Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing.

Long introns with short exons in vertebrate genes are thought to require spliceosome assembly across exons (exon definition), rather than introns, thereby requiring transcription of an exon to splice an upstream intron. Here, we developed CoLa-seq (co-transcriptional lariat sequencing) to investigate the timing and determinants of co-transcriptional splicing genome wide. Unexpectedly, 90% of all introns, including long introns, can splice before transcription of a downstream exon, indicating that exon definition is not obligatory for most human introns. Still, splicing timing varies dramatically across introns, and various genetic elements determine this variation. Strong U2AF2 binding to the polypyrimidine tract predicts early splicing, explaining exon definition-independent splicing. Together, our findings question the essentiality of exon definition and reveal features beyond intron and exon length that are determinative for splicing timing.

Quantification of tRNA m1A modification by templated-ligation qPCR.

N1-methyladenosine (m1A) is a widespread modification in all eukaryotic, many archaeal, and some bacterial tRNAs. m1A is generally located in the T loop of cytosolic tRNA and between the acceptor and D stems of mitochondrial tRNAs; it is involved in the tertiary interaction that stabilizes tRNA. Human tRNA m1A levels are dynamically regulated that fine-tune translation and can also serve as biomarkers for infectious disease. Although many methods have been used to measure m1A, a PCR method to assess m1A levels quantitatively in specific tRNAs has been lacking. Here we develop a templated-ligation followed by a qPCR method (TL-qPCR) that measures m1A levels in target tRNAs. Our method uses the SplintR ligase that efficiently ligates two tRNA complementary DNA oligonucleotides using tRNA as the template, followed by qPCR using the ligation product as the template. m1A interferes with the ligation in specific ways, allowing for the quantitative assessment of m1A levels using subnanogram amounts of total RNA. We identify the features of specificity and quantitation for m1A-modified model RNAs and apply these to total RNA samples from human cells. Our method enables easy access to study the dynamics and function of this pervasive tRNA modification.

Engineered mischarged transfer RNAs for correcting pathogenic missense mutations.

Missense mutations account for approximately 50% of pathogenic mutations in human genetic diseases, and most lack effective treatments. Gene therapies, gene editing, and RNA therapies, including transfer RNA (tRNA) modalities, are common strategies for genetic disease treatments. However, reported tRNA therapies are for nonsense mutations only. It has not been explored how tRNAs can be engineered to correct missense mutations. Here, we describe missense-correcting tRNAs (mc-tRNAs) as a potential therapeutic for correcting pathogenic missense mutations. Mc-tRNAs are engineered tRNAs charged with one amino acid, but read codons of another in translation. We first developed a series of fluorescent protein-based reporters that indicate the successful correction of missense mutations via restoration of fluorescence. We engineered mc-tRNAs that effectively corrected serine and arginine missense mutations in the reporters and confirmed the amino acid substitution by mass spectrometry and mc-tRNA expression by sequencing. We examined the transcriptome response to mc-tRNA expression and found some mc-tRNAs induced minimum transcriptomic changes. Furthermore, we applied an mc-tRNA to rescue a pathogenic CAPN3 Arg-to-Gln mutant involved in LGMD2A. These results establish a versatile pipeline for mc-tRNA engineering and demonstrate the potential of mc-tRNA as an alternative therapeutic platform for the treatment of genetic disorders.

Clinical characteristics and MRI based radiomics nomograms can predict iPFS and short-term efficacy of third-generation EGFR-TKI in EGFR-mutated lung adenocarcinoma with brain metastases.

BACKGROUND: Predicting short-term efficacy and intracranial progression-free survival (iPFS) in epidermal growth factor receptor gene mutated (EGFR-mutated) lung adenocarcinoma patients with brain metastases who receive third-generation epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) therapy was of great significance for individualized treatment. We aimed to construct and validate nomograms based on clinical characteristics and magnetic resonance imaging (MRI) radiomics for predicting short-term efficacy and intracranial progression free survival (iPFS) of third-generation EGFR-TKI in EGFR-mutated lung adenocarcinoma patients with brain metastases. METHODS: One hundred ninety-four EGFR-mutated lung adenocarcinoma patients with brain metastases who received third-generation EGFR-TKI treatment were included in this study from January 1, 2017 to March 1, 2023. Patients were randomly divided into training cohort and validation cohort in a ratio of 5:3. Radiomics features extracted from brain MRI were screened by least absolute shrinkage and selection operator (LASSO) regression. Logistic regression analysis and Cox proportional hazards regression analysis were used to screen clinical risk factors. Single clinical (C), single radiomics (R), and combined (C + R) nomograms were constructed in short-term efficacy predicting model and iPFS predicting model, respectively. Prediction effectiveness of nomograms were evaluated by calibration curves, Harrell's concordance index (C-index), receiver operating characteristic (ROC) curves and decision curve analysis (DCA). Kaplan-Meier analysis was used to compare the iPFS of high and low iPFS rad-score patients in the predictive iPFS R model and to compare the iPFS of high-risk and low-risk patients in the predictive iPFS C + R model. RESULTS: Overall response rate (ORR) was 71.1%, disease control rate (DCR) was 91.8% and median iPFS was 12.67 months (7.88-20.26, interquartile range [IQR]). There were significant differences in iPFS between patients with high and low iPFS rad-scores, as well as between high-risk and low-risk patients. In short-term efficacy model, the C-indexes of C + R nomograms in training cohort and validation cohort were 0.867 (0.835-0.900, 95%CI) and 0.803 (0.753-0.854, 95%CI), while in iPFS model, the C-indexes were 0.901 (0.874-0.929, 95%CI) and 0.753 (0.713-0.793, 95%CI). CONCLUSIONS: The third-generation EGFR-TKI showed significant efficacy in EGFR-mutated lung adenocarcinoma patients with brain metastases, and the combined line plot of C + R can be utilized to predict short-term efficacy and iPFS.

Identification of a Branch Number Locus in Soybean Using BSA-Seq and GWAS Approaches.

The determination of the soybean branch number plays a pivotal role in plant morphogenesis and yield components. This polygenic trait is subject to environmental influences, and despite its significance, the genetic mechanisms governing the soybean branching number remain incompletely understood. To unravel these mechanisms, we conducted a comprehensive investigation employing a genome-wide association study (GWAS) and bulked sample analysis (BSA). The GWAS revealed 18 SNPs associated with the soybean branch number, among which qGBN3 on chromosome 2 emerged as a consistently detected locus across two years, utilizing different models. In parallel, a BSA was executed using an F2 population derived from contrasting cultivars, Wandou35 (low branching number) and Ruidou1 (high branching number). The BSA results pinpointed a significant quantitative trait locus (QTL), designated as qBBN1, located on chromosome 2 by four distinct methods. Importantly, both the GWAS and BSA methods concurred in co-locating qGBN3 and qBBN1. In the co-located region, 15 candidate genes were identified. Through gene annotation and RT-qPCR analysis, we predicted that Glyma.02G125200 and Glyma.02G125600 are candidate genes regulating the soybean branch number. These findings significantly enhance our comprehension of the genetic intricacies regulating the branch number in soybeans, offering promising candidate genes and materials for subsequent investigations aimed at augmenting the soybean yield. This research represents a crucial step toward unlocking the full potential of soybean cultivation through targeted genetic interventions.

Characterization and clinical verification of immune-related genes in hepatocellular carcinoma to aid prognosis evaluation and immunotherapy.

BACKGROUND: Immune-related genes (IRGs) have been confirmed to play an important role in tumorigenesis and tumor microenvironment formation in hepatocellular carcinoma (HCC). We investigated how IRGs regulates the HCC immunophenotype and thus affects the prognosis and response to immunotherapy. METHODS: We investigated RNA expression of IRGs and developed an immune-related genes-based prognostic index (IRGPI) in HCC samples. Then, the influence of the IRGPI on the immune microenvironment was comprehensively analysed. RESULTS: According to IRGPI, HCC patients are divided into two immune subtypes. A high IRGPI was characterized by an increased tumor mutation burden (TMB) and a poor prognosis. More CD8 + tumor infiltrating cells and expression of PD-L1 were observed in low IRGPI subtypes. Two immunotherapy cohorts confirmed patients with low IRGPI demonstrated significant therapeutic benefits. Multiplex immunofluorescence staining determined that there were more CD8 + T cells infiltrating into tumor microenvironment in IRGPI-low groups, and the survival time of these patients was longer. CONCLUSIONS: This study demonstrated that the IRGPI serve as a predictive prognostic biomarker and potential indicator for immunotherapy.

Cancer-coping profile predicts long-term psychological functions and quality of life in cancer survivors.

PURPOSE: Cancer survivors experience significant psychosocial distress even after completion of cancer treatment. The association between cancer coping and cancer recovery is not well established. The present study investigated the cancer-coping profile and cancer outcomes in breast cancer survivors. METHODS: A three-wave longitudinal study was conducted. In 2009 (wave 1), 248 breast cancer survivors completed a package of psychological inventories to evaluate cancer copying style, psychological distress, anxiety and depression, and quality of life. They received follow-up survey in 2012 (wave 2) and 2016 (wave 3). A latent profile analysis (LPA) was conducted among participants in wave 1 to identify cancer-coping class. Identified cancer-coping class was used to predict psychological and survival outcomes in waves 2 and 3. RESULTS: Two cancer-coping classes were identified through LPA, namely adaptive cancer coping (class I; 52%) and maladaptive cancer coping (class II; 47.8%). Demographic and clinical factors did not differ significantly between the two classes. Subsequent analyses demonstrated that the cancer-coping style in wave 1 predicted the psychological symptoms and quality of life outcomes at the two follow-ups (waves 2 and 3). Survivors in the adaptive group (class I) exhibited lower cancer distress, anxiety and depression scores, and higher quality of life scores than those in the maladaptive group did. Cancer coping were not found to be significantly associated with cancer survival or recurrence. CONCLUSIONS: The identified cancer-coping styles were predictive of the survivors' psychological symptoms, psychological well-being, and health-related quality of life but not cancer survival or recurrence.

Revisiting the Continuing Bonds Theory: The Cultural Uniqueness of the Bei Dao Phenomenon in Taiwanese Widows/Widowers.

In the present study, we used the phenomenological approach to rediscover the ontological meaning of relationships with the deceased in Taiwanese widows/widowers. We first revised the original Western definitions of grief, bereavement, and mourning to fit Taiwanese culture. We used the word bei dao to indicate the mixed nature of grief and mourning in the Taiwanese bereavement process. Then we reanalyzed data from a previous study, which was conducted in 2006. In the previous qualitative research, each subject was interviewed 3 to 4 times in the mourning state over an 18-month interval that began at the point of the spouse's death. Results showed that two main themes emerged in the present analysis: (a) a blurred boundary of life and death and (b) a transformation of ethical bonds. The present study reveals the culturally unique aspects of the Taiwanese bei dao process. Limitations of the present study and future directions are discussed and reflected.

Prevalence, risk factors, and the desire for help of distressed newly diagnosed cancer patients: A large-sample study.

OBJECTIVE: Beginning in 2007, all newly diagnosed cancer patients at the Koo Foundation Sun Yat-Sen Cancer Center (KF-SYSCC) were screened for psychosocial distress. Our social workers, as part of the psychosocial care team (PCT), have engaged in proactive outreach with patients identified as distressed. The goal of the present study was to assess the prevalence of psychosocial distress and the extent of contact between the PCT and distressed patients. METHOD: Newly diagnosed patients who were treated at KF-SYSCC between 2007 and 2010 for cancer were eligible if there were at least 100 patients with the same type of cancer. Before treatment began, they were screened with the Pain Scale and the Distress Thermometer (DT) and had the option to specify a desire for help. The rates of distress were analyzed by cancer type and by probable related factors. Information regarding contact with the PCT was retrieved from computerized databases. RESULTS: Overall, some 5,335 cancer patients representing 12 major cancer types were included in our study. Of these, 1,771 (33.20%) were significantly distressed. By multivariate logistic regression, younger age, female gender, higher pain score, and disease stage, but not cancer type, were found to be associated with higher rates of distress. Among these distressed patients, 628 (36%) had some contact with the PCT. SIGNIFICANCE OF RESULTS: This Taiwanese study with a large sample size revealed a prevalence rate of psychosocial distress similar to rates found in Western countries. Contact with the PCT was established in only 36% of significantly distressed patients, despite a proactive outreach program. It is very important to have screening results made available in a timely fashion to the psycho-oncology team so that appropriate care can be offered promptly.

Psychometric analysis of the Chinese version of the Posttraumatic Growth Inventory with cancer patients in Hong Kong and Taiwan.

OBJECTIVE: Cancer patients in Hong Kong and Taiwan share traditional Chinese as a written form of language, but each region has its own sociocultural background. This study examined if the four-factor model (self, spiritual, life orientation, and interpersonal) of the Chinese version of the Posttraumatic Growth Inventory (PTGI-C), developed for Hong Kong cancer survivors, could be applied to cancer survivors in Taiwan. METHODS: Multisample confirmatory factor analyses (MS-CFA) were used to examine the factorial invariance of the PTGI-C among cancer survivors in Taiwan (n = 217) and Hong Kong (n = 223). RESULTS: The goodness-of-fit of the four-factor model was satisfactory, χ²(180) = 372.36 (χ²/df = 2.07), goodness-of-fit index (GFI) = 0.90, adjusted GFI (AGFI) = 0.87, comparative fit index (CFI) = 0.92, Tucker-Lewis index (TLI) = 0.91, root mean square error of approximation (RMSEA) = 0.05, Akaike information criterion (AIC) = 492.36. This result suggests that the factor structure of the PTGI-C developed in Hong Kong could be applied to cancer survivors in Taiwan. The internal reliabilities of the 15-item whole scale, as well as all the subscales, were good and similar to those reported previously. Interregion comparison revealed that the Taiwan sample had higher mean 'spiritual' and 'interpersonal' posttraumatic growth subscale scores than the Hong Kong sample. CONCLUSIONS: The four-factor model of the PTGI-C is invariant among cancer survivors using traditional Chinese as a written form of the language. The differences in the degree of some posttraumatic growth dimensions may be because of differences in cultural factors and in psychosocial support for cancer patients between the two regions.

Efficacy and safety of immunoradiotherapy for advanced non-small cell lung cancer: a retrospective comparative cohort study.

Background: Treatment of radiotherapy (RT) combined with immune checkpoint inhibitor (ICI) may remarkably improve the prognosis in patients with metastatic non-small cell lung cancer (NSCLC). However, the treatment time of RT, irradiated lesion and the optimum combined scheme, have not been fully determined. Methods: Data regarding overall survival (OS), progression-free survival (PFS), treatment response, and adverse events of 357 patients with advanced NSCLC treated with ICI alone or in combination with RT prior to/during ICI treatment were retrospectively collected. Additionally, subgroup analyses for radiation dose, time interval between RT and immunotherapy, and number of irradiated lesions were performed. Results: Median PFS of the ICI alone and ICI + RT groups was 6 and 12 months, respectively (P<0.0001). The objective response rate (ORR) and disease control rate (DCR) were significantly higher in the ICI + RT group than in the ICI alone group (P=0.014; P=0.015, respectively). However, OS, the distant response rate (DRR), and the distant control rate (DCRt) did not differ significantly between the groups. Out-of-field DRR and DCRt were defined in unirradiated lesions only. Compared with RT application prior to ICI, its application concomitant with ICI led to higher DRR (P=0.018) and DCRt (P=0.002). Subgroup analyses revealed that single-site, high biologically effective dose (BED) (≥72 Gy), planning target volume (PTV) size (<213.7 mL) RT groups had better PFS. In multivariate analysis, PTV volume [≥213.7 vs. <213.7 mL: hazard ratio (HR), 1.89; 95% confidence interval (CI): 1.04-3.42; P=0.035] was an independent predictor of immunotherapy PFS. Additionally, radio-immunotherapy increased the incidence rate of grade 1-2 immune-related pneumonitis compared with ICI alone. Conclusions: Combination therapy using ICIs and radiation may improve PFS and tumor response rates in advanced NSCLC patients regardless of programmed cell death 1 ligand 1 (PD-L1) level or previous treatments. However, it may increase the incidence of immune-related pneumonitis.

Constructive, illusory, and distressed posttraumatic growth among survivors of breast cancer: A 7-year growth trajectory study.

A total of 84 breast cancer survivors completed a package of psychological inventories in 2009 (Time 1), 2012 (Time 2), and 2016 (Time 3). Latent class growth analysis revealed three posttraumatic growth trajectory patterns: distressed posttraumatic growth (n = 5, 6.7%), illusory posttraumatic growth (n = 42, 56.0%), and constructive posttraumatic growth (n = 28, 37.3%). Women with more frequent use of helplessness-hopelessness coping and lower depression levels at Time 1 were more likely to display an illusory than a constructive posttraumatic growth trajectory pattern. Illusory posttraumatic growth might represent a form of coping rather than authentic positive changes. Researchers and clinicians should understand different patterns of posttraumatic growth.

Prevalence of Enterobius vermicularis among preschool children in 2003 and 2013 in Xinxiang city, Henan province, Central China.

The present study was performed to assess the prevalence of Enterobius vermicularis infection among preschool children in Xinxiang city, Henan province, China and the changes in the egg positive rate for E. vermicularis over a 10 year period. A total of 510 preschool children in 17 kindergartens were examined using the cellophane-tape perianal swab method in 2003, while 1734 preschool children in 10 kindergartens were examined in 2013 using the same method. The overall egg positive rate for E. vermicularis was 12.75% (65 out of 510) in 2003 and 5.13% (89 out of 1734) in 2013; the former was significantly higher than the latter (p < 0.05). In both 2003 and 2013, the egg positive rate for 5 to 6-year-old children was significantly higher than that of 2 to 4-year-old children (p < 0.05). However, positive rates were not significantly dependent on gender or area. Among selected personal hygiene factors, no hand washing before eating, sucking fingers or toys, and scratching around the anus were all associated with enterobiasis. The present study confirmed that the prevalence of E. vermicularis infection among preschool children decreased significantly over the 10 year period in Xinxiang city, but infection was still prevalent. Improving sanitation and personal hygiene practices, especially hand washing, could help prevent the transmission of E. vermicularis.

Effects of TiO2 and TiC Nanofillers on the Performance of Dye Sensitized Solar Cells Based on the Polymer Gel Electrolyte of a Cobalt Redox System.

Polymer gel electrolytes (PGEs) of cobalt redox system are prepared for dye sensitized solar cell (DSSC) applications. Poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) is used as a gelator of an acetonitrile (ACN) liquid electrolyte containing tris(2,2'-bipyridine)cobalt(II/III) redox couple. Titanium dioxide (TiO2) and titanium carbide (TiC) nanoparticles are utilized as nanofillers (NFs) of this PGE, and the effects of the two NFs on the conductivity of the PGEs, charge-transfer resistances at the electrode/PGE interface, and the performance of the gel-state DSSCs are studied and compared. The results show that the presence of TiC NFs significantly increases the conductivity of the PGE and decreases the charge-transfer resistance at the Pt counter-electrode (CE)/PGE interface. Therefore, the gel-state DSSC utilizing TiC NFs can achieve a conversion efficiency (6.29%) comparable to its liquid counterpart (6.30%), and, furthermore, the cell efficiency can retain 94% of its initial value after a 1000 h stability test at 50 °C. On the contrary, introduction of TiO2 NFs in the PGE causes a decrease of cell performances. It shows that the presence of TiO2 NFs increases the charge-transfer resistance at the Pt CE/PGE interface, induces the charge recombination at the photoanode/PGE interface, and, furthermore, causes a dye desorption in a long-term-stability test. These results are different from those reported for the iodide redox system and are ascribed to a specific attractive interaction between TiO2 and cobalt redox ions.