Functional Divergence in Orthologous Transcription Factors: Insights from AtCBF2/3/1 and OsDREB1C.

Despite traditional beliefs of orthologous genes maintaining similar functions across species, growing evidence points to their potential for functional divergence. C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) are critical in cold acclimation, with their overexpression enhancing stress tolerance but often constraining plant growth. In contrast, a recent study unveiled a distinctive role of rice OsDREB1C in elevating nitrogen use efficiency (NUE), photosynthesis, and grain yield, implying functional divergence within the CBF/DREB1 orthologs across species. Here, we delve into divergent molecular mechanisms of OsDREB1C and AtCBF2/3/1 by exploring their evolutionary trajectories across rice and Arabidopsis genomes, regulatomes, and transcriptomes. Evolutionary scrutiny shows discrete clades for OsDREB1C and AtCBF2/3/1, with the Poaceae-specific DREB1C clade mediated by a transposon event. Genome-wide binding profiles highlight OsDREB1C's preference for GCCGAC compared to AtCBF2/3/1's preference for A/GCCGAC, a distinction determined by R12 in the OsDREB1C AP2/ERF domain. Cross-species multiomic analyses reveal shared gene orthogroups (OGs) and underscore numerous specific OGs uniquely bound and regulated by OsDREB1C, implicated in NUE, photosynthesis, and early flowering, or by AtCBF2/3/1, engaged in hormone and stress responses. This divergence arises from gene gains/losses (∼16.7% to 25.6%) and expression reprogramming (∼62.3% to 66.2%) of OsDREB1C- and AtCBF2/3/1-regulated OGs during the extensive evolution following the rice-Arabidopsis split. Our findings illustrate the regulatory evolution of OsDREB1C and AtCBF2/3/1 at a genomic scale, providing insights on the functional divergence of orthologous transcription factors following gene duplications across species.

Convergent and/or parallel evolution of RNA-binding proteins in angiosperms after polyploidization.

Increasing studies suggest that the biased retention of stress-related transcription factors (TFs) after whole-genome duplications (WGDs) could rewire gene transcriptional networks, facilitating plant adaptation to challenging environments. However, the role of posttranscriptional factors (e.g. RNA-binding proteins, RBPs) following WGDs has been largely ignored. Uncovering thousands of RBPs in 21 representative angiosperm species, we integrate genomic, transcriptomic, regulatomic, and paleotemperature datasets to unravel their evolutionary trajectories and roles in adapting to challenging environments. We reveal functional enrichments of RBP genes in stress responses and identify their convergent retention across diverse angiosperms from independent WGDs, coinciding with global cooling periods. Numerous RBP duplicates derived from WGDs are then identified as cold-induced. A significant overlap of 29 orthogroups between WGD-derived and cold-induced RBP genes across diverse angiosperms highlights a correlation between WGD and cold stress. Notably, we unveil an orthogroup (Glycine-rich RNA-binding Proteins 7/8, GRP7/8) and relevant TF duplicates (CCA1/LHY, RVE4/8, CBF2/4, etc.), co-retained in different angiosperms post-WGDs. Finally, we illustrate their roles in rewiring circadian and cold-regulatory networks at both transcriptional and posttranscriptional levels during global cooling. Altogether, we underline the adaptive evolution of RBPs in angiosperms after WGDs during global cooling, improving our understanding of plants surviving periods of environmental turmoil.

Regulating Tumorigenicity and Cancer Metastasis through TRKA Signaling.

Tropomyosin receptor kinase (TRK) A, TRKA, is a specific binding receptor of nerve growth factor (NGF), which plays an essential role in the occurrence and progression of human cancers. TRKA overexpression has been proven to be a powerful carcinogenic driver and has been verified in many tumors. The TRKA receptor kinase domain is over-activated in an NGF-dependent manner, accompanied by activation of downstream signal pathways, such as RAS-MAPK, PI3K-AKT, JAK2-STAT3 pathway, PLC γ pathway, and Hippo pathway, which participate in tumor cell proliferation, invasion, epithelial-mesenchymal transition (EMT), perineural invasion (PNI), drug resistance, and cancer pain. In addition, chimeric oncogenes produced by the fusion of NTRK1 and other genes are also the direct cause of tumorigenesis and cancer development. The newly developed TRK inhibitors can improve symptoms and tumor regression in cancer patients with overexpression of TRKA or NTRK1 fusion gene. With the emergence of drug resistance, next generation of TRK inhibitors can still maintain strong clinical efficacy in the case of TRK kinase domain mutations, and these inhibitors are in clinical trials. This review summarizes the characteristics and research progress of TRKA, focusing on the regulatory role of the TRKA signal pathway in different tumors. In addition, we have summarized the clinical significance of TRKA and the TRK inhibitors. This review may provide a new reference for the study of the mechanism of TRKA in different tumors, and also provide a new perspective for the in-depth understanding of the role of TRKA as a biomarker and therapeutic target in human cancer.

Differences in alternative splicing and their potential underlying factors between animals and plants.

BACKGROUND: Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW: This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW: We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.

Molecular characterization of ferroptosis in soft tissue sarcoma constructs a prognostic and immunotherapeutic signature through experimental and bioinformatics analyses.

Ferroptosis regulators have been found to affect tumor progression. However, studies focusing on ferroptosis and soft tissue sarcoma (STS) are rare. Somatic mutation, copy number variation, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, consensus clustering, differentially expressed genes analysis (DEGs), principal component analysis (PCA) and gene set enrichment analysis (GSEA) were used to identify and explore different ferroptosis modifications in STS. A nomogram was constructed to predict the prognosis of STS. Moreover, three immunotherapy datasets were used to assess the Fescore. Western blotting, siRNA transfection, EdU assay and reactive oxygen species (ROS) measurement were performed. 16 prognostic ferroptosis regulators were screened and significant differences were observed in somatic mutation, copy number variation (CNV) and RT-qPCR among these ferroptosis regulators. 2 different ferroptosis modification patterns were found (Fe cluster A and B). Fe cluster A with higher Fescore was correlated with p53 pathway and had better prognosis of STS (p = 0.002) while Fe cluster B with lower Fescore was correlated with angiogenesis and MYC pathway and showed a poorer outcome. Besides, the nomogram effectively predicted the outcome of STS and the Fescore could also well predict the prognosis of other 16 tumors and immunotherapy response. Downregulation of LOX also inhibited growth and increased ROS production in sarcoma cells. The molecular characterization of ferroptosis regulators in STS was explored and an Fescore was constructed. The Fescore quantified ferroptosis modification in STS patients and effectively predicted the prognosis of a variety of tumors, providing novel insights for precision medicine.

Overexpression of HSPB6 inhibits osteosarcoma progress through the ERK signaling pathway.

Heat shock protein B6 (HSPB6) plays a certain role in the formation of several cancers, whereas its effect on osteosarcoma remains unclear. In this study, the effect of HSPB6 on osteosarcoma was validated through numerous experiments. HSPB6 was down-regulated in osteosarcoma. As indicated by the result of CCK-8 and colony formation assays, HSPB6 overexpression was likely to inhibit the osteosarcoma cells proliferation, whereas the flow cytometry analysis suggested that apoptosis of osteosarcoma cells was increased after HSPB6 overexpression. Furthermore, transwell and wound healing assays suggested that when HSPB6 was overexpressed, osteosarcoma cells migration and invasion were declined. Moreover, the western blotting assay suggested that the protein level of p-ERK1/2 was down-regulated in osteosarcoma when HSPB6 was overexpressed. Besides, the effect of HSPB6 on osteosarcoma in vivo was examined. As indicated by the result, HSPB6 overexpression was likely to prevent osteosarcoma growth and lung metastasis in vivo. As revealed by the findings of this study, HSPB6 overexpression exerted anticancer effects in osteosarcoma through the ERK signaling pathway and HSPB6 may be suitable target for osteosarcoma molecular therapies.

Intrauterine transmission of SARS-CoV-2 to and prenatal ultrasound abnormal findings in the fetus of a pregnant woman with mild COVID-19.

BACKGROUND: Whether intrauterine transmission of COVID-19 occurs remains uncertain, and it remains unclear whether the disease affects fetuses. We present a case of intrauterine transmission of SARS-CoV-2 infection and the prenatal ultrasonographic findings of the fetus in a pregnant woman with mild COVID-19. CASE PRESENTATION: A 30-year-old woman was admitted to our hospital for ultrasound examination in January 2023 at 26+ 3 weeks' gestation. Twenty-one days prior, her COVID-19 nucleic acid test was positive, and she had mild symptoms, including fever (38.3 °C), headache, chills, ankle pain and cough. After receiving symptomatic treatment, she fully recovered. Prenatal ultrasound revealed that the placenta was diffusely distributed with punctate echogenic foci, hepatomegaly, and the volume of bilateral lungs decreased significantly, with enhanced echo. In addition, we found that the surface of the fetal brain demonstrated widened gyri with a flattened surface. The prenatal MRI confirmed these fetal abnormalities. Amniotic fluid was tested for SARS-CoV-2, and the sample tested was positive for the virus. After careful consideration, the pregnant woman decided to terminate the pregnancy. CONCLUSION: The intrauterine transmission of COVID-19 is certain. Moreover, the intrauterine transmission of COVID-19 may cause abnormalities in various organs of the fetus.

Orthogroup and phylotranscriptomic analyses identify transcription factors involved in the plant cold response: A case study of Arabidopsis BBX29.

C-repeat binding factors (CBFs) are well-known transcription factors (TFs) that regulate plant cold acclimation. RNA sequencing (RNA-seq) data from diverse plant species provide opportunities to identify other TFs involved in the cold response. However, this task is challenging because gene gain and loss has led to an intertwined community of co-orthologs and in-paralogs between and within species. Using orthogroup (closely related homologs) analysis, we identified 10,549 orthogroups in five representative eudicots. A phylotranscriptomic analysis of cold-treated seedlings from eudicots identified 35 high-confidence conserved cold-responsive transcription factor orthogroups (CoCoFos). These 35 CoCoFos included the well-known cold-responsive regulators CBFs, HSFC1, ZAT6/10, and CZF1 among others. We used Arabidopsis BBX29 for experimental validation. Expression and genetic analyses showed that cold-induction of BBX29 is CBF- and abscisic acid-independent, and BBX29 is a negative regulator of cold tolerance. Integrative RNA-seq and Cleavage Under Targets and Tagmentation followed by sequencing analyses revealed that BBX29 represses a set of cold-induced TFs (ZAT12, PRR9, RVE1, MYB96, etc.). Altogether, our analysis yielded a library of eudicot CoCoFos and demonstrated that BBX29 is a negative regulator of cold tolerance in Arabidopsis.

A phylotranscriptomic dataset of angiosperm species under cold stress.

Angiosperms are one of the most diverse and abundant plant groups that are widely distributed on Earth, from tropical to temperate and polar zones. The wide distribution of angiosperms may be attributed to the evolution of sophisticated mechanisms of environmental adaptability, including cold tolerance. Since the development of high-throughput sequencing, transcriptome has been widely utilized to gain insights into the molecular mechanisms of plants in response to cold stress. However, previous studies generally focused on single or two species, and comparative transcriptome analyses for multispecies responding to cold stress were limited. In this study, we selected 11 representative angiosperm species, performed phylotranscriptome experiments at four time points before and after cold stress, and presented a profile of cold-induced transcriptome changes in angiosperms. Our multispecies cold-responsive RNA-seq datasets provide valuable references for exploring conserved and evolutionary mechanisms of angiosperms in adaptation to cold stress.

Near-infrared (NIR) imaging with indocyanine green (ICG) may assist in intraoperative decision making and improving surgical margin in bone and soft tissue tumor surgery.

BACKGROUND AND OBJECTIVES: Negative surgical margins are significant in improving patient outcomes. However, surgeons can only rely on visual and tactile information to identify tumor margins intraoperatively. We hypothesized that intraoperative fluorescence imaging with indocyanine green (ICG) could serve as an assistive technology to evaluate surgical margins and guide surgery in bone and soft tissue tumor surgery. METHODS: Seventy patients with bone and soft tissue tumors were enrolled in this prospective, non-randomized, single-arm feasibility study. All patients received intravenous indocyanine green (0.5 mg/kg) before surgery. Near-infrared (NIR) imaging was performed on in situ tumors, wounds, and ex vivo specimens. RESULTS: 60/70 tumors were fluorescent at NIR imaging. The final surgical margins were positive in 2/55 cases, including 1/40 of the sarcomas. Surgical decisions were changed in 19 cases by NIR imaging, and in 7/19 cases final pathology demonstrated margins were improved. Fluorescence analysis showed that the tumor-to-background ratio (TBR) of primary malignant tumors was higher than that of benign, borderline, metastatic, and tumors ≥5 cm in size had higher TBR than those <5 cm. CONCLUSIONS: ICG fluorescence imaging may be a beneficial technique to assist in surgical decision making and improving surgical margins in bone and soft tissue tumor surgery.

Mild Photothermal-Stimulation Based on Injectable and Photocurable Hydrogels Orchestrates Immunomodulation and Osteogenesis for High-Performance Bone Regeneration.

A photoactivated bone scaffold integrated with minimally invasive implantation and mild thermal-stimulation capability shows great promise in the repair and regeneration of irregularly damaged bone tissues. Developing multifunctional photothermal biomaterials that can simultaneously serve as both controllable thermal stimulators and biodegradable engineering scaffolds for integrated immunomodulation, infection therapy, and impaired bone repair remains an enormous challenge. Herein, an injectable and photocurable hydrogel therapeutic platform (AMAD/MP) based on alginate methacrylate, alginate-graft-dopamine, and polydopamine (PDA)-functionalized Ti3C2 MXene (MXene@PDA) nanosheets is rationally designed for near-infrared (NIR)-mediated bone regeneration synergistic immunomodulation, osteogenesis, and bacterial elimination. The optimized AMAD/MP hydrogel exhibits favorable biocompatibility, osteogenic activity, and immunomodulatory functions in vitro. The proper immune microenvironment provided by AMAD/MP could further modulate the balance of M1/M2 phenotypes of macrophages, thereby suppressing reactive oxygen species-induced inflammatory status. Significantly, this multifunctional hydrogel platform with mild thermal stimulation efficiently attenuates local immune reactions and further promotes new bone formation without the addition of exogenous cells, cytokines, or growth factors. This work highlights the potential application of an advanced multifunctional hydrogel providing photoactivated on-demand thermal cues for bone tissue engineering and regenerative medicine.

Biocompatible scaffolds constructed by chondroitin sulfate microspheres conjugated 3D-printed frameworks for bone repair.

Most bone repair scaffolds are multi-connected channel structure, but the hollow structure is not conducive to the transmission of active factors, cells and so on. Here, microspheres were covalently integrated into 3D-printed frameworks to form composite scaffolds for bone repair. The frameworks composed of double bond modified gelatin (Gel-MA) and nano-hydroxyapatite (nHAP) provided strong support for related cells climbing and growth. Microspheres, which were made of Gel-MA and chondroitin sulfate A (CSA), were able to connect the frameworks like bridges, providing channels for cells migration. Additionally, CSA released from microspheres promoted the migration of osteoblasts and enhanced osteogenesis. The composite scaffolds could effectively repair mouse skull defect and improve MC3T3-E1 osteogenic differentiation. These observations confirm the bridging effect of microspheres rich in chondroitin sulfate and also determine that the composite scaffold can be as a promising candidate for enhanced bone repair.

Graphene dispersant-assisted in situ growth of Re-doped MoS2 nanosheets on carbon cloth and their performance for hydrogen evolution reaction.

Uniform distribution of electrochemically active transition metal compounds on carbon cloth can effective improve their hydrogen evolution reaction (HER) performance, however, harsh chemical treatment of carbon substrates is always unavoidable during this process. Herein, a hydrogen protonated polyamino perylene bisimide (HAPBI) was used as interface active agent for the in situ growth of rhenium (Re) doped MoS2 nanosheets on carbon cloth (Re-MoS2/CC). HAPBI contains a large conjugated core and multiple cationic groups and has been shown to be an effective graphene dispersant. It endowed the carbon cloth excellent hydrophilicity through simple noncovalent functionalization and, meanwhile, provided sufficient active sites to anchor MoO42- and ReO4- via electrostatic interaction. Uniform and stable Re-MoS2/CC composites were facilely obtained by immersing carbon cloth in HAPBI solution followed by hydrothermal treatment in the precursor solution. The doping of Re induced the formation of 1 T phase MoS2, which reached about 40% in the mixture with 2H phase MoS2. Electrochemical measurements showed an overpotential of 183 mV at a current density of 10 mA cm-2 in 0.5 mol L-1 H2SO4 when the molar ratio of Re to Mo is 1:100. This strategy can be further extended to construct other electrocatalysts that using graphene, carbon nanotubes, etc. as conductive additives.

Integrative multi-omics analysis of three early diverged rosid species reveals an ancient hierarchical cold-responsive regulatory network.

Elucidating regulators, including transcription factors (TFs) and RNA-binding proteins (RBPs), underlying gene transcriptional and post-transcriptional co-regulatory network is key to understand plant cold responses. Previous studies were mainly conducted on single species, and whether the regulators are conserved across different species remains elusive. Here, we selected three species that diverged at the early evolution of rosids (~99-113 million years ago), performed cold-responsive phylotranscriptome experiments, and integrated chromatin immunoprecipitation- and DNA affinity purification-sequencing (ChIP/DAP-seq) analysis to explore cold-responsive regulators and their regulatory networks. First, we detected over 10,000 cold-induced differentially expressed genes (DEGs) and alternative splicing genes (DASGs) in each species. Among the DEGs, a set of TFs and RBPs were conserved in rosid cold response. Compared to TFs, RBPs displayed a delayed cold-responsive pattern, implying a hierarchical regulation of DEGs and DASGs. By integrating DEGs and DASGs, we identified 259 overlapping DE-DASG orthogroups (closely-related homologs) that were cold-regulated at both transcriptional and post-transcriptional levels in all three studied species. Notably, pathway analysis on each of the DEGs, DASGs, and DE-DASGs in the three species showed a common enrichment connected to the circadian rhythm. Evidently, 226 cold-responsive genes were directly targeted by at least two circadian rhythm components (CCA1, LHY, RV4, RVE7, and RVE8). Finally, we revealed an ancient hierarchy of cold-responsive regulatory networks at transcriptional and post-transcriptional levels launched by circadian components in rosids. Altogether, this study sheds light on conserved regulators underlying cold-responsive regulatory networks across rosid species, despite a long evolutionary history after their divergence.

A Systematic Review of Perioperative Complications in en Bloc Resection for Spinal Tumors.

STUDY DESIGN: Systematic review. OBJECTIVE: En bloc resection is a major, invasive surgical procedure designed to completely resect a vertebral tumor with a sufficient margin. It is technically demanding and potentially poses risks of perioperative complications. In this systematic review, we investigated the incidence of complications after en bloc resection for spinal tumors. METHODS: We screened PubMed and Embase databases for relevant English publications, from 1980 to 2020, using the following terms: spine OR spinal AND en bloc AND tumor. Using a standard PRISMA template, after the initial screening, full-text articles of interest were evaluated. RESULTS: Thirty-six studies with 961 patients were included. The overall mean age of patients was 49.6 years, and the mean follow-up time was 33.5 months. There were 560 complications, and an overall complication rate of 58.3% (560/961). The 5 most frequent complications were neurological damage (12.7%), hardware failure (12.1%), dural tear and cerebrospinal fluid leakage (10.6%), wound-related complications (7.6%) and vascular injury and bleeding (7.3%). The complication-related revision rate was 10.7% (103/961). The average incidence of complication-related death was 1.2% (12/961). CONCLUSIONS: En bloc resection is a surgical procedure that is very invasive and technically challenging, and the possible risks of perioperative complications should not be neglected. The overall complication rate is high. However, complication-related death was rare. The advantages of surgery should be weighed against the serious perioperative morbidity associated with this technique.

LncRNA STK4 antisense RNA 1 (STK4-AS1) promoted osteosarcoma by inhibiting p53 expression.

BACKGROUND: LncRNA STK4 antisense RNA 1 (STK4-AS1) has been identified as a potential biomarker associated with multiple cancers. We proposed that STK4-AS1 plays a role in the proliferation of osteosarcoma by regulating the cell cycle. METHODS: We compared the expression of STK4-AS1, p53, and p21 in osteosarcoma vs normal samples in clinical tissues and cell lines. We determined the effect of overexpression and knockdown of STK4-AS1 in p53 expressing osteosarcoma cells U2OS, p53 muted osteosarcoma cells MG63, and osteoblast cells hFOB on p53 and p21 expression and the cell viability. For U2OS and MG63, the cell cycle was analyzed and the expression of cyclin proteins was determined. We overexpressed p53 or p21 in STK4-AS1 overexpressed cells to explore the association of STK4-AS1 and p53 in U2OS. RESULTS: The STK4-AS1 expression was higher and p53 and p21 expression were lower in osteosarcoma tissue and cells than in their non-cancer counterparts. The expression of STK4-AS1 was negatively correlated with the expression of p53 or p21. Knockdown of STK4-AS1 in U2OS decreased the cell viability, increased cells in the G0/G1 phase, decreased cells in the S and G2/M phase, decreased expression of cyclin A and B, increased p53 and p21, and had no effect on cyclin D and cyclin E, while overexpression of STK4-AS1 did the opposes. Overexpression of p53 or p21 recovered some changes caused by STK4-AS1 overexpression in U2OS. MG63 expressed no p53 and the expression of p21, cyclin A, and cyclin B, cell viability, and cell cycle were not affected by altered STK4-AS1 levels. In hFOB cells, the expression of p53 and p21 was decreased and the cell viability was increased when STK4-AS1 was overexpressed, but they were not affected when STK4-AS1 was knocked down. CONCLUSION: LncRNA STK4-AS1 promoted the cell cycle of osteosarcoma cells by inhibiting p53 expression.

Evaluation of different scoring systems for spinal metastases based on a Chinese cohort.

INTRODUCTIONS: The spine is one of the most common sites of metastasis for malignancies. This study aimed to compare the predictive performance of seven commonly used prognostic scoring systems for surgically treated spine metastases. It is expected to assist surgeons in selecting appropriate scoring systems to support clinical decision-making and better inform patients. METHODS: We performed a retrospective study involving 268 surgically treated patients with spine metastases between 2017 and 2020 at a single regional oncology center in China. The revised Tokuhashi, Tomita, modified Bauer, revised Katagiri, van der Linden, Skeletal Oncology Research Group (SORG) nomogram, and SORG machine-learning (ML) scoring systems were externally validated. The area under the curve (AUC) of the receiver operating characteristic curve was used to evaluate sensitivity and specificity at different postoperative time points. The actual survival time was compared with the reference survival time provided in the original publication. RESULTS: In the present study, the median survival was 16.6 months. The SORG ML scoring system demonstrated the highest accuracy in predicting 90-day (AUC: 0.743) and 1-year survival (AUC: 0.787). The revised Katagiri demonstrated the highest accuracy (AUC: 0.761) in predicting 180-day survival. The revised Katagiri demonstrated the highest accuracy (AUC: 0.779) in predicting 2-year survival. Based on this series, the actual life expectancy was underestimated compared with the original reference survival time. CONCLUSIONS: None of the scoring systems can perform optimally at all time points and for all pathology types, and the reference survival times provided in the original study need to be updated. A cautious awareness of the underestimation by these models is of paramount importance in relation to current patients.

Innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms.

The C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) have been identified as major regulators of cold acclimation in many angiosperm plants. However, their origin and evolutionary process associated to cold responsiveness are still lacking. By integrating multi-omics data of genomes, transcriptomes, and CBFs/DREB1s genome-wide binding profiles, we unveil the origin and evolution of CBFs/DREB1s and their regulatory network. Gene collinearity and phylogeny analyses show that CBF/DREB1 is an innovation evolved from tandem duplication-derived DREB III gene. A subsequent event of ε-whole genome duplication led to two CBF/DREB1 archetypes (Clades I and II) in ancient angiosperms. In contrast to cold-insensitivity of Clade I and their parent DREB III genes, Clade II evolved a further innovation in cold-sensitive response and was stepwise expanded in eudicots and monocots by independent duplications. In geological time, the duplication events were mainly enriched around the Cretaceous-Paleogene (K-Pg) boundary and/or in the Late Cenozoic Ice Age, when the global average temperature significantly decreased. Consequently, the duplicated CBF/DREB1 genes contributed to the rewiring of CBFs/DREB1s-regulatory network for cold tolerance. Altogether, our results highlight an origin and convergent evolution of CBFs/DREB1s and their regulatory network probably for angiosperms adaptation to global cooling.

Convergent evolution of AP2/ERF III and IX subfamilies through recurrent polyploidization and tandem duplication during eudicot adaptation to paleoenvironmental changes.

Whole-genome duplication (WGD or polyploidization) has been suggested as a genetic contributor to angiosperm adaptation to environmental changes. However, many eudicot lineages did not undergo recent WGD (R-WGD) around and/or after the Cretaceous-Paleogene (K-Pg) boundary, times of severe environmental changes; how those plants survived has been largely ignored. Here, we collected 22 plants from major branches of the eudicot phylogeny and classified them into two groups according to the occurrence or absence of R-WGD: 12 R-WGD-containing plants (R-WGD-Y) and 10 R-WGD-lacking plants (R-WGD-N). Subsequently, we identified 496 gene-rich families in R-WGD-Y and revealed that members of the AP2/ERF transcription factor family were convergently over-retained after R-WGDs and showed exceptional cold stimulation. The evolutionary trajectories of the AP2/ERF family were then compared between R-WGD-Y and R-WGD-N to reveal convergent expansions of the AP2/ERF III and IX subfamilies through recurrent independent WGDs and tandem duplications (TDs) after the radiation of the plants. The expansions showed coincident enrichments in- times around and/or after the K-Pg boundary, when global cooling was a major environmental stressor. Consequently, convergent expansions and co-retentions of AP2/ERF III C-repeat binding factor (CBF) duplicates and their regulons in different eudicot lineages contributed to the rewiring of cold-specific regulatory networks. Moreover, promoter analysis of cold-responsive AP2/ERF genes revealed an underlying cis-regulatory code (G-box: CACGTG). We propose a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF III and IX genes that has contributed to eudicot adaptation during paleoenvironmental changes, and we suggest that TD may be a reciprocal/alternative mechanism for genetic innovation in plants that lack WGD.

Molecular Characteristics of m6A Regulators and Tumor Microenvironment Infiltration in Soft Tissue Sarcoma: A Gene-Based Study.

Background: N6-methyladenosine (m6A) methylation played a key role in tumor growth. However, the relationship between m6A and soft tissue sarcoma (STS) was still unclear. Methods: The characterization and patterns of m6A modification in STS (TCGA-SARC and GSE17674) were analyzed comprehensively through bioinformatics and real-time polymerase chain reaction (RT-PCR). The effects of different m6A modification patterns on prognosis and immune infiltration of STS were further explored. Differentially expressed gene (DEG) analysis was performed. Moreover, an m6Ascore was constructed by principal component analysis (PCA). In addition, two immunotherapy datasets (IMvigor210 and GSE78220) and a sarcoma dataset (GSE17618) were used to evaluate the m6Ascore. Results: Huge differences were found in somatic mutation, CNV, and expression of 25 m6A regulators in STS. Two modification patterns (A and B) in STS were further identified and the m6A cluster A showed a better clinical outcome with a lower immune/stromal score compared with the m6A cluster B (p < 0.050).In addition to , most STS samples from m6A cluster A showed a high m6Ascore, which was related to mismatch repair and a better prognosis of STS (p < 0.001). In contrast, the m6A cluster B, characterized by a low m6Ascore, was related to the MYC signaling pathway, which led to a poor prognosis of STS. A high m6Ascore also contributed to a better outcome of PD-1/PD-L1 blockade immunotherapy. Conclusion: The modification patterns of 25 m6A regulators in the STS microenvironment were explored comprehensively. The novel m6Ascore effectively predicted the characteristics of the tumor microenvironment (TME) and outcome in STS and provided novel insights for future immunotherapy.