T cell receptor ß repertoires in patients with COVID-19 reveal disease severity signatures.

Background: The immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are crucial in maintaining a delicate balance between protective effects and harmful pathological reactions that drive the progression of coronavirus disease 2019 (COVID-19). T cells play a significant role in adaptive antiviral immune responses, making it valuable to investigate the heterogeneity and diversity of SARS-CoV-2-specific T cell responses in COVID-19 patients with varying disease severity. Methods: In this study, we employed high-throughput T cell receptor (TCR) ß repertoire sequencing to analyze TCR profiles in the peripheral blood of 192 patients with COVID-19, including those with moderate, severe, or critical symptoms, and compared them with 81 healthy controls. We specifically focused on SARS-CoV-2-associated TCR clonotypes. Results: We observed a decrease in the diversity of TCR clonotypes in COVID-19 patients compared to healthy controls. However, the overall abundance of dominant clones increased with disease severity. Additionally, we identified significant differences in the genomic rearrangement of variable (V), joining (J), and VJ pairings between the patient groups. Furthermore, the SARS-CoV-2-associated TCRs we identified enabled accurate differentiation between COVID-19 patients and healthy controls (AUC > 0.98) and distinguished those with moderate symptoms from those with more severe forms of the disease (AUC > 0.8). These findings suggest that TCR repertoires can serve as informative biomarkers for monitoring COVID-19 progression. Conclusions: Our study provides valuable insights into TCR repertoire signatures that can be utilized to assess host immunity to COVID-19. These findings have important implications for the use of TCR ß repertoires in monitoring disease development and indicating disease severity.

Rapid and Accurate Detection of SARS Coronavirus 2 by Nanopore Amplicon Sequencing.

Objective: We aimed to evaluate the performance of nanopore amplicon sequencing detection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples. Method: We carried out a single-center, prospective cohort study in a Wuhan hospital and collected a total of 86 clinical samples, including 54 pharyngeal swabs, 31 sputum samples, and 1 fecal sample, from 86 patients with coronavirus disease 2019 (COVID-19) from Feb 20 to May 15, 2020. We performed parallel detection with nanopore-based genome amplification and sequencing (NAS) on the Oxford Nanopore Technologies (ONT) minION platform and routine reverse transcription quantitative polymerase chain reaction (RT-qPCR). In addition, 27 negative control samples were detected using the two methods. The sensitivity and specificity of NAS were evaluated and compared with those of RT-qPCR. Results: The viral read number and reference genome coverage were both significantly different between the two groups of samples, and the latter was a better indicator for SARS-CoV-2 detection. Based on the reference genome coverage, NAS revealed both high sensitivity (96.5%) and specificity (100%) compared with RT-qPCR (80.2 and 96.3%, respectively), although the samples had been stored for half a year before the detection. The total time cost was less than 15 h, which was acceptable compared with that of RT-qPCR (∼2.5 h). In addition, the reference genome coverage of the viral reads was in line with the cycle threshold value of RT-qPCR, indicating that this number could also be used as an indicator of the viral load in a sample. The viral load in sputum might be related to the severity of the infection, particularly in patients within 4 weeks after onset of clinical manifestations, which could be used to evaluate the infection. Conclusion: Our results showed the high sensitivity and specificity of the NAS method for SARS-CoV-2 detection compared with RT-qPCR. The sequencing results were also used as an indicator of the viral load to display the viral dynamics during infection. This study proved the wide application prospect of nanopore sequencing detection for SARS-CoV-2 and may more knowledge about the clinical characteristics of COVID-19.

5-Hydroxymethylcytosine Signatures in Circulating Cell-Free DNA as Early Warning Biomarkers for COVID-19 Progression and Myocardial Injury.

Background: The symptoms of coronavirus disease 2019 (COVID-19) range from moderate to critical conditions, leading to death in some patients, and the early warning indicators of the COVID-19 progression and the occurrence of its serious complications such as myocardial injury are limited. Methods: We carried out a multi-center, prospective cohort study in three hospitals in Wuhan. Genome-wide 5-hydroxymethylcytosine (5hmC) profiles in plasma cell-free DNA (cfDNA) was used to identify risk factors for COVID-19 pneumonia and develop a machine learning model using samples from 53 healthy volunteers, 66 patients with moderate COVID-19, 99 patients with severe COVID-19, and 38 patients with critical COVID-19. Results: Our warning model demonstrated that an area under the curve (AUC) for 5hmC warning moderate patients developed into severe status was 0.81 (95% CI 0.77-0.85) and for severe patients developed into critical status was 0.92 (95% CI 0.89-0.96). We further built a warning model on patients with and without myocardial injury with the AUC of 0.89 (95% CI 0.84-0.95). Conclusion: This is the first study showing the utility of 5hmC as an accurate early warning marker for disease progression and myocardial injury in patients with COVID-19. Our results show that phosphodiesterase 4D and ten-eleven translocation 2 may be important markers in the progression of COVID-19 disease.

Overexpression of HIF-1α, metallothionein and SLUG is associated with high TNM stage and lymph node metastasis in papillary thyroid carcinoma.

Hypoxia inducible factor-1α (HIF-1α) is upregulated by hypoxia, and involved in tumor growth and metastasis in many malignant tumors including papillary thyroid carcinoma (PTC). Metallothionein (MT) is a group of small molecular weight cysteine-rich proteins with a broad variety of functions. SLUG is a member of SNAIL superfamily of zinc finger transcriptional factors implicated in epithelial-mesenchymal transition (EMT). The purpose of this study was to examine HIF-1α, MT and SLUG expression in PTC and assess association of their expression with clinicopathological indicators. HIF-1α, MT and SLUG protein expression in 129 PTCs, 61 nodular hyperplasia and 118 normal thyroid tissue specimens were analyzed using immunohistochemistry. The protein expression levels of these three molecules were up-regulated in PTCs. High protein expression of HIF-1α, MT and SLUG was significantly correlated with high TNM stage (P=0.003, 0.002, 0.024, respectively) and lymph node metastasis (LNM) (P<0.001 for all three molecules). Furthermore, HIF-1α, MT and SLUG protein expression were correlated with one another. Concomitant high expression of any two of these three molecules had stronger correlation with high TNM stage (P≤0.001 for HIF-1α/MT, MT/SLUG and HIF-1α/SLUG) and LNM (P=0.008, 0.002, 0.019 for HIF-1α/MT, MT/SLUG and HIF-1α/SLUG, respectively) than did each alone, and concomitant high expression of all these three molecules is significantly associated with high TNM stage and LNM as compared with cases not showing such expression (P<0.001). These results demonstrated that the evaluation of HIF-1α, MT and SLUG expression in PTC may be useful in predicting the risk of LNM and high TNM stage.

Overexpression of HIF-2α, TWIST, and CXCR4 is associated with lymph node metastasis in papillary thyroid carcinoma.

This study aimed to examine HIF-2α, TWIST, and CXCR4 expression in papillary thyroid carcinoma (PTC) and assesses the association of their expression with clinicopathological indicators. HIF-2α, TWIST, and CXCR4 protein expression in 129 PTCs, 61 nodular hyperplasia, and 118 normal thyroid tissue specimens was analyzed using immunohistochemistry. The protein expression levels of these three molecules were upregulated in PTCs. High protein expression of HIF-2α, TWIST, and CXCR4 was significantly correlated with lymph node metastasis (LNM) (P < 0.001). Furthermore, HIF-2α, TWIST, and CXCR4 protein expression was correlated with one another. Concomitant high expression of these molecules had stronger correlation with LNM than did each alone (P = 0.032 for HIF-2α/TWIST, P < 0.001 for HIF-2α/CXCR4, P = 0.018 for TWIST/CXCR4, and P < 0.001 for HIF-2α/TWIST/CXCR4). Additionally, HIF-2α, TWIST, and CXCR4 mRNA expression were assessed in 30 PTCs, 10 nodular hyperplasia, and 10 normal thyroid tissue specimens using real-time RT-PCR. TWIST and CXCR4 mRNA expression levels were up-regulated in PTCs, and high mRNA expression of TWIST and CXCR4 was significantly correlated with LNM (P = 0.005 and P = 0.010, resp.). These results demonstrated that the evaluation of HIF-2α, TWIST, and CXCR4 expression in PTC may be useful in predicting the risk of LNM.

17ß-estradiol promotes the invasion and migration of nuclear estrogen receptor-negative breast cancer cells through cross-talk between GPER1 and CXCR1.

G protein-coupled estrogen receptor 1 (GPER1) is widely expressed in human breast cancers correlating with increased tumor size and malignancy. Although estrogen signaling via GPER1 was extensively studied in recent years, the underlying molecular mechanism of GPER1-associated metastasis of breast cancer still remains unclear. In this study, the main aims were focused on the potential role of GPER1 in regulating migration and invasion of nuclear estrogen receptor (ER)-negative breast cancer cells upon 17ß-estradiol (E2) stimulation and the involved signaling pathway. Key events in estrogen signaling were chosen for our studies, such as the activation of ERK and AKT, nuclear translocation of NF-κB and secretion of Interleukin-8 (IL-8). The migration and invasion activities upon E2 stimulation were also examined in ER-negative SKBR3 and BT-20 breast cancer cells. Compared with ER-positive MCF-7 breast cancer cells, both SKBR3 and BT-20 cells had very similar expression of GPER1, but relatively high expression of CXC receptor-1 (CXCR1), which is considered as an active regulator for cancer metastasis upon binding IL-8. Results showed that E2 facilitated the activation of ERK, AKT and NF-κB, which could be significantly attenuated by GPER1 blockage or knock-down in both SKBR3 and BT-20 cells. Moreover, increased secretion of IL-8 induced by E2 was also inhibited either by specific inhibitors for GPER1, ERK, AKT, and NF-κB, or by knock-down for GPER1. Furthermore, E2 could activate the migration and invasion of both SKBR3 and BT-20 cells, which in turn could also be inhibited by blocking GPER1, ERK, AKT, NF-κB, and CXCR1, respectively, or knock-down for GPER1 and CXCR1. In conclusion, we demonstrated that estrogen signaling via GPER1 associated with the metastasis of breast cancer, which might be through GPER1/ERK&AKT/NF-κB/IL-8/CXCR1 cascade. The cross-talk between GPER1 and CXCR1 could be another potential target for the therapy of metastatic breast cancer.