Downregulation of CPSF6 leads to global mRNA 3' UTR shortening and enhanced antiviral immune responses.

Alternative polyadenylation (APA) is a widespread mechanism of gene regulation that generates mRNA isoforms with alternative 3' untranslated regions (3' UTRs). Our previous study has revealed the global 3' UTR shortening of host mRNAs through APA upon viral infection. However, how the dynamic changes in the APA landscape occur upon viral infection remains largely unknown. Here we further found that, the reduced protein abundance of CPSF6, one of the core 3' processing factors, promotes the usage of proximal poly(A) sites (pPASs) of many immune related genes in macrophages and fibroblasts upon viral infection. Shortening of the 3' UTR of these transcripts may improve their mRNA stability and translation efficiency, leading to the promotion of type I IFN (IFN-I) signalling-based antiviral immune responses. In addition, dysregulated expression of CPSF6 is also observed in many immune related physiological and pathological conditions, especially in various infections and cancers. Thus, the global APA dynamics of immune genes regulated by CPSF6, can fine-tune the antiviral response as well as the responses to other cellular stresses to maintain the tissue homeostasis, which may represent a novel regulatory mechanism for antiviral immunity.

Intravoxel Incoherent Motion Diffusion-Weighted MR Imaging and Venous Tumor Thrombus Consistency in Renal Cell Carcinoma.

BACKGROUND: Venous tumor thrombus (VTT) consistency of renal cell carcinoma (RCC) is an important consideration in nephrectomy plus thrombectomy. However, evaluation of VTT consistency through preoperative MR imaging is lacking. PURPOSE: To evaluate VTT consistency of RCC through intravoxel incoherent motion-diffusion weighted imaging (IVIM-DWI) derived parameters (Dt , Dp , f, and ADC) and the apparent diffusion coefficient (ADC) value. STUDY TYPE: Retrospective. POPULATION: One hundred and nineteen patients (aged 55.8 ± 11.5 years, 85 male) with histologically-proven RCC and VTT who underwent radical resection. FIELD STRENGTH/SEQUENCES: 3.0-T; two-dimensional single-shot diffusion-weighted echo planar imaging sequence at 9 b-values (0-800 s/mm2 ). ASSESSMENT: IVIM parameters and ADC values of the primary tumor and the VTT were calculated. The VTT consistency (friable vs. solid) was determined through intraoperative findings of two urologists. The accuracy of VTT consistency classification based on the individual IVIM parameters of primary tumors and of VTT, and based on models combining parameters, was assessed. Type of operation, intra-operative blood loss, and operation length were recorded. STATISTICAL TESTS: Shapiro-Wilk test; Mann-Whitney U test; Student's t-test; Chi-square test; Receiver operating characteristic (ROC) analysis. Statistical significance level was P < 0.05. RESULTS: Of the enrolled 119 patients, 33 patients (27.7%) had friable VTT. Patients with friable VTT were significantly more likely to experience open surgery, have significantly more intraoperative blood loss, and significantly longer operative duration. The area under the ROC curve (AUC) values of Dt of the primary tumor and VTT in classifying VTT consistency were 0.758 (95% CI 0.671-0.832) and 0.712 (95% CI 0.622-0.792), respectively. The AUC value of the model combining Dp and Dt of VTT was 0.800 (95% CI 0.717-0.868). Furthermore, the AUC of the model combining Dp and Dt of VTT and Dt of the primary tumor was 0.886 (95% CI 0.814-0.937). CONCLUSION: IVIM-derived parameters had the potential to predict VTT consistency of RCC. EVIDENCE LEVEL: 3 Technical Efficacy: Stage 2.

Nuclear m6 A reader YTHDC1 suppresses proximal alternative polyadenylation sites by interfering with the 3' processing machinery.

N6-methyladenosine (m6 A) and alternative polyadenylation (APA) are important regulators of gene expression in eukaryotes. Recently, it was found that m6 A is closely related to APA. However, the molecular mechanism of this new APA regulation remains elusive. Here, we show that YTHDC1, a nuclear m6 A reader, can suppress proximal APA sites and produce longer 3' UTR transcripts by binding to their upstream m6 A sites. YTHDC1 can directly interact with the 3' end processing factor FIP1L1 and interfere with its ability to recruit CPSF4. Binding to the m6 A sites can promote liquid-liquid phase separation of YTHDC1 and FIP1L1, which may play an important role in their interaction and APA regulation. Collectively, YTHDC1 as an m6 A "reader" links m6 A modification with pre-mRNA 3' end processing, providing a new mechanism for APA regulation.

Crosstalk between alternative polyadenylation and miRNAs in the regulation of protein translational efficiency.

3' UTRs play important roles in the gene regulation network via their influence on mRNA stability, translational efficiency, and subcellular localization. For a given gene, 3' UTRs of different lengths generated by alternative polyadenylation (APA) may result in functional differences in regulation. The mechanistic details of how length changes of 3' UTRs alter gene function remain unclear. By combining APA sequencing and polysome profiling, we observed that mRNA isoforms with shorter 3' UTRs were bound with more polysomes in six cell lines but not in NIH3T3 cells, suggesting that changing 3' UTRs to shorter isoforms may lead to a higher gene translational efficiency. By interfering with the expression of TNRC6A and analyzing AGO2-PAR-CLIP data, we revealed that the APA effect on translational efficiency was mainly regulated by miRNAs, and this regulation was cell cycle dependent. The discrepancy between NIH3T3 and other cell lines was due to contact inhibition of NIH3T3. Thus, the crosstalk between APA and miRNAs may be needed for the regulation of protein translational efficiency.

Small Nuclear Ribonucleoprotein Polypeptide A-Mediated Alternative Polyadenylation of STAT5B during Th1 Cell Differentiation.

T cells are activated and differentiated into Th cells depending on the rapid and accurate changes in the cell transcriptome. In addition to changes in mRNA expression, the sequences of many transcripts are altered by alternative splicing and alternative polyadenylation (APA). We profiled the APA sites of human CD4+ T cell subsets with high-throughput sequencing and found that Th1 cells harbored more genes with shorter tandem 3' untranslated regions (UTRs) than did naive T cells. We observed that STAT5B, a key regulator of Th1 differentiation, possessed three major APA sites and preferred shorter 3' UTRs in Th1 cells. In addition, small nuclear ribonucleoprotein polypeptide A (SNRPA) was found to bind directly to STAT5B 3' UTR and facilitate its APA switching. We also found that p65 activation triggered by TCR signaling could promote SNRPA transcription and 3' UTR shortening of STAT5B. Thus we propose that the APA switching of STAT5B induced by TCR activation is mediated by SNRPA.

APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3'-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3'-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.

The sequence and de novo assembly of the giant panda genome.

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Dynamic landscape of tandem 3' UTRs during zebrafish development.

Tandem 3' untranslated regions (UTRs), produced by alternative polyadenylation (APA) in the terminal exon of a gene, could have critical roles in regulating gene networks. Here we profiled tandem poly(A) events on a genome-wide scale during the embryonic development of zebrafish (Danio rerio) using a recently developed SAPAS method. We showed that 43% of the expressed protein-coding genes have tandem 3' UTRs. The average 3' UTR length follows a V-shaped dynamic pattern during early embryogenesis, in which the 3' UTRs are first shortened at zygotic genome activation, and then quickly lengthened during gastrulation. Over 4000 genes are found to switch tandem APA sites, and the distinct functional roles of these genes are indicated by Gene Ontology analysis. Three families of cis-elements, including miR-430 seed, U-rich element, and canonical poly(A) signal, are enriched in 3' UTR-shortened/lengthened genes in a stage-specific manner, suggesting temporal regulation coordinated by APA and trans-acting factors. Our results highlight the regulatory role of tandem 3' UTR control in early embryogenesis and suggest that APA may represent a new epigenetic paradigm of physiological regulations.

HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies.

Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%-5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.

The genetic basis of population fecundity prediction across multiple field populations of Nilaparvata lugens.

Identifying the molecular markers for complex quantitative traits in natural populations promises to provide novel insight into genetic mechanisms of adaptation and to aid in forecasting population dynamics. In this study, we investigated single nucleotide polymorphisms (SNPs) using candidate gene approach from high- and low-fecundity populations of the brown planthopper (BPH) Nilaparvata lugens Stål (Hemiptera: Delphacidae) divergently selected for fecundity. We also tested whether the population fecundity can be predicted by a few SNPs. Seven genes (ACE, fizzy, HMGCR, LpR, Sxl, Vg and VgR) were inspected for SNPs in N. lugens, which is a serious insect pest of rice. By direct sequencing of the complementary DNA and promoter sequences of these candidate genes, 1033 SNPs were discovered within high- and low-fecundity BPH populations. A panel of 121 candidate SNPs were selected and genotyped in 215 individuals from 2 laboratory populations (HFP and LFP) and 3 field populations (GZP, SGP and ZSP). Prior to association tests, population structure and linkage disequilibrium (LD) among the 3 field populations were analysed. The association results showed that 7 SNPs were significantly associated with population fecundity in BPH. These significant SNPs were used for constructing general liner models with stepwise regression. The best predictive model was composed of 2 SNPs (ACE-862 and VgR-816 ) with very good fitting degree. We found that 29% of the phenotypic variation in fecundity could be accounted for by only two markers. Using two laboratory populations and a complete independent field population, the predictive accuracy was 84.35-92.39%. The predictive model provides an efficient molecular method to predict BPH fecundity of field populations and provides novel insights for insect population management.

[Association of the H770H of PR gene polymorphism with susceptibility to endometriosis].

OBJECTIVE: To investigate the association of PR gene exon 5 region H770H (rs1042839) single nucleotide polymorphism (SNP) with the genetic susceptibility to endometriosis (EM) in southern Han Chinese women. METHODS: Totally 431 EM patients and 499 non-EM women were collected and separated into EM group and control group, that all cases were confirmed by operation and pathology. A case-control study was performed in EM and control groups to evaluate the association of these SNP with the susceptibility to EM by using a fluorescent quantitative PCR-based high resolution melting (HRM) method. RESULTS: The C and T of PR H770H allele frequencies among the EM and control groups were 97.9% (844/862), 2.1% (18/862) and 99.4% (992/998), 0.6% (6/998), respectively. The CC, CT and TT of PR H770H genotype frequencies among the EM and control groups were 95.8% (413/431), 4.2% (18/431), 0 and 98.8% (493/499), 1.2% (6/499), 0, respectively. There were statistical significances in the PR H770H alleles and genotypes distributions between the two groups (χ(2)=7.386, P=0.007; χ(2)=8.135, P=0.004). Carrying allele C reduced the risk of EM (OR=0.986, 95%CI: 0.976-0.996), while carrying allele T enhanced the risk of EM (OR=3.319, 95% CI: 1.323-8.325); carrying genotype CC reduced the risk of EM 0.970 time (OR=0.970, 95% CI: 0.949-0.991), whereas carrying genotype CT enhanced the risk of EM 3.473 times (OR=3.473, 95%CI: 1.391-8.671). CONCLUSION: There is significant association between the polymorphism of PR H770H and genetic susceptibility to EM in southern Han Chinese women.

Polymorphism of DEFA in Chinese Han population with IgA nephropathy.

Our recent genome-wide association study (GWAS) had discovered a new locus at 8p23 (rs2738048) associated with IgA nephropathy (IgAN) in Chinese Han patients, implicating the DEFA gene family within this locus as susceptibility genes. However, it is still unknown whether there are additional variations within these genes associated with the disease susceptibility. The aim of this study is to investigate the polymorphisms of DEFA genes in the susceptibility to IgAN and explore possible disease mechanisms. Sixteen tag single-nucleotide polymorphisms (tag SNPs) were selected for association study in 1,000 IgAN cases and 1,000 controls by using Sequenom MassArray system or TaqMan SNP genotyping assays. We found seven SNPs within DEFA genes that were significantly associated with IgAN, including rs2738048 discovered in our previous GWAS (p = 0.0007, OR = 0.77) and additional 6 SNPs (rs2615787, p = 0.0001, OR = 0.74; rs2738081, p = 0.0003, OR = 0.72; rs2738058, p = 0.0001, OR = 0.73; rs4288398, p = 0.0008, OR = 0.78; rs6984215, p = 0.002, OR = 0.63; rs12716641, p = 0.00002, OR = 0.71). Electrophoretic mobility shift assays and luciferase assays demonstrated that fragments containing rs2738048, rs2738081 and rs6984215 were transcription factor binding sites for CTF, SP1 and CdxA, respectively, and the allele status of rs2738048 and rs6984215 could significantly change the luciferase activity. These results suggest that polymorphisms within DEFA genes are involved in gene transcriptional regulation, and this may have some effect in mediating susceptibility to IgAN in southern Chinese.

Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing.

Tandem 3' UTRs produced by alternative polyadenylation (APA) play an important role in gene expression by impacting mRNA stability, translation, and translocation in cells. Several studies have investigated APA site switching in various physiological states; nevertheless, they only focused on either the genes with two known APA sites or several candidate genes. Here, we developed a strategy to study APA sites in a genome-wide fashion with second-generation sequencing technology which could not only identify new polyadenylation sites but also analyze the APA site switching of all genes, especially those with more than two APA sites. We used this strategy to explore the profiling of APA sites in two human breast cancer cell lines, MCF7 and MB231, and one cultured mammary epithelial cell line, MCF10A. More than half of the identified polyadenylation sites are not included in human poly(A) databases. While MCF7 showed shortening 3' UTRs, more genes in MB231 switched to distal poly(A) sites. Several gene ontology (GO) terms and pathways were enriched in the list of genes with switched APA sites, including cell cycle, apoptosis, and metabolism. These results suggest a more complex regulation of APA sites in cancer cells than previously thought. In short, our novel unbiased method can be a powerful approach to cost-effectively investigate the complex mechanism of 3' UTR switching in a genome-wide fashion among various physiological processes and diseases.

The effects of both single-locus and multi-locus interaction on the clinical manifestations of IgA nephropathy in Southern Han Chinese.

BACKGROUND: Immunoglobulin A nephropathy (IgAN) is one of the most common types of glomerulonephritis throughout the world. It is considered to be a complex disease, to which both genetic and environmental factors contribute. Our previous study has shown a potential interaction of C1GALT1-330G/T and IL5RA31 + 197A/G on the susceptibility of IgAN in Southern Han Chinese. However, the interaction of these gene polymorphisms and the clinical manifestation for IgAN has not been investigated. OBJECTIVE: This study aims to investigate whether genetic variants influence the clinical manifestation for IgAN patients and to assess the relationship between the genotype and phenotype of IgAN. METHODS: Thirty-one SNPs in 24 candidate genes were selected in this study, which were involved in the pathways implicated in the development or progression of IgAN. A total of 480 IgAN patients with integrated clinical data were investigated. Data were analyzed using logistic regression and multifactor dimensionality reduction (MDR). The genotype-phenotype association was studied by correlations of single-locus and multi-locus interaction models with the clinical data. RESULTS: The ADD1 G460W-dominant model for the G allele was significantly associated with hypertension of IgAN patients (P = 0.001, Pc = 0.031 and OR = 1.37). The TGF-ß1-509T/C-dominant model for the C allele was significantly associated with proteinuria (≥1.0 g/d) of IgAN patients (P = 0.001, Pc = 0.031 and OR = 1.49). The MDR analysis of multiple SNPs revealed that P-selectin-2441A/G and CD14-159C/T had combined effects on macroscopic hematuria, whereas TGF-ß1 509T/C, P-selectin-2441A/G and MCP-1 2518A/G had combined effects on the formation of crescents in IgAN patients. CONCLUSION: The effects of both single-locus and multi-locus interaction of these genes may influence the clinical manifestations of IgAN. Further functional studies may be required to confirm the prognostic significance of these genetic polymorphisms.

Assessment of Ki-67 proliferation index in prognosis prediction in patients with nonmetastatic clear cell renal cell carcinoma and tumor thrombus.

PURPOSE: To determine the optimal cut-off value of Ki-67 for predicting the survival of patients with clear cell renal cell carcinoma (ccRCC) and tumor thrombus and to explore the correlation between Ki-67 expression and pathological features. PATIENTS AND METHODS: We retrospectively analyzed Ki-67 immunohistochemical staining of ccRCC and tumor thrombus resected from February 2006 to February 2022. The survival rate was evaluated using the Kaplan-Meier method. The optimal cut-off value of the Ki-67 expression for predicting survival was determined by the minimum P-value method. Clinicopathological data were compared based on Ki-67 status (low versus high expression). Univariate and multivariate Cox regression analysis was used to explore independent predictors. RESULTS: A total of 202 patients (median age, 58 years [IQR, 52-65 years], 147 men) with ccRCC and tumor thrombus were included in the study. The optimal cut-off value of Ki-67 for predicting survival was 30%. 159 (78.7%) and 43 (21.3%) patients were included in the low-expression and high-expression groups. Patients with Ki-67 high expression had significantly worse recurrence-free survival (P < 0.001) and cancer-specific survival (P < 0.001). Ki-67 high expression was associated with adverse pathological features, including tumor necrosis, ISUP nuclear grade, sarcomatoid differentiation, perirenal fat invasion, renal pelvis invasion, and inferior vena cava wall invasion (all P < 0.050). Ki-67 expression ≥ 30% (P = 0.016), tumor side (P = 0.003), diabetes (P = 0.040), blood loss (P = 0.016), inferior vena cava wall invasion (P = 0.016), and sarcomatoid differentiation (P = 0.014) were independent predictors of cancer-specific survival. CONCLUSION: The optimal cut-off level of Ki-67 in predicting the prognosis of ccRCC and tumor thrombus was 30%. The high expression of Ki-67 was associated with the aggressive pathological phenotype and poor prognosis.

Disruption of PABPN1 phase separation by SNRPD2 drives colorectal cancer cell proliferation and migration through promoting alternative polyadenylation of CTNNBIP1.

Generally shortened 3' UTR due to alternative polyadenylation (APA) is widely observed in cancer, but its regulation mechanisms for cancer are not well characterized. Here, with profiling of APA in colorectal cancer tissues and poly(A) signal editing, we firstly identified that the shortened 3' UTR of CTNNIBP1 in colorectal cancer promotes cell proliferation and migration. We found that liquid-liquid phase separation (LLPS) of PABPN1 is reduced albeit with higher expression in cancer, and the reduction of LLPS leads to the shortened 3' UTR of CTNNBIP1 and promotes cell proliferation and migration. Notably, the splicing factor SNRPD2 upregulated in colorectal cancer, can interact with glutamic-proline (EP) domain of PABPN1, and then disrupt LLPS of PABPN1, which attenuates the repression effect of PABPN1 on the proximal poly(A) sites. Our results firstly reveal a new regulation mechanism of APA by disruption of LLPS of PABPN1, suggesting that regulation of APA by interfering LLPS of 3' end processing factor may have the potential as a new way for the treatment of cancer.

Interaction of C1GALT1-IL5RA on the susceptibility to IgA nephropathy in Southern Han Chinese.

IgA nephropathy is one of the most common glomerulonephritis throughout the world, which is thought to be the multifactorial complex diseases, with genetic and environmental factors contributing to this disease. The failure of replicating the single genes in previous association studies may be of that the gene-gene interaction might have more influence on the susceptibility of the complex diseases. In all, 31 single-nucleotide polymorphisms (SNPs) in 24 candidate genes (which were involved in the pathways implicated in the development or progression of IgAN) were selected to conduct a large case-control association study in 527 IgAN patients and 543 healthy controls. Traditional linear logistic regression analyses were used to detect single-locus associations in dominant, recessive and additive genetic models. Bonferroni correction was used to adjust the P-values for multiple testing. The gene-gene interaction effects of multiple SNPs were detected by multifactor-dimensionality reduction (MDR) method. After Bonferroni correction, no significant single-locus associations was observed between IgAN patients and controls (Pc>0.05). The MDR analysis showed a potential interaction of C1GALT1-330G/T (rs1008898) and IL5RA31+197A/G (rs340833) on the susceptibility of IgAN (P<0.001). Gene-gene interaction may have some influence on the susceptibility to IgA nephropathy. This finding proposed a potential gene-gene interactive model for future studies.

[Association of P53 gene polymorphisms with susceptibility to endometriosis].

OBJECTIVE: To assess the association of a single nucleotide polymorphism(SNP) in tumor suppressor gene P53 with the risk of endometriosis (EM) in Han Chinese women. METHODS: For 460 EM patients, 113 patients with endometrial carcinoma and 530 matched unrelated controls, a rs1042522(C/G) SNP of the P53 gene was genotyped by polymerase chain reaction-single strand polymorphism (PCR-SSP) and DNA sequencing. RESULTS: A significant difference has been detected in the distribution of rs1042522 alleles and genotypes between the EM patients and controls (P< 0.01). Allele G has increased the risk of EM by 1.209 times, while allele C has reduced this risk by 0.837 times. Compared with GG genotype, GC and CC genotypes have both increased the risk for EM (OR=2.073, 95%CI: 1.521-2.820, and OR=1.930, 95%CI: 1.363-2.733, respectively). Significant differences were also detected in the distribution of rs1042522 alleles and genotypes between endometrial carcinoma patients and controls (P< 0.01). Allele G has increased the risk to endometrial carcinoma by 1.311 times, while allele C has reduced this risk by 0.757 times. Compared with GG genotypes, individuals with GC and CC genotypes are more likely to be affected with endometrial carcinoma (OR=2.778, 95%CI: 1.585-4.870, and OR=2.864, 95%CI: 1.557-5.263, respectively). CONCLUSION: Our study has suggested a significant association between the rs1042522(G/C) polymorphism and susceptibility to EM in Han Chinese women. The mechanism of EM is similar to carcinoma from genetics point of view.

Objective Value of the Apparent Diffusion Coefficient (ADC) Map from Ultrahigh b-value Diffusion-weighted Imaging (DWI) in 3T MRI could be a Non-invasive Specific Biomarker for Prostate Cancer.

OBJECTIVE: This article aims to explore the ADC value of ultrahigh b-value DWI and the diagnostic cutoff point in prostate cancer. METHODS: A total of 78 patients were included in this study. T2 weighted imaging (T2WI), conventional diffusion-weighted imaging (DWI) (1000 s/mm2), and DWI with ultrahigh b-values of 2000 s/mm2 and 3000 s/mm2 were performed in each patient. With reference biopsy as the gold standard, the apparent diffusion coefficient (ADC)s of each b-value DWI image were analyzed. According to different b-value receiver operating characteristic (ROC) curves, the ADC diagnostic cutoff point for prostate cancer was determined. RESULTS: A total of 154 lesions were identified as prostate cancer. The ADC values for conventional DWI and ultrahigh b-value DWI with 2000 s/mm2 and 3000 s/mm2 were 1.097×10-3 mm2/s (1.040-1.153), 0.809×10-3 mm2/s (0.766-0.851) and 0.622×10-3 mm2/s (0.591-0.652), respectively, in the peripheral zone and 1.085×10-3 mm2/s (1.022-1.147), 0.815×10-3 mm2/s (0.770-0.861) and 0.651×10-3 mm2/s (0.617-0.685) in the transition zone. The area under the curve (AUC)s of the ADC values from ultrahigh b-value DWI (2000 s/mm2 and 3000 s/mm2) were 0.824 and 0.852 in the peripheral zone and 0.905 for the ADC values from ultrahigh b-value DWI (3000 s/mm2) in the transition zone. In the peripheral zone, the ADC diagnostic cutoff values for prostate cancer were 0.75×10-3 mm2/s and 0.685×10-3 mm2/s in DWI at 2000 s/mm2 and 3000 s/mm2, respectively, and the diagnosis of transition zone cancer was 0.8×10-3 mm2/s and 0.634×10-3 mm2/s, respectively. CONCLUSION: The ADC values from ultrahigh b-value DWI demonstrated better consistency and diagnostic efficacy in the diagnosis of prostate cancer.

CPSF6 regulates alternative polyadenylation and proliferation of cancer cells through phase separation.

Cancer cells usually exhibit shortened 3' untranslated regions (UTRs) due to alternative polyadenylation (APA) to promote cell proliferation and migration. Upregulated CPSF6 leads to a systematic prolongation of 3' UTRs, but CPSF6 expression in tumors is typically higher than that in healthy tissues. This contradictory observation suggests that it is necessary to investigate the underlying mechanism by which CPSF6 regulates APA switching in cancer. Here, we find that CPSF6 can undergo liquid-liquid phase separation (LLPS), and elevated LLPS is associated with the preferential usage of the distal poly(A) sites. CLK2, a kinase upregulated in cancer cells, destructs CPSF6 LLPS by phosphorylating its arginine/serine-like domain. The reduction of CPSF6 LLPS can lead to a shortened 3' UTR of cell-cycle-related genes and accelerate cell proliferation. These results suggest that CPSF6 LLPS, rather than its expression level, may be responsible for APA regulation in cancer cells.