Objectives: To define the involvement of CALM and AF10 fusion transcripts in primary leukaemias with t(10; 11). Methods: The AF10 and CALM fusion in five t(10; 11) leukemia samples were checked by reverse transcriptas...Objectives: To define the involvement of CALM and AF10 fusion transcripts in primary leukaemias with t(10; 11). Methods: The AF10 and CALM fusion in five t(10; 11) leukemia samples were checked by reverse transcriptase-polymerase chain reaction (RT-PCR), and effects of CALM/AF10 antisense phosphorothioate oligodeoxynucleotides (AS PS-ODNs) on chemotherapy sensitivity and apoptosis of leukemia cells in vitro were observed. Results: Five different-sized AF10-CALM products and four different-sized CALM/AF10 products were detected by RT-PCR. The chemotherapy sensitivity of leukemic cells with t(10; 11) to drugs in vitro was lower than that of leukemic cells without t(10; 11). AS PS-ODNs increased the chemotherapy sensitivity and apoptotic rate. There were 4 cases positive at 5 μmol/L concentration, all cases positive at 10 μmol/L and 20 μmol/L concentration, P<0.01 vs only chemotherapeutic drugs (3 cases positive), and chemotherapeutic drugs + S-PS-ODNs (10 μmol/L) (3 cases positive). After cells were treated with 10 μmol/L AS-PS-ODNs + chemotherapeutic drugs for 48 h, 72 h, 96 h, the apoptotic indexes were 14.22±2.86, 29.39±3.57, and 41.26±4.52, respectively. These were significantly higher than those of only chemotherapeutic drugs-treated cells and chemotherapeutic drugs + S-PS-ODNs-treated cells at corresponding time (P<0.01). There was no difference between only drugs group and S-PS-ODNs group at corresponding time (P>0.05). Conclusion: The CALM and AF10 fusion transcripts are involved in the pathogenesis of haematological malignancies with t(10, 11), and is associated with a poor prognosis. AS-PS-ODNs might be useful in therapy of t(10, 11) leukemia. Key words AF10 - CALM - Fusion transcript - Primary leukemia cell - In vitro sensitivity - Antisense oligodeoxynucleotide CLC number R733.7 Biography: LIU Ge-xiu (1968–), male, associate professor, Institute of Hematology, Medical College, Jinan University, majors in hematology.展开更多
1.INTRODUCTION Hematological malignancies with NUP98 rearrangement(NUP98r)were included as recurrent genetic abnormali-ties due to their distinctive clinicopathologic characteristics in the 2022 European LeukmiaNet(EL...1.INTRODUCTION Hematological malignancies with NUP98 rearrangement(NUP98r)were included as recurrent genetic abnormali-ties due to their distinctive clinicopathologic characteristics in the 2022 European LeukmiaNet(ELN)classification,the 2022 World Health Organization(WHO)classification,and the International Consensus Classification.展开更多
The transcriptome serves as a bridge that links genomic variation to phenotypic diversity.A vast number of studies using next-generation RNA sequencing(RNA-seq)over the last 2 decades have emphasized the essential rol...The transcriptome serves as a bridge that links genomic variation to phenotypic diversity.A vast number of studies using next-generation RNA sequencing(RNA-seq)over the last 2 decades have emphasized the essential roles of the plant transcriptome in response to developmental and environmental conditions,providing numerous insights into the dynamic changes,evolutionary traces,and elaborate regulation of the plant transcriptome.With substantial improvement in accuracy and throughput,direct RNA sequencing(DRS)has emerged as a new and powerful sequencing platform for precise detection of native and full-length transcripts,overcoming many limitations such as read length and PCR bias that are inherent to short-read RNA-seq.Here,we review recent advances in dissecting the complexity and diversity of plant transcriptomes using DRS as the main technological approach,covering many aspects of RNA metabolism,including novel isoforms,poly(A)tails,and RNA modification,and we propose a comprehensive workflow for processing of plant DRS data.Many challenges to the application of DRS in plants,such as the need for machine learning tools tailored to plant transcriptomes,remain to be overcome,and together we outline future biological questions that can be addressed by DRS,such as allele-specific RNA modification.This technology provides convenient support on which the connection of distinct RNA features is tightly built,sustainably refining our understanding of the biological functions of the plant transcriptome.展开更多
Background Colorectal cancer(CRC)is a complex,heterogeneous disease characterized by frequent relapses and metastasis.Previous studies have reported that the invasion and progression of CRC in several cases can be con...Background Colorectal cancer(CRC)is a complex,heterogeneous disease characterized by frequent relapses and metastasis.Previous studies have reported that the invasion and progression of CRC in several cases can be controlled by targeting fusion genes.This study aimed to screen for potent fusion transcripts as potential molecular biomarkers and therapeutic targets for metastatic CRC(mCRC)using an in silico approach.Methods RNA sequencing(RNA-seq)data from 18 patients with primary CRC and matched normal and mCRC samples were derived from the same patient set.Novel fusion transcripts were screened using the Kallisto and Pizzly software,followed by Gene Ontology(GO),pathway analysis,transcription factor enrichment,and survival for functional enrichment analysis.Furthermore,the fusion transcripts’utility as biomarkers was evaluated using a pan-cancer analysis.Results In total,32 fusion genes unique to mCRC were identified.Hub gene analysis identified 17 novel fusion transcripts,and GO analysis revealed that these genes were enriched in different biological and molecular functions.Pathways significantly correlated with CRC included the complement and coagulation cascades,ferroptosis,interleukin-17(IL-17)signaling pathway,and estrogen signaling pathway.We identified albumin-eukaryotic translation elongation factor 1 alpha 1(ALB-EEF1A1)as unique to mCRC based on significant gene expression and survival outcomes.Moreover,its utility as a prognostic biomarker was confirmed using a pan-cancer analysis.Conclusions ALB-EEF1A1 may play a pivotal role in the metastatic transformation of primary CRC and significantly increase the risk of death.The identified ALB-EEF1A1 fusion transcripts are promising novel molecular targets that may serve as prognostic and diagnostic biomarkers and treatment targets for mCRC in the future.展开更多
Hepatitis B virus(HBV),one of the well-known DNA oncogenic viruses,is the leading cause of hepatocellular carcinoma(HCC).In infected hepatocytes,HBV DNA can be integrated into the host genome through an insertional mu...Hepatitis B virus(HBV),one of the well-known DNA oncogenic viruses,is the leading cause of hepatocellular carcinoma(HCC).In infected hepatocytes,HBV DNA can be integrated into the host genome through an insertional mutagenesis process inducing tumorigenesis.Dissection of the genomic features surrounding integration sites will deepen our understanding of mechanisms underlying integration.Moreover,the quantity and biological activity of integration sites may reflect the DNA damage within affected cells or the potential survival benefits they may confer.The wellknown human genomic features include repeat elements,particular regions(such as telomeres),and frequently interrupted genes(e.g.,telomerase reverse transcriptase[i.e.TERT],lysine methyltransferase 2B[i.e.KMT2B],cyclin E1[CCNE1],and cyclin A2[CCNA2]).Consequently,distinct genomic features within diverse integrations differentiate their biological functions.Meanwhile,accumulating evidence has shown that viral proteins produced by integrants may cause cell damage even after the suppression of HBV replication.The integration-derived gene products can also serve as tumor markers,promoting the development of novel therapeutic strategies for HCC.Viral integrants can be single copy or multiple copies of different fragments with complicated rearrangement,which warrants elucidation of the whole viral integrant arrangement in future studies.All of these considerations underlie an urgent need to develop novel methodology and technology for sequence characterization and function evaluation of integration events in chronic hepatitis B-associated disease progression by monitoring both host genomic features and viral integrants.This endeavor may also serve as a promising solution for evaluating the risk of tumorigenesis and as a companion diagnostic for designing therapeutic strategies targeting integration-related disease complications.展开更多
文摘Objectives: To define the involvement of CALM and AF10 fusion transcripts in primary leukaemias with t(10; 11). Methods: The AF10 and CALM fusion in five t(10; 11) leukemia samples were checked by reverse transcriptase-polymerase chain reaction (RT-PCR), and effects of CALM/AF10 antisense phosphorothioate oligodeoxynucleotides (AS PS-ODNs) on chemotherapy sensitivity and apoptosis of leukemia cells in vitro were observed. Results: Five different-sized AF10-CALM products and four different-sized CALM/AF10 products were detected by RT-PCR. The chemotherapy sensitivity of leukemic cells with t(10; 11) to drugs in vitro was lower than that of leukemic cells without t(10; 11). AS PS-ODNs increased the chemotherapy sensitivity and apoptotic rate. There were 4 cases positive at 5 μmol/L concentration, all cases positive at 10 μmol/L and 20 μmol/L concentration, P<0.01 vs only chemotherapeutic drugs (3 cases positive), and chemotherapeutic drugs + S-PS-ODNs (10 μmol/L) (3 cases positive). After cells were treated with 10 μmol/L AS-PS-ODNs + chemotherapeutic drugs for 48 h, 72 h, 96 h, the apoptotic indexes were 14.22±2.86, 29.39±3.57, and 41.26±4.52, respectively. These were significantly higher than those of only chemotherapeutic drugs-treated cells and chemotherapeutic drugs + S-PS-ODNs-treated cells at corresponding time (P<0.01). There was no difference between only drugs group and S-PS-ODNs group at corresponding time (P>0.05). Conclusion: The CALM and AF10 fusion transcripts are involved in the pathogenesis of haematological malignancies with t(10, 11), and is associated with a poor prognosis. AS-PS-ODNs might be useful in therapy of t(10, 11) leukemia. Key words AF10 - CALM - Fusion transcript - Primary leukemia cell - In vitro sensitivity - Antisense oligodeoxynucleotide CLC number R733.7 Biography: LIU Ge-xiu (1968–), male, associate professor, Institute of Hematology, Medical College, Jinan University, majors in hematology.
基金supported by grant from the National Key R&D Program of China(2019YFA0111000,2022YFC2502700)the National Natural Science Foundation of China(82170158,82470166,82200149,82100175,82200149,82100170)+1 种基金the priority academic program development of Jiangsu Higher Education Institution,the Natural Science Foundation of Jiangsu Province(BK20231195,BK20210087)the Open Project of Jiangsu Biobank of Clinical Resources(SBK202003001,SBK202003003).
文摘1.INTRODUCTION Hematological malignancies with NUP98 rearrangement(NUP98r)were included as recurrent genetic abnormali-ties due to their distinctive clinicopathologic characteristics in the 2022 European LeukmiaNet(ELN)classification,the 2022 World Health Organization(WHO)classification,and the International Consensus Classification.
基金Guangxi Natural Science Foundation(2024GXNSFGA010003)National Natural Science Foundation of China(32270712 and 31871269)Guangxi Science and Technology Major Program(AA23062085).
文摘The transcriptome serves as a bridge that links genomic variation to phenotypic diversity.A vast number of studies using next-generation RNA sequencing(RNA-seq)over the last 2 decades have emphasized the essential roles of the plant transcriptome in response to developmental and environmental conditions,providing numerous insights into the dynamic changes,evolutionary traces,and elaborate regulation of the plant transcriptome.With substantial improvement in accuracy and throughput,direct RNA sequencing(DRS)has emerged as a new and powerful sequencing platform for precise detection of native and full-length transcripts,overcoming many limitations such as read length and PCR bias that are inherent to short-read RNA-seq.Here,we review recent advances in dissecting the complexity and diversity of plant transcriptomes using DRS as the main technological approach,covering many aspects of RNA metabolism,including novel isoforms,poly(A)tails,and RNA modification,and we propose a comprehensive workflow for processing of plant DRS data.Many challenges to the application of DRS in plants,such as the need for machine learning tools tailored to plant transcriptomes,remain to be overcome,and together we outline future biological questions that can be addressed by DRS,such as allele-specific RNA modification.This technology provides convenient support on which the connection of distinct RNA features is tightly built,sustainably refining our understanding of the biological functions of the plant transcriptome.
文摘Background Colorectal cancer(CRC)is a complex,heterogeneous disease characterized by frequent relapses and metastasis.Previous studies have reported that the invasion and progression of CRC in several cases can be controlled by targeting fusion genes.This study aimed to screen for potent fusion transcripts as potential molecular biomarkers and therapeutic targets for metastatic CRC(mCRC)using an in silico approach.Methods RNA sequencing(RNA-seq)data from 18 patients with primary CRC and matched normal and mCRC samples were derived from the same patient set.Novel fusion transcripts were screened using the Kallisto and Pizzly software,followed by Gene Ontology(GO),pathway analysis,transcription factor enrichment,and survival for functional enrichment analysis.Furthermore,the fusion transcripts’utility as biomarkers was evaluated using a pan-cancer analysis.Results In total,32 fusion genes unique to mCRC were identified.Hub gene analysis identified 17 novel fusion transcripts,and GO analysis revealed that these genes were enriched in different biological and molecular functions.Pathways significantly correlated with CRC included the complement and coagulation cascades,ferroptosis,interleukin-17(IL-17)signaling pathway,and estrogen signaling pathway.We identified albumin-eukaryotic translation elongation factor 1 alpha 1(ALB-EEF1A1)as unique to mCRC based on significant gene expression and survival outcomes.Moreover,its utility as a prognostic biomarker was confirmed using a pan-cancer analysis.Conclusions ALB-EEF1A1 may play a pivotal role in the metastatic transformation of primary CRC and significantly increase the risk of death.The identified ALB-EEF1A1 fusion transcripts are promising novel molecular targets that may serve as prognostic and diagnostic biomarkers and treatment targets for mCRC in the future.
基金This work was supported by the 111Project(Project No.:B13003)Innovation Promotion Association CAS(2016098)National Natural Science Foundation of China(81201700)to D.Z。
文摘Hepatitis B virus(HBV),one of the well-known DNA oncogenic viruses,is the leading cause of hepatocellular carcinoma(HCC).In infected hepatocytes,HBV DNA can be integrated into the host genome through an insertional mutagenesis process inducing tumorigenesis.Dissection of the genomic features surrounding integration sites will deepen our understanding of mechanisms underlying integration.Moreover,the quantity and biological activity of integration sites may reflect the DNA damage within affected cells or the potential survival benefits they may confer.The wellknown human genomic features include repeat elements,particular regions(such as telomeres),and frequently interrupted genes(e.g.,telomerase reverse transcriptase[i.e.TERT],lysine methyltransferase 2B[i.e.KMT2B],cyclin E1[CCNE1],and cyclin A2[CCNA2]).Consequently,distinct genomic features within diverse integrations differentiate their biological functions.Meanwhile,accumulating evidence has shown that viral proteins produced by integrants may cause cell damage even after the suppression of HBV replication.The integration-derived gene products can also serve as tumor markers,promoting the development of novel therapeutic strategies for HCC.Viral integrants can be single copy or multiple copies of different fragments with complicated rearrangement,which warrants elucidation of the whole viral integrant arrangement in future studies.All of these considerations underlie an urgent need to develop novel methodology and technology for sequence characterization and function evaluation of integration events in chronic hepatitis B-associated disease progression by monitoring both host genomic features and viral integrants.This endeavor may also serve as a promising solution for evaluating the risk of tumorigenesis and as a companion diagnostic for designing therapeutic strategies targeting integration-related disease complications.
