A comprehensive multi-omics analysis identifies a robust scoring system for cancer-associated fibroblasts and intervention targets in colorectal cancer.

BACKGROUND: Cancer-associated fibroblasts (CAF) play a critical role in promoting tumor growth, metastasis, and immune evasion. While numerous studies have investigated CAF, there remains a paucity of research on their clinical application in colorectal cancer (CRC). METHODS: In this study, we collected differentially expressed genes between CAF and normal fibroblasts (NF) from previous CRC studies, and utilized machine learning analysis to differentiate two distinct subtypes of CAF in CRC. To enable practical application, a CAF-related genes (CAFGs) scoring system was developed based on multivariate Cox regression. We then conducted functional enrichment analysis, Kaplan-Meier plot, consensus molecular subtypes (CMS) classification, and Tumor Immune Dysfunction and Exclusion (TIDE) algorithm to investigate the relationship between the CAFGs scoring system and various biological mechanisms, prognostic value, tumor microenvironment, and response to immune checkpoint blockade (ICB) therapy. Moreover, single-cell transcriptomics and proteomics analyses have been employed to validate the significance of scoring system-related molecules in the identity and function of CAF. RESULTS: We unveiled significant distinctions in tumor immune status and prognosis not only between the CAF clusters, but also across high and low CAFGs groups. Specifically, patients in CAF cluster 2 or with high CAFGs scores exhibited higher CAF markers and were enriched for CAF-related biological pathways such as epithelial-mesenchymal transition (EMT) and angiogenesis. In addition, CAFGs score was identified as a risk index and correlated with poor overall survival (OS), progression-free survival (PFS), disease-free survival (DFS), and recurrence-free survival (RFS). High CAFGs scores were observed in patients with advanced stages, CMS4, as well as lymphatic invasion. Furthermore, elevated CAFG scores in patients signified a suppressive tumor microenvironment characterized by the upregulation of programmed death-ligand 1 (PD-L1), T-cell dysfunction, exclusion, and TIDE score. And high CAFGs scores can differentiate patients with lower response rates and poor prognosis under ICB therapy. Notably, single-cell transcriptomics and proteomics analyses identified several molecules related to CAF identity and function, such as FSTL1, IGFBP7, and FBN1. CONCLUSION: We constructed a robust CAFGs score system with clinical significance using multiple CRC cohorts. In addition, we identified several molecules related to CAF identity and function that could be potential intervention targets for CRC patients.

Rational design of a SOCS1-edited tumor-infiltrating lymphocyte therapy using CRISPR/Cas9 screens.

Cell therapies such as tumor-infiltrating lymphocyte (TIL) therapy have shown promise in the treatment of patients with refractory solid tumors, with improvement in response rates and durability of responses nevertheless sought. To identify targets capable of enhancing the antitumor activity of T cell therapies, large-scale in vitro and in vivo clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 screens were performed, with the SOCS1 gene identified as a top T cell-enhancing target. In murine CD8+ T cell-therapy models, SOCS1 served as a critical checkpoint in restraining the accumulation of central memory T cells in lymphoid organs as well as intermediate (Texint) and effector (Texeff) exhausted T cell subsets derived from progenitor exhausted T cells (Texprog) in tumors. A comprehensive CRISPR tiling screen of the SOCS1-coding region identified sgRNAs targeting the SH2 domain of SOCS1 as the most potent, with an sgRNA with minimal off-target cut sites used to manufacture KSQ-001, an engineered TIL therapy with SOCS1 inactivated by CRISPR/Cas9. KSQ-001 possessed increased responsiveness to cytokine signals and enhanced in vivo antitumor function in mouse models. These data demonstrate the use of CRISPR/Cas9 screens in the rational design of T cell therapies.

High-performing polysulfate dielectrics for electrostatic energy storage under harsh conditions.

High capacity polymer dielectrics that operate with high efficiencies under harsh electrification conditions are essential components for advanced electronics and power systems. It is, however, fundamentally challenging to design polymer dielectrics that can reliably withstand demanding temperatures and electric fields, which necessitate the balance of key electronic, electrical and thermal parameters. Herein, we demonstrate that polysulfates, synthesized by sulfur(VI) fluoride exchange (SuFEx) catalysis, another near-perfect click chemistry reaction, serve as high-performing dielectric polymers that overcome such bottlenecks. Free-standing polysulfate thin films from convenient solution processes exhibit superior insulating properties and dielectric stability at elevated temperatures, which are further enhanced when ultrathin (~5 nm) oxide coatings are deposited by atomic layer deposition. The corresponding electrostatic film capacitors display high breakdown strength (>700 MV m-1) and discharged energy density of 8.64 J cm-3 at 150 °C, outperforming state-of-the-art free-standing capacitor films based on commercial and synthetic dielectric polymers and nanocomposites.

Impact of neoadjuvant chemoradiotherapy on the local recurrence and distant metastasis pattern of locally advanced rectal cancer: a propensity score-matched analysis.

BACKGROUND: Previous studies have demonstrated different predominant sites of distant metastasis between patients with and without neoadjuvant chemoradiotherapy (NCRT). This study aimed to explore whether NCRT could influence the metastasis pattern of rectal cancer through a propensity score-matched analysis. METHODS: In total, 1296 patients with NCRT or post-operative chemoradiotherapy (PCRT) were enrolled in this study between January 2008 and December 2015. Propensity score matching was used to correct for differences in baseline characteristics between the two groups. After propensity score matching, the metastasis pattern, including metastasis sites and timing, was compared and analyzed. RESULTS: After propensity score matching, there were 408 patients in the PCRT group and 245 patients in the NCRT group. NCRT significantly reduced local recurrence (4.1% vs. 10.3%, P = 0.004), but not distant metastases (28.2% vs. 27.9%, P = 0.924) compared with PCRT. In both the NCRT and PCRT groups, the most common metastasis site was the lung, followed by the liver. The NCRT group developed local recurrence and distant metastases later than the PCRT group (median time: 29.2 [18.8, 52.0] months vs. 18.7 [13.3, 30.0] months, Z = -2.342, P = 0.019; and 21.2 [12.2, 33.8] vs. 16.4 [9.3, 27.9] months, Z = -1.765, P = 0.035, respectively). The distant metastases occurred mainly in the 2nd year after surgery in both the PCRT group (39/114, 34.2%) and NCRT group (21/69, 30.4%). However, 20.3% (14/69) of the distant metastases appeared in the 3rd year in the NCRT group, while this number was only 13.2% (15/114) in the PCRT group. CONCLUSIONS: The predominant site of distant metastases was the lung, followed by the liver, for both the NCRT group and PCRT group. NCRT did not influence the predominant site of distant metastases, but the NCRT group developed local recurrence and distant metastases later than the PCRT group. The follow-up strategy for patients with NCRT should be adjusted and a longer intensive follow-up is needed.

A risk score system for predicting complicated appendicitis and aid decision-making for antibiotic therapy in acute appendicitis.

BACKGROUND: Exclusive antibiotic therapy is a feasible treatment option for uncomplicated appendicitis, but the pre-treatment diagnosis of uncomplicated appendicitis is challenging. This study aimed to develop a risk score system to predict complicated appendicitis and aiding decision-making regarding antibiotic therapy for acute appendicitis. METHODS: The risk score system for predicting complicated appendicitis was constructed and validated by a surgical therapy cohort (n=543). Furthermore, we applied an independent antibiotic treatment cohort (n=169) to verify whether the risk score system could guide antibiotic treatment decision-making in patients with acute appendicitis (AA). RESULTS: A total of 543 patients were included in the surgical therapy cohort and was split into the primary (n=375) and validation (n=168) cohorts with repeated random sampling. In the primary cohort, multivariate analysis confirmed that periappendiceal fat stranding (PFS, P<0.001, OR =67.80), the C-reactive protein level (CRP ≥38 mg/L, P<0.001, OR =5.77) and the neutrophil-to-lymphocyte ratio (NLR ≥7, P<0.001, OR =3.51) were independent risk factors for complicated appendicitis. The PFS, CRP and NLR scores were 10.0, 4.0 and 3.0 points, respectively. Fourteen patients (3.7%, 14/375) and seven patients (4.2%, 7/168) with pathologically confirmed complicated appendicitis were classified as having uncomplicated appendicitis in the primary and validation cohorts based on the risk score system, respectively. In the independent antibiotic treatment cohort (n=169), the failure rate of antibiotic treatment was 49.2% and 5.3% for the risk score system predicted complicated AA and uncomplicated AA. Furthermore, the predictive accuracy of the risk score system for antibiotic treatment failure as measured by the area under the curve (AUC) was 0.823 (95% CI: 0.757-0.878). CONCLUSIONS: We found that the proposed risk score system based on biological and CT features not only enables the accurate identification of complicated appendicitis patients before pre-treatment but also serves to guide antibiotic treatment decisions.

Log odds of positive lymph nodes is an excellent prognostic factor for patients with rectal cancer after neoadjuvant chemoradiotherapy.

BACKGROUND: Neoadjuvant chemoradiotherapy (NCRT) results in fewer lymph nodes harvested and causes staging migration. Therefore, we compared the prognostic value of the logarithmic odds of positive lymph nodes (LODDS) with the lymph node ratio (LNR) and the American Joint Committee on Cancer (AJCC) ypN stage in patients with locally advanced rectal cancer (LARC) after NCRT. METHODS: A total of 445 patients with LARC who received NCRT and underwent radical surgery between January 2004 and December 2015 were recruited, and data from 4881 patients included in the Surveillance, Epidemiology and End Results (SEER) database between 2010 and 2013 were analyzed to verify our results. The time-dependent area under the receiver operating characteristic curve (TimeROC) was used to evaluate the discriminative ability of the different lymph node staging systems. RESULTS: ypN staging failed to satisfactorily stratify the patients treated with NCRT [the 3-year disease-free survival (DFS) rates were 65.7% and 55.4% for the ypN1 and ypN2 groups, respectively, P=0.252]. The LODDS classification was significantly associated with DFS, and the 3-year DFS rates for the LODDS0, LODDS1, and LODDS2 groups were 89.9%, 72.4%, and 53.9%, respectively (P<0.05 across all groups). Furthermore, the LODDS classification system was able to subclassify patients with ypN0 stage tumors regardless of whether ≥12 or <12 total lymph nodes (TLNs) were harvested. TimeROC analysis showed that the LODDS classification (AUC, median: 0.722, range: 0.692-0.754) had a higher accuracy for determining the prognosis than the ypN stage (AUC, median: 0.691, range: 0.684-0.712) or the LNR (AUC, median: 0.703, range: 0.685-0.730) classification, regardless of lymph node status. These results were verified using the SEER database. CONCLUSIONS: The LODDS was a better prognostic factor for DFS than ypN staging or the LNR-based approach in patients with LARC after NCRT, particularly those with <12 TLNs harvested or ypN0 stage disease.

Prognostic and staging value of tumor deposits in patients with rectal cancer after neoadjuvant chemoradiotherapy.

BACKGROUND: The presence of tumor deposits (TDs) is only considered in the absence of lymph node metastases (LNMs) in the current TNM staging system. However, the prognostic value of TDs when concomitant with LNM for rectal cancer after neoadjuvant chemoradiotherapy (NCRT) remains unclear. This study aimed to evaluate the prognostic value of TDs and when concomitant with LNMs in rectal cancer after NCRT. METHODS: Patients with rectal cancer who had received NCRT between 2010 and 2016 were obtained from the Surveillance, Epidemiology and End Results (SEER) 18 (year range, 1975-2016) database. Data were extracted on the following: age, sex, race, TNM stage, total LNs harvested, positive LNs, histologic type, perineural invasion, grade, carcinoma embryonic antigen status, TD number, and cancer-specific survival (CSS) rates. The primary objective was to determine the prognostic impact of TDs on CSS. The effect of the addition of TD to the LNM count for a novel N stage was also evaluated. Univariate and multivariate analyses were performed using the Kaplan-Meier method and Cox models. RESULTS: Of 9,620 patients, 865 (9.0%) had TDs. TD-positive patients showed a worse prognosis than TD-negative patients (HR =2.39, 95% CI: 2.04-2.80, P<0.001), and multivariate analysis showed that the presence of TDs was an independent poor prognostic factor (HR =1.41, 95% CI: 1.19-1.67, P<0.001). Regarding the LN status, TDs were associated with a higher risk of cancer-specific death in the LNM- group (HR =2.43, 95% CI: 1.86-3.18, P<0.001), M1 group (HR =1.51, 95% CI: 1.08-2.10, P<0.001), and ypN1 group (HR =2.08, 95% CI: 1.61-2.70, P<0.001), but not in the ypN2 group (HR =0.97, 95% CI: 0.69-1.36, P=0.84). Patients with concomitant TDs and LNM showed significantly worse survival than those with TDs or LNM alone (5-year CSS: 48.2%, 72.2%, and 67.8%, respectively). The 5-year CSS rates were 86.2%, 77.4%, 65.1%, 53.8%, and 46.5% for the novel N0, N1a, N1b, N2a, and N2b groups, respectively (P<0.05 across all groups). Time dependent receiver operating characteristic curve analysis and decision curve analysis showed that the novel N stage was superior to the current ypN stage. CONCLUSIONS: The presence of TDs is an independent poor prognostic factor for LARC patients after NCRT. The concomitant presence of TDs and LNM indicates a significantly worse survival, and the addition of TD to LNM may help to better prompt appropriate risk stratification.

Risk factors for nonclosure of defunctioning stoma and stoma-related complications among low rectal cancer patients after sphincter-preserving surgery.

BACKGROUND: Defunctioning stoma is widely used to reduce anastomotic complications in rectal cancer surgery. However, the complications of stoma and stoma reversal surgery should not be underestimated. Furthermore, in some patients, stoma reversal failed. Here, we investigated the complications of defunctioning stoma surgery and subsequent reversal surgery and identify risk factors associated with the failure of getting stoma reversed. METHODS: In total, 154 patients who simultaneously underwent low anterior resection and defunctioning stoma were reviewed. Patients were divided into two groups according to whether their stoma got reversed or not. The reasons that patients received defunctioning stoma and experienced stoma-related complications and the risk factors for failing to get stoma reversed were analysed. RESULTS: The mean follow-up time was 47.54 (range 4.0-164.0) months. During follow-up, 19.5% of the patients suffered stoma-related long-term complications. Only 79 (51.3%) patients had their stomas reversed. The morbidity of complications after reversal surgery was 45.6%, and these mainly consisted of incision-related complications. Multivariate analyses showed that pre-treatment comorbidity (HR = 3.17, 95% CI 1.27-7.96, P = 0.014), postoperative TNM stage (HR = 2.55, 95% CI 1.05-6.18, P = 0.038), neoadjuvant therapy (HR = 2.75, 95% CI 1.07-7.05, P = 0.036), anastomosis-related complications (HR = 4.52, 95% CI 1.81-11.29, P = 0.001), and disease recurrence (HR = 24.83, 95% CI 2.90-213.06, P = 0.003) were significant independent risk factors for a defunctioning stoma to be permanent. CONCLUSIONS: Defunctioning stoma is an effective method to reduce symptomatic anastomotic leakage, but the stoma itself and its reversal procedure are associated with high morbidity of complications, and many defunctioning stomas eventually become permanent. Therefore, surgeons should carefully assess preoperatively and perform defunctioning stomas in very high risk patients. In addition, doctors should perform stoma reversal surgery more actively to prevent temporary stomas from becoming permanent.

Mapping the spreading routes of lymphatic metastases in human colorectal cancer.

Lymphatic metastases are closely associated with tumor relapse and reduced survival in colorectal cancer (CRC). How tumor cells disseminate within the lymphatic network remains largely unknown. Here, we analyze the subclonal structure of 94 tumor samples, covering the primary tumors, lymph node metastases (LNMs), and liver metastases from 10 CRC patients. We portray a high-resolution lymphatic metastatic map for CRC by dividing LNMs into paracolic, intermediate, and central subgroups. Among the 61 metastatic routes identified, 38 (62.3%) are initiated from the primary tumors, 22 (36.1%) from LNMs, and 1 from liver metastasis (1.6%). In 5 patients, we find 6 LNMs that reseed 2 or more LNMs. We summarize 3 diverse modes of metastasis in CRC and show that skip spreading of tumor cells within the lymphatic network is common. Our study sheds light on the complicated metastatic pattern in CRC and has great clinical implications.

A comprehensive review of computational prediction of genome-wide features.

There are significant correlations among different types of genetic, genomic and epigenomic features within the genome. These correlations make the in silico feature prediction possible through statistical or machine learning models. With the accumulation of a vast amount of high-throughput data, feature prediction has gained significant interest lately, and a plethora of papers have been published in the past few years. Here we provide a comprehensive review on these published works, categorized by the prediction targets, including protein binding site, enhancer, DNA methylation, chromatin structure and gene expression. We also provide discussions on some important points and possible future directions.

Regulatory annotation of genomic intervals based on tissue-specific expression QTLs.

MOTIVATION: Annotating a given genomic locus or a set of genomic loci is an important yet challenging task. This is especially true for the non-coding part of the genome which is enormous yet poorly understood. Since gene set enrichment analyses have demonstrated to be effective approach to annotate a set of genes, the same idea can be extended to explore the enrichment of functional elements or features in a set of genomic intervals to reveal potential functional connections. RESULTS: In this study, we describe a novel computational strategy named loci2path that takes advantage of the newly emerged, genome-wide and tissue-specific expression quantitative trait loci (eQTL) information to help annotate a set of genomic intervals in terms of transcription regulation. By checking the presence or the absence of millions of eQTLs in a set of input genomic intervals, combined with grouping eQTLs by the pathways or gene sets that their target genes belong to, loci2path build a bridge connecting genomic intervals to functional pathways and pre-defined biological-meaningful gene sets, revealing potential for regulatory connection. Our method enjoys two key advantages over existing methods: first, we no longer rely on proximity to link a locus to a gene which has shown to be unreliable; second, eQTL allows us to provide the regulatory annotation under the context of specific tissue types. To demonstrate its utilities, we apply loci2path on sets of genomic intervals harboring disease-associated variants as query. Using 1 702 612 eQTLs discovered by the Genotype-Tissue Expression (GTEx) project across 44 tissues and 6320 pathways or gene sets cataloged in MSigDB as annotation resource, our method successfully identifies highly relevant biological pathways and revealed disease mechanisms for psoriasis and other immune-related diseases. Tissue specificity analysis of associated eQTLs provide additional evidence of the distinct roles of different tissues played in the disease mechanisms. AVAILABILITY AND IMPLEMENTATION: loci2path is published as an open source Bioconductor package, and it is available at http://bioconductor.org/packages/release/bioc/html/loci2path.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Altered 5-Hydroxymethylcytosine Landscape in Primary Gastric Adenocarcinoma.

Multiple factors, including genetic and epigenetic fluctuations, have been linked to gastric cancer formation and progression. Cytosine methylation (5mC) has been recognized as a critical epigenetic mark in the mammalian genome. The recent discovery of 5-hydroxymethylcytosine (5hmC), which is generated by ten-eleven translocation (TET) enzymes, provides new perspectives to understand DNA methylation-related plasticity. In this study, we show that gastric tumors display significant loss of 5hmC. Using matched distant normal, peripheral, and tumor primary tissues, we performed genome-wide profiling of 5hmC and identified differentially hydroxymethylated regions (DhMRs) specifically associated with gastric tumors. Gene ontology analyses indicated that DhMRs (both loss of 5hmC and gain of 5hmC) were enriched among the genes involved in specific pathways. Interestingly, the binding motif of hypoxia-inducible factor 1 (HIF1) is enriched among both peripheral and tumor DhMRs, while the Myc-binding motif is specifically enriched among only tumor DhMRs. Tumor progression analyses revealed a unique set of DhMRs that correlate with tumor progression. These data together suggest that alteration of 5hmC could potentially contribute to the tumorigenesis of gastric tumors.

TRIB3 Interacts With ß-Catenin and TCF4 to Increase Stem Cell Features of Colorectal Cancer Stem Cells and Tumorigenesis.

BACKGROUND & AIMS: Activation of Wnt signaling to ß-catenin contributes to the development of colorectal cancer (CRC). Expression of tribbles pseudo-kinase 3 (TRIB3) is increased in some colorectal tumors and associated with poor outcome. We investigated whether increased TRIB3 expression promotes stem cell features of CRC cells and tumor progression by interacting with the Wnt signaling pathway. METHODS: We performed studies with C57BL/6J-ApcMin/J mice injected with an adeno-associated virus vector that expresses a small hairpin RNA against Trib3 mRNA (ApcMin/J-Trib3KD) or a control vector (ApcMin/J-Ctrl). We created BALB/c mice that overexpress TRIB3 from an adeno-associated virus vector and mice with small hairpin RNA-mediated knockdown of ß-catenin. The mice were given azoxymethane followed by dextran sodium sulfate to induce colitis-associated cancer. Intestinal tissues were collected and analyzed by histology, gene expression profiling, immunohistochemistry, and immunofluorescence. Leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5)-positive (LGR5Pos) and LGR5-negative (LGR5Neg) HCT-8 CRC cells, with or without knockdown or transgenic expression of TRIB3, were sorted and analyzed in sphere-formation assays. We derived organoids from human and mouse colorectal tumors to analyze the function of TRIB3 and test the effect of a peptide inhibitor. Wnt signaling to ß-catenin was analyzed in dual luciferase reporter, chromatin precipitation, immunofluorescence, and immunoblot assays. Proteins that interact with TRIB3 were identified by immunoprecipitation. CRC cell lines were grown in nude mice as xenograft tumors. RESULTS: At 10 weeks of age, more than half the ApcMin/J-Ctrl mice developed intestinal high-grade epithelial neoplasia, whereas ApcMin/J-Trib3KD mice had no intestinal polyps and normal histology. Colon tissues from ApcMin/J-Trib3KD mice expressed lower levels of genes regulated by ß-catenin and genes associated with cancer stem cells. Mice with overexpression of Trib3 developed more tumors after administration of azoxymethane and dextran sodium sulfate than BALB/c mice. Mice with knockdown of ß-catenin had a lower tumor burden after administration of azoxymethane and dextran sodium sulfate, regardless of Trib3 overexpression. Intestinal tissues from mice with overexpression of Trib3 and knockdown of ß-catenin did not have activation of Wnt signaling or expression of genes regulated by ß-catenin. LGR5Pos cells sorted from HCT-8 cells expressed higher levels of TRIB3 than LGR5Neg cells. CRC cells that overexpressed TRIB3 had higher levels of transcription by ß-catenin and formed larger spheroids than control CRC cells; knockdown of ß-catenin prevented the larger organoid size caused by TRIB3 overexpression. TRIB3 interacted physically with ß-catenin and transcription factor 4 (TCF4). TRIB3 overexpression increased, and TRIB3 knockdown decreased, recruitment of TCF4 and ß-catenin to the promoter region of genes regulated by Wnt. Activated ß-catenin increased expression of TRIB3, indicating a positive-feedback loop. A peptide (P2-T3A6) that bound ß-catenin disrupted its interaction with TRIB3 and TCF4. In primary CRC cells and HCT-8 cells, P2-T3A6 decreased expression of genes regulated by ß-catenin and genes associated with cancer stem cells and decreased cell viability and migration. Injection of C57BL/6J-ApcMin/J mice with P2-T3A6 decreased the number and size of tumor nodules and colon expression of genes regulated by ß-catenin. P2-T3A6 increased 5-fluorouracil-induced death of CRC cells and survival times of mice with xenograft tumors. CONCLUSION: TRIB3 interacts with ß-catenin and TCF4 in intestine cells to increase expression of genes associated with cancer stem cells. Knockdown of TRIB3 decreases colon neoplasia in mice, migration of CRC cells, and their growth as xenograft tumors in mice. Strategies to block TRIB3 activity might be developed for treatment of CRC.

Fragile X mental retardation protein modulates the stability of its m6A-marked messenger RNA targets.

N6-methyladenosine (m6A) is the most prevalent internal modification of mammalian messenger RNAs (mRNAs) and long non-coding RNAs. The biological functions of this reversible RNA modification can be interpreted by cytoplasmic and nuclear 'm6A reader' proteins to fine-tune gene expression, such as mRNA degradation and translation initiation. Here we profiled transcriptome-wide m6A sites in adult mouse cerebral cortex, underscoring that m6A is a widespread epitranscriptomic modification in brain. Interestingly, the mRNA targets of fragile X mental retardation protein (FMRP), a selective RNA-binding protein, are enriched for m6A marks. Loss of functional FMRP leads to Fragile X syndrome (FXS), the most common inherited form of intellectual disability. Transcriptome-wide gene expression profiling identified 2035 genes differentially expressed in the absence of FMRP in cortex, and 92.5% of 174 downregulated FMRP targets are marked by m6A. Biochemical analyses indicate that FMRP binds to the m6A sites of its mRNA targets and interacts with m6A reader YTHDF2 in an RNA-independent manner. FMRP maintains the stability of its mRNA targets while YTHDF2 promotes the degradation of these mRNAs. These data together suggest that FMRP regulates the stability of its m6A-marked mRNA targets through YTHDF2, which could potentially contribute to the molecular pathogenesis of FXS.

Active N6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons.

A ten-eleven translocation (TET) ortholog exists as a DNA N6-methyladenine (6mA) demethylase (DMAD) in Drosophila. However, the molecular roles of 6mA and DMAD remain unexplored. Through genome-wide 6mA and transcriptome profiling in Drosophila brains and neuronal cells, we found that 6mA may epigenetically regulate a group of genes involved in neurodevelopment and neuronal functions. Mechanistically, DMAD interacts with the Trithorax-related complex protein Wds to maintain active transcription by dynamically demethylating intragenic 6mA. Accumulation of 6mA by depleting DMAD coordinates with Polycomb proteins and contributes to transcriptional repression of these genes. Our findings suggest that active 6mA demethylation by DMAD plays essential roles in fly CNS by orchestrating through added epigenetic mechanisms.

EWS/ETS-Driven Ewing Sarcoma Requires BET Bromodomain Proteins.

The EWS/ETS fusion transcription factors drive Ewing sarcoma (EWS) by orchestrating an oncogenic transcription program. Therapeutic targeting of EWS/ETS has been unsuccessful; however, identifying mediators of the EWS/ETS function could offer new therapeutic options. Here, we describe the dependency of EWS/ETS-driven transcription upon chromatin reader BET bromdomain proteins and investigate the potential of BET inhibitors in treating EWS. EWS/FLI1 and EWS/ERG were found in a transcriptional complex with BRD4, and knockdown of BRD2/3/4 significantly impaired the oncogenic phenotype of EWS cells. RNA-seq analysis following BRD4 knockdown or inhibition with JQ1 revealed an attenuated EWS/ETS transcriptional signature. In contrast to previous reports, JQ1 reduced proliferation and induced apoptosis through MYC-independent mechanisms without affecting EWS/ETS protein levels; this was confirmed by depleting BET proteins using PROTAC-BET degrader (BETd). Polycomb repressive complex 2 (PRC2)-associated factor PHF19 was downregulated by JQ1/BETd or BRD4 knockdown in multiple EWS lines. EWS/FLI1 bound a distal regulatory element of PHF19, and EWS/FLI1 knockdown resulted in downregulation of PHF19 expression. Deletion of PHF19 via CRISPR-Cas9 resulted in a decreased tumorigenic phenotype, a transcriptional signature that overlapped with JQ1 treatment, and increased sensitivity to JQ1. PHF19 expression was also associated with worse prognosis in patients with EWS. In vivo, JQ1 demonstrated antitumor efficacy in multiple mouse xenograft models of EWS. Together these results indicate that EWS/ETS requires BET epigenetic reader proteins for its transcriptional program and can be mitigated by BET inhibitors. This study provides a clear rationale for the clinical utility of BET inhibitors in treating EWS.Significance: These findings reveal the dependency of EWS/ETS transcription factors on BET epigenetic reader proteins and demonstrate the potential of BET inhibitors for the treatment of EWS. Cancer Res; 78(16); 4760-73. ©2018 AACR.

CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens.

Major challenges in vaccine development include rapidly selecting or designing immunogens for raising cross-protective immunity against different intra- or inter-subtypic pathogens, especially for the newly emerging varieties. Here we propose a computational method, Conformational Epitope (CE)-BLAST, for calculating the antigenic similarity among different pathogens with stable and high performance, which is independent of the prior binding-assay information, unlike the currently available models that heavily rely on the historical experimental data. Tool validation incorporates influenza-related experimental data sufficient for stability and reliability determination. Application to dengue-related data demonstrates high harmonization between the computed clusters and the experimental serological data, undetectable by classical grouping. CE-BLAST identifies the potential cross-reactive epitope between the recent zika pathogen and the dengue virus, precisely corroborated by experimental data. The high performance of the pathogens without the experimental binding data suggests the potential utility of CE-BLAST to rapidly design cross-protective vaccines or promptly determine the efficacy of the currently marketed vaccine against emerging pathogens, which are the critical factors for containing emerging disease outbreaks.

5-Hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder.

Autism spectrum disorders (ASDs) include a group of syndromes characterized by impaired language, social and communication skills, in addition to restrictive behaviors or stereotypes. However, with a prevalence of 1.5% in developed countries and high comorbidity rates, no clear underlying mechanism that unifies the heterogeneous phenotypes of ASD exists. 5-hydroxymethylcytosine (5hmC) is highly enriched in the brain and recognized as an essential epigenetic mark in developmental and brain disorders. To explore the role of 5hmC in ASD, we used the genomic DNA isolated from the postmortem cerebellum of both ASD patients and age-matched controls to profile genome-wide distribution of 5hmC. We identified 797 age-dependent differentially hydroxymethylated regions (DhMRs) in the young group (age ≤ 18), while no significant DhMR was identified in the groups over 18 years of age. Pathway and disease association analyses demonstrated that the intragenic DhMRs were in the genes involved in cell-cell communication and neurological disorders. Also, we saw significant 5hmC changes in the larger group of psychiatric genes. Interestingly, we found that the predicted cis functions of non-coding intergenic DhMRs strikingly associate with ASD and intellectual disorders. A significant fraction of intergenic DhMRs overlapped with topologically associating domains. These results together suggest that 5hmC alteration is associated with ASD, particularly in the early development stage, and could contribute to the pathogenesis of ASD.

Epitranscriptomic m6A Regulation of Axon Regeneration in the Adult Mammalian Nervous System.

N6-methyladenosine (m6A) affects multiple aspects of mRNA metabolism and regulates developmental transitions by promoting mRNA decay. Little is known about the role of m6A in the adult mammalian nervous system. Here we report that sciatic nerve lesion elevates levels of m6A-tagged transcripts encoding many regeneration-associated genes and protein translation machinery components in the adult mouse dorsal root ganglion (DRG). Single-base resolution m6A-CLIP mapping further reveals a dynamic m6A landscape in the adult DRG upon injury. Loss of either m6A methyltransferase complex component Mettl14 or m6A-binding protein Ythdf1 globally attenuates injury-induced protein translation in adult DRGs and reduces functional axon regeneration in the peripheral nervous system in vivo. Furthermore, Pten deletion-induced axon regeneration of retinal ganglion neurons in the adult central nervous system is attenuated upon Mettl14 knockdown. Our study reveals a critical epitranscriptomic mechanism in promoting injury-induced protein synthesis and axon regeneration in the adult mammalian nervous system.