2004 and 2018 in accordance to Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. We summarized the test performance using random effects models. RESULTS: General pooled diagnostic sensitivity and specificity of RS to kidney cancer were 94% (95% CI 0.93-0.95) and 92% (95% CI 0.90-0.93). The pooled positive LR was 10.00 (95%CI 5.66-17.65) while the negative LR was 0.09 (95%CI 0.06-0.14). The pooled DOR was 139.53 (95% CI 54.60-356.58). The AUC of SROC was 0.9717. CONCLUSION: Through this meta-analysis, we found a promisingly high sensitivity and specificity of RS in the diagnosis of suspected bladder masses and tumors. Other parameters like positive, negative LR, DOR, and AUC of the SROC curve all helped to illustrate the high efficacy of RS in bladder cancer diagnosis.