U4 snRNP inhibits premature cleavage and polyadenylation of pre-mRNAs.

The essential role of U4 snRNP in pre-messenger RNA (mRNA) splicing has been well established. In this study, we utilized an antisense morpholino oligonucleotide (AMO) specifically targeting U4 snRNA to achieve functional knockdown of U4 snRNP in HeLa cells. Our results showed that this knockdown resulted in global intronic premature cleavage and polyadenylation (PCPA) events, comparable to the effects observed with U1 AMO treatment, as demonstrated by mRNA 3'-seq analysis. Furthermore, our study suggested that this may be a common phenomenon in both human and mouse cell lines. Additionally, we showed that U4 AMO treatment disrupted transcription elongation, as evidenced by chromatin immunoprecipitation sequencing (ChIP-seq) analysis for RNAPII. Collectively, our results identified a unique role for U4 snRNP in the inhibition of PCPA and indicated a model wherein splicing intrinsically inhibits intronic cleavage and polyadenylation in the context of cotranscriptional mRNA processing.

Clarifying the Temperature-Dependent Lithium Deposition/Stripping Process and the Evolution of Inactive Li in Lithium Metal Batteries.

The deposition/stripping behavior of lithium metal is intriguing, and the associated formation of inactive lithium at various temperatures remains elusive, which hinders the practical application of lithium metal batteries. Here, utilizing the variable-temperature operando solid-state nuclear magnetic resonance (SS NMR) technique, we reveal the temperature effects on the lithium microstructure evolution in a carbonate-based electrolyte system. In addition, the mass spectrometry titration (MST) method is used to quantify the evolution of inactive lithium components, including dead lithium, solid electrolyte interface (SEI), and lithium hydride (LiH). Combined SS NMR and MST results show that the morphology of lithium metal is reasonably correlated to the amount of inactive Li formed. At low/ambient temperature, the lithium microstructure has a similar evolution pattern, and its poor morphology leads to a large amount of dead lithium, which dominates capacity loss; however, at high temperature large and dense lithium deposits form with less dead Li detected, and the intensified electrolyte consumption in SEI formation is the major cause for capacity loss. Our phase-field simulation results reveal that the compact lithium deposition formed at higher temperature is due to the more uniformly distributed electric field and Li+ concentration. Lastly, two strategies in forming a dense Li deposit are proposed and tested that show performance-enhancing results.

The applications of solid-state NMR and MRI techniques in the study of rechargeable sodium-ion batteries.

In order to develop new electrode and electrolyte materials for advanced sodium-ion batteries (SIBs), it is crucial to understand a number of fundamental issues. These include the compositions of the bulk and interface, the structures of the materials used, and the electrochemical reactions in the batteries. Solid-state NMR (SS-NMR) has unique advantages in characterizing the local or microstructure of solid electrode/electrolyte materials and their interfaces-one such advantage is that these are determined in a noninvasive and nondestructive manner at the atomic level. In this review, we provide a survey of the recent advances in the understanding of the fundamental issues of SIBs using advanced NMR techniques. First, we summarize the applications of SS-NMR in characterizing electrode material structures and solid electrolyte interfaces (SEI). In particular, we elucidate the key role of in-situ NMR/MRI in revealing the complex reactions and degradation mechanisms of SIBs. Next, the characteristics and shortcomings of SS-NMR and MRI techniques in SIBs are also discussed in comparison to similar Li-ion batteries. Finally, an overview of SS-NMR and MRI techniques for sodium batteries are briefly discussed and presented.

Inhibitor AN3661 reveals biological functions of Arabidopsis CLEAVAGE and POLYADENYLATION SPECIFICITY FACTOR 73.

Cleavage and polyadenylation specificity factor (CPSF) is a protein complex that plays an essential biochemical role in mRNA 3'-end formation, including poly(A) signal recognition and cleavage at the poly(A) site. However, its biological functions at the organismal level are mostly unknown in multicellular eukaryotes. The study of plant CPSF73 has been hampered by the lethality of Arabidopsis (Arabidopsis thaliana) homozygous mutants of AtCPSF73-I and AtCPSF73-II. Here, we used poly(A) tag sequencing to investigate the roles of AtCPSF73-I and AtCPSF73-II in Arabidopsis treated with AN3661, an antimalarial drug with specificity for parasite CPSF73 that is homologous to plant CPSF73. Direct seed germination on an AN3661-containing medium was lethal; however, 7-d-old seedlings treated with AN3661 survived. AN3661 targeted AtCPSF73-I and AtCPSF73-II, inhibiting growth through coordinating gene expression and poly(A) site choice. Functional enrichment analysis revealed that the accumulation of ethylene and auxin jointly inhibited primary root growth. AN3661 affected poly(A) signal recognition, resulted in lower U-rich signal usage, caused transcriptional readthrough, and increased the distal poly(A) site usage. Many microRNA targets were found in the 3' untranslated region lengthened transcripts; these miRNAs may indirectly regulate the expression of these targets. Overall, this work demonstrates that AtCPSF73 plays important part in co-transcriptional regulation, affecting growth, and development in Arabidopsis.

Gas induced formation of inactive Li in rechargeable lithium metal batteries.

The formation of inactive lithium by side reactions with liquid electrolyte contributes to cell failure of lithium metal batteries. To inhibit the formation and growth of inactive lithium, further understanding of the formation mechanisms and composition of inactive lithium are needed. Here we study the impact of gas producing reactions on the formation of inactive lithium using ethylene carbonate as a case study. Ethylene carbonate is a common electrolyte component used with graphite-based anodes but is incompatible with Li metal anodes. Using mass spectrometry titrations combined with 13C and 2H isotopic labeling, we reveal that ethylene carbonate decomposition continuously releases ethylene gas, which further reacts with lithium metal to form the electrochemically inactive species LiH and Li2C2. In addition, phase-field simulations suggest the non-ionically conducting gaseous species could result in an uneven distribution of lithium ions, detrimentally enhancing the formation of dendrites and dead Li. By optimizing the electrolyte composition, we selectively suppress the formation of ethylene gas to limit the formation of LiH and Li2C2 for both Li metal and graphite-based anodes.

A vortex-enhanced magnetic solid phase extraction for the selective enrichment of four quaternary ammonium alkaloids from Zanthoxyli Radix.

Zanthoxyli Radix, the dried root of Zanthozylum nitidum (Roxb.) DC, one of traditional Chinese medicines (TCMs), exhibits various pharmacological activities such as anti-bacterial, anti-inflammatory, anti-tumor, analgesic activity. A sustainable vortex-enhanced magnetic solid phase extraction (VE-MSPE) method combined with ultra-high performance liquid chromatography (UHPLC) was established to enrich and analyze the bioactive quaternary ammonium alkaloids (QAAs) of Zanthoxyli Radix. Fe3O4@C@CMCS magnetic nanoparticles (MNPs) was first synthesized for selectively adsorbing target QAAs (magnolinine, sanguinarine, nitidine chloride and chelerythrine), which possess excellent adsorption performance after being reused 10 times. The results revealed that the great adsorption rate of Fe3O4@C@CMCS MNPs for the four QAAs could reach 55.1-78.7 %. In addition, a reliable linear relationship (r ≥ 0.9995) and good recovery (97.5-104 %) was obtained. Consequently, the VE-MSPE method applying Fe3O4@C@CMCS MNPs as a sustainable adsorbent exhibited great potential in the selective enrichment of QAAs in TCM.

[Effects of electroacupuncture on sexual development and ovarian estrogen receptor ß expression in female adolescent obese rats].

OBJECTIVE: To observe the effect of electroacupuncture on sexual development and ovarian estrogen receptor ß(ER-ß) expression in female adolescent obese rats induced by high-fat diet, so as to explore its underlying mechanisms of improving adolescent obesity. METHODS: Female SD rats (age of 21 days) were randomly divided into control, model and acupuncture groups, with 6 rats in each group. The obese model was established by feeding high-fat diet for 6 weeks. Rats of the acupuncture group received electroacupuncture(2 Hz, 0.5-1.2 mA)stimulation at bilateral "Sanyinjiao"(SP6), "Fenglong"(ST40) and "Zusanli"(ST36) for 30 min, once a day for 14 days. The body mass and abdominal circumference of rats were measured before and after treatment. The contents of serum follicle stimulating hormone (FSH), luteinizing hormone (LH) and estradiol (E2) were detected by ELISA. The number of corpus luteum and follicle were observed by HE staining. The expression levels of ER-ß mRNA and protein in ovary were detected by fluorescence quantitative PCR and Western blot, respectively. RESULTS: Compared with the control group, the body mass and abdominal circumference, the contents of serum FSH and E2, and the expression levels of ER-ß mRNA and protein in ovary were significantly increased (P<0.05)in the model group, while the number of mature follicles and corpus luteum increased significantly. Compared with the model group, the body mass and abdominal circumference, the contents of serum FSH and E2, and the expression levels of ER-ß mRNA and protein in ovary were significantly decreased (P<0.05) in the acupuncture group, while the number of mature follicles and corpus luteum decreased significantly. CONCLUSION: Electroacupuncture can effectively improve the levels of sex hormone and the development of ovary, down-regulate the expression levels of ER-ß mRNA and protein in ovary, so as to regulate the process of sexual development of female adolescent obese rats induced by high-fat diet.

Quantifying the Evolution of Inactive Li/Lithium Hydride and Their Correlations in Rechargeable Anode-free Li Batteries.

Electrolyte optimization, such as using fluoride-bearing electrolytes, is regarded as an effective way to improve the cycle performance of lithium metal batteries (LMBs), but the promotion mechanisms of the electrolytes are in controversy due to the lack of quantitative understanding of the reaction products during cycling. Here, taking several fluorinated electrolytes as models, we use mass spectrometry titration (MST) and solid state nuclear magnetic resonance (NMR) techniques to quantify the evolution of dead Li metal, solid electrolyte interphases (SEI) and lithium hydride (LiH) during cycling. Our quantitative results clearly disclose that lithium difluoro(oxalato)borate (LiODFB) is able to inhibit the formation of SEI and LiH while fluoroethylene carbonate (FEC) mainly inhibits the formation of dead Li metal. Furthermore, we surprisingly observe a linear correlation between LiH and SEI formation, whereas the commonly mentioned lithium fluoride (LiF) shows a weak correlation with either dead Li metal or SEI. Guided by the clear failure mechanism, we can provide a reasonable explanation for the synergistic effect with the combination of LiODFB and FEC from a quantitative perspective. We believe that a quantitative insight of electrolytes on the failure mechanism of LMBs will guide us to explore the functional electrolytes to achieve the practical application of LMBs.

Phosphorylation of PBK/TOPK Tyr74 by JAK2 promotes Burkitt lymphoma tumor growth.

Burkitt lymphoma (BL), which is characterized by high invasiveness, is a subgroup of non-Hodgkin lymphoma. Although BL is regarded as a highly curable disease, especially for children, some patients unfortunately still do not respond adequately. The understanding of the etiology and molecular mechanisms of BL is still limited, and targeted therapies are still lacking. Here, we found that T-LAK cell-derived protein kinase (TOPK) and phosphorylated Janus kinase 2 (p-JAK2) are highly expressed in the tissues of BL patients. We report that TOPK directly binds to and is phosphorylated at Tyr74 by JAK2. Histone H3, one of the downstream targets of TOPK, is also phosphorylated in vivo and in vitro. Furthermore, we report that the phosphorylation of TOPK at Tyr74 by JAK2 plays a vital role in the proliferation of BL cells and promotes BL tumorigenesis in vivo. Phosphorylation of TOPK at Tyr74 by JAK2 enhances the stability of TOPK. Collectively, our results suggest that the JAK2/TOPK/histone H3 axis plays a key role in the proliferation of BL cells and BL tumorigenesis in vivo.

Mitigating the Surface Reconstruction of Ni-Rich Cathode via P2-Type Mn-Rich Oxide Coating for Durable Lithium Ion Batteries.

Ni-rich materials have received widespread attention as one of the mainstream cathodes in high-energy-density lithium-ion batteries for electric vehicles. However, Ni-rich cathodes suffer from severe surface reconstruction in a high delithiation state, constraining their rate capabilities and life span. Herein, a novel P2-type NaxNi0.33Mn0.67O2 (NNMO) is rationally selected as the surficial modification layer for LiNi0.8Co0.1Mn0.1O2 (NCM811) cathode, which undergoes a spontaneous Na+-Li+ exchange reaction to form an O2-type LixNi0.33Mn0.67O2 (LNMO) layer revealed by combining X-ray diffraction and solid-state nuclear magnetic resonance techniques. Owing to the specific oxygen stacking sequence, O2-type LNMO significantly prevents the initial layered structure of NCM811 from transforming to the spinel or rock-salt phases during cycling, thus effectively maintaining the integral surficial structure and the Li+ diffusion channels of NCM811. Eventually, the NNMO@NCM811 electrode yields enhanced thermal stability, outstanding rate performance, and long cycling stability with 80% capacity retention after 294 cycles at 200 mA g-1, and its life span is further extended to 531 cycles while enhancing the mechanical stability of the bulk material.

Establishing and evaluating physician-pharmacist collaborative clinics to manage patients with type 2 diabetes in primary hospitals in Hunan province: study protocol of a multi-site randomized controlled trial in the era of COVID-19 pandemic.

BACKGROUND: The COVID-19 pandemic has exerted an unprecedented and universal impact on global health system, resulting in noticeable challenges in traditional chronic disease care, of which diabetes was reported to be most influenced by the reduction in healthcare resources in the pandemic. China has the world's largest diabetes population, and current diabetes management in China is unsatisfactory, particularly in rural areas. Studies in developed countries have demonstrated that physician-pharmacist collaborative clinics are efficient and cost-effective for diabetes management, but little is known if this mode could be adapted in primary hospitals in China. The aim of this proposed study is to develop and evaluate physician-pharmacist collaborative clinics to manage type 2 diabetes mellitus (T2DM) in primary hospitals in Hunan province. METHODS: A multi-site randomized controlled trial will be conducted to evaluate the effectiveness and cost-effectiveness of the physician-pharmacist collaborative clinics compared with usual care for Chinese patients with T2DM. Six primary hospitals will participate in the study, which will recruit 600 eligible patients. Patients in the intervention group will receive services from both physicians and pharmacists in the collaborative clinics, while the control group will receive usual care from physicians. Patients will be followed up at the 3rd, 6th, 9th and 12th month. Comparison between the two groups will be conducted by assessing the clinical parameters, process indicators and costs on diabetes. A satisfaction survey will also be carried out at the end of the study. DISCUSSION: If effective, the physician-pharmacist collaborative clinics can be adapted and used in primary hospitals of China to improve glycemic control, enhance medication adherence, decrease incidence of complications and reduce patients' dependence on physicians. Findings from the present study are meaningful for developing evidence-based diabetes care policy in rural China, especially in the COVID-19 pandemic era. TRIAL REGISTRATION: Chinese Clinical Trial Registry, ChiCTR2000031839 , Registered 12 April 2020.

EWSR1::SMAD3-rearranged fibroblastic tumor: A case with twice recurrence and literature review.

EWSR1::SMAD3-rearranged fibroblastic tumor is a recently described entity that mostly occurs in acral locations. Only 15 cases have been reported in the English literature, with a wide age range and marked female predominance. The most common sites are the foot, followed by the hand and the distal lower leg. There are four cases that recurred locally during 5-120 months of follow-up, with no metastases to date. Herein, we presented a case of EWSR1::SMAD3-rearranged fibroblastic tumor that recurred twice in a 20-year-old man. The patient presented with a second recurrent painful nodule in the left plantar of the second toe. Grossly, the lesion was pale solid and well-defined, measuring 9 × 8 × 9 mm in size. Histological examination revealed a monomorphic spindle cell tumor composed of cellular fascicles of bland fibroblasts in a collagenous to myxoid stroma with low mitotic activity, which evoked a wide spectrum of differential diagnoses. Immunohistochemically, the tumor cells were diffusely and strongly positive for ERG while negative for S100, α-SMA, CD34, and other vascular markers. An unbalanced rearrangement of EWSR1 was demonstrated by fluorescence in situ hybridization (FISH), and a gene fusion between EWSR1 exon 7 and SMAD3 exon 6 was confirmed by RT-PCR and Sanger sequencing. This case recurred twice within 6 years with no sign of further relapse and metastasis at another 9-month follow-up since the last surgery, indicating that this tumor was benign but prone to local recurrence. Nevertheless, more cases and further studies are needed to better interpret the biological behavior of this new entity.

Comparison of two different methods of establishment of canine urethroplasty model: an experimental trial.

BACKGROUND: Graft substitute urethroplasty is recommended for patients with long segment anterior urethral stricture. The therapeutic effects of the grafts need to be validated on the animal models. Therefore the aim of this study was to compared the operative time, blood loss, intra- and post- operative complications of two different methods of establishment of canine urethroplasty model. METHODS: Twelve Beagle dogs were randomly separated into control and experimental group using a random number table. Six animals in the control group received the conventional urethroplasty, while the other 6 in the experimental group received the modified procedures. Tube cystostomy and urethroplasty were performed in the control group. The cystostomy not the tube cystostomy were performed in the experimental group, and the testes were simultaneously removed with the scrotum. Per- and postoperative outcomes, complications were evaluated. RESULTS: The urethroplasty were successfully performed for all dogs and all of these procedures were done by the same surgeon. The median operative time in the control and experimental groups was 186.8 min and 188.7 min respectively. The blood loss in the control and experimental groups was 40.8 ml and 45.8 ml respectively. No intraoperative complications occurred. 3 animals in the control group developed acute urinary retention after the accidental removal of suprapubic bladder tube and the cystostomy was done again. There was no occurrence of urinary retention in the experimental group. 4 animals in the control group developed the perineal hematoma, in which one animal had the urine leakage and incision infection. Perineal hematoma occurred in only one animal in the experimental group. CONCLUSION: The occurrence of urinary retention and perineal hematoma decreased in the modified group, in which the cystostomy not the tube cystostomy were performed and the testes with the scrotum were simultaneously removed.

Poor histologic tumor response after adjuvant therapy in basal-like HER2-positive breast carcinoma.

AIMS: HER2-positive breast carcinomas are all treated with first-line anti-HER2 therapy. However, immunohistochemical and molecular profiling demonstrates significant heterogeneity among HER2-positive carcinomas. Basal-like HER2-positive breast carcinomas are poorly differentiated from pure HER2-positive breast carcinomas. MATERIALS AND METHODS: Seventy-five patients with HER2-positive, ER- and PR-negative breast carcinomas who received anti-HER2 based neoadjuvant therapy were retrospectively analyzed. Thirty-seven cases were classified as basal-like HER2-positive breast carcinoma with any positivity for CK5/6, and thirty-eight cases were classified as pure HER2-positive breast carcinoma with completely negativity for CK5/6. The clinicopathological features and tumor responses after neoadjuvant therapy and outcomes were analyzed. RESULTS: Compared to non-basal HER2-positive breast carcinoma, basal-like HER2-positive breast carcinoma showed distinctive histologic features including poor differentiation and syncytial tumor cells with pushing, invasive borders and a significantly higher proportion of apocrine metaplasia. They also demonstrated significantly higher histologic grade; 18/37 (48.6%) of basal-like carcinomas were grade 3, whereas only 5/38 (13.2%) of non-basal carcinomas were grade 3 (p = 0.001), Furthermore, basal-like HER2-positive breast carcinomas were more likely to be positive or completely negative for p53 (p = 0.009), and demonstrated a higher percentage of TP53 mutation (p = 0.17). These tumors were less responsive to anti-HER2 based neoadjuvant therapy, with Miller-Payne grades 1-3 higher than pure HER2-positive breast carcinoma (25/37 [67.6%] vs 16/38 [42.1%]), and the percentage of grade 4-5 was lower (12/37 [32.4%] vs 22/38 [57.9%]; p = 0.027). CONCLUSIONS: Basal-like HER2-positive breast carcinoma has distinctive clinicopathological features and less histologic tumor response after neoadjuvant therapy. There is urgent need to recognize basal-like HER2-positive breast carcinoma to be treated precisely.

TOPK: A new predictor of the therapeutic response to neoadjuvant chemotherapy and prognosis in triple-negative breast cancer.

BACKGROUND: Triple-negative breast cancer (TNBC) has a high probability of relapse and poor overall survival. Neoadjuvant chemotherapy (NACT) is currently a routine treatment strategy for TNBC, but some patients do not respond well. T-LAK cell-originated protein kinase (TOPK) is highly expressed in breast cancer cells and contributes to cancer cell proliferation. The present study aimed to investigate the correlation of TOPK expression with NACT treatment response and prognosis in TNBC. METHODS: We collected 66 pairs of TNBC samples before and after NACT with docetaxel+ epirubicin+ cyclophosphamide (TEC). The Miller-Payne (MP) system was used to assess the therapeutic response to NACT in TNBC patients. RESULTS: Immunohistochemistry analysis showed that TNBC patients with high TOPK expression before NACT had a poor treatment response and a poor prognosis. The expression of TOPK after NACT was significantly higher than that before NACT in patients with MP grade 1-3. In contrast, patients with MP grade 4-5 had significantly lower TOPK expression after NACT than before NACT, and the expression change in Ki-67 in patients with MP grade 4-5 exhibited the same trend. Survival analysis revealed that patients with TNBC accompanied by elevated TOPK expression before NACT had a worse prognosis than those with lower TOPK expression. CONCLUSION: TOPK may be a novel predictor for the therapeutic response to NACT and prognosis for patients with TNBC.

Tumor Immune Microenvironment Components and Checkpoint Molecules in Anaplastic Variant of Diffuse Large B-Cell Lymphoma.

BACKGROUND: Anaplastic diffuse large B-cell lymphoma(A-DLBCL) is a rare morphological subtype characterized by the presence of polygonal, bizarre-shaped tumor cells. Our previous research found that A-DLBCL displays many genetic alterations and biological features that differ greatly from those of ordinary DLBCL. However, the status of tumor immune microenvironment components and checkpoint molecules in A-DLBCL remains unclear. METHODS: Thirty A-DLBCL patients were enrolled to study tumor immune microenvironment components and checkpoint molecules and their associations with clinicopathological features and prognosis. RESULTS: Patients with A-DLBCL presented higher expression of PD-L1 (40% vs 10%, P=0.004) than patients with ordinary DLBCL. FISH analysis showed that extra copies of PD-L1 were more frequent in A-DLBCL cases than in ordinary DLBCL cases (23.3% vs 4.0%, P=0.001). The numbers of PD-1+ TILs (tumor infiltrating lymphocytes) and CD8+T cells were significantly lower in A-DLBCL versus ordinary DLBCL. In contrast, the numbers of GATA3+ Th2 cells, FOXP3+ Tregs and CD33+ myeloid-derived suppressor cells (MDSCs) were significantly higher in A-DLBCL than in ordinary DLBCL. The associations between clinicopathological features and tumor immune microenvironment cell frequency were analyzed in A-DLBCL patients. Briefly, the number of PD-1+ TILs was lower and the number of CD33+ MDSCs was higher in patients with mutated TP53 compared to those with wild-type TP53. The number of FOXP3+ Tregs was much lower in patients with a noncomplete response (CR) to chemotherapy than in those with a complete response. The number of CD8+ T cells showed a decreasing trend in patients with high International Prognostic Index (IPI) scores and in those with concurrent MYC and BCL2 and/or BCL6 abnormalities. Univariate survival analysis showed that patients with PD-L1+, mPD-L1+(PD-L1+ nonmalignant stromal cells) or mPD-L1+ status had a significantly poorer overall survival (OS) than those with PD-L1- status. An increase in the number of CD3+ T cells, FOXP3+ Treg cells and T-bet+ Th1 cells was significantly associated with prolonged OS in patients with A-DLBCL. CONCLUSION: Our study suggests that A-DLBCL displays a distinct pattern of tumor immune microenvironment components and checkpoint molecules that distinguish it from ordinary DLBCL. The analysis of tumor immune microenvironment components and checkpoint molecules could help in predicting the prognosis of A-DLBCL patients and determining therapeutic strategies targeting the tumor immune microenvironment.

Some pleomorphic adenomas of the breast share PLAG1 rearrangements with the analogous tumour of the salivary glands.

AIMS: Pleomorphic adenoma (PA) of the breast, and especially its malignant transformation, is extremely rare and represents a diagnostic pitfall. Molecular alterations in this entity have not been investigated. We aimed to examine the clinicopathological features of our breast PAs and perform molecular analysis. METHODS AND RESULTS: Seven cases of breast PA, including two cases of carcinoma ex PA, were analysed. PLAG1 and HMGA2 gene rearrangements were assayed by fluorescence in-situ hybridisation (FISH) and RNA sequencing (RNA-Seq), respectively. Reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing were used to verify RNA sequencing results. All seven cases of breast PA occurred in women. The histological features were similar to the analogous tumour in salivary glands, including a dual epithelial-myoepithelial component and negativity of oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) by immunohistochemistry. Of the two cases with carcinoma ex PA, one demonstrated minimal invasion and one was extensively invasive. PLAG1 rearrangements were identified in two cases (28.6%), but no rearrangements of HMG2A were found. A novel fusion product in PAs, TRPS1-PLAG1, was identified in one case. No patients had recurrence or metastasis with a follow-up period of 6-158 months. CONCLUSIONS: Breast PA is rare, but it is an important differential diagnosis of breast pathology with the potential to develop carcinoma ex PA. We report a novel TRPS1-PLAG1 fusion gene in breast PA.

QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering.

The dynamic choice of different polyadenylation sites in a gene is referred to as alternative polyadenylation, which functions in many important biological processes. Large-scale messenger RNA 3' end sequencing has revealed that cleavage sites for polyadenylation are presented with microheterogeneity. To date, the conventional determination of polyadenylation site clusters is subjective and arbitrary, leading to inaccurate annotations. Here, we present a weighted density peak clustering method, QuantifyPoly(A), to accurately quantify genome-wide polyadenylation choices. Applying QuantifyPoly(A) on published 3' end sequencing datasets from both animals and plants, their polyadenylation profiles are reshaped into myriads of novel polyadenylation site clusters. Most of these novel polyadenylation site clusters show significantly dynamic usage across different biological samples or associate with binding sites of trans-acting factors. Upstream sequences of these clusters are enriched with polyadenylation signals UGUA, UAAA and/or AAUAAA in a species-dependent manner. Polyadenylation site clusters also exhibit species specificity, while plants ones generally show higher microheterogeneity than that of animals. QuantifyPoly(A) is broadly applicable to any types of 3' end sequencing data and species for accurate quantification and construction of the complex and dynamic polyadenylation landscape and enables us to decode alternative polyadenylation events invisible to conventional methods at a much higher resolution.