Fecal gene detection based on next generation sequencing for colorectal cancer diagnosis.

BACKGROUND: Colorectal cancer (CRC) is one of the most common malignancies worldwide. Given its insidious onset, the condition often already progresses to advanced stage when symptoms occur. Thus, early diagnosis is of great significance for timely clinical intervention, efficacy enhancement, and prognostic improvement. Featuring high throughput, fastness, and rich information, next generation sequencing (NGS) can greatly shorten the detection time, which is a widely used detection technique at present. AIM: To screen specific genes or gene combinations in fecal DNA that are suitable for diagnosis and prognostic prediction of CRC, and to establish a technological platform for CRC screening, diagnosis, and efficacy monitoring through fecal DNA detection. METHODS: NGS was used to sequence the stool DNA of patients with CRC, which were then compared with the genetic testing results of the stool samples of normal controls and patients with benign intestinal disease, as well as the tumor tissues of CRC patients. Specific genes or gene combinations in fecal DNA suitable for diagnosis and prognostic prediction of CRC were screened, and their significances in diagnosing CRC and predicting patients' prognosis were comprehensively evaluated. RESULTS: High mutation frequencies of TP53, APC, and KRAS were detected in the stools and tumor tissues of CRC patients prior to surgery. Contrastively, no pathogenic mutations of the above three genes were noted in the postoperative stools, the normal controls, or the benign intestinal disease group. This indicates that tumor-specific DNA was detectable in the preoperative stools of CRC patients. The preoperative fecal expression of tumor-associated genes can reflect the gene mutations in tumor tissues to some extent. Compared to the postoperative stools and the stools in the two control groups, the pathogenic mutation frequencies of TP53 and KRAS were significantly higher for the preoperative stools (χ 2 = 7.328, P < 0.05; χ 2 = 4.219, P < 0.05), suggesting that fecal TP53 and KRAS genes can be used for CRC screening, diagnosis, and prognostic prediction. No significant difference in the pathogenic mutation frequency of the APC gene was found from the postoperative stools or the two control groups (χ 2 = 0.878, P > 0.05), so further analysis with larger sample size is required. Among CRC patients, the pathogenic mutation sites of TP53 occurred in 16 of 27 preoperative stools, with a true positive rate of 59.26%, while the pathogenic mutation sites of KRAS occurred in 10 stools, with a true positive rate of 37.04%. The sensitivity and negative predictive values of the combined genetic testing of TP53 and KRAS were 66.67% (18/27) and 68.97%, respectively, both of which were higher than those of TP53 or KRAS mutation detection alone, suggesting that the combined genetic testing can improve the CRC detection rate. The mutation sites TP53 exon 4 A84G and EGFR exon 20 I821T (mutation start and stop positions were both 7579436 for the former, while 55249164 for the latter) were found in the preoperative stools and tumor tissues. These "undetected" mutation sites may be new types of mutations occurring during the CRC carcinogenesis and progression, which needs to be confirmed through further research. Some mutations of "unknown clinical significance" were found in such genes as TP53, PTEN, KRAS, BRAF, AKT1, and PIK3CA, whose clinical values is worthy of further exploration. CONCLUSION: NGS-based fecal genetic testing can be used as a complementary technique for the CRC diagnosis. Fecal TP53 and KRAS can be used as specific genes for the screening, diagnosis, prognostic prediction, and recurrence monitoring of CRC. Moreover, the combined testing of TP53 and KRAS genes can improve the CRC detection rate.

Safety and immunogenicity of a recombinant COVID-19 vaccine (Sf9 cells) in healthy population aged 18 years or older: two single-center, randomised, double-blind, placebo-controlled, phase 1 and phase 2 trials.

COVID-19 vaccines from multiple manufacturers are needed to cope with the problem of insufficient supply. We did two single-center, randomised, double-blind, placebo-controlled phase 1 and phase 2 trials to assess the safety, tolerability and immunogenicity of a recombinant COVID-19 vaccine (Sf9 cells) in healthy population aged 18 years or older in China. Eligible participants were enrolled, the ratio of candidate vaccine and placebo within each dose group was 3:1 (phase 1) or 5:1 (phase 2). From August 28, 2020, 168 participants were sequentially enrolled and randomly assigned to receive the low dose vaccine, high dose vaccine or placebo with the schedule of 0, 28 days or 0, 14, 28 days in phase 1 trial. From November 18, 2020, 960 participants were randomly assigned to receive the low dose vaccine, high dose vaccine or placebo with the schedule of 0, 21 days or 0, 14, 28 days in phase 2 trial. The most common solicited injection site adverse reaction within 7 days in both trials was pain. The most common solicited systematic adverse reactions within 7 days were fatigue, cough, sore throat, fever and headache. ELISA antibodies and neutralising antibodies increased at 14 days, and peaked at 28 days (phase 1) or 30 days (phase 2) after the last dose vaccination. The GMTs of neutralising antibody against live SARS-CoV-2 at 28 days or 30 days after the last dose vaccination were highest in the adult high dose group (0, 14, 28 days), with 102.9 (95% CI 61.9-171.2) and 102.6 (95% CI 75.2-140.1) in phase 1 and phase 2 trials, respectively. Specific T-cell response peaked at 14 days after the last dose vaccination in phase 1 trial. This vaccine is safe, and induced significant immune responses after three doses of vaccination.

Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution.

The fast development of single-particle cryogenic electron microscopy (cryo-EM) has made it more feasible to obtain the 3D structure of well-behaved macromolecules with a molecular weight higher than 300 kDa at ~3 Å resolution. However, it remains a challenge to obtain the high-resolution structures of molecules smaller than 200 kDa using single-particle cryo-EM. In this work, we apply the Cs-corrector-VPP-coupled cryo-EM to study the 52 kDa streptavidin (SA) protein supported on a thin layer of graphene and embedded in vitreous ice. We are able to solve both the apo-SA and biotin-bound SA structures at near-atomic resolution using single-particle cryo-EM. We demonstrate that the method has the potential to determine the structures of molecules as small as 39 kDa.

Near-Atomic Resolution Structure Determination in Over-Focus with Volta Phase Plate by Cs-Corrected Cryo-EM.

Volta phase plate (VPP) is a recently developed transmission electron microscope (TEM) apparatus that can significantly enhance the image contrast of biological samples in cryoelectron microscopy, and therefore provide the possibility to solve structures of relatively small macromolecules at high-resolution. In this work, we performed theoretical analysis and found that using phase plate on objective lens spherical aberration (Cs)-corrected TEM may gain some interesting optical properties, including the over-focus imaging of macromolecules. We subsequently evaluated the imaging strategy of frozen-hydrated apo-ferritin with VPP on a Cs-corrected TEM and obtained the structure of apo-ferritin at near-atomic resolution from both under- and over-focused dataset, illustrating the feasibility and new potential of combining VPP with Cs-corrected TEM for high-resolution cryo-EM.

The effect of CD33 expression on inflammatory response in chronic obstructive pulmonary disease.

OBJECTIVE: In this article, the effects of CD33 expression from peripheral blood granulocytes and monocytes on inflammatory response in chronic obstructive pulmonary disease (COPD) were examined. METHODS: CD33 and CD64 expression on peripheral blood granulocytes and monocytes from patients with acute exacerbation of chronic obstructive pulmonary disease and healthy control were detected by flow cytometry. To evaluate the effect of CD33 on inflammation immunity in COPD, the correlation between CD33 expression and CD64 expression, as well as inflammatory indices were investigated. RESULTS: We found that the expression of CD64 on granulocytes and monocytes, as well as the levels of C-reacting protein (CRP) and myoglobin (MYO) or the proportion of neutrophils (N%) significantly increased in COPD patients compared to normal control group (p < 0.01). The expression of CD33 on granulocytes was significantly and negatively correlated with the level of CRP (r = -0.311, p = 0.012), as well as to the level of MYO (r = -0.295. p = 0.018). CONCLUSIONS: The granulocytes and monocytes in peripheral blood were activated in patients of acute exacerbation in COPD. CD33 on granulocytes had the potential to inhibit inflammation and prevent tissue damage.

Changes in the proportions of CD4(+)T cell subsets defined by CD127 and CD25 expression during HBV infection.

CD4(+)T cell counts are closely related to the progression of HBV infection. Here, we investigated how the proportions of three CD4(+)T cell subsets - CD127(-)CD25(-), CD127(+)CD25(low/-) and CD127(low)CD25(high) - changed during HBV infection, as is little known. Compared with healthy controls, the proportions of CD127(-)CD25(-) in chronic hepatitis B (CHB) patients and HBV carriers significantly increased, while that of CD127(+)CD25(low/-) significantly decreased. The proportion of CD127(low)CD25(high) in CHB patients was significantly higher than those in HBV carriers or healthy controls. Compared with HBV-DNA negative group, the proportion of CD127(-)CD25(-) in positive group significantly decreased and that of CD127(+)CD25(low/-) significantly increased. In the follow-up study for CHB patients treated with interferon-α2b for 12 weeks or 24 weeks, the proportions of CD127(-)CD25(-) significantly decreased, while that of CD127(low/-)CD25(high) significantly increased. The results suggested that specific changes in the fraction of CD4(+)T cell subsets expressing CD127 and/or CD25 were associated with hepatitis B progression.

[Protein array technology applied in high throughput monoclonal antibody generation].

UNLABELLED: To reduce the huge labor-cost in the screening in traditional monoclonal antibody generation, We established a new system for monoclonal antibody generation integrating with protein array. BALB/c mice were immunized by eight recombinant proteins respectively, and the positive hybridoma cells were obtained by cell fusion and ELISA screening. All the eight kinds of positive hybridoma cells were mixed, cloned, screened by protein array, and definite dilution cloned. RESULTS: 175 single cell clones were obtained by complex cloning, and 119 of those were positive clones. Then 8 positive cell lines were generated by the following 2 rounds definite dilution cloning. By comparing with the traditional method, we got 8 monoclonal antibodies using the combined protein array screening and multiplex cloning method in 1 cycle, and fewer amounts of antigens were used. As a result, the combined protein array and multiplex cloning method could be used as an economical, rapid and simple tool applying in high throughput monoclonal antibody generation.

Frustrated molecular packing in highly ordered smectic phase of side-chain liquid crystalline polymer with rigid polyacetylene backbone.

Using poly(5-{[(4'-heptoxy-4-biphenylyl)carbonyl]oxy}-1-pentyne) as an example, we demonstrate the incorporative accommodation of the rigid polyacetylene backbones and the mesogenic pendants, which leads to a highly ordered smectic (Sm) phase with a frustrated structure. The polymer exhibits a recognizable sheetlike molecular shape due to its rigid backbone and relatively short spacer (three methylene units), and the building block of the liquid crystalline (LC) phase is the whole molecule. In the LC phase, five layers of the molecules stack as a smectic A (SmA) block, and adjacent SmA blocks glide halfway of the molecular width from one to another. In scanning tunneling microscopy (STM) experiments, the STM tip scrape is found to generate a regular nanopattern with periodic electron conductivity, of which the spacing is determined by the side-chain length.