| 1 | Expression dynamics of periodic transcripts during cancer cell cycle progression and their correlation with anticancer drug sensitivity显示文摘Background:The cell cycle is at the center of cellular activities and is orchestrated by complex regulatory mechanisms,among which transcriptional regulation is one of the most important components.Alternative splicing dramatically expands the regulatory network by producing transcript isoforms of genes to exquisitely control the cell cycle.However,the patterns of transcript isoform expression in the cell cycle are unclear.Therapies targeting cell cycle checkpoints are commonly used as anticancer therapies,but none of them have been designed or evaluated at the alternative splicing transcript level.The utility of these transcripts as markers of cell cycle-related drug sensitivity is still unknown,and studies on the expression patterns of cell cycle-targeting drug-related transcripts are also rare.Methods:To explore alternative splicing patterns during cell cycle progression,we performed sequential transcriptomic assays following cell cycle synchronization in colon cancer HCT116 and breast cancer MDA-MB-231 cell lines,using flow cytometry and reference cell cycle transcripts to confirm the cell cycle phases of samples,and we developed a new algorithm to describe the periodic patterns of transcripts fluctuating during the cell cycle.Genomics of Drug Sensitivity in Cancer(GDSC)drug sensitivity datasets and Cancer Cell Line Encyclopedia(CCLE)transcript datasets were used to assess the correlation of genes and their transcript isoforms with drug sensitivity.We identified transcripts associated with typical drugs targeting cell cycle by determining correlation coefficients.Cytotoxicity assays were used to confirm the effect of ENST00000257904 against cyclin dependent kinase 4/6(CDK4/6)inhibitors.Finally,alternative splicing transcripts associated with mitotic(M)phase arrest were analyzed using an RNA synthesis inhibition assay and transcriptome analysis.Results:We established high-resolution transcriptome datasets of synchronized cell cycle samples from colon cancer HCT116 and breast cancer MDA-MB-231 cells.The results of the cell cycle assessment showed that 43,326,41,578 and 29,244 transcripts were found to be periodically expressed in HeLa,HCT116 and MDA-MB-231 cells,respectively,among which 1280 transcripts showed this expression pattern in all three cancer cell lines.Drug sensitivity assessments showed that a large number of these transcripts displayed a higher correlation with drug sensitivity than their corresponding genes.Cell cycle-related drug screening showed that the level of the CDK4 transcript ENST00000547281 was more significantly associated with the resistance of cells to CDK4/6 inhibitors than the level of the CDK4 reference transcript ENST00000257904.The transcriptional inhibition assay following M phase arrest further confirmed the M-phase-specific expression of the splicing transcripts.Combined with the cell cycle-related drug screening,the results also showed that a set of periodic transcripts,for example,ENST00000314392(a dolichylphosphate mannosyltransferase polypeptide 2 isoform transcript),was more associated with drug sensitivity than the levels of their corresponding gene transcripts.Conclusions:In summary,we identified a panel of cell cycle-related periodic transcripts and found that the levels of transcripts of drug target genes showed different values for predicting drug sensitivity,providing novel insights into alternative splicing-related drug development and evaluation. | Chun‑Xiao Li Jin‑Song Wang Wen‑Na Wang Dong‑Kui Xu Yan‑Tong Zhou Fang‑Zhou Sun Yi‑Qun Li Feng‑Zhu Guo Jia‑Lu Ma Xue‑Yan Zhang Meng‑Jiao Chang Bing‑He Xu Fei Ma Hai‑Li Qian | 2023 | Military Medical Research2023，10，4： | 0 |
| 2 | Taxonomy and phylogeny of hyaline‑spored coelomycetes显示文摘Coelomycete is a general term used for asexual fungi which produce conidia in fruiting bodies:pycnidial,acervular,cupulate,pycnothyria or stromatic conidiomata.The group contains numerous plant pathogenic,saprobic and endophytic species associated with a wide range of hosts.Traditionally,morphological characters and host associations have been used as criteria to identify and classify coelomycetes,and this has resulted in a poor understanding of their generic and species boundaries.DNA based taxonomic studies have provided a better outlook of the phylogenetic and evolutionary trends in coelomycetes.However,the present outcomes represent only a preliminary step towards the understanding of coelomycetes.Many genera have not been revisited since they were first described.The present study revises the classification of the hyaline-spored coelomycetes and provides a modern taxonomic framework based on both morphology and phylogeny.In total,248 genera were investigated,of which less than 100 are known to have sequence data.Multi-locus sequence data analyses of 28S nrDNA,18S nrDNA,ITS,RNA polymerase II second largest subunit(rpb2),and part of the translation elongation factor 1-alpha gene(tef1)andβ-tubulin(tub2)gene regions were analysed.As a result,three new genera and 23 new species are introduced.In addition,three new links between sexual and asexual genera are provided.There are 138 genera that lack sequence data,and these are treated as Ascomycota,genera incertae sedis.Line drawings and descriptions are provided based on the examination of types and fresh collections and on the literature. | Wen‑Jing Li Eric H.C.McKenzie Jian‑Kui(Jack)Liu D.Jayarama Bhat Dong‑Qin Dai Erio Camporesi Qing Tian Sajeewa S.N.Maharachchikumbura Zong‑Long Luo Qiu‑Ju Shang Jin‑Feng Zhang Narumon Tangthirasunun Samantha C.Karunarathna Jian‑Chu Xu Kevin D.Hyde | 2020 | Fungal Diversity2020，，1： | 0 |
| 3 | Fungal diversity notes 1151-1276:taxonomic and phylogenetic contributions on genera and species of fungal taxa显示文摘Fungal diversity notes is one of the important journal series of fungal taxonomy that provide detailed descriptions and illustrations of new fungal taxa,as well as providing new information of fungal taxa worldwide.This article is the 11th contribution to the fungal diversity notes series,in which 126 taxa distributed in two phyla,six classes,24 orders and 55 families are described and illustrated.Taxa in this study were mainly collected from Italy by Erio Camporesi and also collected from China,India and Thailand,as well as in some other European,North American and South American countries.Taxa described in the present study include two new families,12 new genera,82 new species,five new combinations and 25 new records on new hosts and new geographical distributions as well as sexual-asexual reports.The two new families are Eriomycetaceae(Dothideomycetes,family incertae sedis)and Fasciatisporaceae(Xylariales,Sordariomycetes).The twelve new genera comprise Bhagirathimyces(Phaeosphaeriaceae),Camporesiomyces(Tubeufiaceae),Eriocamporesia(Cryphonectriaceae),Eriomyces(Eriomycetaceae),Neomonodictys(Pleurotheciaceae),Paraloratospora(Phaeosphaeriaceae),Paramonodictys(Parabambusicolaceae),Pseudoconlarium(Diaporthomycetidae,genus incertae sedis),Pseudomurilentithecium(Lentitheciaceae),Setoapiospora(Muyocopronaceae),Srinivasanomyces(Vibrisseaceae)and Xenoanthostomella(Xylariales,genera incertae sedis).The 82 new species comprise Acremonium chiangraiense,Adustochaete nivea,Angustimassarina camporesii,Bhagirathimyces himalayensis,Brunneoclavispora camporesii,Camarosporidiella camporesii,Camporesiomyces mali,Camposporium appendiculatum,Camposporium multiseptatum,Camposporium septatum,Canalisporium aquaticium,Clonostachys eriocamporesiana,Clonostachys eriocamporesii,Colletotrichum hederiicola,Coniochaeta vineae,Conioscypha verrucosa,Cortinarius ainsworthii,Cortinarius aurae,Cortinarius britannicus,Cortinarius heatherae,Cortinarius scoticus,Cortinarius subsaniosus,Cytospora fusispora,Cytospora rosigena,Diaporthe camporesii,Diaporthe nigra,Diatrypella yunnanensis,Dictyosporium muriformis,Didymella camporesii,Diutina bernali,Diutina sipiczkii,Eriocamporesia aurantia,Eriomyces heveae,Ernakulamia tanakae,Falciformispora uttaraditensis,Fasciatispora cocoes,Foliophoma camporesii,Fuscostagonospora camporesii,Helvella subtinta,Kalmusia erioi,Keissleriella camporesiana,Keissleriella camporesii,Lanspora cylindrospora,Loratospora arezzoensis,Mariannaea atlantica,Melanographium phoenicis,Montagnula camporesii,Neodidymelliopsis camporesii,Neokalmusia kunmingensis,Neoleptosporella camporesiana,Neomonodictys muriformis,Neomyrmecridium guizhouense,Neosetophoma camporesii,Paraloratospora camporesii,Paramonodictys solitarius,Periconia palmicola,Plenodomus triseptatus,Pseudocamarosporium camporesii,Pseudocercospora maetaengensis,Pseudochaetosphaeronema kunmingense,Pseudoconlarium punctiforme,Pseudodactylaria camporesiana,Pseudomurilentithecium camporesii,Pseudotetraploa rajmachiensis,Pseudotruncatella camporesii,Rhexocercosporidium senecionis,Rhytidhysteron camporesii,Rhytidhysteron erioi,Septoriella camporesii,Setoapiospora thailandica,Srinivasanomyces kangrensis,Tetraploa dwibahubeeja,Tetraploa pseudoaristata,Tetraploa thrayabahubeeja,Torula camporesii,Tremateia camporesii,Tremateia lamiacearum,Uzbekistanica pruni,Verruconis mangrovei,Wilcoxina verruculosa,Xenoanthostomella chromolaenae and Xenodidymella camporesii.The five new combinations are Camporesiomyces patagoniensis,Camporesiomyces vaccinia,Camposporium lycopodiellae,Paraloratospora gahniae and Rhexocercosporidium microsporum.The 22 new records on host and geographical distribution comprise Arthrinium marii,Ascochyta medicaginicola,Ascochyta pisi,Astrocystis bambusicola,Camposporium pellucidum,Dendryphiella phitsanulokensis,Diaporthe foeniculina,Didymella macrostoma,Diplodia mutila,Diplodia seriata,Heterosphaeria patella,Hysterobrevium constrictum,Neodidymelliopsis ranunculi,Neovaginatispora fuckelii,Nothophoma quercina,Occultibambusa bambusae,Phaeosphaeria chinensis,Pseudopestalotiopsis theae,Pyxine berteriana,Tetraploa sasicola,Torula gaodangensis and Wojnowiciella dactylidis.In addition,the sexual morphs of Dissoconium eucalypti and Phaeosphaeriopsis pseudoagavacearum are reported from Laurus nobilis and Yucca gloriosa in Italy,respectively.The holomorph of Diaporthe cynaroidis is also reported for the first time. | Kevin DHyde Yang Dong Rungtiwa Phookamsak Rajesh Jeewon DJayarama Bhat EBGareth Jones Ning‑Guo Liu Pranami DAbeywickrama Ausana Mapook Deping Wei Rekhani HPerera Ishara SManawasinghe Dhandevi Pem Digvijayini Bundhun Anuruddha Karunarathna Anusha HEkanayaka Dan‑Feng Bao Junfu Li Milan CSamarakoon Napalai Chaiwan Chuan‑Gen Lin Kunthida Phutthacharoen Sheng‑Nan Zhang Indunil CSenanayake Ishani DGoonasekara Kasun MThambugala Chayanard Phukhamsakda Danushka STennakoon Hong‑Bo Jiang Jing Yang Ming Zeng Naruemon Huanraluek Jian‑Kui(Jack)Liu Subodini NWijesinghe Qing Tian Saowaluck Tibpromma Rashika SBrahmanage Saranyaphat Boonmee Shi‑Ke Huang Vinodhini Thiyagaraja Yong‑Zhong Lu Ruvishika SJayawardena Wei Dong Er‑Fu Yang Sanjay KSingh Shiv Mohan Singh Shiwali Rana Sneha SLad Garima Anand Bandarupalli Devadatha MNiranjan VVenkateswara Sarma Kare Liimatainen 馻‑ Tuula Niskanen Andy Overall Renato Lúcio Mendes Alvarenga Tatiana Baptista Gibertoni Walter PPfliegler EnikőHorváth Alexandra Imre Amanda Lucia Alves Ana Carla da Silva Santos Patricia Vieira Tiago Timur SBulgakov Dhanushaka NWanasinghe Ali HBahkali Mingkwan Doilom Abdallah MElgorban Sajeewa SNMaharachchikumbura Kunhiraman CRajeshkumar Danny Haelewaters Peter EMortimer Qi Zhao Saisamorn Lumyong Jianchu Xu Jun Sheng | 2020 | Fungal Diversity2020，，1： | 0 |
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