The outbreak of 2019 coronavirus disease has been a challenge for hospital laboratories because of the huge number of samples that must be tested for the presence of the causative pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Simple and rapid immunodiagnostic methods are urgently needed to identify positive cases. Here we report the development of a rapid and sensitive lateral flow immunoassay (LFIA) that uses lanthanide-doped polysterene nanoparticles (LNPs) to detect anti-SARV-CoV-2 IgG in human serum. A recombinant nucleocapsid phosphoprotein of SARS-CoV-2 was dispensed onto a nitrocellulose membrane to capture specific IgG. Mouse anti-human IgG antibody was labeled with self-assembled LNPs that served as a fluorescent reporter. A 100-μL aliquot of serum samples (1:1000 dilution) was used for this assay and the whole detection process took 10 min. The results of the validation experiment met the requirements for clinical diagnostic reagents. A value of 0.0666 was defined as the cutoff value by assaying 51 normal samples. We tested 7 samples that were positive by reversetranscription (RT-)PCR and 12 that were negative but clinically suspicious for the presence of anti-SARS-CoV-2 IgG. One of the negative samples was determined to be SARS-CoV-2 IgG positive, while the results for the other samples were consistent with those obtained by RT-PCR. Thus, this assay can achieve rapid and sensitive detection of anti-SARS-CoV-2 IgG in human serum and allow positive identification in suspicious cases; it can also be useful for monitoring the progression COVID-19 and evaluating patients' response to treatment.

Super-enhancers (SEs) are enriched with a cluster of mediator binding sites, which are major contributors to cell-type-specific gene expression. Currently, a large quantity of long non-coding RNAs has been found to be transcribed from or to interact with SEs, which constitute super-enhancer associated long non-coding RNAs (SE-lncRNAs). These SE-lncRNAs play essential roles in transcriptional regulation through controlling SEs activity to regulate a broad range of physiological and pathological processes, especially tumorigenesis. However, the pathological functions of SE-lncRNAs in tumorigenesis are still obscure. In this paper, we characterized 5056 SE-lncRNAs and their associated genes by analysing 102 SE data sets. Then, we analysed their expression profiles and prognostic information derived from 19 cancer types to identify cancer-related SE-lncRNAs and to explore their potential functions. In total, 436 significantly differentially expressed SE-lncRNAs and 2035 SE-lncRNAs with high prognostic values were identified. Additionally, 3935 significant correlations between SE-lncRNAs and their regulatory genes were further validated by calculating their correlation coefficients in each cancer type. Finally, the SELER database incorporating the aforementioned data was provided for users to explore their physiological and pathological functions to comprehensively understand the blocks of living systems.

Development of sensitive homogeneous assays is a high-priority research target for clinical diagnostics. Quantum dots (QDs) present favorable photophysical properties, which implies their potential as an exceptional dye in fluorescence detection. QDs-based biosensors have been described in the literature; however, few of them have truly progressed to widespread clinical usage. In this work, a chemiluminescent homogeneous detecting biosensor is fabricated using QDs-doped polystyrene nanospheres to sensitively detect biomarkers in low-volume serum samples. Phthalocyanine-dyed and QDs-encapsulated carboxylate-functionalized polystyrene nanospheres with surface carboxyl groups (PPs and QPs, respectively) were fabricated and served as triggers and fluorescent probes, respectively, in this biosensing system. In this sandwich-format immunoassay, the PPs produced singlet oxygen once sensitized by 680 nm diode lasers, and the QPs, conjugated with antibodies, and then reacted with the singlet oxygen in the presence of specific antigens and emitted anti-Stokes fluorescence with wavelengths around 605 nm, as a result of fluorescence resonance energy transfer (FRET) within the QPs. We demonstrated the determination of carcinoembryonic antigen as a model protein target in 25 μL of serum samples with an unprecedented detection limit of 2.56 × 10–13 M (46 pg/mL) using this biosensor. Furthermore, excellent correlations (R 2 = 0.99718, n = 107) were obtained between utilizing this biosensor and commercialized chemiluminescence immunoassay kits in clinical serum detection. These results demonstrate that our flexible and reliable biosensor is suitable for direct integration into clinical diagnostics, and it is expected to be a promising diagnostic tool for early detection and screening tests as well as prognosis evaluation for patients.

Micropeptides (≤100 amino acids) are essential regulators of physiological and pathological processes, which can be encoded by small open reading frames (smORFs) derived from long non-coding RNAs (lncRNAs). Recently, lncRNA-encoded micropeptides have been shown to have essential roles in tumorigenesis. Since translated smORF identification remains technically challenging, little is known of their pathological functions in cancer. Therefore, we created classifiers to identify translated smORFs derived from lncRNAs based on ribosome-protected fragment sequencing and machine learning methods. In total, 537 putative translated smORFs were identified and the coding potential of five smORFs was experimentally validated via green fluorescent protein-tagged protein generation and mass spectrometry. After analyzing 11 lncRNA expression profiles of seven cancer types, we identified one validated translated lncRNA, ZFAS1, which was significantly up-regulated in hepatocellular carcinoma (HCC). Functional studies revealed that ZFAS1 can promote cancer cell migration by elevating intracellular reactive oxygen species production by inhibiting nicotinamide adenine dinucleotide dehydrogenase expression, indicating that translated ZFAS1 may be an essential oncogene in the progression of HCC. In this study, we systematically identified translated smORFs derived from lncRNAs and explored their potential pathological functions in cancer to improve our comprehensive understanding of the building blocks of living systems

Simple, rapid SA-MPs based TRFIA, is applied in therapeutic drug monitoring and the analytical performance is comparable with LC-MS/MS.

Breast cancer is the second cause of cancer-associated death among women and seriously endangers women’s health. Therefore, early identification of breast cancer would be beneficial to women’s health. At present, circular RNA (circRNA) not only exists in the extracellular vesicles (EVs) in plasma, but also presents distinct patterns under different physiological and pathological conditions. Therefore, we assume that circRNA could be used for early diagnosis of breast cancer. Here, we developed classifiers for breast cancer diagnosis that relied on 259 samples, including 144 breast cancer patients and 115 controls. In the discovery stage, we compared the genome-wide long RNA profiles of EVs in patients with breast cancer (n=14) and benign breast (n=6). To further verify its potential in early diagnosis of breast cancer, we prospectively collected plasma samples from 259 individuals before treatment, including 144 breast cancer patients and 115 controls. Finally, we developed and verified the predictive classifies based on their circRNA expression profiles of plasma EVs by using multiple machine learning models. By comparing their circRNA profiles, we found 439 circRNAs with significantly different levels between cancer patients and controls. Considering the cost and practicability of the test, we selected 20 candidate circRNAs with elevated levels and detected their levels by quantitative real-time polymerase chain reaction. In the training cohort, we found that BCExoC, a nine-circRNA combined classifier with SVM model, achieved the largest AUC of 0.83 [95% CI 0.77-0.88]. In the validation cohort, the predictive efficacy of the classifier achieved 0.80 [0.71-0.89]. Our work reveals the application prospect of circRNAs in plasma EVs as non-invasive liquid biopsies in the diagnosis and management of breast cancer.

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Dear Editor, Neoadjuvant radiotherapy and concomitant fluorouracil-based chemoradiotherapy (CRT) followed by total mesorectal excision is the conventional treatment for locally advanced rectal cancer (LARC). 1 However, there are individual differences in the sensitivity of cancer patients to cancer therapies. 2 The effectiveness prediction before treatment would assist clinical decisions, effectively avoid indiscriminately using drugs, reduce side effects, and improve the curative effect and quality of life. 3 Therefore, it is important to develop a novel noninvasive methodology to predict the effectiveness of cancer therapy before cancer treatment, which would enable timely interventions and provide a more individualized approach for better treatment outcomes. Cell-free DNA (cfDNA) is mainly derived from tumor and hematopoietic cells in cancer patients and it can reflect the characteristics of its tissue of origin. 4,5 For instance, the promoter coverage of cfDNA could be used to infer the expression status of tumor tissue. 5 As tumor expression status is closely related to patient's responses to cancer therapy, 6 we hypothesized that the promoter profiling of cfDNA could be used for pathologic complete response (pCR) prediction after neoadjuvant CRT. In this study, we first compared the local chromatin changes of cfDNA between the pCR and non-pCR groups of LARC patients. We further evaluated the potentials of promoter profiling of cfDNA for predicting the effectiveness of cancer therapy by developing classifiers for distinguishing pCR and non-pCR patients (Figure 1A). By comparing the local cfDNA signal between 10 pCR and 10 non-pCR patients, we observed a related loss of cfDNA signals in the mean coverage of transcriptional start site (TSS) in LARC patients with non-pCR (Figure 1B, P-value = 3.4 × 10 −21 , Wilcoxon rank-sum test). But the cfDNA signals around transcriptional terminal site (TTS) did not show significant difference (Figure 1C, Pvalue = 1, Wilcoxon rank-sum test). Therefore, we further compared their promoter profiling for each TSS, we iden-This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.