Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing RNA-Binding Protein Family in Cinnamomum camphora.

N6-methyladenosine (m6A) is one of the most abundant chemical modifications on mRNA in eukaryotes. RNA-binding proteins containing the YT521-B (YTH) domain play crucial roles in post-transcriptional regulation of plant growth, development, and stress response by reading the m6A mark. However, the YTH domain-containing RNA-binding protein family has not been studied in a valuable and medicinal tree such as Cinnamomum camphora (C. camphora) yet. In this study, we identified 10 YTH genes in C. camphora, located on eight out of 12 chromosomes. Phylogenetic analysis revealed that these genes can be classified into two major classes, YTHDF (CcDF) and YTHDC (CcDC). Closely related CcYTHs within the same class exhibited a similar distribution of conserved motifs and domain organization, suggesting functional similarities among these closely related CcYTHs. All CcYTH proteins possessed a highly conserved YTH domain, with CcDC1A containing an additional CCCH domain. The liquid-liquid phase separation (LLPS) predictions indicate that CcDC1A, CcDF1A, CcDF1C, CcDF3C, CcDF4C, and CcDF5C may undergo phase transitions. Quantitative expression analysis revealed that tissue-specific expression was observed fo CcYTHs. Notably, there were two genes, CcDF1A and CcDF5C; both exhibited significantly higher expression levels in various tissues than other genes, indicating that the m6A-YTH regulatory network in C. camphora might be quite distinct from that in most plants such as Arabidopsis thaliana (A. thaliana) with only one abundant YTH protein. According to the analysis of the up-stream cis-regulatory elements of these YTH genes, these genes could be closely related to stress, hormones, and development. The following stress response experiments further verified that their expression levels indeed changed under both PEG and NaCl treatments. These findings not only provide a foundation for future functional analysis of CcYTHs in C. camphora, but also provide insights into the functions of epigenetic mark m6A in forest trees.

Identification and Expression Patterns of WOX Transcription Factors under Abiotic Stresses in Pinus massoniana.

WUSCHEL-related homeobox (WOX) transcription factors (TFs) play a crucial role in regulating plant development and responding to various abiotic stresses. However, the members and functions of WOX proteins in Pinus massoniana remain unclear. In this study, a total of 11 WOX genes were identified, and bioinformatics methods were used for preliminary identification and analysis. The phylogenetic tree revealed that most PmWOXs were distributed in ancient and WUS clades, with only one member found in the intermediate clade. We selected four highly conserved WOX genes within plants for further expression analysis. These genes exhibited expressions across almost all tissues, while PmWOX2, PmWOX3, and PmWOX4 showed high expression levels in the callus, suggesting their potential involvement in specific functions during callus development. Expression patterns under different abiotic stresses indicated that PmWOXs could participate in resisting multiple stresses in P. massoniana. The identification and preliminary analysis of PmWOXs lay the foundation for further research on analyzing the resistance molecular mechanism of P. massoniana to abiotic stresses.

Enhancement of the liver's neuroprotective role ameliorates traumatic brain injury pathology.

Traumatic brain injury (TBI) is a pervasive problem worldwide for which no effective treatment is currently available. Although most studies have focused on the pathology of the injured brain, we have noted that the liver plays an important role in TBI. Using two mouse models of TBI, we found that the enzymatic activity of hepatic soluble epoxide hydrolase (sEH) was rapidly decreased and then returned to normal levels following TBI, whereas such changes were not observed in the kidney, heart, spleen, or lung. Interestingly, genetic downregulation of hepatic Ephx2 (which encodes sEH) ameliorates TBI-induced neurological deficits and promotes neurological function recovery, whereas overexpression of hepatic sEH exacerbates TBI-associated neurological impairments. Furthermore, hepatic sEH ablation was found to promote the generation of A2 phenotype astrocytes and facilitate the production of various neuroprotective factors associated with astrocytes following TBI. We also observed an inverted V-shaped alteration in the plasma levels of four EET (epoxyeicosatrienoic acid) isoforms (5,6-, 8,9-,11,12-, and 14,15-EET) following TBI which were negatively correlated with hepatic sEH activity. However, hepatic sEH manipulation bidirectionally regulates the plasma levels of 14,15-EET, which rapidly crosses the blood-brain barrier. Additionally, we found that the application of 14,15-EET mimicked the neuroprotective effect of hepatic sEH ablation, while 14,15-epoxyeicosa-5(Z)-enoic acid blocked this effect, indicating that the increased plasma levels of 14,15-EET mediated the neuroprotective effect observed after hepatic sEH ablation. These results highlight the neuroprotective role of the liver in TBI and suggest that targeting hepatic EET signaling could represent a promising therapeutic strategy for treating TBI.

Deletion of Transferrin Receptor 1 in Parvalbumin Interneurons Induces a Hereditary Spastic Paraplegia-Like Phenotype.

Hereditary spastic paraplegia (HSP) is a severe neurodegenerative movement disorder, the underlying pathophysiology of which remains poorly understood. Mounting evidence has suggested that iron homeostasis dysregulation can lead to motor function impairment. However, whether deficits in iron homeostasis are involved in the pathophysiology of HSP remains unknown. To address this knowledge gap, we focused on parvalbumin-positive (PV+) interneurons, a large category of inhibitory neurons in the central nervous system, which play a critical role in motor regulation. The PV+ interneuron-specific deletion of the gene encoding transferrin receptor 1 (TFR1), a key component of the neuronal iron uptake machinery, induced severe progressive motor deficits in both male and female mice. In addition, we observed skeletal muscle atrophy, axon degeneration in the spinal cord dorsal column, and alterations in the expression of HSP-related proteins in male mice with Tfr1 deletion in the PV+ interneurons. These phenotypes were highly consistent with the core clinical features of HSP cases. Furthermore, the effects on motor function induced by Tfr1 ablation in PV+ interneurons were mostly concentrated in the dorsal spinal cord; however, iron repletion partly rescued the motor defects and axon loss seen in both sexes of conditional Tfr1 mutant mice. Our study describes a new mouse model for mechanistic and therapeutic studies relating to HSP and provides novel insights into iron metabolism in spinal cord PV+ interneurons and its role in the regulation of motor functions.SIGNIFICANCE STATEMENT Iron is crucial for neuronal functioning. Mounting evidence suggests that iron homeostasis dysregulation can induce motor function deficits. Transferrin receptor 1 (TFR1) is thought to be the key component in neuronal iron uptake. We found that deletion of Tfr1 in parvalbumin-positive (PV+) interneurons in mice induced severe progressive motor deficits, skeletal muscle atrophy, axon degeneration in the spinal cord dorsal column, and alterations in the expression of hereditary spastic paraplegia (HSP)-related proteins. These phenotypes were highly consistent with the core clinical features of HSP cases and partly rescued by iron repletion. This study describes a new mouse model for the study of HSP and provides novel insights into iron metabolism in spinal cord PV+ interneurons.

Effects of repetitive functional magnetic stimulation in the sacral nerve in patients with neurogenic detrusor overactivity after suprasacral spinal cord injury: a study protocol for a randomized controlled trial.

BACKGROUND: Neurogenic detrusor overactivity (NDO) is a serious and common complication after spinal cord injury, affecting patients' quality of life seriously. Therefore, we developed this research protocol to evaluate the efficacy of repetitive functional magnetic stimulation (rFMS) in the sacral nerve in patients with neurogenic detrusor overactivity (NDO) after suprasacral spinal cord injury (SCI) and provide more options for rFMS in treating NDO after suprasacral SCI. METHODS: This study is a single-center, randomized, parallel-group clinical trial. We will recruit the patients with NDO after suprasacral SCI in the Rehabilitation Department of the Affiliated Hospital of Southwest Medical University from September 2022 to August 2023. They will be assigned to the rFMS group and the sham stimulation group randomly. The sample size is 66, with 33 patients in each group. The rFMS group will receive real rFMS treatment of the sacral nerve (100% stimulation intensity, 5 Hz, 20 min each time, five times a week), and the sham group will receive sham stimulation. Both groups will receive similar treatment strategies, including medication, standard urine management, acupuncture treatment, and health education. The bladder compliance (bladder capacity/detrusor pressure) and pudendal nerve electromyography will be evaluated at baseline, 8th week of treatment. The residual volume of the bladder and bladder diary will be recorded once a week during 8 weeks of treatments. SCI-QOL and NBSS will be evaluated at baseline, the 4th and 8th week of treatment. In addition, the above assessments will be followed up at 8 weeks after the end of treatment. DISCUSSION: It is expected that the bladder function, symptoms, and quality of life might be significantly improved after rFMS of the sacral nerve. TRIAL REGISTRATION: The China Clinical Trials Registry has approved this study, registration number: ChiCTR2100045148. Registered on April 7, 2021.

Degradation of Perineuronal Nets in the Cerebellar Interpositus Nucleus Ameliorated Social Deficits in Shank3-deficient Mice.

Perineuronal nets (PNNs) are structures that contain extracellular matrix chondroitin sulfate proteoglycan and surround the soma and dendrites of various neuronal cell types. They are involved in synaptic plasticity and undertake important physiological functions. Altered expression of PNNs has been demonstrated in the brains of autism-related animal models. However, the underlying mechanism is still unknown. In this study, we demonstrated that the PNNs in the cerebellum are involved in modulating social and repetitive/inflexible behaviors in Shank3B-/- mice, an established animal model of autism spectrum disorder. First, we performed wisteria floribunda agglutinin staining of the whole brain of Shank3B-/- mice, and found wisteria floribunda agglutinin-positive PNNs are significantly increased in the cerebellar interpositus nucleus (IntP) in Shank3B-/- mice compared to control littermates. After degradation of PNNs in the IntP by chondroitinase ABC, the repetitive behaviors of Shank3B-/- mice were decreased, while their social behaviors were ameliorated. These results suggested that PNNs homeostasis is involved in the regulation of social behavior, revealing a potential therapeutic strategy targeting PNNs in the IntP for the treatment of autism spectrum disorder.

Promoting Strategies for Healthy Environments in University Halls of Residence under Regular Epidemic Prevention and Control: An Importance-Performance Analysis from Zhejiang, China.

In the post-epidemic era, regular epidemic prevention and control is a daunting and ongoing task for nations all around the world. University halls of residence have been important spaces where university students balance their studies, work, and personal lives after COVID-19. Therefore, a healthy physical living environment deserves more attention. This paper compares situations before and after COVID-19 in an effort to evaluate the impact of indoor environments in university halls of residence on students. The study proposed eight vital dimensions for creating a healthy university hall of residence environment and, from 14 September to 4 October 2022, used an online questionnaire to collect data from 301 university students studying in Zhejiang, China. The key quality of service characteristics for fostering a healthy environment in university halls of residence were discovered using descriptive statistical analysis and revised importance-performance analysis (IPA). We found that an improved indoor physical environment and efficient arrangement of indoor space were crucial for the health of university students. The quality of educational services could be improved, and indoor exercise should be utilized effectively, both of which can contribute significantly to a healthy indoor environment. This study aims to contribute to the development of future initiatives to support healthy physical living environments in university halls of residence.

Transcriptomics-metabolomics joint analysis: New highlight into the triterpenoid saponin biosynthesis in quinoa (Chenopodium quinoa Willd.).

Quinoa (Chenopodium quinoa Willd.) contains various physiologically active substances, including vitamins, polyphenols, flavonoids, phytosterols, and saponins. Research showed that saponins were the protective substances in the outer layer of quinoa seeds to defend against microbes, herbivores, and insects. Because the aglycones of quinoa saponins are triterpenoids, they are called triterpenoid saponins (TSs). In addition, the presence of TS imparted bitterness in quinoa and resulted in anticancer and anti-inflammatory effects. In this study, the seeds of low-saponin quinoa, NT376-2 (N), and high-saponin quinoa, B-12071(B), at 30 and 60 days after flowering (DAF) were used to measure the TS content and evaluated for their transcriptomic and metabolomic profiles. The amounts of TS were found to significantly differ between all possible comparisons: N and B at 30 DAF (N1_vs_B1), N and B at 60 DAF (N2_vs_B2), N at 30 DAF and 60 DAF (N1_vs_N2), and B at 30 DAF and 60 DAF (B1_vs_B2). RNA sequencing (RNA-seq) was used to screen differentially expressed genes (DEGs) and revealed 14,703 upregulated DEGs and 26,267 downregulated DEGs in the four comparison groups. The 311 overlapping DEGs found in the four comparisons were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to screen for DEGs related to TS biosynthesis in quinoa. Metabolomics analysis identified acetyl-CoA, 1-hydroxy-2-methyl-2-butenyl-4-diphosphate, farnesal, and (S)-2,3-epoxysqualene as the key differentially accumulated metabolites (DAMs). Transcriptomics-metabolomics joint analysis showed that triterpenoid biosynthesis and terpenoid backbone biosynthesis were the enriched pathways of TS biosynthesis; farnesal were the key DAMs shared in the four comparison groups and associated with 10 key candidate DEGs related to TS biosynthesis in quinoa. These results provided important references for in-depth research on the metabolic mechanism of TS in quinoa.

Corrigendum: Multi-Omics and miRNA Interaction Joint Analysis Highlight New Insights Into Anthocyanin Biosynthesis in Peanuts (Arachis hypogaea L.).

[This corrects the article DOI: 10.3389/fpls.2022.818345.].

Multi-Omics and miRNA Interaction Joint Analysis Highlight New Insights Into Anthocyanin Biosynthesis in Peanuts (Arachis hypogaea L.).

Peanut (Arachis hypogaea L.) is one of the most important economic and oil crops in the world. At present, peanut varieties with rich anthocyanin in testa are rare in the market, but the selection and breeding of varieties with the related traits has always attracted the attention of breeders. In this study, two peanut varieties with the pink and purple testa, G110 (G) and Z18-40 (Z) were used to conduct interaction joint analysis of multi-omics and miRNA-target gene. The anthocyanin content of Z18-40 was 7.49-8.62-folds higher than G110 on 30 DAF (days after flowering) and 45 DAF via Ultraviolet-visible Spectrophotometer (UV-5800, Shanghai, China). And then, a total of 14 candidate genes related with the anthocyanin biosynthesis were identified for correlation in different comparison groups (R 2 ≥ 0.80), among of a novel gene Ah21440 related with hydroxycinnamoyl transferase (HCT) biosynthesis was identified. In addition, Cyanidin 3-O-glucoside (Kuromanin, pmb0550) was the only common differentially accumulated metabolite (DAM) identified using multi-omics joint analysis in G1_vs_G2, Z1_vs_Z2, G1_vs_Z1, and G2_vs_Z2, respectively. Correlation analysis of miRNA-target genes and DEGs in the transcriptome shows that, AhmiR2950, AhmiR398, AhmiR50, and AhmiR51 regulated to HCT and chalcone biosynthesis related candidate genes (Ah21440, AhCHS, AhCHI). Lastly, all of 14 candidate genes and 4 differentially expressed miRNAs were validated using quantitative real-time PCR (qRT-PCR), which trends were consistent with that of the former transcriptome data. The results provide important reference for in-depth research on the anthocyanin metabolism mechanism in peanut testa.

PHF5A promotes colorectal cancerprogression by alternative splicing of TEAD2.

Dysregulated alternative splicing (AS) plays critical roles in driving cancer progression, and the underlying mechanisms remain largely unknown. Here, we demonstrated that PHF5A, a component of U2 small nuclear ribonucleoproteins, was frequently upregulated in colorectal cancer (CRC) samples and associated with poor prognosis. PHF5A promoted proliferation and metastasis of CRC cells in vitro and in vivo. Transcriptomic analysis identified PHF5A-regulated AS targets and pathways. Particularly, PHF5A induced TEAD2 exon 2 inclusion to activate YAP signaling, and interference of TEAD2-L partially reversed the PHF5A-mediated tumor progression. Pharmacological inhibition of PHF5A using pladienolide B had potent antitumor activity. Collectively, these data revealed the oncogenic role of PHF5A in CRC through regulating AS and established PHF5A as potential therapeutic target.

Delivery of Anti-miRNA-221 for Colorectal Carcinoma Therapy Using Modified Cord Blood Mesenchymal Stem Cells-Derived Exosomes.

Background: Exosomes, as natural intercellular information carriers, have great potential in the field of drug delivery. Many studies have focused on modifying exosome surface proteins to allow drugs to specifically target cancer cells. Methods: In this study, human cord blood mesenchymal stromal cell-derived exosomes were used in the delivery of anti-miRNA oligonucleotides so as to be specifically ingested by tumor cells to perform anti-tumor functions. Mesenchymal stem cells modified by the fusion gene iRGD-Lamp2b were constructed to separate and purify exosomes, and the anti-miRNA-221 oligonucleotide (AMO) was loaded into the exosomes by electroporation. Results: The AMO-loaded exosomes (AMO-Exos) effectively inhibited the proliferation and clonal formation of colon cancer cells in vitro, and it was further found that AMO-Exos was taken up by tumor cells through interaction with the NRP-1 protein. The results of a xenograft tumor model also showed that iRGD-modified exosomes were obviously enriched in tumor sites, exerting excellent anti-tumor efficacy. In vivo imaging showed that exosomes were mainly distributed in liver, spleen, and lung tissues. Conclusion: Our results suggest that genetically modified exosomes could be an ideal natural nanostructure for anti-miRNA oligonucleotide delivery.

Clinical Effects of Stereotactic Body Radiation Therapy Targeting the Primary Tumor of Liver-Only Oligometastatic Pancreatic Cancer.

AIM: To investigate the efficacy and safety of stereotactic body radiotherapy (SBRT) targeting the primary tumor for liver-only oligometastatic pancreatic cancer. METHODS: We compared the efficacy and safety of SBRT plus chemotherapy with chemotherapy alone in patients with liver-only oligometastatic pancreatic cancer. The populations were balanced by propensity score-weighted and propensity score-matched analyses based on baseline variables. The primary outcome was overall survival (OS). The secondary outcomes included progression free survival (PFS), local progression, metastatic progression and symptomatic local control. RESULTS: This is a retrospective study of 89 pancreatic cancer patients with liver-only oligometastasis. Overall, 34 (38.2%) and 55 (61.8%) patients received SBRT plus chemotherapy and chemotherapy alone, respectively. After propensity score matching, 1-year OS rate was 34.0% (95%CI, 17.8-65.1%) in the SBRT plus chemotherapy group and 16.5% (95%CI, 5.9-46.1%) in chemotherapy alone group (P=0.115). The 6-month PFS rate was 29.4% (95%CI, 15.4-56.1) in SBRT plus chemotherapy and 20.6% (95%CI, 8.8-48.6) in chemotherapy alone group (P=0.468), respectively. Further subgroup analysis indicated that the addition of SBRT improved OS in patients with primary tumor located in the head of pancreas (stratified HR, 0.28; 95% CI, 0.09 to 0.90) or good performance status (stratified HR, 0.24; 95% CI, 0.07 to 0.86). In terms of disease control, SBRT delayed local progression of pancreas (P=0.008), but not distant metastatic progression (P=0.56). Besides, SBRT offered significant abdominal/back pain relief (P=0.016) with acceptable toxicities. CONCLUSIONS: The addition of SBRT to chemotherapy in patients with liver-only oligometastatic pancreatic cancer improves the OS of those with primary tumor located in the head of pancreas or good performance status. In addition, it is a safe and effective method for local progression control and local symptomatic palliation in patients with metastatic pancreatic cancer.

CRISPR screen in cancer: status quo and future perspectives.

Clustered regularly interspaced short palindromic repeats (CRISPR) system offers a powerful platform for genome manipulation, including protein-coding genes, noncoding RNAs and regulatory elements. The development of CRISPR screen enables high-throughput interrogation of gene functions in diverse tumor biologies, such as tumor growth, metastasis, synthetic lethal interactions, therapeutic resistance and immunotherapy response, which are mostly performed in vitro or in transplant models. Recently, direct in vivo CRISPR screens have been developed to identify drivers of tumorigenesis in native microenvironment. Key parameters of CRISPR screen are constantly being optimized to achieve higher targeting efficiency and lower off-target effect. Here, we review the recent advances of CRISPR screen in cancer studies both in vitro and in vivo, with a particular focus on identifying cancer immunotherapy targets, and propose optimizing strategies and future perspectives for CRISPR screen.

Efficient sparse estimation on interval-censored data with approximated L0 norm: Application to child mortality.

A novel penalty for the proportional hazards model under the interval-censored failure time data structure is discussed, with which the subject of variable selection is rarely studied. The penalty comes from an idea to approximate some information criterion, e.g., the BIC or AIC, and the core process is to smooth the ℓ0 norm. Compared with usual regularization methods, the proposed approach is free of heavily time-consuming hyperparameter tuning. The efficiency is further improved by fitting the model and selecting variables in one step. To achieve this, sieve likelihood is introduced, which simultaneously estimates the coefficients and baseline cumulative hazards function. Furthermore, it is shown that the three desired properties for penalties, i.e., continuity, sparsity, and unbiasedness, are all guaranteed. Numerical results show that the proposed sparse estimation method is of great accuracy and efficiency. Finally, the method is used on data of Nigerian children and the key factors that have effects on child mortality are found.

Outcomes of Stereotactic Body Radiotherapy for Metastatic Colorectal Cancer With Oligometastases, Oligoprogression, or Local Control of Dominant Tumors.

AIM: To evaluate the clinical outcomes of metastatic colorectal cancer (mCRC) patients with oligometastases, oligoprogression, or local control of dominant tumors after stereotactic body radiotherapy (SBRT) and establish a nomogram model to predict the prognosis for these patients. METHODS AND MATERIALS: A cohort of 94 patients with 162 mCRC metastases was treated with SBRT at a single institution. Treatment indications were oligometastases, oligoprogression, and local control of dominant tumors. End points of this study were the outcome in terms of progression-free survival (PFS), overall survival (OS), local progression (LP), and cumulative incidence of starting or changing systemic therapy (SCST). In addition, univariate and multivariable analyses to assess variable associations were performed. The predictive accuracy and discriminative ability of the nomogram were determined by concordance index (C-index) and calibration curve. RESULTS: Median PFS were 12.6 months, 6.8 months, and 3.7 months for oligometastases, oligoprogression, and local control of dominant tumors, respectively. 0-1 performance status, < 10 ug/L pre-SBRT CEA, and ≤ 2 metastases were significant predictors of higher PFS on multivariate analysis. Median OS were 40.0 months, 26.1 months, and 6.5 months for oligometastases, oligoprogression, and local control of dominant tumors, respectively. In the multivariate analysis of the cohort, the independent factors for survival were indication, performance status, pre-SBRT CEA, and PTV, all of which were selected into the nomogram. The calibration curve for probability of survival showed the good agreement between prediction by nomogram and actual observation. The C-index of the nomogram for predicting survival was 0.848. CONCLUSIONS: SBRT for metastases derived from colorectal cancer offered favorable survival and symptom palliation without significant complications. The proposed nomogram could provide individual prediction of OS for patients with mCRC after SBRT.