Photo-Facilitated Detection and Sequencing of 5-Formylcytidine RNA.

5-Formylcytidine (f5 C) is one of the epigenetic nucleotides in tRNA. Despite the evident importance of f5 C in gene expression regulation, little is known about its exact amount and position. To capture this information, we developed a modification-specific functionalization with a semi-stabilized ylide. The chemical labelling exhibited a high selectivity towards f5 C and allowed distinction from similar 5-formyluridine. We realized a detection strategy based on the fluorescence signal of the cyclization product 4,5-pyridin-2-amine-cytidine paC, which exhibited a high quantum yield. The results clearly identified f5 C with a limit of detection at 0.58 nM. This method altered the hydrogen bonding activities of f5 C and modulated its reverse transcription signature in its sequencing profile. We showed that f5 C can be detected from tRNA segments with a single-base resolution. Taken together, this approach is a sensitive, antibody-free, and applicable detection and sequencing method for f5 C-containing RNA.

MicroRNA-494 sensitizes colon cancer cells to fluorouracil through regulation of DPYD.

Chemoresistance of colon cancer cells to the chemotherapeutics is still a main obstacle in treatment of this malignancy. The microRNA (miRNA) mediated chemosensitivity regulation in colon cancer cells is still largely unknown. Here we constructed a fluorouracil (5-Fu) resistant SW480 cell line (SW480/5-Fu) and discovered that miRNA miR-494 was down-regulated in the drug resistant cells compared with the parental cells. miR-494 level was found to be correlated with 5-Fu sensitivity in colon cancer cells, and artificial alteration of miR-494 affects the sensitivity of colon cancer cell lines to 5-Fu. miR-494 also promoted apoptosis of colon cancer cells at present of 5-Fu. Importantly, as a regulatory enzyme in the 5-Fu catabolic pathway, DPYD was confirmed to be a direct target of miR-494 through the interaction of miR-494 and its binding site within DPYD 3' untranslated region (3'UTR). miR-494 also negatively regulated endogenous DPYD expression in SW480 cells. Overexpression or knockdown of DPYD could attenuate miR-494 mediated 5-Fu sensitivity regulation, suggesting the dependence of DPYD regulation in miR-494 activity. miR-494 inhibited SW480/5-Fu derived xenograft tumors growth in vivo at present of 5-Fu. Thus, we concluded that in colon cancer cells, tumor suppressor miR-494 enhanced 5-Fu sensitivity via regulation of DPYD expression.

m6 A promotes planarian regeneration.

Regeneration is the regrowth of damaged tissues or organs, a vital process in response to damages from primitive organisms to higher mammals. Planarian possesses active whole-body regenerative capability owing to its vast reservoir of adult stem cells, neoblasts, providing an ideal model to delineate the underlying mechanisms for regeneration. RNA N6 -methyladenosine (m6 A) modification participates in many biological processes, including stem cell self-renewal and differentiation, in particular the regeneration of haematopoietic stem cells and axons. However, how m6 A controls regeneration at the whole-organism level remains largely unknown. Here, we demonstrate that the depletion of m6 A methyltransferase regulatory subunit wtap abolishes planarian regeneration, potentially through regulating genes related to cell-cell communication and cell cycle. Single-cell RNA-seq (scRNA-seq) analysis unveils that the wtap knockdown induces a unique type of neural progenitor-like cells (NP-like cells), characterized by specific expression of the cell-cell communication ligand grn. Intriguingly, the depletion of m6 A-modified transcripts grn, cdk9 or cdk7 partially rescues the defective regeneration of planarian caused by wtap knockdown. Overall, our study reveals an indispensable role of m6 A modification in regulating whole-organism regeneration.

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer featured with high intra-tumoral heterogeneity and poor prognosis. To comprehensively delineate the PDAC intra-tumoral heterogeneity and the underlying mechanism for PDAC progression, we employed single-cell RNA-seq (scRNA-seq) to acquire the transcriptomic atlas of 57,530 individual pancreatic cells from primary PDAC tumors and control pancreases, and identified diverse malignant and stromal cell types, including two ductal subtypes with abnormal and malignant gene expression profiles respectively, in PDAC. We found that the heterogenous malignant subtype was composed of several subpopulations with differential proliferative and migratory potentials. Cell trajectory analysis revealed that components of multiple tumor-related pathways and transcription factors (TFs) were differentially expressed along PDAC progression. Furthermore, we found a subset of ductal cells with unique proliferative features were associated with an inactivation state in tumor-infiltrating T cells, providing novel markers for the prediction of antitumor immune response. Together, our findings provide a valuable resource for deciphering the intra-tumoral heterogeneity in PDAC and uncover a connection between tumor intrinsic transcriptional state and T cell activation, suggesting potential biomarkers for anticancer treatment such as targeted therapy and immunotherapy.

Author Correction: Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Possibilities and potential roles of estrogen in the pathogenesis of proliferation hemangiomas formation.

Hemangiomas, often categorized as angiogenic diseases, are the most common tumors of infancy, the life span of which is generally divided into proliferating phase, involuting phase, and involuted phase. Despite their high prevalence, the mechanism leading to proliferation hemangiomas formation is poorly understood and the best approach to their management remains controversial. None of the current therapeutic modalities is ideal, partly because the pathogenesis of hemangioma and the mechanism of its proliferation are far from clear. Many clues reveal that estrogen has an important role in developing the vascular system, experimental and clinical evidences accumulated in recent years also suggest the potential for estrogen to influence neovascularization. Based on those, we hypothesize that estrogen play a potential role in the development of hemangiomas, mainly by regulating some key angiogenic factors, including MMP-9, EPCs, VEGF, NO, etc. Accepting the hypothesis to be correct, a therapy that identify estrogen as a potential target for the design of new, more specific treatments can be used to prevent the proliferation hemangiomas formation. The hypothesis may lead a new direction in the study of mechanisms for proliferation hemangiomas formation, and further study of the precise mechanisms for estrogen-induced hemangiomas will produce effective antiestrogens and estrogen receptor antagonists as new medication for the very difficult problem.

Clinical features and outcome of patients with HIV-negative multicentric Castleman's disease treated with combination chemotherapy: a report on 10 patients.

To investigate the clinical characteristics and outcome of patients with HIV-negative multicentric Castleman's disease (MCD) treated exclusively with combination chemotherapy, and review literature to improve the diagnosis and management of this disease. A retrospective study was performed on the medical records of 10 patients with HIV-negative MCD treated exclusively with combination chemotherapy at one medical institution from May 2004 to April 2012. And relevant clinical, pathological, radiographic, and laboratory data were examined in order to evaluate treatment responses, with symptom onsets and survival period serving as the endpoints of the assessment. All patients have multifocal lymphadenopathy, and the associated system symptoms are found in 80 % of the cases. All patients were treated with lymphoma-based chemotherapy alone. The duration of follow-up ranged from 5 to 77 months for nine patients. Four patients were treated with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) alone: One was alive with no evidence of disease, and three were alive with disease. Three patients received cyclophosphamide, vincristine, and prednisone (COP) alone: One remained alive with disease, and two experienced recurrences and passed away. Two had only minimal response to COP and were switched to CHOP, and they were still alive with disease. MCD is a more progressive clinical entity, and long-term follow-up is necessary. CHOP chemotherapy may be an effective treatment option for patients with MCD, whereas when to start chemotherapy, how many cycles of chemotherapy required, and the role of combined radiotherapy remain to be further studied.

FDG PET-CT in non-small cell lung cancer: relationship between primary tumor FDG uptake and extensional or metastatic potential.

OBJECTIVE: To explore the relationships between primary tumor 18F-FDG uptake measured as the SUVmax and local extension, and nodal or distant organ metastasis in patients with NSCLC on pretreatment PET-CT. METHODS: 93 patients with NSCLC who underwent 18F-FDG PET-CT scans before the treatment were included in the study. Primary tumor SUVmax was calculated; clinical stages, presence of local extension, nodal and distant organ metastases were recorded. The patients with SUVmax ≥ 2.5 were divided into low and high SUVmax groups by using the median SUVmax. The low SUVmax group consisted of 45 patients with SUVmax<10.5, the high SUVmax group consisted of 46 patients with SUVmax ≥ 10.5. Their data were compared statistically. RESULTS: 91 cases with SUVmax≥2.5 were included for analysis. The mean SUVmax in patients without any metastasis was 7.42 ± 2.91 and this was significantly lower than that (12.18 ± 4.94) in patients with nodal and/or distant organ metastasis (P=0.000). In the low SUV group, 19 patients had local extension, 22 had nodal metastasis, and 9 had distant organ metastasis. In the high SUV group, 31 patients had local extension, 37 had nodal metastasis, and 18 had distant organ metastases. There was a significant difference in local extension (P =0.016), distant organ metastasis (P =0.046), and most significant difference in nodal metastasis rate (P =0.002) between the two groups. In addition, there was a moderate correlation between SUVmax and tumor size (r = 0.642, P<0.001), tumor stage (r = 0.546, P<0.001), node stage (r = 0.388, P<0.001), and overall stage (r = 0.445, P= 0.000). CONCLUSION: Higher primary tumor SUVmax predicts higher extensional or metastatic potential in patients with NSCLC. Patients with higher SUVmax may need a close follow-up and more reasonable individual treatment because of their higher extensional and metastatic potential.