title: Gene expression by LASP1 knocked down in PC3 cells

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

summary: The aim of this research was to confirm the regulatory effect of LASP1 on gene expression in the development of prostate cancer.

overall_design: In this research, there were two samples examed including sample of negtive control cells (PC3-NC) and sample of LASP1 knocked down cells (PC3-siLASP1).

first: Hongwei

last: Guo

first: Bo

last: Han


title: Microarray for Rice Hitomebore

status: Public on Jun 30 2022

city: Changchun

first: Ningning

last: Wang

address: 2888, Xinchen Street

country: China

institute: Jilin Agricultural University

summary: Detection gene expression variation in Rice Hitomebore

overall_design: CK(3 replicates)

first: Bao

last: Liu


title: Highly-sensitive DNA hydroxymethylation analysis to aid clinic evaluation of myelodysplastic syndromes (MDS)

status: Public on Jul 01 2022

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

country: USA

institute: Guangzhou Medical University

type: Methylation profiling by high throughput sequencing

summary: Aberrant DNA hydroxymethylation (5hmC) has been reported in patients with myelodysplastic syndromes (MDS). The dysregulation of 5hmC is not only observed in patients with TET2 mutations, but also those bearing other genetic defects, suggesting that 5hmC might act as a valuable epigenetic mark to reflect the status of MDS. To further evaluate the function of 5hmC during MDS pathogenesis, we reported herein an improved highthroughput 5hmC analysis method based on CMS-IP using low input DNA (10 ng) purified from bone marrow aspirates of MDS patients. Our analysis revealed relatively higher heterogeneity of 5hmC signals in MDS patients compared with those of healthy donors, CMML and AML patients. Our systematic bioinformatic analysis further unveiled that 5hmC signatures could be used to separate patients with good and poor clinical outcomes. At the molecular level, we observed dynamic changes of 5hmC within several key transcription factor binding motifs that are essential for hemopoiesis and myeloid lineage specification, which might result in impaired transcriptional outputs during leukemogenesis. Interestingly, we also observed massive changes in 5hmC and transcriptomes in patient showing response to hypomethylating agents (HMA) treatment, suggesting the prognostic value of 5hmC in evaluating epigenetic therapy. Overall, our high-sensitive 5hmC analysis method provides a useful means to greatly facilitate the clinic evaluation for MDS.

overall_design: We collected total 82 human bone marrow samples (7 healthy; 4 AML patients; 71 MDS patients) and performed CMS-IP sequencing.

first: Deqiang

last: Sun

first: Yun

last: Huang

first: Guillermo

last: Garcia-Manero


title: The molecular and cellular basis of divergent dose-dependent ionising radiation response

city: Leiden

first: Bharath

last: Sampadi

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

type: Expression profiling by high throughput sequencing

summary: Cancer risk from medical exposure to low dose (LD) ionizing radiation (IR) is linearly extrapolated from high dose (HD) IR without sufficient mechanistic understanding and definitive evidence. The long-term health effects of radiotherapy for cancer are unclear as secondary tumours possibly arise from the ‘low-dose bath’ of normal tissue,. By the age of ~45 years, most (>90%) of the survivors of paediatric cancers develop secondary tumours from cancer therapy (including radiotherapy). Here, we show that LD and HD drive molecular and cellular responses to reactive oxygen species (ROS) production and DNA damage, respectively. We found dose-proportionality only for the phosphorylation events in the DNA damage response (DDR); signalling via PPP1R7 and global (de)phosphorylation events govern the G2/M checkpoint, whereas impaired DSB repair affected the DDR signalling duration rather than amplitudes. Contrastingly, LD specifically activated NRF2-regulated antioxidant defence, redox-sensitive ERK1/2/MAPK signalling, kinome/phosphatome, mitochondrial metabolic and glycolytic pathways, whereas HD induced replication stress signalling, p53 transcription and proliferation inhibition. Dose-proportional (10-200 mGy) chromosomal damage induction suggests non(slowly) repairable DNA breaks generation without a threshold, whereas LD-specific enhanced ROS-related responses induction implies survival of cells with residual DNA damage.

overall_design: Dynamic nascent BrU-RNA profiles of mouse embroyonic stem cells were generated over five different time points and three different conditions, in duplicates, using Illumina HiSeq 2500 sequencers.

first: Brian

last: Magnuson


title: BRD4 promotes gastric cancer progression and metastasis through acetylation-dependent stabilization of Snail

city: Chongqing

first: Zhon-gyi

last: qin

address: Changjiang Road, Yuzhong District

department: Gastroenterology

institute: Daping Hospital, Army Military Medical University (Third Military Medical University)

summary: The puropose of this study is to reveal a noncanonical post-transcriptional regulatory function of BRD4 that maintains cancer growth and dissemination, with immediate translational implication for treating metastatic malignancies with clinically available bromodomain inhibitors. The next-generation RNA sequencing was used to confirm the transcriptom overlapping change after BRD4 and Snail knockout separately.

overall_design: mRNA profiles of gastric cancer cells which were generated by depletion of control, Snail and BRD4 were generated by deep sequencing, in triplicate, using Illumina hiseqxten .

first: Zhong-yi

last: Qin

first: Bin


title: Contribution of skeletal muscle-specific microRNA to insulin resistance in heart failure

city: Baltimore

first: Samarjit

last: Das

state: MD

address: 720 Rutland Avenue

department: Anesthesiology and Critical Care Medicine

institute: Johns Hopkins School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Exercise intolerance (EI) and insulin resistance (IR) are hallmarks of heart failure (HF). Abnormalities in skeletal muscle metabolism, where glucose is a major energy source, have been identified in HF and may be a link between EI and IR but the underlying mechanisms are poorly understood.

overall_design: Comparative miRNA expression profiling analysis of RNA-seq data for skeletal muscle of mice with HF induced by transverse aortic constriction (TAC)

first: Fernanda

last: Carrizo Velasquez

first: Barbara

last: Roman

first: Erick

middle: O

last: Hernández-Ochoa

first: Michelle

middle: K

last: Leppo

first: Sharon

last: Truong

first: Charles

last: Steenbergen

first: Martin

middle: F

last: Schneider

first: Robert

middle: G

last: Weiss


title: Dynamic analysis of m6A methylation spectroscopy during progression and reversal of hepatic fibrosis

city: shanghai jingan district

first: ZHONGQI

last: CUI

state: shanghai

address: 301 yanchangzhong road

institute: shanghai tenth people hospital

summary: We constructed a model of progression and reversal of hepatic fibrosis by intraperitoneal injection of carbon tetrachloride (CCl4). Dynamic m6A methylation was evaluated using MeRIP-Seq technique in the progression and reversal of hepatic fibrosis, and of the normal age-matched control groups. Genes with differentially m6A methylated sites and expression were analyzed to reveal the over-represented gene ontologies and pathways at different stages

overall_design:
Dynamic analysis of differential methylation and expression of genes during the first, third and sixth weeks of progression of liver fibrosis and the first and second weeks of reversal, to explore the dynamic changes of methylation during hepatic fibrosis
contributor: National Natural Science Foundation of China (81608129/ 81772941)
contributor: Cloudseq


title: Single-cell RNA sequencing of cortical samples in Fam69c knockout mice

city: Beijing

first: Fan

last: Mei

address: 38 Xueyuan Road

institute: Peking University Health Science Center

summary: Synapse loss and memory decline are the primary features of neurodegenerative dementia. However, molecular underpinnings that drive memory loss remain largely unknown. Here, we report that FAM69C is a novel kinase critically involved in neurodegenerative dementia. Biochemical analyses uncovered that FAM69C is a serine/threonine kinase. We generated the Fam69c knockout mice, and showed by single-cell RNA sequencing that FAM69C deficiency drives cell-type-specific transcriptional changes relevant to synapse dysfunction. Electrophysiological, morphological and behavioral experiments demonstrated impairments in synaptic plasticity, dendritic spine density and memory in Fam69c knockout mice, as well as stress-induced neuronal death. Phosphoproteomic characterizations revealed FAM69C substrates involved in synaptic structure and function. Finally, reduced levels of FAM69C were found in postmortem brains of AD. Our study demonstrates that FAM69C is a protective regulator of memory and suggests FAM69C as a potential therapeutic target for memory loss in neurodegenerative dementia.

overall_design: Study of cell-type-specific transcriptional changes in Fam69c wildtype and knockout cortical tissues using 10x Genomics platform.

first: Guangze

last: Zhang

first: Anhang

last: Liu

first: Xiangyan

last: Meng


title: Pre-mRNA processing complex in Trypanosoma brucei: structural assembly and function of core polyA factors

city: hengyang

first: Logen

state: --- Select a state ---

address: 35. Libration Ave. the second affiliated hospital

institute: university of south china

summary: Pre mRNA 3 end processing is unique in trypanosomes as it involves polycistronic transcription, polyadenylation coupled to trans splicing and elusive polyadenylation signals. The mechanism is poorly understood. Here we reported that nine putative polyA factors from Trypanosoma brucei form a stable complex which then subsequently develops into two tight subcomplexes. One contains the proteins tbCPSF160, tbCPSF30, tbFip1 and tbWdr33 with tbCPSF160 as the scaffold; while the other contains tbCPSF100, tbCPSF73, tbSYMK and two trypanosome unique proteins, designated CPF30 and CPF15. No CstF homologs were found. The protein tbCPSF100 seems to coordinate the association of these two subcomplexes by interacting with tbCPSF160. RNAi knockdown of these polyA factors resulted in RNA processing disorders and variable disruption of the complex and RNA processing disorders. Depletion of either factors caused dicistronic transcripts formation; depletion of either tbCPSF30, tbFip1 or tbWdr33 caused increased usage of proximal polyadenylation sites of the transcripts; depletion of tbCPSF30 caused mRNA polyA tail shortening. This indicates that these two polysA factors have a critical role in polyadenylation site selection. Genome-wide UV crosslinking assays showed that tbCPSF30 and tbFip1 have strong RNA-binding activity in this complex. Altogether, these data indicate that the 3 end processing complex of T. brucei is more like the human CPSF homolog. However, it displays trypanosome specific features in composition, structural assembly and function of components, which facilitate a common, yet unique, cleavage polyadenylation reaction.

overall_design: CPSF30 were knockdown or not, poly(A)  enriched RNA were extracted, direct RNA sequencing were performed (Minion, sequencing kit SQK-RNA002), poly(A) tail length were evaculated with tailfindr software. Direct sequencing of poly(A) RNA from cells of TRRM2 knockdown or not were used as control.

first: Xuemin

last: Guo


title: Single-cell transcriptomic analysis of mouse pancreas: characteristic features of pancreatic ductal cells in chronic pancreatitis

city: Shanghai

first: Wenbin

last: Zou

address: No. 168, Changhai Road, Yangpu District, Shanghai

institute: Shanghai Institute of Pancreatic Diseases

summary: Chronic pancreatitis (CP) is a pathogenically complex fibro-inflammatory disorder of the pancreas. Our understanding of CP pathogenesis is partly limited by the incomplete characterization of pancreatic cell types. Here, we performed single-cell RNA sequencing on 3,386 cells from the pancreas of one control mouse and mice with caerulein-induced CP. These data provides a preliminary description of the single-cell transcriptome profiles of mouse pancreata and accurately demonstrates the characteristics of pancreatic ductal cells in CP.

overall_design: Single-cell RNA sequencing of pancreatic cells from one control mouse and mice with caerulein-induced CP.

first: Xiaotong

last: Mao

first: Shenghan

first: Zhuan

last: Liao


title: Transcriptomic analysis of TCF-7 cKO CD8 T cells

city: Syracuse

first: Mobin

last: Karimi

state: NY

address: 766 Irving Ave Suite 2281

department: Microbiology/Immunology

institute: Suny Upstate Medical University

summary:
T Cell Factor-1, encoded by TCF-7, is a transcription factor that plays an essential role during T cell development and differentiation. In this manuscript we utilized a pre-clinical model provided evidence that TCF-7 is dispensable for the anti-tumor response, and that TCF-7 suppresses key transcriptional factors Eomes and T-bet and molecules responsible for peripheral CD8 T cell cytolytic function. We discovered that TCF-7 regulates NKG2D expression on naïve and activated mouse CD8 T cells, and that peripheral CD8 T cells from TCF-7 cKO utilize NKG2D to clear tumor cells.
We also provide evidence that TCF-7 regulates key signaling molecules, including LCK, LAT, ITK, PLC-y1, P65, ERKI/II, and JAK/STATs required for peripheral CD8 T cell persistent function.  Our data transcriptomic and protein data uncovered the mechanism of how TCF-7 impacting peripheral CD8 T cell inflammatory cytokine production, CD8 T cell activation, and apoptosis. Our pre-clinical model showed that CD8 T cells from TCF-7 cKO mice did not cause GVHD, but effectively cleared primary tumor cells.

overall_design: We analyzed FACS purified CD8 T cells of 3 different  TCF-7 cKO and WT mouse labeled this group of samples as pre-transplanted samples. For post-transplanted samples 1 x10^6 CD3 T Cells from  TCF-7 cKO and WT mice were initially transplanted into lethally irradiated recipent Balb/c mouse and at day 7 post-transplant H2kb+ donor CD4 and CD8 T cells  FACS sorted  from the spleen of recipients into the Trizol.

first: Mahinbanu

last: Mammadli


title: Vitamins and their derivatives synergistically promote hair shaft elongation ex vivo via PlGF/VEGFR-1 signaling activation

city: KIzugawa

first: Shun

last: Kimura

state: Kyoto

address: 6-5-4 Kunimidai

country: Japan

institute: Rohto Pharmaceutical co. ltd.

summary: Background: Despite that vitamins or their derivatives (Vits), such as panthenyl ethyl ether, tocopherol acetate, or pyridoxine have been widely used in topical hair care products, their efficacy and mode of action have been insufficiently studied.  Objective: To elucidate biological influence of Vits on hair follicles and dissect underlying mechanisms.   Methods: Mouse vibrissa hair follicle organ culture model was utilized to evaluate the effects of Vits on hair shaft elongation. Gene and protein expression analyses, and histological investigation were conducted to elucidate responsible mechanisms. Human hair follicle cell culture was adopted to assess clinical relevance.   Results: In organ culture models, the combination of panthenyl ethyl ether, tocopherol acetate, and pyridoxine (namely PPT) supplementation significantly promoted hair shaft elongation. PPT-treatment enhanced hair matrix cell proliferation by 1.9 folds compared to controls, as demonstrated by Ki-67 positive immunoreactivity. PPT-treated mouse dermal papillae up-regulated Placental growth factor (Plgf) by 1.6 folds, compared to non-treated controls. Importantly, addition of PlGF neutralizing antibodies to the ex vivo culture diminished the promotive effect on hair growth and the increase in VEGFR1 phosphorylation achieved by PPT. A VEGFR1 inhibitor also repressed the promotion of hair shaft elongation. Microarray analysis suggested synergistic summation of individual Vit bioactivity, putatively explaining the effect of PPT. Moreover, PPT increased PlGF secretion in cultured human dermal papilla cells.  Conclusion: Our findings suggested that PPT promoted hair shaft elongation via activating PlGF/VEGFR-1 signaling. The current study can shed light on the previously underrepresented advantage of utilizing Vits for ameliorating hair care products.

overall_design: Mouse vibrissae respectively treated with a single, double, or triple mixture of Panthenyl ethyl ether(PEE), Pyridoxine hydrochloride(PH), and Tocopherol Acetate(TA) for 24 hr, were used for gene expression analysis. One sample was total RNA from 10 hair follicles and 3 independent experiments were performed.

first: Liuying

last: Hu

first: Masatoshi

last: Haga

first: Sayo

last: Kashiwagi

first: Kyoko

last: Takagi

first: Takashi

last: Shimizu

first: Tsuyoshi

last: Ishii

first: Manabu

last: Ohyama


title: Virulence, cellular masking, and grazing resistance in the struggle to survive under long term protozoan predation; the genetics of survival

city: Christchurch

first: Heather

last: Hendrickson

department: Biological Sciences

country: New Zealand

institute: University of Cantebury

summary:
Purpose: Generalist protozoan predators change the pace of evolution in microbial communities, but investigations into the molecular consequences of predation for the genomic evolution of defence or coadaptation are scarce. We have previously performed a 90-day co-evolution experiment to address these effects using the bacterium Pseudomonas fluorescens SBW25 on solid media in the presence and absence of a wild Acanthamoeba sp. predator. Coevolution led to genomic divergence, altered phenotypes and resistance to predation in coevolved bacterial lineages. Strong parallel phenotypic evolution was observed among the coevolved replicates leading to Wrinkly Spreader, Volcano and Mountain colony phenotypes. Here, we describe the genomic mutations underlying this parallelism with a focus on these morphotypes.
Methods: Pseudomonas fluorescens SBW25 and a wild Acanthamoeba sp. isolate as a predator prey pair co-evolved for 90 days yielded novel colony morphotype (Mountain; MNT, and Volcano; VOL) isolates with conferred grazing resistance. These isolates were subjected to RNAseq profiling with and without predation to determine transcriptional changes contributing to grazing resistance.
Results: We made a profile of differentially expressed genes (DEG) for the coevolved Vol-L1 (Volcano L1; ∆fadD2-fadD1 & luxR T2675G) while predated by ancestral Acanthamoebae. WT P. fluorescens SBW25 was used as the baseline and significant differential expression was considered for genes with log2 FC ≥ 2, P-value ≤ 0.05 between conditions. We identified a total of 953 DEGs, of which 293 were upregulated and 660 were downregulated. Differentially expressed gene (DEG) profiles were made for the coevolved strains Mnt-L2 (Mountain L2; ∆4974-4975 & PFLU_0924 C790T) while under predation by ancestral Acanthamoebae. In this case we also used WT P. fluorescens SBW25 without predation as a baseline as described previously. In this condition and compared to the WT SBW25, we identified a total of 209 DEGs, of which 118 were upregulated and 91 were downregulated.
Conclusions:  In this study, from the DEG profile of Mnt-L2 and Vol-L1 while predated by the ancestral Acanthamoebae we found 12 and 21 upregulated genes in O-antigen biosynthesis, respectively. The polysaccharide capsule (LPS) is considered as one of the main virulence factors produced by pathogenic bacteria to protect bacteria against phagocytosis by the host’s immune system as well. We found enrichments in lipopolysaccharide-A production and three viscosin genes in Vol-L1 (a finding unique to the Vol-L1 strain). Vol-L1 had significant downregulation of seven efflux genes, most significantly PFLU_3263 (an efflux transporter), as well as a fatty acid transporter (PFLU4903). These results, taken with the finding of altered survivability only when evolved strains are grown with Acanthamoebae and the abundance of mutations found in FadD genes, led to our hypothesis that the evolved bacteria might be altering transporters to counter increased exposure to LC fatty acids from the Acanthamoeba by increased oxidative stress from LC fatty acid degradation, masking, etc. Furthermore, we found upregulation of an efflux RND transporter downstream of the deletion (PFLU_4976) and a unique enrichment (5 genes) in the cyclophilin-like domain (immunophilin) in Mnt-L2. Among all DEGs, 72 upregulated and 66 downregulated genes were shared between the Vol-L1 and Mnt-L2 conditions.

sample_organism:
Pseudomonas fluorescens
Acanthamoeba sp.

overall_design: mRNA profiles of Co-evolved predator (Acathamoeba sp.) and prey (Pseudomonas fluorescens SBW25)

first: Farhad

last: Golzar

first: Michael

last: Miller


title: mRNA m6A MeRIP-seq of Mesocricetus auratus cell infected with Senecavirus A

city: Qingdao City

first: Bo

last: Ni

state: Shandong Province

address: No.369 Nanjing Road

institute: China Animal Health And Epidemiology Center

summary: To investigate the mRNA m6A modification profiling in Mesocricetus auratus cells that infected with Senecavirus,  we used passage-5 Senecavirus A to infect BSR-T7/5 cells. We then performed m6A MeRIP-seq(GenSeq® m6A MeRIP Kit) at at two time points (12hrs or 72 hrs after infection), each time point with three replicates.

overall_design: Comparative mRNA m6A modification profiling analysis of MeRIP-seq data for BSR-T7/5 cells infected with passage-5 Senecavirus A at two time point(12 hrs or 72 hrs after infection) . Each time point has three replicates, i.e. S-A, S-B, S-C at 12 hrs, and S-D, S-E, S-F at 72 hrs.

first: Fuxiao

last: Liu

first: Ziwei

last: Li

first: Rong

last: Wei


title: Gene expression of human mesenchymal stem cells in 3D cell culture

city: Tulln

first: Vanessa

last: Dobernig

address: Konrad-Lorenz-Straße

country: Austria

institute: LifeTaq Analytics GmbH

summary: Two-dimensional (2D) monolayer cell cultures are inevitable for drug development to identify drug candidate molecules because they are extremely potent for screening procedures. They can be used to predict in vivo drug responses for a variety of targets and pathways but they also face disadvantages like a lack of cell-to-cell and cell-to-matrix interaction as well as the loss of tissue-specific architecture. To overcome the drawbacks of 2D systems, three-dimensional (3D) cell culture was designed to provide cells a more physiological environment. In light of the multiple benefits of 3D cell culture it is important to note that this cultivation system is not automated and thus not ideal for high throughput screening (HTS) so far. An automated technique is critical for reproducible and standardized in vitro cultivation and it can greatly speed up preclinical research and total drug development. This procedure also requires a quality control system to monitor results and ensure that it is suitable for customers´ applications. For this purpose, the physiological condition of 2 D and 3D cell cultures will be assessed analyzing gene expression profiles of human mesenchymal stem cells (hMSCs). This will be accomplished by extracting total ribonucleic acid (RNA) from 2D and 3D cells followed by Affymetrix microarrays to get transcription profiles. The resulting data from both cell systems can be compared, and changes in cell behaviour caused by the 3D system can be observed.

overall_design: 3 samples are analyzed, the 2 D standard culture (sample 1) is a reference for the other samples.


title: An autoregulatory feedback loop converging on H2AK119ub1 drives synovial sarcoma [ChIP-seq]

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The SS18-SSX fusion drives oncogenic transformation in synovial sarcoma by bridging SS18, a member of mSWI/SNF complex, to polycomb repressive complex 1 (PRC1) target genes. Here we show that the SSX C-terminus, via its SSXRD domain, directs SS18-SSX chromatin binding independently of SS18. SSXRD specific targeting is mediated by interaction with H2AK119ub1 and histone MacroH2A with which the fusion overlaps genome wide. Variant Polycomb Repressive Complex 1.1 (PRC1.1) acts as the main depositor of H2AK119ub1 and consequently is required for SS18-SSX occupancy. Importantly, SSX C-terminus not only depends on H2AK119ub1 for localization but also further promotes it and consequently, high H2AK119ub1 levels are acquired during synovial sarcoma development. These results reveal an SS18-SSX/PRC1 autoregulatory feedback-loop that enforces fusion binding and could play a role in a wide-range of cancers and physiological settings where SSX proteins are overexpressed.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for eGFP, SSX-C and SSX-CDeltaRD in human synovial sarcoma cells HS-SY-II using their HA tag.

middle: S

first: Ana

last: Banito


title: Afadin and Zyxin contribute to coupling between cell junctions and contracting actomyosin networks during apical constriction

city: New York

first: Sophia

middle: C

last: Tintori

address: 29 Washington Pl - rm 951

institute: New York University

summary: One of the most common cell shape changes driving morphogenesis in diverse animals is the constriction of the apical surface. Apical constriction depends on contraction of an actomyosin network in the apical cell cortex, but such actomyosin networks have been shown to undergo continual, conveyor belt-like contractions even before the shrinking of an apical surface begins. This finding suggests that apical constriction is not necessarily triggered by the contraction of actomyosin networks, but rather by unidentified, temporally-regulated mechanical linking of actomyosin to the cell junctions. Here, we used C. elegans gastrulation as a model to identify proteins that contribute to such linkage. We found that α-catenin and β-catenin initially failed to move centripetally with contracting cortical actomyosin networks, suggesting that linkage is regulated between cadherin-catenin complexes and actomyosin. We used a proteomic approach to identify AFD-1/afadin and transcriptomics to identify ZYX-1/zyxin as contributors to C. elegans gastrulation. We found that a zyxin family of LIM domain proteins have transcripts that become enriched in multiple cells just before they undergo apical constriction. Using a new, semi-automated image analysis tool, we found that AFD-1/afadin and ZYX-1/zyxin both contribute to cell-cell junctions’ centripetal movement along contracting actomyosin networks. These results identify two key proteins as important for actomyosin networks to effectively pull cell-cell junctions inward during apical constriction. The transcriptional upregulation of zyxin/ZYX-1 in specific cells points to one way that developmental patterning spatiotemporally regulates cell biological mechanisms in vivo. Because afadin- and zyxin-family proteins contribute to membrane-cytoskeleton linkage in other systems, we anticipate that their roles in regulating apical constriction in this manner may be conserved.

overall_design: RNA-seq datasets for 9 embryonic tissues at the ~100-cell stage, in 4 sets of embyo-matched samples. ABp descendents (ABp+) and the rest of the embryo (ABp-), MS descendents (MS+) and the rest of the embryo (MS-), D descendents (D+) and the rest of the embryo (D-), and Cxp cells (Cin), Cxa cells (Cout) and the rest of the embryo (C-). Samples labeled "_rejected" were from embryos in which one sample did not pass QC (more than 10% of transcripted were ERCC spike-ins).

first: Mark

middle: M

last: Slabodnick

first: Mangal

last: Prakash

first: Christopher

middle: D

last: Higgins

first: Alicia

middle: H

last: Chen

first: Timothy

last: Cupp

first: Terrence

last: Wong

first: Emily

last: Bowie

first: Florian

last: Jug

first: Bob

last: Goldstein


title: MECP2-related pathways are dysregulated in a cortical organoid model of Myotonic dystrophy

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: MECP2-related pathways are dysregulated in a cortical organoid model of Myotonic dystrophy [eCLIP]

summary:
Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3’ untranslated region of the dystrophia myotonica-protein kinase (DMPK) gene. Despite its prominence as the most common adult-onset muscular dystrophy, patients with congenital to juvenile-onset forms of DM1 can present with debilitating neurocognitive symptoms along the autism spectrum, characteristic of possible in utero   cortical defects. However, the molecular mechanism by which CTG MREs lead to these developmental central nervous system (CNS) manifestations is unknown. Here, we showed that CUG foci discovered early in maturation of three-dimensional cortical organoids from DM1 patient-derived induced pluripotent stem cells, cause hyperphosphorylation of CUGBP Elav-Like Family Member 2 (CELF2 ) protein. Integrative single-cell RNA-seq and enhanced crosslinking and immunoprecipitation (eCLIP ) analysis revealed reduced CELF2 protein-RNA substrate interactions resulting in mis-regulation of genes critical for excitatory synaptic signaling in glutamatergic neurons, including key components of the Methyl-CpG binding protein 2 (MECP2) pathway. Comparisons to MECP2(-/-) cortical organoids revealed convergent molecular and cellular defects such as glutamate toxicity and neuronal loss. Our findings provide evidence suggesting that early-onset DM1 might involve neurodevelopmental disorder-associated pathways and identify N-Methyl-D-aspartic acid (NMDA ) antagonists as potential treatment avenues for neuronal defects in DM1.
To evaluate if the post-translational modification of CELF2 impacts its RNA targets, we generated transcriptome-wide eCLIP maps of CELF2 protein-RNA interactions  in mature, 6-month-old control and DM1 cortical organoids. All CELF2 eCLIP libraries per organoid line were performed in biologically independent duplicates, with each replicate experiment consisting of a CELF2 (IP) and a paired size-matched input (SMInput) library . We used CLIPper  to identify clusters of reads representing regions in the transcriptome significantly associated with CELF2 binding in both neurotypical lines and compared them to DM1 cortical organoids with 600 and 1200 CUG repeats.

overall_design: Comparative CELF2 eCLIP data generated from cortical organoid lines  differentiated from 2 DM1 iPSC lines (DM1200 and DM600) and 2 Neurotypical Control Lines (CSO and Kin).

first: Shashank

last: Shathe

first: Kathryn

last: Morelli


title: Comparative study of transcriptome in the hearts isolated from mice, rats, and human

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The heart is a major organ in mammalian life, and the study of transcription factors, particularly those that regulate cardiac rhythm, has been an important focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences. In this study, we reanalyzed mouse, rat, and human transcriptome data obtained from different platforms by calculating specificity measure (SPM) values in consideration of species differences. SHOX2 and HOXA2 were found to be important as sinoatrial node-specific transcription factors throughout the species. In particular, the SPM value of SHOX2 is very high. Similarly, by calculating SPM values, we identified 3 atrial-specific, 11 ventricular-specific, and 17 SA-specific markers. Ontology analysis identified 70 cardiac region- and species-specific ontologies. These results suggest that reanalyzing existing data by calculating SPM values may identify novel tissue-specific genes and species-dependent gene expression. Within this study, we identified the importance of SHOX2 as a SA-specific transcription factor, a novel cardiac regional marker, and ontologies.

overall_design: Total RNA from sinoatrial nodes and left and right ventricles and atria were examined using Illumina mouse Ref-8 microarrays (N = 4 for each of the five groups).

first: Daigo

last: Okada

first: Yosuke

last: Okamoto

first: Toshiro

last: Io

first: Miho

last: Oka

first: Daiki

last: Kobayashi

first: Ryo

last: Yamada

first: Kuniaki

last: Ishii

first: Kyoichi

last: Ono


title: Effects of SRSF5  knock down on gene expression in HaCaT cells

city: Tokushima

last: Sumi

state: Not US or Canada

address: 180, Yamashiro-cho

department: Faculty of Pharmaceutical Sciences

institute: Tokushima Bunri University

summary: To seach for factors with altered gene expression under the suppression of SRSF5 expression

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SRSF5 knockdown with siRNA


title: Overdominant expression of related genes of ion homeostasis improves K+ content advantage in hybrid tobacco leaves

city: Guiyang

first: kai

last: pi

state: Guizhou

department: Key Laboratory for Tobacco Quality Research Guizhou Province

institute: Guizhou University

summary: Through a two-year field experiment, G70×GDH11 with strong heterosis and K326×GDH11 with weak heterosis were screened out. Transcriptome analyses revealed that 80.89% and 57.28% of the differentially expressed genes (DEGs) in the strong and weak heterosis combinations exhibited an overdominant expression pattern, respectively. The genes that up-regulated the overdominant expression in the strong heterosis hybrids were significantly enriched in the ion homeostasis. Genes involved in K+ transport (KAT1/2, GORK, AKT2 and KEA3), activity regulation complex (CBL-CIPK5/6), and vacuole (TPKs) genes were overdominant expressed in strong heterosis hybrids, which contributed to K+ homeostasis and heterosis in tobacco leaves.

overall_design: 18 samples were analyzed, including 6 plant materials, each with three replicates.

first: Kai

last: Pi

first: Wen

last: Luo


title: Expression of miRNAs from HPV-positive penile cancer patients

city: São Luís

first: Silma

middle: Regina

last: Pereira

state: Maranhão

address: Av. dos Portugueses, 1966, Bacanga

department: Department of Biology

country: Brazil

institute: Federal University of Maranhão

summary: PeCa is a rare carcinoma in developed countries, but it presents higher incidence rates in South America, Asia, and Africa, where limited economic and social conditions play a large impact leading to delay in diagnosis, and treatment initiation. The infection by HPV is a the risk factors and can occur through the canonical HPV/p53/RB1 pathway mediated by the E2/E6/E7 viral oncoproteins. During the transformation process, HPV inserts its genetic material into host Integration Sites (IS), affecting coding genes and miRNAs. In penile cancer (PeCa) there is limited data on the miRNAs. Considering the high frequency of HPV infection in PeCa patients in Northeast Brazil, global miRNA expression profiling was performed in high-risk HPV-associated PeCa. A panel of differentially expressed miRNAs (miRDE) was successfully constructed using 22 PeCa tissues and five non-tumor penile tissues.

overall_design: Fresh tissues of 22 primary tumors were collected from 22 patients with squamous cell penile carcinoma who underwent surgical treatment between Jan/2014 and Dez/2016. As control, five paired non-tumors tissues was used. Total RNA from tumors and non-tumor tissues was isolated using the TRIzol protocol (Invitrogen Carlsbad, CA, USA). Expression of miRNAs was determined using the nCounter® Human v.3 miRNA expression platform (Nanostring Technologies™, Seattle, Wa, USA), which contains human probes from miRBase v.22 (http://www.mirbase.org) targeting human miRNAs, six positive controls, eight negative controls, three positive binding controls, three negative binding controls, five internal reference genes (ACTB, B2M, GAPDH, RPL19, and RPL0) and five miRNA controls (ath-miR- 159a, cel-miR-248, cel-miR-133, osa-miR-414, and osa-miR-442).

middle: R

first: Rui

last: Reis

first: Luciane

last: Sussuchi

first: Ana

last: Laus

first: Jenilson

last: Silva


title: Transcriptional profiling of whole blood leukocytes obtained from critically ill patients with sepsis treated with clarithromycin, or not, and healthy particpants

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: To evaluate whether clarithromycin improves 28-day mortality among patients with sepsis, respiratory and multiple-organ dysfunction syndrome. The INntravenous CLArithromycin in Sepsis and multiple organ dysfunction Syndrome trial was a phase 3, randomized, double blind, placebo-controlled clinical study, conducted in 11 intensive care units and 2 Internal Medicine wards in 2 countries. Patients with sepsis, respiratory failure and total sequential organ failure assessment score of ≥7 were enrolled between December 2017 and September 2019. Follow-up lasted 90 days. Patients were randomized to receive 1 gr of intravenous clarithromycin or placebo once daily for 4 consecutive days.

overall_design: Examination of PAXgene blood leukocyte RNA expression in critically-ill patients due to sepsis treated with clarithromycin after the first day of study inclusion (INC_D1_A) and in the same patients after five days (INC_D5_A). Placebo-treated patients after one day of study inclusion (INC_D1_B) and same patients treated with placebo after five days (INC_D5_B). Healthy pariticpants were also included and assessed (healthy).

middle: P

first: Evangelos

middle: J

last: Giamarellos Bourboulis

first: Eleni

last: Karakike


title: MECP2-related pathways are dysregulated in a cortical organoid model of Myotonic dystrophy [scRNA-Seq]

first: Gene

last: Yeo

summary: As cortical organoids consist of a heterogeneous population of cell-types, 6-month-old DM1  and Rett syndrome cortical organoids were subjected to single cell RNA-seq (scRNA-seq) analysis to determine which cell type(s) CELF2’s RNA targets are expressed in. Unsupervised clustering was implemented on the combined dataset of 8595 cells from control, DM600, and DM1200 cortical organoids that consisted of ~2865 cells per organoid line and ~17,575 reads per cell to identify genotype-specific clusters at 6-months post-differentiation. Uniform Manifold Approximation and Projection (UMAP) for dimension reduction revealed clear differences between control and DM1 organoids. From the expression of established cell-type specific gene markers, smaller sub-clusters were combined to represent four major cell classes: neural progenitors, intermediate neural progenitors, glutamatergic cortical neurons, and glial cells.

overall_design: Gene expression profile at single cell level of cortical organoids differentiated  from myotonic dystrophy 1(DM1200 and Dm600) and Rett Syndrome (MECP2) patient stem cells as well as 2 neurotypical control stem cells (MECP2_KO and MECP2_WT)

first: Wenhao

last: Jin

first: Kathryn

last: Morelli


title: NUF2-HMGA2 axis drives cell proliferation, migration, and invasion in clear cell renal cell carcinoma

city: Shenzhen

first: Xina

last: Xie

state: Guangdong

institute: Shenzhen Second People's Hospital

summary: The relatively poor sensitivity of clear cell renal cell carcinoma (ccRCC) to conventional chemotherapy and radiotherapy makes its treatment challenging. The Ndc80 kinetochore complex component (NUF2) is involved in the development and progression of several cancers. However, its role in ccRCC remains unclear. In an effort to identify novel treatment targets and prognostic markers for ccRCC, we investigated the role of NUF2 in ccRCC progression. We found that the expression of NUF2 was increased in ccRCC tissues and cells, and the elevated NUF2 levels were significantly associated with worse clinicopathological parameters and shorter survival. In addition, NUF2 was an independent prognostic biomarker for ccRCC. Knocking down NUF2 expression affected the proliferation, migration, and invasion of ccRCC cells and the expression of epithelial–mesenchymal transition (EMT)-related markers. Moreover, RNA sequencing and in vitro experiments identified the oncogene high-mobility group AT-hook 2 (HMGA2) as the target factor regulated by NUF2 in ccRCC. Restoring HMGA2 levels ameliorated the inhibitory effects of NUF2 depletion on cell proliferative, migratory, and invasive capacities and recovered the expression of EMT-related markers to basal levels.These results suggest that NUF2 promotes proliferation, migration, and invasion of ccRCC cells, at least partly by regulating HMGA2, and that the NUF2-HMGA2 axis could be an ideal therapeutic target and a promising prognostic indicator for ccRCC.

overall_design: mRNA profiles of  769-P and ACHN cells after transfecting with siRNA-NUF2  for 48 h.

first: Jiatian

last: Lin

first: Xiangling

last: Chen


title: Systematic mutagenesis identifies p52/Tfb2 residues required for XPB/Ssl2 function within TFIIH and genetic interactions with TFB6

city: Boulder

first: Dylan

last: Taatjes

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

summary: TFIIH is an evolutionarily conserved complex that plays central roles in both RNA polymerase II (pol II) transcription and DNA repair. As an integral component of the pol II Pre-Initiation Complex, TFIIH regulates the activity of the pol II enzyme in numerous ways. One of the essential functions of TFIIH resides in its XPB/Ssl2 subunit. XPB/Ssl2 is an ATP-dependent DNA translocase that stimulates promoter opening prior to transcription initiation. Crosslinking-mass spectrometry and cryo-EM results have shown a conserved interaction network involving XPB/Ssl2 and the C-terminal Hub region of the p52/Tfb2 core subunit. Here, we systematically mutagenized the HubA region of Tfb2 and screened for growth phenotypes in a TFB6 deletion background in Saccharomyces cerevisiae. We identified six lethal and twelve conditional mutants. Growth phenotypes of all but three of the conditional mutants were suppressed in the presence of Tfb6, thus identifying a functional interaction between Tfb2 HubA mutants and Tfb6, a protein that dissociates Ssl2 from TFIIH. Biochemical analysis of p52/Tfb2 mutants with severe growth phenotypes revealed defects in XPB/Ssl2 association. Further characterization of these Tfb2 mutant cells revealed defects in induction of Gal genes, and reduced occupancy TFIIH and pol II at Gal gene promoters, suggesting that functional TFIIH is required for proper Pol II recruitment to PICs in vivo. Consistent with recent structural models of TFIIH, our results identify key residues in the p52/Tfb2 HubA domain that are required for stable incorporation of XPB/Ssl2 into TFIIH, and for pol II transcription.

overall_design: Examination of the role mutations in the HubA region of TFb2 play in transcriptional regulation in yeast cells.

first: Jacob

last: Bassett

first: Jenna

last: Rimel

first: Krysta

last: Engel


title: Transcriptome profiling of SW480 cells and cells derived from xenograft tumors from serial transplantation of SW480 cells by RNA-sequencing

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

summary: SW480 is a colorectal cancer cell line. We have shown that cancer cells are characteristic of neural stem cells and neural stemness contributes to cell tumorigenicity. We found that during serial transplantation of SW480 cells into nude mice via subcutaneous injection (in vivo passaging), the cells enhanced their neural stemness, tumorigenicity and pluripotent differentiation potential.

overall_design: SW480 cells (designated as S0) were injected subcutaneously into 6 nude mice at a does of 3x10^6 cells per mouse. 49 days later, tumors were dissected and tumor cells (designated as S1) were cultured in neural stem cell specific serum-free medium (Ndiff227 medium) for 9 days. Cell spheres formed in the serum-free medium were collected and dissociated by trituration. Each 3x10^6 of the cells of the tumors at the first transplantation were injected subcutaneously into nude mice, and tumors were dissected again after 49 days after transplantation. The tumors of the second transplantation (S2) were the cell source for the third transplantation (S3), which was done exactly as the first and second time. SW480 cells cultured in serum-free medium for 9 days (S0), sphere-forming cells from the first (S1), second (S2) and the third (S3) transplantation were subjected to RNA sequencing.

first: Min

last: Zhang


title: Isoleucine and valine correct hepatic lipid processing, reduce liver steatosis and suppress inflammation in obese mice with manifest NASH

city: Rijswijk

first: Eveline

last: Gart

state: Zuid-Holland

address: Van vredenburchweg 659

institute: TNO

summary: Abstract:   Non-alcoholic steatohepatitis (NASH) is associated with a disturbed metabolism in liver and excessive accumulation of ectopic fat. Branched-chain amino acids (BCAAs) may beneficially modulate hepatic lipids, however it remains unclear whether individual BCAAs can attenuate already established NASH and oxidative-inflammatory stress associated with it. Therefore, mice were first put on a run-in fast food diet (FFD) for 26 weeks, these obese mice were then treated with individual BCAAs valine or isoleucine (3% of FFD) for another 12 weeks and compared to FFD controls.  Valine and isoleucine treatment did not affect obesity, dyslipidemia, gut permeability or fecal fatty acid excretion, although significantly reduced hyperinsulinemia compared with FFD. Valine and isoleucine significantly reduced ALT, CK-18M30, and liver steatosis with a particularly pronounced effect on the microvesicular component (-61% by valine and -71% by isoleucine). Hepatic 4-hydroxynonenal (4-HNE) immunoreactivity, a marker for oxidative stress-induced lipid peroxidation, was also significantly decreased. Functional genomics analysis demonstrated that valine and isoleucine upregulated BCAA metabolism, deactivated master regulators of anabolic pathways related to steatosis (e.g. SREBPF1) and activated master regulators of mitochondrial biogenesis (e.g. PPARGC1a) and lipid catabolism (e.g. ACOX1, AMPK). The correction of critical metabolic pathways by valine and isoleucine was accompanied by a significant decrease of liver inflammation, and suppression of many FFD-stimulated cytokine and chemokine pathways including IL-1β, TNFα and CCR2 signaling. In conclusion, the dietary intervention with either valine or isoleucine corrected multiple metabolic processes in liver and reduced steatosis and inflammation with profound effects on oxidative stress and inflammatory pathways.  Methods: Putative antifibrotic effects of butyrate were studied in Ldlr-/-.Leiden mice fed an obesogenic NASH-inducing diet (HFD) containing 2.5% (w/w) butyrate for 38 weeks and compared to an HFD control group. Antifibrotic mechanisms of butyrate were further investigated in TGF-β-stimulated primary human hepatic stellate cells (HSC).   Results: HFD-fed mice developed obesity, insulin resistance, increased levels of plasma leptin, adipose tissue inflammation, gut permeability, dysbiosis and NASH-associated fibrosis. Butyrate corrected hyperinsulinemia, lowered plasma leptin levels and attenuated adipose tissue inflammation, without affecting gut permeability or microbiota composition. Butyrate lowered plasma ALT and CK-18M30 and attenuated hepatic steatosis and inflammation. Butyrate inhibited fibrosis development as demonstrated by decreased hepatic collagen content and Sirius-red-positive area. In TGF-β-stimulated HSC, butyrate dose-dependently reduced collagen deposition and decreased procollagen1α1 and PAI-1 protein expression. Transcriptomic analysis and subsequent pathway and upstream regulator analysis revealed deactivation of specific non-canonical TGF-β signaling pathways RhoA/Rock and PI3K/AKT and other important pro-fibrotic regulators (e.g. YAP/TAZ and MYC) by butyrate, providing a potential rationale for its antifibrotic effects.   Conclusions: Butyrate protects against the development of obesity and insulin resistance-associated NASH and liver fibrosis. These antifibrotic effects are at least in part attributable to a direct effect on collagen production in hepatic stellate cells, as a result of inhibiting non-canonical TGF-β signaling.

overall_design: Mice were first put on a run-in fast food diet (FFD) for 26 weeks, these obese mice were then treated with individual BCAAs valine or isoleucine (3% of FFD) for another 12 weeks and compared to FFD controls. A reference group remained on a low-fat chow diet.

first: Wim

last: van Duyvenvoorde

first: Martien

last: Caspers

first: Nikki

last: van Trigt

first: Aswin

last: Menke

first: Jaap

last: Keijer

first: Kanita

last: Salic

first: Martine

last: Morrison

first: Robert

last: Kleemann


title: Effects of CHCHD10 G58R and S59L mutations on global gene expression in the presence and absence of OMA1

city: Bethesda

first: Mario

middle: K.

last: Shammas

address: 35 Convent Dr.

department: Neurogenetics Branch

institute: National Institute of Neurological Disorders and Stroke, National Institutes of Health

summary:
Differential gene expression in CHCHD10 mutants with OMA1 present or knocked out
This experiment used the Clariom_S_Mouse Microarray from Affymetrix to analyze the effect of CHCHD10 mutations on gene expression, and the effect of congenital OMA1 KO on gene expression in these CHCHD10 mutants.

overall_design: CHCHD10 WT, CHCHD10 G58R/+, or CHCHD10 S59L/+ mouse hearts on the OMA1+/- or OMA1-/- background. 4 mouse hearts per genotype were analyzed, and there were no technical replicates. The G58R OMA1 cohort was 14 weeks old, and the S59L OMA1 cohort was 20 weeks old.

first: Pedro

last: Quirós

first: Carlos

last: Lopez-Otin

first: Derek

last: Narendra


title: Epigenetic inheritance mediates phenotypic evolution in natural populations

city: Norwich

first: Jaemyung

last: Choi

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

summary: Genetic variation is regarded as a prerequisite for evolution. Theoretical models suggest epigenetic information inherited independently of DNA sequence can also enable evolution. However, whether epigenetic inheritance mediates phenotypic evolution in natural populations is unknown. Here we show that natural epigenetic DNA methylation variation in gene bodies regulates genes expression, and thereby influences the natural variation of complex traits in Arabidopsis thaliana. Notably, the effects of methylation variation on phenotypic diversity and gene expression variance are comparable with those of DNA sequence polymorphism. We also identify methylation epialleles in numerous genes associated with environmental conditions in native habitats, suggesting that intragenic methylation facilitates adaptation to fluctuating environments. Our results demonstrate that methylation variation fundamentally shapes phenotypic diversity in natural populations and provides an epigenetic basis for adaptive Darwinian evolution independent of genetic polymorphism.

overall_design: Bisulfite and RNA sequencing was performed using one h1;met1+/- plant and six h1 plants segregated from h1;met1+/- (h1;met1+/+). For bisulfite sequencing, we constructed one bs-seq library per plant. To profile RNA expression, we constructed three RNA-seq libraries per h1;met1+/- plant (3 replicates), and one RNA-seq library for h1;met1+/-.

first: Zaigham

last: Shahzad

first: Jonathan

last: Moore


title: The Bap1-SMN axis in Dpp4+ skeletal muscle mesenchymal cells regulates survival of motor neurons

city: Seoul

first: Kyusang

last: Yoo

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences Department

country: South Korea

institute: Seoul National University

summary: Spinal muscular atrophy (SMA) is a neuromuscular disease caused by mutations in the survival of motor neuron (SMN) gene. Although the primary manifestation of SMA is degeneration of motor neurons in a dying-back manner, deficient SMN intrinsic to motor neurons does not cause severe motor neuron loss, as is the case in SMA mouse models. Thus, the involvement of non-neuronal cells in the pathogenesis of SMA has been suggested. Here, we report that a novel subset of fibro-adipogenic progenitors expressing Dpp4 (Dpp4+ FAPs) is required for the survival of motor neurons, in which BRCA1-associating protein 1 (Bap1) is crucial for the stabilization of SMN by preventing its ubiquitination-dependent degradation. Inactivation of Bap1 in FAPs decreased SMN levels and accompanied degeneration of the neuromuscular junction, leading to dying-back loss of motor neurons and muscle atrophy, reminiscent of SMA pathogenesis. Overexpression of ubiquitination-resistant SMN variant, SMNK186R, in Bap1-null FAPs completely prevented neuromuscular degenerations. In addition, transplantation of Dpp4+ FAPs, but not Dpp4- FAPs, completely rescued neuromuscular defects in the mutant mice. Our data revealed that Bap1-mediated stabilization of SMN in Dpp4+ FAPs is crucial for the survival of motor neurons and provided a new therapeutic approach to treat SMA.

overall_design: Single cell RNA-sequencing analysis was performed using FACS-sorted FAPs from limb muscles of 3-week-old Bap1 conditional knockout (Prx1-Cre; Bap1f/f) mouse and littermate control (Bap1f/f) mouse.

first: Young-yun

last: Kong


title: Single-cell RNA-seq and chromatin accessibility profiling decipher mouse gd T cell heterogeneity in peripheral lymph nodes, spleen and thymus

city: GuangZhou

first: Quanli

last: Yang

address: Huangpu Road

institute: Jinan University

summary: Qur data represent a comprehensive mapping on the transcriptome and chromatin accessibility dynamics of mouse gd T cells, providing a valuable reference for future studies of the application and function of gd T cells

overall_design: Single-cell analyses revealed transcriptome and chromatin accessibility landscape of mouse gd T cells in peripheral lymph node, spleen and thymus

first: Zhenhua

last: Li

first: Guangchao

last: Cao


title: Whole genome bisulfite sequencing data of Russian wheat aphid biotypes US-RWA1 (co-fed), US-RWA2 (co-fed) and US-RWA2 (isolated)

city: Stellenbosch

first: Anna-Maria

last: Oberholster

state: Western Cape

address: JC Smuts Building, Van der Bijl Street

department: Genetics

country: South Africa

institute: University of Stellenbosch

summary: The aim for this study was to compare the differences in the methylome of three Russian wheat aphid populations that differ in virulence and bacterial load. Differences in the methylome of US Russian wheat aphid biotype 2 (US-RWA2) that have undergone removal of their phytobiomes through isolation of newly born nymphs from their mothers compared to nymphs who stayed in close proximity to their progenitors. US-RWA1 is the least virulent biotype and US-RWA2 is the most virulent biotype. The isolated US-RWA2 population (with a reduced bacterial load) has been shown to be less virulent than the co-fed population (Luna et al., 2018).  The corresponding two methylomes were then compared to the methylome of US Russian wheat aphid biotype 1 (US-RWA1 is less virulent than US-RWA2) to ascertain the contribution (or lack thereof) of the phytobiome in regards to the increased/decreased virulence of phytobiome present and absent aphids. We investigated the overall, genic, intergenic, exonic and intronic methylation - as well as genic and intergenic hemimethylation -all three available contexts ( CpG, CHG and CHH) through use of the Bismark pipeline. These findings were used to ascertain to what effect the phytobiome (bacterial load) had on methylation within the US Russian wheat aphid biotypes.

overall_design: Compare the methylation from three pooled sample (of 100 aphids) each of three Russian wheat aphid population (US-RWA1 (co-fed); US-RWA2 (co-fed); US-RWA2 (isolated))

first: Nicholas

last: de Jager

first: Pieter

last: du Preez

first: N

last: Burger

last: Botha-Oberholster


title: Transcriptome profiling of NE-4C cells and NE-4C cells with knockdown of Setdb1 by RNA-sequencing

first: Ying

summary: NE-4C is a mouse neural stem cell line used for study of neuronal differentiation. Setdb1 is an epigenetic modification factor responsible for catalyzing the histone modification H3K9me3. Transcription of Setdb1 gene is enriched in embryonic neural cells during vertebrate embryogenesis. Setdb1 is upregulated in cancer cells and promotes cancers. We found that knockdown of Setdb1 in NE-4C cells led to neuronal differentiation.

overall_design: Setdb1 was knocked down with specific short-hairpin RNA (shSetdb1) in NE-4C cells using lentiviral infection (NE4C_B), while cells infected with virus carrying only the empty vector was used as control (NE4C_A). Knockdown cells showed neuronal differentiation phenotype. Control cells and knockdown cells were cultured in MEM supplemented with 1% MEM non-essential amino acids, 1% Glutamax and 10% FBS, at 37°C plus 5% CO2 for 5 days, and then collected and subjected to RNA-sequencing.

first: Min

last: Zhang


title: Identification and analysis of plasmin-related miRNA in Sipunculus nudus

city: QuanZhou

first: LuJie

last: Lu

state: FuJian

address: Chenghua north road

institute: HuaQiao University

summary:
Purpose:Sipunculus nudus is a marine organism with high application value, and the fibrinolytic enzyme (SNFE) extracted from the visceral homogenate has been proved to have an antithrombotic effect by experiments. MicroRNAs(MiRNAs) play an important role in the molecular mechanisms related to plasmin. However, the research on plasmin-related miRNA of Sipunculus nudus is relatively rare.
Methods:In this paper, high-throughput sequencing technology was used to sequence and analyze the small RNA and transcriptome of Sipunculus nudus.
Conclusion:After data analysis, 198 known miRNAs were identified and 46 new miRNAs were predicted, followed by statistical analysis of miRNA base preference. At the same time, 76 miRNAs differentially expressed in different tissues were found, and a total of 76 known and new miRNAs were predicted for target genes, from which 7,161 candidate target genes were obtained. In addition, we found that six plasmin-related target genes were significantly annotated with 28 GO terms, and three plasmin-related target genes were rich in eight KEGG biological pathways. Finally, four joint regulatory networks including four candidate target genes, 32 differentially expressed miRNA and related proteins were constructed according to the four related species, and it was found that there existed interactions between the candidate target genes Cluster-15745.8440 and Cluster-3821.0 with unclear mechanisms.This study will provide a reference for in-depth exploration of the regulatory relationship between the plasmin-related genes and miRNA in Sipunculus nudus and understanding the molecular mechanisms related to plasmin in Sipunculus nudus.

overall_design: High-throughput sequencing technology was used to sequence and analyze the small RNA and transcriptome of Sipunculus nudus

first: Jie

first: Ming

middle: Q

last: Tang


title: RNA-seq of intestinal epithelial cells isolated from DSS colitis model mice

city: Shanghai

first: Qian

last: Cai

address: No.130 Dongan road

department: Immunology

institute: Fudan University

summary: In the present study, we demonstrated that mice deficient in chemerin or IEC-specific CMKLR1 expression were highly susceptible to DSS-induced colitis and subsequent tumorigenesis, which was reversed by suppressing colonic neutrophilic inflammation using CXCR2 inhibitor. Surprisingly, we found that lack of the Chemerin-CMKLR1 signaling specifically reduced colonic epithelial expression of lactoperoxidase (LPO), an epithelial peroxidase which could utilize H2O2 to oxidase thiocyanates to antibiotic compound (Bafort et al., 2014). Importantly, we demonstrated that impaired epithelial LPO expression accounted for outgrowth of potentially pathogenic Gram-negative bacteria following epithelial injury, which led to overproduction of CXCL1/2 and pathological neutrophilic inflammation in mice with epithelial Chemerin-CMKLR1 signaling deficiency. Finally, lack of epithelial Chemerin-CMKLR1 signaling impaired early host defense against enteric bacteria, which was reversed by LPO supplementation. Taken together, our study uncovers a critical role of epithelial Chemerin-CMKLR1 signaling in restricting pathological colonic neutrophilia via potentiating LPO-mediated epithelial innate defense, thereby rendering protection against microbiota-driven colitis and tumorigenesis.

overall_design: 18 samples in total was analyzed, including IEC RNA-seq data from DSS treated WT and Rarres2-/- mice at 0,2, and 7 days post DSS, there are 3 replicated samples in each group.

first: Yuli

last: Lin

first: Rui

last: He


title: Effects of acute OMA1 knockdown on global gene expression in CHCHD10 G58R mutants

first: Mario

last: Shammas

state: MD

summary:
Differential gene expression in CHCHD10 G58R mouse hearts treated with nontargeting or OMA1-targeting antisense oligomers (ASOs) provided by Ionis Pharmaceuticals (Carlsbad, CA)
This experiment used the Clariom_S_Mouse Microarray from Affymetrix to analyze the effect of acute OMA1 KD on gene expression in CHCHD10 G58R mouse hearts.

overall_design: OMA1+/- C10 G58R mice were treated with a nontargeting ASO or one of 2 OMA1-targeting ASOs (OMA1 ASO1, OMA1 ASO2). There were no technical replicates. Mice were 33-weeks-old.

first: Andrew

last: Powers

first: Pedro

last: Quirós

first: Carlos

last: Lopez-Otin

first: Derek

last: Narendra


title: Transcriptome profiling of HCT116 cells and HCT116 cells with knockdown of SETDB1 by RNA-sequencing

last: Cao

summary: HCT116 is a colorectal cancer cell line. SETDB1 is an epigenetic modification factor responsible for catalyzing the histone modification H3K9me3. Transcription of SETDB1 gene is enriched in embryonic neural cells during vertebrate embryogenesis. SETDB1 is upregulated in cancer cells and promotes cancers. We found that knockdown of SETDB1 in HCT116 cells led to a neuronal-like differentiation phenotype.

overall_design: SETDB1 was knocked down with specific short-hairpin RNA (shSETDB1) in HCT116 cells using lentiviral infection (HCT116_B), while cells infected with virus carrying only the empty vector was used as control (HCT116_A). Knockdown and control cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 for 5 days. Control cells and knockdown cells were then collected and subjected to RNA-sequencing.


title: Transcriptome profiling of five mixed tissues for juvenile Eriocheir sinensis

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

summary: The transcriptome profiling five tissues of juvenile Eriocheir sinensis, including gill, muscle, thoracic ganglion, eyestalk and hepatopancreas, were sequenced to get the basic dataset for constructed a genome-scale metabolic network model for E. sinensis. The model was used to predict the optimal nutrient requirements of E. sinensis in feed and suggestions for feed improvement were put forward based on the simulation results.

overall_design: Five tissues of crabs, including gill, muscle, thoracic ganglion, eyestalk and hepatopancreas, were collected.Total RNA from mixed E. sinensis tissues was sequenced with the Illumina high-throughput sequencing technology by Novogene Inc.The sequenced unigenes were subsequently aligned against the NR, Nt and PFAM databases. GO and KO annotations was obtained by Blast2GO and KAAS (KEGG Automatic Annotation Server).

first: Jingjing

last: Li

first: Jinsheng

last: Sun


title: Single cell analysis reveals the molecular signaling and cellular composition of the regenerating Hydra head

city: Peoria

first: Aide

last: Macias-Khan

state: Arizona

address: 9565 W Patrick Ln

institute: UC Irvine

summary: We use single cell RNA-seq from a regeneration time course to identify the molecular and cellular features of Hydra head regeneration

overall_design: We bisected Hydra and allowed them to regenerate for 0, 4, and 12 hours. We also extracted RNA from the hypostome tissue.

last: Macias-Munoz

first: Lisa

last: Mesrop

first: Heidi

last: Liang

first: Ali

last: Mortazavi


title: Bulk and single cell profiling of the transcriptional response to Trichostatin A and Valproic Acid using CAGE

city: Yokohama

middle: Tae-Jun

last: Kwon

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

institute: RIKEN

summary: To better understand the transcriptomic changes that occur in response to HDACi treatment, we perform CAGE on dermal fibroblasts, HepG2, and MCF7 cells after TSA or VPA treatment, at both bulk and single cell level. We make detailed annotation of the identified coding and noncoding RNA transcription start sites and enhancers, in addition to their expression levels.

overall_design: Overall, 3 cell types are subjected to 3 different treatments, including control, TSA, and VPA. For bulk CAGE, 3 replicates of each cell type x treatment were made. For C1 CAGE,

middle: T

first: Takahiro

last: Arakawa

first: Satoshi

last: Takizawa

first: Efthymios

last: Motakis

first: Bogumil

last: Kaczkowski

first: Masaaki

last: Furuno

first: Harukazu

last: Suzuki

first: Erik

last: Arner


title: Dynamic profiling of histone Kcr and Kla during neural differentiation in P19 embryonal carcinoma cells

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

summary: To gain a deeper insight into dynamic changes of histone lysine crotonylation and lactylation during embryonic neurogenesis, ChIP-seq, ATAC-seq and RNA-seq were performed to analyze the genome-wide changes of histone Kcr and Kla in the P19 embryonal carcinoma cells.

overall_design: ChIP-seq, ATAC-seq and RNA-seq were both performed with two biological replicates, and sequenced on Illumina NovaSeq 6000 platform.

first: Shang

middle: K

last: Dai


title: High-dimensional single cell analysis of T cells infiltrating human intrahepatic cholangiocarcinoma [RNA-Seq]

city: Rozzano

first: Alberto

last: Termanini

state: MI

address: Via Manzoni, 113

country: Italy

institute: Istituto Clinico Humanitas

summary: In tumors, CD4+ T regulatory cells (Tregs), a specialized subtype of cells indispensable for maintaining immune homeostasis and tolerance, inhibit anti-tumor immunity and response to immunotherapy. Selective targeting of the hyperactive Tregs promote tumor regression and synergizes with checkpoint blockade without severe, systemic autoimmunity, that is otherwise observed with non-specific Treg depletion. However, is poorly defined how Treg hyper-activation regulated in the tumor microenvironment. We found that mesenchyme homeobox-1 (MEOX1) a transcription factor with an important role in skeleton formation during development, is specifically overexpressed by intrahepatic cholangiocarcinoma infiltrating Treg compared to Treg cells present in the peritumoral tissue. Integration of transcriptomic data revealed that MEOX1 positively regulates several molecules involved in immunosuppression, including CTLA-4, ICOS and IL10, as well as a tumor Treg-specific signature associated with disease progression. Thus, interfering with the MEOX1-dependent molecular program may represent a novel immunotherapeutic approach capable to block immunosuppression in the tumor microenvironment without inducing autoimmunity in peripheral tissues.

overall_design: Transcriptional profiling of human activated Tregs overexpressing MEOX1.

first: Giorgia

last: Alvisi

first: Cristiana

last: Soldani

first: Federica

last: Portale

first: Roberta

last: Carriero

first: Karolina

last: Pilipow

first: Guido

last: Costa

first: Michela

last: Polidoro

first: Barbara

last: Franceschini

first: Ines

last: Malenica

first: Simone

last: Puccio

first: Veronica

last: Lise

first: Giovanni

last: Galletti

last: Zanon

first: Federico

last: Colombo

first: Gabriele

last: De Simone

first: Michele

last: Tufano

first: Alessio

last: Aghemo

first: Luca

last: Di Tommaso

first: Clelia

last: Peano

first: Javier

last: Cibella

first: Matteo

last: Iannacone

first: Rahul

last: Roychoudhuri

first: Teresa

last: Manzo

last: Donadon

last: Torzilli

first: Paolo

last: Kunderfranco

first: Diletta

last: Di Mitri

first: Enrico

last: Lugli

first: Ana

last: Lleo


title: Hyperactivated Tregs abundantly infiltrate human intrahepatic cholangiocarcinoma and are controlled by transcription factor MEOX1

first: Alberto

last: Termanini

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: High-dimensional single cell analysis of T cells infiltrating human intrahepatic cholangiocarcinoma [scRNA-Seq]

overall_design: A total of twelve samples; two conditions (normal and tumor) matched from six patients.

first: Giorgia

last: Alvisi

first: Cristiana

last: Soldani

first: Federica

last: Portale

first: Roberta

last: Carriero

first: Karolina

last: Pilipow

first: Guido

last: Costa

first: Michela

last: Polidoro

first: Barbara

last: Franceschini

first: Ines

last: Malenica

first: Simone

last: Puccio

first: Veronica

last: Lise

last: Galletti

last: Zanon

last: Colombo


title: Intercellular heterogeneity of the p53 transcriptional response to oncogenic stress

city: New Haven

first: Atreyo

last: Pal

state: CT

address: 333 Cedar St, SHMI I 120

institute: Yale University

summary: We use scRNA-seq to investigate the intercellular heterogeneity of the p53 transcriptional response to oncogenic stress. Comparisons of the transcriptomes of cells collected in the absence and in the presence of p53 activation revealed the expected upregulation of direct p53 target genes as well as the downregulation of E2F- and Myc-target genes, previously indirectly linked to the p53 pathway. Strikingly, the majority of previously defined p53 core target genes were induced in only a fraction of the cells. In addition, we identified two distinct subsets of cells within the p53-responsive group, differentiated by their expression of proliferative and metabolic signatures. While one group was characterized by gene expression changes consistent with a robust halt in cell cycle progression, the second group exhibited a strong activation of genes linked to oxidative phosphorylation. Inhibition of oxidative phosphorylation impaired the ability of cells to undergo p53-induced senescence, highlighting the importance of this pathway in mediating p53 tumor suppressive functions.

overall_design: scRNA-seq profiles of lung adenocarcinoma (LA2) cells from the p53-restorable K-rasLA2; p53LSL/LSL; Rosa26-CreERT2 (KPR)  mouse model, untreated or treated with 4-hydroxytamoxifen (4-OHT) for 16h

first: Nadya

last: Dimitrova

first: Elena

last: Martinez-Terroba


title: Dynamic profiling of histone Kcr and Kla during neural differentiation in vivo

first: Dai

last: Kun

summary: To gain a deeper insight into dynamic changes of histone lysine crotonylation and lactylation during embryonic neurogenesis, ChIP-seq, ATAC-seq and RNA-seq were performed to analyze the genome-wide changes of histone Kcr and Kla in the developing telencephalon.

first: Shang-Kun

last: Dai


title: Impact of brequinar treatment on gene expression in bone marrow progenitors of tumor-bearing mice

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Immune checkpoint inhibitors (ICIs) have transformed the therapeutic landscape in oncology; however, ICIs are effective in subsets of patients. A major limitation of their efficacy is tumor-driven immune suppression, and one key mechanism is the ‘biogenesis’ of myeloid-derived suppressor cells (MDSCs). A fundamental gap in MDSC biology is the dearth of approaches that target their biogenesis. We hypothesized that targeting MDSC biogenesis will mitigate MDSC burden and bolster responses to ICIs. We focused on a class of agents, dihydroorotate dehydrogenase (DHODH) inhibitors, recently found to restore terminal differentiation of leukemic myeloid progenitors and is in clinical trials of AML. One such DHODH inhibitor is brequinar. Using preclinical models of mammary cancer that elicit robust MDSC responses, we demonstrated that brequinar suppressed MDSC biogenesis, enhancing the antitumor and anti-metastatic activity of PD-1-based ICI therapy. In this single-cell RNA transcriptomics study, we sought to determine the impact of brequinar treatment of tumor-bearing mice on altering gene expression in bone marrow myeloid progenitors.  Thus, this cutting-edge molecular approach enabled us to test the hypothesis that brequinar acted in the bone marrow at a qualitative level to mitigate MDSC biogenesis.

overall_design: Bone marrow cells enriched for cKit+ progenitors were isolated from 3 separate mice each from the following groups: 1) non-tumor-bearing controls, 2) 4T1 tumor-bearing mice treated with the vehicle control and 3) 4T1 tumor-bearing mice treated with brequinar. Non-tumor-bearing samples served as the reference control

first: Sean

last: Colligan

first: Scott

last: Abrams

first: Michael

last: Nemeth

first: Prishant

last: Singh

first: Elliot

last: Kramer


title: Glutamine synthetase gene glnA plays an important role in curdlan biosynthesis of Agrobacterium sp. CGMCC 11546

first: Deming

last: Jiang

address: No. 500, Dongchuan Road, Minhang District, Shanghai

institute: East China Normal University

summary:
Purpose： The goal of this study is compare the effect of glnA gene in curdlan synthesis in Agrobacterium  sp. CGMCC 11546.
methods:  The transcriptional and metabolomics analysis the function of glnA in Agrobacterium  sp. CGMCC 11546.
Results: The transcriptional and metabolomics showed that the decrease of curdlan production in the ΔglnA mutants may be caused by the insufficient supply of energy ATP
conclusion: glnA play an important role in curdlan synthesis in Agrobacterium  sp. CGMCC 11546

overall_design: The total RNA of each sample from the wild type strain and the gene deletion mutants after 24 hours fermentation, samples from glnA deletion mutant named glnA-1, glnA-2 and glnA-3; three biological repeats. samples from the wild type strain named WT-1, WT-2 and WT-3; three biological repeats

first: Hongliang

last: Gao


title: Adipocyte Specific Tribbles1 Regulates Plasma Adiponectin and Plasma Lipids in Mice

city: New York

first: Robert

last: Bauer

department: Medicine

institute: Columbia University Irving Medical Center

summary: The goal of this study is to understand the role of adipocyte-specific Trib1 in adiponectin and plasma lipid regulation. Here, we report that adipocyte-specific Trib1 knockout mice (Trib1_ASKO) have increased plasma adiponectin levels and decreased plasma cholesterol and triglycerides. We demonstrate that loss of Trib1 increases adipocyte production and secretion of adiponectin independent of the known TRIB1 function of regulating proteasomal degradation. RNA-seq analysis of adipocytes and livers from Trib1_ASKO mice suggests that alterations in adipocyte function underlie the plasma lipid changes observed in these mice. Secretomics and RNA-seq analysis revealed that Trib1_ASKO mice have increased production of Lpl and decreased production of Angptl4 in adipose tissue, and fluorescent substrate assays confirm an increase in adipose tissue Lpl activity, which likely underlies the observed triglyceride phenotype. In summary, we demonstrate here a novel role for adipocyte Trib1 in regulating plasma adiponectin, total cholesterol, and triglycerides in mice, confirming previous genetic associations observed in humans and providing a novel avenue through which Trib1 regulates plasma lipids and coronary artery disease.

overall_design: Individual adipocyte and hepatocyte mRNA profiles from 4 male wild-type and 4 male adipocyte-specific Trib1 knockout mice (16 samples overall)

first: Elizabeth

middle: E

last: Ha


title: phbC and glnA play important roles in curdlan biosynthesis of Agrobacterium sp. CGMCC 11546


title: phbC plays an important role in curdlan biosynthesis of Agrobacterium sp. CGMCC 11546

summary:
Purpose： The goal of this study is compare the effect of phbC gene in curdlan synthesis in Agrobacterium  sp. CGMCC 11546.
methods:  The transcriptional and metabolomics analysis the function of phbC in Agrobacterium  sp. CGMCC 11546.
Results:The transcriptional and metabolomics showed that the decrease of curdlan production in the ΔphbC mutants may be caused by the insufficient supply of energy ATP
conclusion:phbC play an important role in curdlan synthesis in Agrobacterium  sp. CGMCC 11546

overall_design: The total RNA of each sample from the wild type strain and the gene deletion mutants after 24 hours fermentation, samples from phbC deletion mutant named phbC-1, phbC-2 and phbC-3; three biological repeats. samples from the wild type strain named WT-1, WT-2 and WT-3; three biological repeats


title: Gene expression analysis of mulberry (Morus atropurpurea) response to cadmium stress

city: Guangzhou

first: fanwei

last: dai

address: The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences

summary: Mulberry (Morus atropurpurea) is an important economic woody tree with rapid growth rate and large biomass, which had great potential for heavy metals remediation. To further understand the mechanisms involved in cadmium accumulation and detoxification in mulberry, we carried out a transcriptomic study to get insights into the molecular mechanisms of the mulberry response to cadmium stress using RNA-seq analysis with BGISEQ-500.

overall_design: mRNA profiles of CMulberry fruit stressed with different concentrations of CdCl2 (5, 10, 20mM).

first: Fanwei

first: Zhenjiang

first: Guoqing

last: Luo

first: Cuiming

last: Tang


title: miRNA expression profiling in cervical cancer cells following emodin treatment

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Cervical cancer is one of the most common cancers in women worldwide. The role of HPV in cervical cancer is well studied, however, the underlying mechanism promoting cervical tumorigenesis is still not fully understood. Recently, emodin was shown to induce cell cycle arrest, induction of differentiation, downregulation of TGF β signaling pathway and apoptosis in cervical cancer cell lines. Further, recent studies have shown the role of miRNAs in mediating abnormal regulatory mechanisms leading to the pathogenesis of cervical cancer and large scale miRNA profiling studies have examined the use of miRNAs as cervical cancer diagnostic markers. However, to date, there is no study being performed to analyze the changes in miRNAs following emodin treatment to determine whether emodin mediates its effects by regulating the expression of miRNAs. Therefore, the aim of the current study is to perform miRNA profiling in cervical cancer cells following emodin treatment and to analyze the roles of differentially expressed miRNAs in regulating the pathogenesis and treatment of cervical cancer.

overall_design: miRNA profiling was performed at 24 h following emodin treatment (n=2) to SiHa cervical cancer cells.  DMSO (0.4%) was used as a vehicle control (n=3) for all the experiments. Agilent one-color experiment,Organism: Homo sapiens ,Agilent Human miRNA 8x60k Arrays AMADID: 070156

first: Priyanka

last: Samji

first: Akshayaa

last: Ganesh

first: Vidya

last: Warrier

first: Manoj

last: Rajendran

first: D

last: Karunagaran


title: B Cells Polarize Pathogenic Inflammatory T Helper Subsets through ICOSL-Dependent Glycolysis

first: Dongming

last: Kuang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

summary:
B cells constitute abundant cellular components in inflamed human tissues, but their role in pathogenesis of inflammatory T helper (Th) subsets is still unclear. Here, we demonstrate that B cells, particularly resting naïve B cells, have a previously unrecognized helper function that is involved in shaping the metabolic process and subsequent inflammatory differentiation of T-cell-receptor-primed Th cells. ICOS/ICOSL axis-mediated glucose incorporation and utilization were crucial for inflammatory Th subset induction by B cells, and activation of mTOR was critical for T cell glycolysis in this process. Consistently, upon encountering ICOSL+ B cells, activated effector memory Th cells from patients with rheumatoid arthritis or systemic lupus erythematosus spontaneously differentiated into inflammatory Th subsets. Immunotherapy using an anti-CD20 antibody that specifically depleted B cells in patients with rheumatoid arthritis efficiently abrogated the capabilities of memory Th cells to incorporate and utilize glucose, thereby impairing the pathogenic differentiation of inflammatory Th subsets.
To examine the metabolic process of Th cells after interacting with autologous B cells, we applied RNA-sequencing to analyze their transcriptional profiles.

overall_design: T cells, cultured in medium or with B cells for 7 days in the presence of CD3-cross-linking Abs, were sorted for RNA-sequencing.

first: Qiu

last: Zeng


title: Comparison of Transcriptional Signatures of Three Staphylococcal Superantigenic Toxins in Human Epidermal Melanocytes

city: Silver Spring

first: Aarti

last: Gautam

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: Staphylococcus aureus, a gram-positive bacterium, causes food poisoning and toxic shock syndrome through the production of superantigenic toxins known as Staphylococcal enterotoxins serotypes A-J (SEA, SEB, etc.) and toxic shock syndrome toxin-1 (TSST-1). A subset of these toxins have been classified as potential biothreat agents. The chronology of molecular events that could potentially characterize superantigenic toxicity and early pathogenesis is not well understood.  The focus of this study was to determine the distinct and shared mechanisms of response to three toxins of the superantigenic family, namely SEA, SEB and TSST-1. Since skin functions as the front line of the host’s defense mechanism, melanocytes were selected for the study and treated with 25 µg/mL of one of these three toxins. Cells were collected after treatment for six different time periods, ranging from 0.5 h to 48 h. Total RNA was investigated using gene expression microarrays containing approximately 50,000 probes, and a subset of the results were validated using NanoString assays. Transcriptomic expression data indicated that each of these three toxins had a unique longitudinal trajectory. In particular, the gene expression profiles of SEB post-exposure was very distinct from those for SEA and TSST-1 superantigens. All three superantigens showed enriched biological networks related to necrosis, skin disorders, and inflammation. The three superantigens share some similarities in acting on the mechanisms underlying apoptosis, innate immunity, and other biological processes. Pathways related to innate immunity, such as the patterns of cytokine production and acute-phase response, showed toxin-specific regulation. The differentially regulated networks can be logical targets for early therapeutic intervention and can potentially serve as early diagnostic markers for superantigen-induced toxicity.

overall_design: Normal Human Epidermal Melanocytes (NHEM) was cultured and treated with SEA, SEB, and TSST-1 toxins at a final concentration of 200 ng/ml (25ug stock). Three comparitive groups i.e., melanocytes treated by SEA, SEB and TSST-1 for six different durations i.e., 0.5, 2, 6, 12, 24, 48 hours post-exposure. As controls, untreated melanocytes were grown in parallel and harvested at the same time points.

first: Seshamalini

last: Srinivasan

first: Nabarun

last: Chakraborty

first: Ruoting

last: Yang

first: Stacy

last: Ann-Miller

first: Abdulnaser

last: Alkhalil

first: Lauren

last: Moffatt

first: Bonnie

last: Carney

first: Marti

last: Jett

first: Jeffrey

middle: W

last: Shupp

first: Rasha

last: Hammamieh


title: miRNA expression profiling in cervical cancer cells following curcumin treatment

first: Genotypic

last: technology

summary: Cervical cancer is the second most common cancer in women worldwide. In addition to the important role played by HPV, the underlying mechanism promoting cervical tumorigenesis is complex and involves deregulation of key signaling pathways. Recently, role of miRNA mediated abnormal regulatory mechanisms is implicated in the pathogenesis of cervical cancer. Micro RNAs are regulatory, non‐coding RNAs about 21–23 nucleotides in length and effects the expression of a number of genes at the post‐transcriptional level. For the past few decades, role of curcumin in inhibiting the growth of cervical cancer and increasing the chemo and radio- sensistivity has been studied extensively. Interestingly, curcumin was shown to downregulate NF-κB, Wnt/β-catenin, TGF‐β and various other signaling pathways in cervical cancer cells. Although, a number of microarray studies have examined the use of miRNAs as cancer diagnostic markers, the regulation of miRNAs upon treatment with curcumin in cervical cancer cells has not been studied. The current study is aimed to perform miRNA profiling in cervical cancer cells following curcumin treatment and to study the role of miRNAs in regulating the different signaling pathways.

overall_design: miRNA profiling was performed at 24 h following curcumin treatment (n=3) to SiHa cervical cancer cells.  DMSO (0.4%) was used as a vehicle control (n=3) for all the experiments.  Agilent one-color experiment,Organism: Homo sapiens ,Agilent Human miRNA 8x60k Arrays AMADID: 070156

first: Priyanka

last: Samji

first: Akshayaa

last: Ganesh


title: TWIST1 is required for HSC maintenance under steady state and stress condition by inhibiting mitochondrial metabolism gene program

city: TianJin

first: Xiao Tong

last: Ma

state: TianJin

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

summary: RNA-seq and ATAC-seq were performed to determine possible downstream molecular mechamisms and the changes in chromatin accessibility in long-term hematopoietic stem cell when TWIST1 was absent following irradiation stress. We found that mitochondrial metabolism pathway was strongly turned on in the Twist1-deficient LT-HSCs upon irradiation stress.

overall_design: a) RNA-seq in Twist1-deleted and control  LT-HSCs following irradiation treatment; b) ATAC-seq in Twist1-deleted and control  LT-HSCs following irradiation treatment; c) RNA-seq in Twist1-deleted  and control LT-HSCs under steady state.

first: Xiaotong

last: Wang


title: Establishment of radioresistant U87MG glioblastoma cell line

status: Public on Jun 29 2022

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

institute: Pusan National University

summary: To explore factors contributing to radioresistance in GBM, we established GBM radioresistant cell line using U87MG human GBM cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U87MG cell liness and its radioresistant cell lines.

first: Hyunkoo

last: Kang

first: Kyeongmin

last: Kim

first: Haksoo

last: Lee


title: Decreased synapse-associated proteins are associated with the onset of epileptic memory impairment in endothelial CDK5-deficient mice

city: Nanjing

first: chen

last: xiang

address: chunhua street

institute: nanjing medical university

summary: Epilepsy accompanying cognitive impairment has been verified by accumulating clinical cases, but the mechanism remains unclear. Here, we discover that persistent epileptic seizures impaired the ability of mice to recognize either novel objects or novel locations at 6 months old but not at 2 months old by utilizing the spontaneous epilepsy model of Cdh5-CreERT2; CDK5f/f mice after tamoxifen treatment. To the best of our knowledge, this is the first report that the levels of synapse-related proteins, such as NMDA receptors (NR1 and NR2B), PSD95, and phosphorylation of CaMKII, are progressively decreased during epileptic seizures in the hippocampus of spontaneous epileptic mice. Notably, we also found that valproate (VPA) augment synapse-related genes and protein expression and ameliorate progressive cognitive impairment. Hence, our study describes a mechanism of cognitive deficits in epilepsy and identifies new effects of VPA on synapses, which provides new insights into preventive or therapeutic interventions for epileptic cognitive deficits.

overall_design: Examination of CDK5f/f mice and Cdh5-CreERT2;CDK5f/f mice hiappocampus CA1 region different genes expression

first: zhengmao

last: li

first: xiuxiu

last: liu

first: xiang

last: chen


title: Activated-memory T cells influence naïve T cell fate: A non-cytotoxic function of human CD8 T cells

city: Pittsburgh

first: Khodor

middle: I

last: Abou-Daya

state: PA

address: 200 Lothrop Street

department: Surgery

institute: Starzl Transplantation Institute

summary: T cells are endowed with the capacity to sense their environment including other T cells 48 around them. They do so to set their numbers and activation thresholds. This form of regulation has been well-studied within a given T cell population – i.e., within the naïve or memory pool; however, less is known about the cross-talk between T cell subsets. Here, we tested whether memory T cells interact with and influence surrounding naïve T cells. We report that human naïve CD8 T cells (TN) undergo phenotypic and transcriptional changes in the presence of autologous activated-memory CD8 T cells (TMem). Following in vitro co-culture with activated central memory cells (TCM), ~3% of the TN acquired activation/memory canonical markers (CD45RO and CD95) in an MHC-I dependent-fashion. Using scRNA-seq, we also observed that ~3% of the TN acquired an activated/memory signature, while ~84% developed a unique activated transcriptional profile hybrid between naïve and activated memory. Pseudotime trajectory analysis provided further evidence that TN with an activated/memory or hybrid phenotype were derived from TN. Our data reveal a non-cytotoxic function of TMem with potential to activate autologous TN into the activated/memory pool. These findings may have implications for host-protection and autoimmunity that arises after vaccination, infection or transplantation

overall_design: CD8 T cells subsets were sorted from one healthy donor pbmcs. Activated TCM cells (150K) were labeled with CFSE and co-cultured with resting CTV labeled naïve CD8 T cells (50K) at a 3:1 ratio respectively for 7 days. As for controls, isolated naïve T cells or activated TCM were cultured separately in similar conditions. Thereafter, live naïve and activated TCM cells were sorted, while only CTV+ cells (which included both CTV+ CD45RO- and CD45RO+ subpopulations) were sorted following co-culture of naïve with activated TCM cells. Each sorted sample was then labelled with cell hashing antibodies (Totalseq-C, Biolegend) for later demultiplexing, then pooled together and sequenced in one flow cell.

first: Hossam

middle: A

last: Abdelsamed


title: Gene expression profiles of electrically pulse-stimulated human myotubes

city: Oslo

first: G. Hege

last: Thoresen

address: Sem Sælands vei 3

department: Section for Pharmacology and Pharmaceutical Biosciences

country: Norway

institute: University of Oslo

summary: In this study, we aimed to investigate transcriptomic profile changes in human skeletal muscle cells that are triggered by a well-established in vitro model of exercise using electrical pulse stimulation (EPS).

overall_design: Skeletal muscle cells isolated from muscle biopsies from seven donors were used. The cells from each donor were then exposed to prolonged EPS (i.e. 10 V, 2 ms, 0.1 Hz for 24 h), and non-stimulated cells from the same donor were used as a control.

first: Abel

middle: M

last: Mengeste

first: Arild

middle: C

last: Rustan

first: G


title: Plasma exosomes miRNAs high-throughput sequencing in patients after STEMI 3-6 months

first: Yang

last: yanqi

address: YanjiangXi Road 107

institute: Sun Yat-Sen Memorial Hospital

summary:
ST-segment elevated myocardial infarction (STEMI) is one of the most severe forms of cardiovascular heart diseases. In the present study, we aim to describe differential expressed plasma exosome-miRNAs in patients with post-STEMI 3-6 months. Methods: Consecutive patients with ages from 40 to 80 years and 25 males among them 3-6 months after STEMI (n=11) were compared to sex-matched healthy control (n=10). The mean age of the patient was 64.71±10.40 years and 89.2% were male. Compared to the healthy control group, the plasma exosome-miRNAs were assessed by using microarray assay (IIIumnia Hiseq 2500). Profile of plasma exosome-miRNAs related to heart diseases was established both in the patient and control groups. The specificity of the lowest expressed exosome-miRNAs for all subjects was evaluated by using a quantitative real-time polymerase chain (qPCR).
plasma exosomes miRNAs were obtained from STEMI patients after 3-6 months and healthy subjects

overall_design: we explored the plasma exosomes miRNAs profile of 10 STEMI after 3-6 months, and 10 healthy individuals by RNA sequencing analyses to investigate its features and potential targets for postponing myocardium remodeling.

last: Yanqi

first: Guanrui

last: Cong


title: Analysis of Wild Type and Siah2 KO time series liver transcriptome from male and female mice

city: Atlanta

first: Jason

last: DeBruyne

state: GA

address: 720 Westview Dr, Research Wing 315

department: Pharmacology & Toxicology

institute: Morehouse School of Medicine

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Treatment of MCF-7 cells with TRAIL and Smac mimetic (LCL-161) [array]

city: Lund

first: Christer

last: Larsson

address: Medicon Village, Bldg 404:C3

department: Laboratory Medicine

country: Sweden

institute: Lund university

summary: The aim was to identify changes in gene expression in MCF-7 cells induced by a combination of TRAIL and LCL-161. Treated samples and control samples were collected after 24 h of treatment and after 96 h of treatment followed by a three-day period in normal medium.

overall_design: Four treatments with three biological replicates. The groups were C24 (control cells 24 h) LT24 (cells treated with LCL-161 and TRAIL for 24 h, C963 (control cells grown for 96 h in regular medium followed by a change of medium and culture for additional three days), and LT963 (cells treated with LCL-161 and TRAIL for 96 h followed by growth for three days in regular medium).

first: Christian

last: Holmgren

first: Victoria

last: Granqvist


title: EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma [CUT&RUN]

status: Public on Jun 28 2022

city: Boston

first: April

last: Apfelbaum

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-farber Cancer Institute

summary: Posterior homeobox D genes, in particular HOXD13, are over-expressed by Ewing sarcoma, a tumor driven by the oncogenic fusion protein EWS-FLI1. Here, we have found that EWS-FLI1 maintains HOXD13 expression through a GGAA microsatellite enhancer in the developmental posterior HOXD regulatory domain. RNA-seq of shHOXD13 defined HOXD13-ergulated genes, so we performed CUT&RUN for HOXD13 and histone marks (H3K27ac, H3K4me3, H3K4me1, and H3K27me3) to determine how it regulates target genes.

overall_design: A673 and CHLA10 cells were run through the automated CUT&RUN protocol (Janssens et al. 2018 Methodology). In brief, 250,000-500,000 cells were collected and incubated with concavalin A beads for 10min. Cells were then washed and permeabilized with 0.05% digitonin wash buffer solution and incubated with primary antibodies for 24-48 hours at 4C. Samples were then run through the automated platform (https://www.protocols.io/view/autocut-run-genome-wide-profiling-of-chromatin-pro-ufeetje)

first: Feinan

last: Wu

first: Beth

last: Lawlor