title: Transcriptome sequencing of Wild Type and msoA mutant type in Mycolicibacterium smegmatis

city: Nanning

first: Hao

state: Guangxi

address: No. 100, University East Road, Xixiangtang District

department: College of Life Science and Technology

institute: Guangxi University

summary: We identified a novel transcription factor, MsoA, in response to oxidative stress in Mycolicibacterium smegmatis. We hope to discover the regulatory network and target genes of transcription factor msoA by transcriptome sequencing of wild-type and msoA mutants, so as to help us further elucidate the molecular mechanism of msoA involved in regulation of Mycolicibacterium oxidation.

overall_design: mRNA profiles of wild-type and msoA mutant strains of Mycolicibacterium smegmatis at logarithmic stage

first: Weihui


title: Increased cardiac macrophages in Sorbs2-deficient hearts: revealing a potential role for macrophage in responding to embryonic myocardial abnormalities

status: Public on Dec 22 2024

city: shanghai

first: Beibei

last: Hu

address: No 1678, Dongfang Road, Pudong New Area

country: China

institute: shanghai children's medical center

type: Expression profiling by high throughput sequencing

summary: Macrophages are known to support cardiac development and homeostasis, contributing to tissue remodeling and repair in the adult heart. However, it remains unclear whether embryonic macrophages also respond to abnormalities in the developing heart. Previously, we reported that the structural protein Sorbs2 promotes the development of the second heart field, with its deficiency resulting in atrial septal defects (ASD). In analyzing RNA-seq data, we noted an upregulation of macrophage-related genes in Sorbs2-/- hearts. Immunostaining and lineage-tracing confirmed an increase in macrophage numbers, underscoring a macrophage response to myocardial abnormalities. Partial depletion of macrophages led to downregulation of genes involved in lipid metabolism, muscle development and organ regeneration, alongside upregulation of genes associated with DNA damage-induced senescence and cardiomyopathy. Additionally, a non-significant increase in septal defects in macrophage-depleted Sorbs2-/- hearts suggests a potential reparative function for macrophages in maintaining structural integrity. Valve formation, however, remained unaffected. Our findings suggest that embryonic macrophages might sense abnormalities in embryonic cardiomyocytes and could adaptively support cardiac structure and function development in response to myocardial abnormalities.

overall_design: RNA profiling of wild-type embryonic hearts, Sorbs2 mutant hearts, and macrophage-depleted hearts at embryonic stages E12.5, E15.5, and E18.

first: Min

last: Zhang

first: Shanshan

last: Xiong


title: Transdifferentiation of Rat Keratinocyte Progenitors to Corneal Epithelial Cells by Limbal Niche via the STAT3/PI3K/AKT signaling pathway

city: Wuhan

first: Bei

last: Wang

address: 1277 Jiefang Avenue, Wuhan, Hubei Province, China

institute: Huazhong University of Science and Technology

summary: PURPOSE. To develop a method for enriching keratinocyte progenitor cells (KPCs) and establish a limbal niche (LN)-mediated transdifferentiation protocol to induce KPCs transdifferentiation into corneal epithelial cells. METHODS. Limbal niche cells (LNCs) were isolated from limbal tissues through enzymatic digestion and characterized. Conditioned medium from LNCs cultures was collected. KPCs were enriched by rapid adhesion of Matrigel and subsequently cultured in either an LNCs-conditioned medium supplemented with KSFM (LN-KS) or SHEM (LN-SH) for 14 days. Corneal-specific marker expression was assessed to evaluate transdifferentiation efficiency. Key transcription factors and signaling pathways involved in the transdifferentiation process were identified through single-cell and RNA sequencing, and validated using western blot and quantitative real-time PCR. RESULTS. Both LN-KS and LN-SH protocols successfully induced corneal epithelial cell transdifferentiation from KPCs, with LN-KS demonstrating higher efficiency in generating CK12+ and p63+ cells (p<0.001). RNA sequencing analysis and western blot have revealed significant activation of STAT3 and PI3K/AKT signaling pathways. Inhibition of STAT3 blocked PI3K/AKT activation and impaired corneal epithelial cell transdifferentiation. CONCLUSIONS. This study demonstrates the ability of LN to promote KPCs transdifferentiation into corneal epithelial cells in vitro, a process partially mediated by the STAT3 and PI3K/AKT signaling pathways.

overall_design: Primary keratinocyte progenitors were transferred to Matrigel-coated six-well plates for 14 days, with daily medium changes. This induction phase was conducted under one of three culture conditions: (1) KSFM condition, employing commercial keratinocyte serum-free medium supplemented with rhEGFand BPE; (2) LNCs-KS condition, utilizing KSFM supplemented with LNCs conditioned medium at a 1:1 ratio; (3) LNC-SH condition, employing supplemented hormonal epithelial medium(SHEM) supplemented with LNCs conditioned medium at a 1:1 ratio.


title: Early life myeloid immune cells in the neonatal liver

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

country: Germany

institute: RWTH Aachen University Hospital

summary: The translocation of macromolecules across the mammalian intestinal epithelial barrier is enhanced in early life before ceasing at what has been termed gut closure. However, the translocated macromolecules, the mechanism of translocation, and the functional consequences for the neonatal liver, which is still a hematopoietic organ at this age in mice, have not been defined. Microbiota profiling identified a transiently increased abundance of small intestinal lipopolysaccharide (LPS)-producing g-Proteobacteria early after birth. Orally administered LPS was translocated across the mucosal barrier during this early postnatal window, resulting in increased hepatic cytokine expression. LPS translocation was independent of disabled homolog 2 (Dab2)-mediated endocytosis by fetal-like enterocytes, but was mediated by the fatty acid translocase CD36, which showed transient overexpression early after birth. Postnatal LPS exposure altered hepatic haematopoiesis, innate immune reactivity and the bacterial clearance capacity of the neonatal liver. Taken together, our results identify and characterise a postnatal time window of hepatic tissue stimulation by gut-derived LPS as a novel immune priming event in early life.

overall_design: To investigate the effect of gut-derived LPS on neonatal hepatic immune cells, mice were daily treated with oral LPS (2.5 µg/g BW) from P1 to P4 every 24h (N=3). 2h after the last LPS treatment on P4, mice were analysed by single-cell RNA sequencing of hepatic immune cells.

first: Eva-Lena

last: Stange

first: Julian

last: Brück

first: Trong Hieu

first: Mathias

last: Hornef


title: Assessing biosimilarity of Trastuzumab monoclonal antibody therapeutics using RNA sequencing of treated SKBR3 cells

city: Waterloo

first: Karsten

last: Rinas

state: ON

address: 200 University Ave W

department: Biology

country: Canada

institute: University of Waterloo

summary: Patents of some therapeutic monoclonal antibodies (mAb) used for cancer treatment are ending soon, allowing for the entry of similar analogs (biosimilars) onto the market. To have a biosimilar approved by health agencies, the manufacturer must typically demonstrate functional and physicochemical similarity between the biosimilar and the approved reference product. Functional similarity is often validated with cell-based assays, but the information gained is limited. In contrast, RNA-seq methods enable a sensitive transcriptomic analysis, providing detailed information on pathways and cellular responses. Trastuzumab inhibits signaling of the cell-surface receptor HER2, which is overexpressed in approximately 30% of all breast cancer patients. Here, we compare the functional effect of the mAb Trastuzumab and a corresponding biosimilar.   The SKBR3 breast cancer cell line was treated with the reference product, Trastuzumab (Herceptin®), or a proposed biosimilar (ApoTras), and the cellular transcriptomes were analyzed by RNA-seq. Functional similarity was assessed using two statistical contrasts. One contrast evaluated the mechanism of action by comparing treated samples (Her and ApoTras, n = 16) vs. untreated controls (n = 8). The other contrast directly compared ApoTras (n = 8) vs. Her (n = 8) to determine differences in expression between treatments. A gene set overrepresentation analysis of DEG for mAb treatments revealed mechanisms of action, which were consistent with known trastuzumab effects.

overall_design: We compared changes in gene expression of mRNAs in SKBR3 cells untreated or treated with Herceptin or a biosimilar of it by RNA-seq.  Paired-End Sequencing of samples with Illumina HiSeq Sequencing

first: Brendan

last: McConkey


title: Responses to temperature shocks in Zymoseptoria tritici reveal specific transcriptional reprogramming and novel candidate genes for thermal adaptation

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

summary: The transcriptomic response of Zymoseptoria tritici IPO323 spores under heat and cold shock.

overall_design: The pre-culture of the reference strain IPO323 was prepared as described previously for heat and cold shock response phenotyping. We then investigated the transcriptomic response of IPO323 under two experimental conditions: i) A “shock” treatment, where 25 mL spore suspensions (7.5 x 10⁵ spores/mL) were incubated for 15 hours at either 30°C (heat shock), 0°C (cold shock), or 18°C (control), with three replicates for each condition. ii) A “shock and recovery” treatment, where 25 mL spore suspensions were exposed to 15 hours at 0°C, 30°C, or 18°C, followed by an additional 75 hours at 18°C, with three replicates per condition. For each experiment, we transferred 2 mL of spore suspension, centrifuged the samples at approximately 9400g for 2 minutes to remove the media, and immediately flash-froze the spore pellets before storing them at -80°C. The frozen samples were sent for RNA extraction and sequencing to Biomarker Technologies GmbH (BMKgene, Münster, Germany). The sequencing was performed with Illumina NovaSeq X, pair-end 150bp reads.

first: Silvia

last: Minana-Posada


title: Genome-wide reconstruction of the bacterial response to single and multiple stress in Shigella flexneri 2a str. 2457T (S fflexneri ChIP-exo)

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The genome-wide analysis were carried out to find out the genes reponsible for single and multiple stress in Shigella flexneri 2a str. 2457T. This results can be offered to explain bacterial responses such as the capacity of survive and elicit infections.

overall_design: Shigella sflexneri 2a str. 2457T is cultured in modified M9 minimal medium with 0.2% (w/v) glucose as the carbon source upto exponential phase.

first: Khoi

middle: N

last: Pham

first: Joon

middle: Y

last: Park

first: Nong

middle: K

last: Linh


title: Genome-wide reconstruction of the bacterial response to single and multiple stress in Shigella flexneri 2a str. 2457T (S. flexneri RNA-Seq)

summary: The genome-wide analysis was carried out to find out the genes responsible for single and multiple stress in Shigella flexneri 2a str. 2457T. This result can be offered to explain bacterial responses, such as the capacity to survive and elicit infections.


title: Genome-wide reconstruction of the bacterial response to single and multiple stress in Shigella flexneri 2a str. 2457T

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

sample_organism:
Escherichia coli
Shigella flexneri

platform_organism:
Escherichia coli
Shigella flexneri

overall_design: Refer to individual Series


title: E3 ligase SYVN1-Mediated Polyubiquitination of CPSF6 Promotes Alternative Polyadenylation and Antivirus Effects of Macrophages

status: Public on Dec 21 2024

city: Guangzhou

first: Wu

last: Runze

address: SUN YAT-SEN UNIVERSITY

institute: SUN YAT-SEN UNIVERSITY

summary: Down-regulation of CPSF6 protein, one of 3′ end processing factors, mediates APA in macrophage with responses to virus infection and plays an important role in its anti-virus effect. However, the signal pathway and molecular mechanism underlying the downregulation of the CPSF6 protein remain elusive. Here, we found that MAVS triggers the nucleus import of E3 ligase SYVN1 mediated by NUP153 in response to vesicular stomatitis virus infection. Then, SYVN1 catalyzes K48-linked polyubiquitination of CPSF6, resulting in the degradation of CPSF6 via proteasome, and then transcriptome wide APA and anti-virus effect subsequently.

overall_design: Compare the changes in APA length between IVT-SAPAS groups

first: Xin

last: Lu

first: Chao

last: Liu

first: Runze

last: Wu


title: RNA-sequencing data of T-AP1-labeled NCI-N87 xenograft tumor cells sorted according to the fluorescence

status: Public on Dec 23 2024

city: Kyoto

first: Yoshifumi

last: Ueda

address: Katsura, Kyoto-daigaku

department: Department of Synthetic Chemistry and Biological Chemistry

country: Japan

institute: Graduate School of Engineering, Kyoto University

summary: Oxidative stress is recognazed as a hallmark of cancer. However, little is known about intratumor heterogeneity of reactive oxygen species (ROS) and its influence on tumor behavior, largely due to technical challenges inherent in detecting intratumor ROS at single-cell resolution. We have developed a tumor-targeted H2O2 probe (T-AP1) by conjugating trastuzumab with both Alexa Fluor 647 (AF647), an H2O2-insensitive fluorophore, and peroxy green 1 (PG1), an irreversible H2O2-sensitive chemical probe to provide a “ratiometric” readout, allowing H2O2 measurements independent of accumulated T-AP1 levels. Given the ability of T-AP1 to persistently mark tumor cells that experience H2O2 exposure, we employed cell sorting to isolate tumor cells with high (PG1highAF647+) and low (PG1lowAF647+) H2O2 exposure levels from T-AP1–labeled NCI-N87 xenograft tumors. PG1highAF647+ and PG1lowAF647+ cells obtained via cell sorting from three biologically independent N87 tumors were subjected to RNA sequencing.

overall_design: N87 xenograft tumors were resected from male athymic nude mice (BALB/c Slc-nu/nu) 3 weeks post-subcutaneous inoculation. T-AP1 was administered 12 hours before the harvestion of the tumors. Resected tumors were minced into small fragments in ice-cold RPMI 1640 containing DNase I, Liberase DH (Roche), and catalase. The fragments were incubated in a shaker for 1 h at 37°C and filtered through 40 μm cell strainers (BD Falcon). Filtrated cells were suspended in PBS and stored on ice until cell sorting. The cells were treated with 5 μM propidium iodide (PI, Dojindo) for 10 min to exclude dead cells, and PI-negative cells were sorted according to the fluorescence intensity of PG1 and AF647. Total RNA from the sorted tumor cells was purified using an RNeasy Micro kit (Qiagen). cDNA libraries were prepared using a SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara Bio). Sequencing libraries were then prepared with Nextera XT Index Kit v2 SetA/B/C/D (Illumina). The prepared library was sequenced on NovaSeq 6000 system (Illumina).


title: Genome-wide reconstruction of the bacterial response to single and multiple stress in Shigella flexneri 2a str. 2457T (E. coli RNA-Seq)

summary: The genome-wide analysis was carried out to find out the genes responsible for single and multiple stress in Shigella flexneri 2a str. 2457T. E. coli used as a reference strain. This is RNA-seq data of E.coli K-12 MG1655.

overall_design: E.coli strain is cultured in modified M9 minimal medium with 0.2% (w/v) glucose as the carbon source upto exponential phase.


title: Gene expression profiles of complete hydatidiform moles and XBP1-overexpressing cell lines associated with progression to gestational trophoblastic tumors

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University


title: Identification of B cell stimulation-specific A20-repressed genesets

city: München

first: Marc

last: Schmidt-Supprian

address: Isamninger Str. 22

department: Klinikum rechts der Isar

institute: Technical University of Munich (TUM)

summary:
Loss of one copy of the negative feedback regulator A20 is implicated in the development of autoimmunity. In mouse models the B cell specific loss of A20 can induce autoimmune phenotypes.
To identify genesets which are repressed by A20 in B cell, we stimulated A20-deficient and control B cells in vitro with αIgM, αCD40 or LPS for 3 or 14 hours to reflect B cell receptor engagement, T cell help and innate/TLR signals, respectively, and analyzed the effect on gene expression.

overall_design: Per biological replicate, splenocytes from three mice were pooled and follicular B cells were enriched by depletion of CD9+ (marginal zone B) and CD43+ (T) cell.  7 million cells were stimulated with anti-IgM, anti-CD40 or LPS or not stimulated (control) for 3 hours or 14 hours.

first: Yuanyuan

last: Chu


title: TurboCas: A method for locus-specific labeling of genomic regions and isolating their associated protein interactome [ChIPseq]

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

summary: Regulation of gene expression during development and stress response requires the concerted action of transcription factors and chromatin-binding proteins. Because this process is cell-type specific and varies with cellular conditions, mapping of chromatin factors at individual regulatory loci is crucial for understanding cis-regulatory control. Previous methods only characterize static protein binding. We present “TurboCas,” a method combining a proximity-labeling (PL) enzyme, miniTurbo, with CRISPR-dCas9 that allows for efficient and site-specific labeling of chromatin factors in mammalian cells. Validating TurboCas at the FOS promoter, we identify proteins recruited upon heat shock, cross-validated via RNA polymerase II and P-TEFb immunoprecipitation. These methodologies reveal canonical and uncharacterized factors that function to activate expression of heat-shock-responsive genes. Applying TurboCas to the MYC promoter, we identify two P-TEFb coactivators, the super elongation complex (SEC) and BRD4, as MYC co-regulators. TurboCas provides a genome-specific targeting PL, with the potential to deepen our molecular understanding of transcriptional regulatory pathways in development and stress response.

overall_design:
The miniTurbo proximity labeling enzyme was fused to the N terminus of a catalytically dead Cas9 and cloned into a lentiviral expression vector with an in-frame blasticidin selection cassette, separated by a 2A autocatalytic peptide. HEK293T human embryonic kidney cells and HCT116 human colon carcinoma cells were used to stably express TurboCas or MiniTurbo. To target TurboCas to the FOS locus, sgRNA were designed against regions ~600bp and ~300bp upstream of the transcription start site (TSS) and the first FOS exon (hereafter referred to as FOS-600, FOS-300, FOX-EX1). TurboCas or MiniTurbo cell lines were then transduced with LentiGuide-Puro virus containing the sgRNA and selected with Puromycin to generate stable sgRNA-expressing cell lines. To confirm that TurboCas was specifically binding at the intended sgRNA target sites, we assessed TurboCas chromatin binding by performing ChIP-seq with a commercial polyclonal dCas9 antibody. In addition to the three sgRNA cell lines (TurboCas-Fos600, TurboCas-Fos300, TurboCas-FosEX1), the experiments were also performed in the MiniTurbo and TurboCas-empty controls. To functionally validate hits identified through TurboCas mass spectrometry, we selected the top hits as targets  and performed shRNA knockdown of these genes in HCT116 cells. Cells were selected with puromycin for 10 days and then heat shocked for 3 hours, followed by RNA extraction and RNA-seq both to evaluate shRNA efficiency and to assess gene expression patterns.
For dCas9 ChIP, 5 x 107 cells were used. For Pol2 ChIP, 1 x 107 cells were used. In brief, HCT116 or HEK293T cells were fixed in 1% formaldehyde for 15 minutes, followed by quenching, cell lysis and chromatin shearing with an E220 focused ultrasonicator (Covaris). Sheared chromatin was subjected to immunoprecipitation with a Cas9 antibody (Diagenode, #C15310258-100) or a Pol2 antibody (Cell Signaling Technologies, 14958). Immunoprecipitated DNA was then washed, eluted, revers-crosslinked and purified using a ChIP DNA Clean&Concentrator kit (Zymo Research, D5205) prior to library preparation using the KAPA HTP library preparation kit (KAPA Biosystems). RNA from HCT116 cells was isolated using the RNeasy mini kit (Qiagen, #74106) as per manufacturer’s instructions. RNA-seq libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, # E7760L).
ChIP-seq and RNA-seq libraries were paired-end read sequenced on the NovaSeq 6000 (Illumina). Raw BCL output files were processed using bcl2fastq (Illumina, version 2.20) prior to quality trimming using CutAdapt1.14. Trimmed ChIP-seq reads were aligned to the human genome (University of California at Santa Cruz [UCSC] hg38 build) using Bowtie v2.2.6. Only uniquely mapped reads satisfying the two-mismatch maximum threshold within the entire length of the gene were considered for ensuing analyses. Mapped ChIP-seq reads with MAPQ quality score >=30 were extended to 150bp to represent sequenced fragments. Raw read counts from both ChIP-seq were normalized to total reads per million (RPM). Output BAM files were converted into bigwig coverage plots to generate UCSC genome browser tracks. Peak calling was performed using MACS2 with the  default (narrow) option. Called peaks were annotated with HOMER program annotatePeaks.pl. Heatmaps and metaplots from bigwig files were generated using deepTools v3.1.1. For region-based categorization of dCas9 signal, bed files were split by chromosome and coordinate (in the case of chromosome 14), these split files were then used as inputs for profile plotting with deepTools. RNA-seq reads were aligned to the hg38 human genome using STAR aligner v2.5.2 and outputted bam files were sorted using samtools v1.6. For RNA-seq, exonic reads were assigned to specific genes from Ensembl release 72 and genome assembly GRCh38.p13 using the python package HTSeq-0.6.1.

first: Bercin

last: Cenik

first: Yuki

last: Aoi

first: Marta

last: Iwanaszko


title: 25-hydroxycholesterol mediates brain cytokine production and neutrophil infiltration in a mouse model of LPS-induced neuroinflammation.

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Neuroinflammation has been implicated in the pathogenesis of several neurologic and psychiatric disorders. Microglia are key drivers of neuroinflammation and in response to different inflammatory stimuli overexpress a proinflammatory signature of genes. Among these, Ch25h is a gene overexpressed in brain tissue from Alzheimer’s disease as well as various mouse models of neuroinflammation. Ch25h encodes cholesterol 25-hydroxylase, an enzyme that hydroxylates cholesterol to form 25-hydroxycholesterol (25HC). 25HC, an immune-oxysterol primarily produced by activated microglia, is further metabolized to 7,25-dihydroxycholesterol, which is a potent chemoattractant for leukocytes. We have also previously shown that 25HC increases production and secretion of the proinflammatory cytokine, IL-1, by mouse microglia treated with lipopolysaccharide (LPS). In the present study, wildtype (WT) and Ch25h-knockout (CKO) mice were peripherally administered LPS to induce an inflammatory state in the brain. In LPS-treated WT mice, Ch25h expression and 25HC levels increased in brain relative to vehicle-treated WT mice. Interestingly, 25HC levels were significantly higher in LPS-treated WT female compared to male mice. Activation of microglia and astrocytes in response to systemic LPS was suppressed in CKO mice relative to WT mice. Proinflammatory cytokine production and intra-parenchymal infiltration of neutrophils strongly correlated with brain 25HC levels and were significantly lower in CKO compared to WT mice. Overall, our results show that 25HC mediates a sex-specific proinflammatory response in the brain characterized by activation of both microglia and astrocytes but also by neutrophil migration into the brain parenchyma presumably due to 7,25-diHC produced from 25HC.

overall_design: Wild-type (C57BL/6J) and ch25h-/- (CKO) mice from the Jackson Laboratory were used in this study. At 23-26 weeks of age, mice were intraperitoneally (i.p.) administered LPS (2 mg/kg per dose) or vehicle (PBS) twice with a 24-hours interval. Animals were perfused 24 hours after the last injection. Left hemisphere was fixed in 4% paraformaldehyde for immunostaining. Hippocampus from the right hemisphere was flash frozen and stored at -80˚C until RNA isolation using Zymo Research Quick-RNA MiniPrep Plus kit (Cat. #: R1058).

first: Johnathan

last: Romero

first: Danira

last: Toral-Rios

first: Steven

last: Paul

first: Anil

middle: G

last: Cashikar


title: TurboCas: A method for locus-specific labeling of genomic regions and isolating their associated protein interactome [RNAseq]


title: Transcriptome analysis for XBP1 overexpressing complete hydatidiform mole-derived cell lines

summary: The trophoblastic disease is a general term for diseases that cause abnormal growth of trophoblasts, the most frequent form of which is called hydatidiform mole (CHM). CHM cell lines (Hmol1-3B and Hmol1-2C) were established in our laboratory (Yamamoto E, et al. Int J Mol Med. 2017 Sep; 40(3): 614–622). In this study, XBP1 was overexpressed, and RNA sequencing was performed to investigate the role of XBP1 in CHM.

overall_design: The control and XBP1 lentiviral vectors (pLV[Exp]-Puro-EF1A>EGFP and pLV[Exp]-EGFP:T2A:Puro-EF1A>hXBP1) were purchased from Vector Builder (Chicago, IL). Transduction of the viral vectors was performed according to the protocol of the Lenti-XTM Packaging Single Shots (Takara, Shiga, Japan). Then, the total RNA of cell lines was extracted using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany), and RNA sequencing was performed by Novogene, Inc. (Beijing, China).

first: Mayu

last: Shibata

first: Akira

last: Yokoi

first: Kaoru

last: Niimi


title: The gene expression profiles of complete hydatidiform mole which developed post molar gestational trophoblast neoplasia

summary: A complete hydatidiform mole (CHM) is a common disease known to develop post-molar gestational trophoblast neoplasia (GTN). However, the details of the molecular biological mechanisms underlying the progression to post-molar GTN from hydatidiform moles are still largely unknown. In this study, we performed RNA sequencing (RNA-seq) using archival fresh frozen tissues of patients with CHM and compared the gene expression profiles of patients who achieved spontaneous remission and those who developed post-molar GTN after the evacuation.

overall_design: We prospectively collected CHM tissues from patients who underwent the evacuation at the Nagoya University Hospital (Nagoya, Japan). In this study, we included seven patients with CHM who eventually developed low-risk GTN between 2015 to 2021. Moreover, we included six patients with CHM who achieved spontaneous remission as controls. The total RNA of their archival fresh frozen tissues was extracted using the miRNeasy® Mini Kit (QIAGEN, Hilden, Germany), and the library construction and pair-end sequencing were conducted by Rarevariant, Inc. (Tokyo, Japan).


title: Transcriptome statistics of wild-type  and KO-Dectin-1 mice in adipose tissue

city: Changsha

first: Jie

last: Ma

address: street of nongda road

institute: Hunan Agricultural University

summary: transcriptional map of wild-type mice and Ko-Dectin1 mice was analysed in adipose tissue, we screened 185 differentially expressed genes, and further identified 38 differentially expressed genes (including 9 up-regulated genes and 29 down-regulated genes), Log2FC > 2, P < 0.05. These differentially expressed genes play an important role in regulating fat deposition and metabolism in adipose tissue.

overall_design: MRNA profiles were measured in 7 wild-type mice and 7 KO-Dectin1 mice

last: Yin


title: Breast cancer brain metastasis

city: sadel crick road

first: Mohd

middle: wasim

last: Nasser

state: Omaha

address: 42 and Emile

department: BMB

institute: UNMC

summary: Investigating the differential expression of gene during breast cancer brain metastasis

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of cells. Comparative gene expression profiling analysis of RNA-seq data of cells (Breast cancer and breast cancer brain metastatic cells).

first: Surinder

last: Batra

middle: W

first: Jawed

middle: A

last: Siddiqui


title: Next Generation Sequencing of chromatin structure remodeling RSC1 during growth mycelia in the Magnaporthe oryzae [RNA-seq]

city: Hangzhou

first: mengting

last: xu

state: ZheJiang

address: Zhejiang University

institute: mengtingxu

summary: A bromodomain and BAH containing Remodels the Structure of Chromatin 1 (RSC1), which play key roles  in the filamentous fungus Magnaporthe oryzae.

overall_design: Examination of 3 different mutants in Magnaporthe oryzae strain

first: Zeng

last: Tao


title: DDB1 Prepares Brown Adipocytes for Cold-Induced Thermogenesis

first: Guosheng

last: Hu

state: shanghai

address: 2005 Songhu Road, Yangpu District, Shanghai

institute: fudan university


title: DDB1 Prepares Brown Adipocytes for Cold-Induced Thermogenesis [RNA-seq]

summary: Adipose tissues play a pivotal role in energy homeostasis.  They are existent in two forms: white adipose tissue and brown adipose tissue (BAT). Being the primary source of non-shivering thermogenesis of mammals, BAT plays an irreplaceable role in maintaining body temperature .  Damaged DNA binding protein 1 (DDB1) is usually recognized as a component of the CUL4-DDB1 E3 complex. We have previously shown that DDB1 functions independently of CUL4 to promote adipogenesis.  In the thesis, we focus on the function of DDB1 in mature adipocytes.   We crossed Ddb1f/f mice with Adipoq-Cre or Ucp1-Cre mice to generate adipose tissue or BAT-specific mice, designated Ddb1-AKO and Ddb1-BKO mice respectively. At 8-12 weeks, BAT in these mice was servely whitened with decreased mitochdiral content. The thermogenic genes were also significantly downregulated at both RNA and protein levels. To further characterize the effect of DDB1 on thermogenesis, we first examined the bdy temperature of the pulps on postnatal day 3, and found that depletion of DDB1 caused a significant decrease in surface temperature.When the adult mice were subjected to cold challenge, both Ddb1-AKO and Ddb1-BKO mice showed dramatically decreased body temperature compared with control mice.  At the end of the experiment, Ddb1-AKO and Ddb1-BKO mice had higher contents in BAT triglycerides and lower blood glucose level. Furthermore, the oxygen comsumption in Ddb1-AKO and Ddb1-BKO mice failed to respond to epinephrine injection. . All these results above demonstrated that lacking of DDB1 in brown adipocytes leads to a destruction in thermogenesis of BAT. We have also examined the phenotypes of Ddb1-AKO and Ddb1-BKO mice on high-fat-diet feeding. Compared with control mice, these mice showed decreased body weight, but significantly glucose intolerance and increased triglycierde content in liver, indicating that these mice have partial lipodystrophy.   To study whether the effect of DDB1 was dependent on CUL4, we generated adipose tissue-specific Cul4a or CUl4b knockout mice, and found that these mice have no visible defect in BAT morphology compared with control mice, indicating a CUL4-independent function of DDB1. RNA-Seq analysis revealed that DDB1 is required for cold-induced expression of around 900 genes. ChIP-Seq analysis revelaed that these genes were subjected to regulation of promoter-proximally paused RNA polymerase II (Pol II), and that DDB1 is required for the release of paused Pol II upon cold stimulation.   Our findings have thus revealed that DDB1 plays an important role in maintaining the theremogenic function of BAT by regulating the expression of thermogenic genes upon cold stimulation. Our studies will shed insights into transcriptional regulation of thermogenic gene

overall_design: RNA-seq performed in this study was designed to understand the molecular mechanisms underlying DDB1 in gene transcription regulation.

first: Xu

last: Wang

first: Tong-Jin

last: Zhao

first: Guo-Sheng


title: DDB1 Prepares Brown Adipocytes for Cold-Induced Thermogenesis [ChIP-seq]

overall_design: ChIP-seq performed in this study was designed to understand the molecular mechanisms underlying DDB1 in gene transcription regulation.

first: Hao-Yan


title: RNA-seq analysis in esophageal squamous cell carcinoma (ESCC) cell line KYSE510

city: Zhengzhou

first: Yunfeng

last: Gao

address: No.127 at Dongming road

institute: China-US (Henan) Hormel Cancer Institute

summary: We report the application of RNA-seq analysis in three kinds of KYSE510 cell lines. One group of cells was transfected with scremble RNA as control and the other two groups of cells were transfected with TCONS_02256997 shRNAs individually to knockdown transcript TCONS_02256997. We did RNA-seq aim to explore  the potential target fectors that TCONS_02256997 might effect to and try to explain the mechanism it caused tumor progression.

overall_design: Screen the potential targets of transcript TCONS_02256997

first: Ming

last: Jiang


title: Single-cell profiling reveals pathogenic role and differentiation trajectory of Granzyme K+ tissue resident memory CD8+T cells in primary Sjögren’s syndrome

status: Public on Dec 20 2024

first: Ting

last: Xu

address: No. 106, Zhongshan Second Road

institute: Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences

summary: This study was conducted to depict the immune landscape of primary Sjögren’s syndrome (pSS) and to explore the pathogenic role of CD8+T cell subsets.

overall_design:
single-cell RNA sequencing (including Gene expression, TCR and BCR) for labial glands (LG) and peripheral blood mononuclear cells (PBMC) from pSS patients (n = 3) and PBMC from age-/gender- matched healthy control (n = 4).

***************************************************************
The raw data have been deposited into the CNGB Sequence Archive (CNSA) of the China National GeneBank DataBase (CNGBdb) with accession number CNP0003733 for controlled access to the personally identifiable sequence data.
***************************************************************

first: Jinfen

first: Haoxian

last: Zhu

first: Xing

last: You

first: Yang

last: Li

first: Zhexiong

last: Lian

first: Caiyue


title: RPA1 Remodels Liver Chromatin Architecture to Maintain Lipid Metabolic Homeostasis

city: Beijing

first: Chengqi

last: Yi

address: Yiheyuan Road

department: School of Life Sciences

institute: Peking University

summary: Replication protein A(RPA), a ssDNA binding protein complex, participates in DNA replication, recombination and damage repair, but its physiological function remains elusive. Here, we show that heterozygous Rpa1 knockout mice were developmentally normal, but hypersensitive to ageing and high-fat-diet (HFD) induced hepatic steatosis. Liver specific deletion of Rpa1 leads to impaired lipid beta-oxidation, hepatic steatosis and subsequently hepatocellular carcinoma (HCC). Assays for RNA-seq, pull-down and transposase-accessible chromatin sequencing (ATAC-seq) reveal that RPA1 is required for transcription of a subgroup of lipid metabolic genes via altering chromatin accessibility landscape. Thus, our results suggest that RPA1 is a critical regulator of gene transcription and chromatin remodeling, linking a guardian of genome stability to lipid metabolic homeostasis.

overall_design: Liver mRNA profiles of 3 liver specific Rpa1 knockout mice and 3 wild type (WT) mice were generated for RNA-seq. And chromatin accessibility in liver tissue of 4 liver specific Rpa1 knockout mice and 4 wild type (WT) mice were examinated by ATAC-seq.

first: Qi

first: Zhe

last: Zhou

first: Yuxin


title: Gene expression profile at single cell level of two colored skin (red and white) from koi carp.

city: Wuxi

first: Mingkun

last: Luo

state: Jiangsu

address: No. 9, Shanshui East Road, Binhu District, Wuxi City, Jiangsu Province, China

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

summary: Fish are richly and diversely coloured and have a complex palette of pigment cells. We first investigated the diversity of skin cells in Kohaku koi by single-cell sequencing.

overall_design: We collected red and white skin from three Kohaku koi and performed single-cell sequencing simultaneously.


title: Time-series analysis of gene expression of Oryza sativa tropical japonica subgroup (Azucena) under saline stress conditions at the seedling stage

city: New York

first: Maricris

middle: Lanuzo

last: Zaidem

email: mzaidem@gmail.com, mz82@nyu.edu

state: New York

address: 12 Waverly Pl

department: Center for Genomics and Systems Bi8ology

institute: New York University

summary: Salinity stress has both immediate and long-term effects on the growth, in order to model the dynamics of the transcriptome response upon salt imposition we conducted a time-series analysis of the rice transcriptome. The data set is used in mutliple analysis including inferring the global regulatory network for a rice adaptive response and aiding the analysis of boundaries of actively transcribed sequences enriched for sequence conservation signatures in conserved topologically associating domains (TADs).

overall_design: RNA-seq profiling of a salinity susceptible rice variety Azucena by subjecting the seedlings to salt stress (10mM NaCl). A corresponding seedling subset was concurrently grown with no salt stress (0mM NaCl), as control. Time-series samples were collected at 0mins, 60mins, 180mins, 240mins and 5days time-points based on the start of salt-imposition.

first: Michael

last: Purugganan

first: Christopher

last: Jackson


title: A simple method to efficiently generate structural variation in plants [short read]

city: Toronto

first: Satyaki

last: Rajavasireddy

address: 1265 Military Trail, Toronto,, SY246

department: Biological Sciences (Scarborough)

institute: University of Toronto

summary: Phenotypic variation is essential for the selection of new traits of interest. Structural variants, consisting of deletions, duplications, inversions, and translocations, have greater potential for phenotypic consequences than single nucleotide variants. Indeed, pan-genome studies have highlighted the importance of structural variation in the evolution and selection of novel traits. Here, we describe a simple method to induce structural variation in plants. We demonstrate that a short period of growth on the topoisomerase II inhibitor etoposide induces heritable structural variation and altered phenotypes in Arabidopsis thaliana at high frequency. Using long-read sequencing and genetic analysis, we identified causative deletions and inversions underlying semi-dominant and recessive phenotypes. This method is potentially applicable to any plant species, with minimal resources required, and is suitable to replace irradiation as a source of induced large-effect structural variation.

overall_design: Short-read DNA sequencing of M2 and M3 descendants of plants treated with etoposide or DMSO. M2 and M3 plants of etoposide-treated lines were a mix of plants with and without a phenotype.

first: Lindsey

middle: L

last: Bechen

first: Naiyara

last: Ahsan

first: Alefiyah

last: Bahrainwala

first: Mary

last: Gehring

first: PRV

last: Satyaki


title: A simple method to efficiently generate structural variation in plants [long read]

overall_design: Long-read DNA sequencing of M2 and M3 descendants of plants treated with etoposide or DMSO. M3 plants of etoposide-treated lines either exhibited a phenotype (termed BR-like dwarf, short-internode dwarf, virescent, and variegated), or do not show a phenotype but are genetic relatives of those that do. Untreated Col-0 plant also included as an additional control.


title: A simple method to efficiently generate structural variation in plants [RNA-Seq]

overall_design: RNA sequencing of M2 and M3 descendants of plants treated with etoposide or DMSO. M3 plants of etoposide-treated lines either exhibited a phenotype (termed BR-like dwarf, short-internode dwarf, virescent, and variegated), or do not show a phenotype but are genetic relatives of those that do.


title: Selective translational control by PABPC1 phase separation regulates blast crisis and target therapy resistance of chronic myeloid leukemia [RNA-seq]

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

summary: Tyrosine kinase inhibitors (TKIs) targeting the BCR-ABL1 fusion tyrosine kinase have revolutionized the treatment of chronic myeloid leukemia (CML). However, the development of TKI resistance and the subsequent transition from the chronic phase (CP) to blast crisis (BC) threaten CML patients. Accumulating evidence suggests that translational control is crucial for cancer development and progression. Here, we performed high throughput CRISPR/Cas9 screening and identified poly(A) binding protein cytoplasmic 1 (PABPC1) as a driver for CML-BC progression. PABPC1 preferentially improved the translation efficiency of multiple leukemogenic mRNAs with long and highly structured 5' untranslated regions, including BCR-ABL1 and its TKI-resistant mutants, through forming biomolecular condensates. Inhibiting PABPC1 significantly suppressed CML cell proliferation and attenuated disease progression, but did not affect normal hematopoiesis seriously. More importantly, we identified two novel PABPC1 inhibitors, 1,10-Phen and ML324, which inhibited BC progression and overcame TKI resistance in murine and human CML. Overall, our work identified PABPC1 as a selective translation enhancing factor in CML-BC, the genetic or pharmacological inhibition of which overcame TKI resistance and suppressed BC progression in CML.

overall_design: RNA-seq in K562 cells.

first: Chenguang

last: Sun

first: Yanni

last: Ma

first: Jia

last: Yu


title: Selective translational control by PABPC1 phase separation regulates blast crisis and target therapy resistance of chronic myeloid leukemia [Polysome-seq]

overall_design: Polysome-seq in K562 cells.


title: ACSL4 mediated H3K9 and H3K27 hyperacetylation upregulates SNAIL to drive TNBC metastasis

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Triple-Negative Breast Cancer (TNBC) has profound unmet medical need globally for its devastating clinical outcome associated with rapid metastasis and lack of targeted therapies. Recently, lipid metabolic reprogramming especially fatty acid oxidation (FAO) has emerged as a major driver of breast cancer metastasis. Analyzing the expression of major FAO regulatory genes in breast cancer, we found selective overexpression of acyl-CoA synthetase 4 (ACSL4) in TNBC, which is primarily attributed by the absence of progesterone receptor (PR). Loss of ACSL4 function, by genetic ablation or pharmacological inhibition significantly reduces metastatic potential of TNBC. Global transcriptome analysis reveals that ACSL4 activity positively influences the gene expression related to TNBC migration and invasion. Mechanistically, ACSL4 modulates FAO and intracellular acetyl-CoA levels, leading to hyper-acetylation of particularly H3K9ac and H3K27ac marks resulting in overexpression of SNAIL during the course of TNBC metastatic spread to lymph node and lung. Further, human TNBC metastasis exhibits positive correlation among ACSL4, H3K9ac, H3K27ac, and SNAIL expression. Altogether, our findings provide new molecular insights regarding the intricate interplay between metabolic alterations and epigenetic modifications, intertwined to orchestrate TNBC metastasis and posit a rational understanding for the development of ACSL4 inhibitors as a targeted therapy against TNBC.

overall_design: Overall design : MDA-MB-231 (Human Breast Cancer Cell) were made stable by transducing Control (pLKO.1 empty vector) and ACSL4 knockdown (KD) (pLKO.1-shACSL4) plasmids. Three different batches of respective cells (Control, ACSL4 KD, and control cells treated with ACSL4 inhibitor (PRGL493)) from each group were subjected to RNA seq analysis-Gene expression profiling by high throughput sequencing.

first: Abhipsa

last: Sinha

first: Madavan

last: Vasudevan

first: Dipak

last: Datta


title: Characterization of the cellular components of mouse collecting lymphatic vessels reveals that lymphatic muscle cells are the innate pacemaker cells regulating lymphatic contractions

city: Columbia

first: Sathesh

last: Sivasankaran

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: Collecting lymphatic vessels (cLVs) exhibit spontaneous contractions with a pressure-dependent frequency, but the identity of the lymphatic pacemaker cell is still debated. By analogy to pacemakers in the GI and lower urinary tracts, proposed cLV pacemaker cells include interstitial cells of Cajal like cells (ICLC) or the lymphatic muscle (LMCs) cells themselves. Here we examined the cellular constituents of the mouse cLV wall and assessed whether any cell type exhibited morphological and functional processes characteristic of pacemaker cells: a continuous if not contiguous network; spontaneous Ca2+ transients;  and depolarization-induced propagated contractions. We employed inducible Cre (iCre) mouse models routinely used to target these specific cell populations including: c-kitCreERT2 to target ICLC; PdgfrβCreERT2 to target pericyte like cells; PdgfrαCreERTM to target CD34+ adventitial cells and ICLC; and Myh11CreERT2 to target LMCs directly. These specific inducible Cre lines were crossed to the fluorescent reporter ROSA26mT/mG, the genetically encoded Ca2+ sensor GCaMP6f, and the light-activated cation channel rhodopsin2 (ChR2). c-KitCreERT2 labeled both a sparse population of LECs and round adventitial cells that responded to the mast cell activator compound 48-80. PdgfrβCreERT2 drove recombination in both adventitial cells and LMCs, limiting its power to discriminate a pericyte specific population. PdgfrαCreERTM labeled a large population of interconnected, oak leaf-shaped cells primarily along the adventitial surface of the vessel. Of these cells, only LMCs consistently, but heterogeneously, displayed spontaneous Ca2+ events during the diastolic period of the contraction cycle, and whose frequency was modulated in a pressure-dependent manner. Optogenetic depolarization through the expression of ChR2 under control of Myh11CreERT2, but not PdgfrαCreERTM or c-KitCreERT2, resulted in a propagated contraction upon photo-stimulation. Membrane potential recording in LMCs demonstrated that the diastolic depolarization was significantly correlated with contraction frequency. These findings support the conclusion that LMCs, or a subset of LMCs, are responsible for mouse cLV pacemaking.

overall_design: IALVs we used a total of 10 Rosa26mTmGmice, without Cre and no tamoxifen, with equivalent representation of sex (5 males and 5 females). Full length IALVs from both the left and right side of each mouse ROSA26mTmG were isolated and cleaned of excessive matrix and adipose tissue. Isolated vessels were digested into single cell suspensions as described above and the cells were kept on ice following single cell suspension until all the tissues had been processed. Cells from all vessels were combined and FACs purified by tdTomato expression to remove debris and concentrate the cells for downstream single cell 3’ RNA-Seq libraries creation with 10x Genomics Chromium Chip and Chromium Next GEM Single Cell 3’ RNA-Seq reagents. Samples were sequenced with the NovaSeq 6000 S4-PE100 flow cell

first: S

middle: D

last: Zawieja

first: G

last: Pea

middle: E

last: Broyhill

first: A

last: Patro

first: K

middle: H

last: Bromert

first: C

last: Norton

first: H

middle: J

last: Kim

first: M

last: Li

first: J

last: Castorena-Gonzalez

first: B

middle: T

last: Drumm

last: Davis


title: Transcriptional profiling of sorted THP1 cells infected with wild-type Mtb (H37Rv) or ESX-1-mutant Mtb

city: Cambridge

first: Amy

middle: K.

last: Barczak

state: MA

address: The Ragon Institute, 400 Technology Square

department: Medicine/Infectious Diseases

institute: Massachusetts General Hospital

summary: THP1 cells were infected with wild-type or ESX-1-mutant Mtb expressing GFP. Cells were then sorted into infected and bystander populations, and RNAseq was performed.

overall_design: PMA-differentiated THP1 cells were infected with wild-type H37Rv-GFP or ∆ESX-1-Rv-GFP at an MOI of 10:1. 4 hours were allowed for phagocytosis, then cells were washed with PBS and the media was replaced. Cells were flow sorted into infected (GPF+) and bystander (GFP-) populations at 2, 4, 8, and 16 hours after the wash. Total RNA was isolated and bulk RNA sequencing was performed.


title: R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning

city: Freiburg im Breisgau

first: Manuel

last: Brenes-Álvarez

address: Schänzlestraße 1

department: Genetics and Experimental Bioinformatics

institute: University of Freiburg

summary: RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria is an example of cell differentiation in prokaryotes. Although multiple non-coding transcripts are involved in this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation of RNA-protein complexes after RNase treatment in density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates in Nostoc sp. PCC 7120. We validated in vivo the RNA-binding capacity of 6 RBP candidates. Alr1700 is an RBP with two OB-fold domains that is differentially expressed in heterocysts and interacts with non-coding regulatory RNAs. Deletion of alr1700 led to complete deregulation of the cell differentiation process, a striking increase in the number of heterocyst-like cells, and was ultimately lethal in the absence of combined nitrogen. These observations characterize this RBP as a master regulator of the heterocyst patterning and differentiation process, leading us to rename Alr1700 to PatR.

overall_design: CLIP-seq data of Alr1700-3xFLAG pull-down compared to a negative control (WT without FLAG-tagged proteins).

first: Halie

middle: R

last: Ropp

first: Dimitrios

last: Papagiannidis

first: Clement

last: Potel

first: Frank

last: Stein

first: Ingeborg

last: Scholz

first: Claudia

last: Steglich

first: Mikhail

last: Savitski

first: Agustín

last: Vioque

first: Alicia

middle: M

last: Muro-Pastor

first: Wolfgang

last: Hess


title: Selective translational control by PABPC1 phase separation regulates blast crisis and target therapy resistance of chronic myeloid leukemia [RIP-seq]

first: Zhongyang

last: Chen

overall_design: RIP-seq in K562 cells.

first: Chenguang

last: Sun

first: Yanni

last: Ma

first: Jia

last: Yu


title: Single Nucleus RNAseq Dataset of Soma-Germline Nucleoside Transport in Regulating Reproduction in C. elegans

city: Ashburn

first: Shihong

middle: Max

last: Gao

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: We presents a single-nucleus transcriptome analysis in the Wild-type(N2), ent-1KO mutant, ent-2KO mutant and ent-1KO;ent-2KD mutants which revealed that genes involved in purine metabolism were specifically up-regulated in the germline, suggesting the possible specificity of ENT-1/2 in transporting purine nucleosides.

overall_design: To perfom snRNAseq for wild-type, ent-1KO mutant, ent-2KO mutant and ent-1KO;ent-2KD mutant, we harvested and homogenized ~3,000 worms for each genotype/condition. Nuclei were isolated using fluorescence-activated cell sorting (FACS) based on the DNA content signal and then proceed with 10x Chromium sequcing.

first: Youchen

last: Guan

first: Meng

last: Wang


title: Transcriptomic Analysis of Circulating Extracellular Vesicles and Serum during the Perioperative period of Fontan and Glenn Surgery

city: Atlanta

first: Felipe

last: Takaesu

state: Georgia

address: 1562 Haygood Drive

institute: Emory University

type: Non-coding RNA profiling by high throughput sequencing

summary: Single-ventricle defects are palliatively corrected using the Glenn and Fontan procedures that provide lifesaving relief but lead to early mortality rates and poor prognosis post-operatively. The pathophysiology of these complications is diverse, and there are no clear predictors for these outcomes. As such, we aimed to identify novel biomarkers for single-ventricle associated outcomes through the characterization of the serum transcriptome and small extracellular vesicles (sEVs). We report on molecular responses in serum and sEVs pre-operatively and post-operatively in patients undergoing either Glenn or Fontan operations. We found that transcriptomes of serum RNA and sEV RNA are distinctly different, whereas differences between the Fontan and Glenn transcriptomes did not show any significant changes. An in vitro wound healing assay further confirmed that post-operative sEVs have higher angiogenic potential. Moreover, we used a partial-least square regression model to identify 100 RNAs and 50 microRNAs that are involved in angiogenesis-related pathways and accurately predict our wound healing results and compared them with our previously published models of ovine Fontan surgery. Lastly, an EV-origin analysis showed decreased secretion of sEV from cardiac tissue in post-operative samples and increased secretion of sEVs from stomach and nervous tissue. Overall, this study provided evidence that the circulating sEVs transcriptome are potent biomarkers and demonstrated the role of sEVs as a possible mediator for formation of veno-venous collaterals.

overall_design: We compared the transcriptome of serum and sEVs from patients undergoing Glenn or Fontan surgery and compared them pre-operatively. and post-operatively.

first: Michael

last: Davis


title: Phenotypic Screens Identify SCAF1 as Critical Activator of RNAPII Elongation and Global Transcription

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

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

overall_design: Refer to individual Series

first: Pranjali

last: Bhandare

first: Ashwin

last: Narain

first: Julia

last: Hofstetter

first: Teresa

last: Rummel

last: Wenzel

first: Christina

last: Schülein-Völk

first: Stephanie

last: Lamer

first: Ursula

last: Eilers

first: Andreas

last: Schlosser

first: Martin

first: Florian

last: Erhard


title: Targeting WNT Signaling for Improved Glioma Immunotherapy [IL13R?2-targeted CAR T cells]

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

summary: Metabolic gene expression analysis to explore ICG-001’s impact on metabolic changes  associated with glioma differentiation after disrupting the CBP/β-Catenin interaction by treating patient-derived  GBM cell lines PBT147 and PBT030 with ICG-001 (0, 5, or 10 µM) for 24 and 72 h using Nanostring nCounter platform

overall_design: Gene expression analysis using nanostring ecounter platform Nanostring nCounter mouse PanCancer Immune profiling panel

first: Margarita

last: Gutova

first: Raju

last: Pillai

first: Holly

last: Yin


title: Multifactoral Immune Modulation Potentiates Durable Remission in Multiple Models of Aggressive Malignancy

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

summary: Tumors typically lack canonical danger signals required to activate adaptive immunity and also frequently employ substantial immunomodulatory mechanisms that downregulate adaptive responses and contribute to escape from immune surveillance. Given the variety of mechanisms involved in shielding tumors from immune recognition, it is not surprising that single agent immunomodulatory approaches have been largely unsuccessful in generating durable antitumor responses. Here we report a unique combination of immunomodulatory and cytostatic agents that recondition the tumor microenvironment and eliminate complex and/or poor-prognosis tumor types including the aggressive MOC-2 model of HNSCC. scRNAseq analysis implicated up-regulation of innate immune responses and antigen presentation in tumor cells and the myeloid cell compartment as critical early events.

overall_design: Single cell suspensions were generated from six MOC-2 tumor-bearing male mice at 24 hours after intratumoral drug or vehicle treatment. Live cells were isolated by FACS sorting. Each tumor sample was tagged with a Multiplexing Oligo (10x Genomics) and sequenced with NovaSeq X Plus PE150 by the Novogene Corporation. Data processing was performed using Cell Ranger v.7.1 and Seurat v4.1.0.

first: William

last: Decker

first: Henry

last: Withers


title: RNA-Seq of GB2-treated and untreated RAW264.7 cells

city: xi'an

first: Wei

last: Gaofei

state: Shaanxi

address: beilin

institute: Northwestern Polytechnical University

summary: RAW264.7 cells treated with GB2 or not were collected and then the total RNA was isolated. After removal of the remaining genomic DNA, MRNA was purified from total RNA using polyT and then fragmented with 10x RNA fragmentation buffer and the RNA-seg library was constructed using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit and was sequenced.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GB2 treated group and untreated group. Each group was replicated for three times.

first: Aohua

last: Deng

first: Gaofei

last: Wei


title: RNA-Seq of GB2-treated and untreated MC38 tumors

summary: MC38 tumors from C57BL/6 mice treated with GB2 or PBS were collected and then the total RNA was isolated. After removal of the remaining genomic DNA, MRNA was purified from total RNA using polyT and then fragmented with 10x RNA fragmentation buffer and the RNA-seg library was constructed using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit and was sequenced.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for GB2 treated group and PBS treated group. Each group was replicated for three times.


title: Dysfunctional effector memory CD8 T cells in the bronchoalveolar compartment of people living with HIV

city: Durban

first: Emily

middle: Beth

last: Wong

state: KwaZulu-Natal

address: 719 Umbilo Road

department: Basic science laboratory

country: South Africa

institute: Africa Health research Institute

summary: Mechanisms by which HIV causes susceptibility to respiratory pathogens remain incompletely understood. We obtained whole blood and bronchoalveolar lavage (BAL) from people with latent TB infection in the presence or absence of ARV-naïve HIV co-infection. Transcriptomic and flow cytometric analyses demonstrated HIV-associated cell proliferation and type I interferon activity in blood and effector memory CD8 T-cells in BAL. Both compartments displayed reduced induction of CD8 T cell-related IL-17A in people with HIV, associated with elevated T cell regulatory molecule expression. We propose dysfunctional CD8 T cell responses in uncontrolled HIV contribute to susceptibility to secondary bacterial infections, including tuberculosis.

overall_design: BAL mini populations of specific immune cell subsets from people living with HIV

first: M

last: Mthembu

first: V

last: Voillet

first: G

last: Pollara

first: E

middle: B


title: Single-cell RNA Sequencing Reveals Tumor Subtypes Within Salivary Gland Pleomorphic Adenoma

city: Wuhan

first: qiwen

last: man

state: Hubei

address: Luyu road

institute: wuhan university

summary: Here, we performed single cell RNA sequencing (scRNA-seq) analysis for 27, 810 cells from 2 donors with primary salivary gland pleomorphic adenoma

overall_design: Single cell RNA sequencing (scRNA-seq) analysis of salivary gland pleomorphic adenoma

first: Xi-Qian

last: Wang

first: Li

last: Li


title: Effect of pemafibrate on gene expression under Th17 differentiation condition

city: Suita

first: Satoshi

last: Masuyama

state: Osaka

address: 2-2, Yamada-oka

department: Nephrology

institute: Osaka university

summary:
To investigate the effect of pemafibrate to Th17 cells,  we differentiated naive T cells under Th17 condition.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 groups at 48hr after polarization.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  vehicle and pemafibrate-treated cells.

first: Masayuki

last: Mizui


title: Longitudinal prospective and multicentric peripheral blood immune cell profiling of corneal transplant with acute rejection

city: Edinburgh

first: Max

last: Bylesjo

state: Scotland

address: BioCube 1, Edinburgh BioQuarter, 13 Little France Road

country: United Kingdom

institute: Fios Genomics Ltd

summary: This study evaluates the peripheral blood mononuclear cell transcriptomes of cornea transplant (CT) recipients from a prospective multi-center clinical study. 244 CT patients were recruited in 5 European clinical centers and biological samples were collected before and 6- and 12-months after the CT. Two groups of patients were recruited: 102 CT patients with a high risk of rejection and 142 with a low risk of rejection. The risk of rejection was defined according to consensus clinical features associated with higher or lower risk of rejection. The gene expression profiles from a total of 572 samples (277 high-risk and 296 low-risk) were generated using Affymetrix transcriptome-wide gene-level expression profiling microarray.

overall_design: To identify immunological biomarkers associated with the occurrence of acute rejection of CT, 244 CT patients were recruited in 5 European clinical centers and biological samples were collected before and during the 1st post-transplant year. Two groups of patients were recruited: 102 CT patients with a high risk of rejection and 142 with a low risk of rejection. The risk of rejection was defined according to consensus clinical features associated with higher or lower risk of rejection. Gender and age were equally distributed among the acute rejection and stable groups. Pre-existing systemic disease, clinical reason for CT, initial diagnosis in case of regraft, immunological event leading to regraft and the use of topical immunosuppressive drugs were equally distributed between CT patients who will later experience acute rejection. Microarray gene expression profiling was analyzed at each time point between samples with and without rejection separately for the high- and low-risk groups.

first: Jesper

last: Hjortdal

first: Matthew

last: Griffin

first: Marion

last: Cadoux

first: W

last: Armitage

first: Peadar

last: Mac Gabhann

first: Conor

middle: C

last: Murphy

first: Uwe

last: Pleyer

first: Derek

last: Tole

first: Bertrand

last: Vabres

first: Malcolm

last: Walkinshaw

first: Richard

last: Danger

first: Sophie

last: Brouard

first: Nicolas

last: Degauque


title: Dicer-2 senses a 5' secondary structural element of picorna-like viruses for priming antiviral RNA interference

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

country: France

institute: CNRS

summary:
Introduction: Insects as well as plants base their innate antiviral immunity on RNA interference (RNAi). In the model organism Drosophila melanogaster the replicating virus is sensed by the RNase III enzyme Dicer-2, which processes double stranded (ds) viral RNA into 21 nt long small interfering (si) RNAs. A distinctive advantage of the fly antiviral immune system is that these siRNAs provide a footprint of its action.
Methods: We use a combination of high throughput sequencing and genetics to unravel the mechanisms involved in viral RNA sensing in Drosophila. Particularly, we cloned and sequenced small RNAs from virus-infected flies. The sequencing was performed by Illumina HiSeq2000. Sequence strategy was 1 x 50 base pairs (bp).
Results: We identify a conserved RNA structure in the virus that serves as entry point for Dicer-2 to initiate RNA interference. The recognition of this structure is independent to the helicase activity of the protein. However, the hydrolysis of ATP is essential to mantain the enzyme fully processive.

overall_design: Flies were infected with Drosophila C Virus (DCV) and Cricket Paralysis Virus (CrPV). Total RNA was extracted from 12 flies (males and females in equal number) following Trizol (Ambion) datasheet. Small RNAs under 30 nucleotides in size were electrophoretically purified using 15% polyacrylamide gels and subsequently cloned following the protocol described by Sorefan et al., 2012.

first: Simona

last: Paro

first: Eric

last: Guimarães Rocha Aguiar

first: Laurent

last: Troxler

first: João

last: Trindade Marques

last: Westhof

first: Carine

last: Meignin


title: Chronic Interferon Stimulated Gene Transcription Promotes Oncogene Induced Breast Cancer

city: New York

first: Hexiao

last: Wang

state: NY

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center


title: Cerebellar organoids model cell type-specific FOXP2 expression during human cerebellar development

status: Public on Dec 19 2024

city: London

first: Elizabeth

last: Apsley

address: New Hunt's House, Guys campus

department: CDN

institute: Kings College London

summary: Cerebellar organoids differentiated from human induced pluripotent stem cells (iPSCs) contain key cerebellar cell types and are increasingly used to study cerebellar diseases. In this study, we demonstrate the potential of cerebellar organoids for studying features of early human cerebellar development. Forkhead box protein P2 (FOXP2) is a transcription factor associated with speech and language development that is highly expressed in the developing brain. However, little attention has been directed to the study of FOXP2 in the early developing cerebellum. Here we used CRISPR gene editing in human iPSCs to generate a fluorescent FOXP2-reporter line. By combining transcriptomic analysis of iPSC-derived cerebellar organoids with published cerebellar datasets, we describe the expression and identify potential downstream targets of FOXP2 in the early developing human cerebellum. Our results highlight expression of FOXP2 in early human Purkinje cells and cerebellar nuclei neurons, and the vulnerability of these cell populations to neurodevelopmental disorders. Our study demonstrates the power of cerebellar organoids to model early human developmental processes and disorders.

overall_design: RNA sequencing of populations of cells from day 63 cerebellar organoids sorted on the basis of FOXP2-mNeon expression.

first: Esther

last: Becker


title: eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency

first: Jianlong

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Translational control has emerged as a fundamental regulatory layer of proteome complexity that governs cellular identity and functions. As initiation is the rate-limiting step of translation, we carried out an RNAi screen for key translation initiation factors required to maintain embryonic stem cell (ESC) identity. We identified eIF4A2 and defined its mechanistic action through Rps26-independent and -dependent ribosomes in translation initiation activation of mRNAs encoding pluripotency factors and the histone variant H3.3 with demonstrated roles in maintaining stem cell pluripotency. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent 2-cell transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Accordingly, knockdown of eIF4A2 disrupts ESC proteome causing the loss of ESC identity. Collectively, we establish a translational paradigm of the protein synthesis of pluripotency transcription factors and epigenetic regulators imposed on their established roles in controlling pluripotency.

overall_design: RNA sequencing analysis was performed using the total RNA extracted from the sorted 2C double reporter ESCs infected with shNT or sheIF4A2. The double positive and double negative subpopulations were sorted.

first: Dan

last: Li

first: Jihong

last: Yang


title: BnaA07.WRKY40 transcription factor confers enhanced defensive response to sclerotinia sclerotiorum in Brassica napus

city: yangzhou

first: xvwen

last: shen

state: JiangSu

address: wenhui

institute: Yangzhou University

summary: Oilseed rape (Brassica napus, B. napus) is one of the most important oil crops globally, contributing significantly to the world's supply of vegetable oil. However, its production is severely threatened by Sclerotinia stem rot, a disease caused by the broad-host-range fungus Sclerotinia sclerotiorum (Lib.) de Bary (S. sclerotiorum). We have investigated the gene expression of J9712 and W40-OE2 during different time periods of Sclerotinia sclerotiorum infection through RNA-Seq analysis.

overall_design: W40-OE2 after 3h, 6h and 12h Sclerotinia sclerotiorum infection

first: Chen

last: Lin

first: Jian

last: Wu

first: Youping


title: Intranasal administration of a multiplex targeting SCLMs@FEN1-hpDNAs with synergistic baicalein for pulmonary anti-viral treatment

city: Nanjing

first: Shu

last: Xu

state: Jiangsu Province

address: China Pharmaceutical University

institute: China Pharmaceutical University

summary: Here we reported an anti-viral strategy for SARS-CoV-2 infection: intranasal administration of silica cross-linked micelles (SCLMs) encapsulating in vitro purified NES-FEN1-NES protein and a set of hpDNAs (shorted as SCLMs@FEN1-hpDNAs). The set of hpDNAs multiplex targeted SARS-CoV-2’s N gene RNA and the host Ctsl gene mRNA. In vitro experiments demonstrated the purified NES-FEN1-NES protein transfected into cells has efficient mRNA knockdown ability when guided by hpDNAs. The intranasal administration of SCLMs exhibited high pulmonary accessibility, and SCLMs@FEN1-hpDNAs effectively downregulated targeted gene expression in vivo. The efficacy is enhanced by synergistic intranasal baicalein by improving cellular uptake and anti-inflammatory effects. In a mouse model of SARS-CoV-2 infection, the combination with baicalein and SCLMs@FEN1-hpDNAs inhibited the virus replication, improved survival rates, and reduced neuroinflammation. This study highlights the potential of intranasal SCLMs@FEN1-hpDNAs with baicalein as a promising approach for treating respiratory diseases.

overall_design: To examine the intensity of the collateral effects of the FEN1-hpDNA, we performed total RNA integrity analysis and transcriptome-wide RNA-seq of A549 cells treated with FEN1-hpDNA. Data showed that ~ 44 and 107 genes were significantly up-regulated and down-regulated in FEN1-hpDNA group compared with the NT control, respectively .


title: Elucidating Sex-specific Immune Profiles in a Breast Cancer Model

city: Nashville

first: Ebony

last: Hargrove-Wiley

state: TN

address: 2220 Pierce Ave 738 PRB

department: Cancer Biology

institute: Vanderbilt University

summary: This study demonstrates sex differences in the hormonal and immune landscape of the MMTV-PyMT transgenic murine model of female and male ER+ breast cancer using single-cell RNA sequencing

overall_design: Matched whole tumors from MMTV-PyMT transgenic female (n=2) and male (n=2) mice.

first: Brianna

last: Caldwell

first: Barbara

last: Fingleton


title: Human Induced Pluripotent Stem Cells-Derived Neural Organoids as a Novel In Vitro Platform for Developmental Neurotoxicity Assessment

city: Kanagawa

first: Tsunehiko

last: Hongen

address: Fujisawa Jyonan

institute: Yokohama University of Pharmacy

summary: Rotenone is a neurotoxic substance that inhibits mitochondrial respiratory chain complex I, decreases ATP production and increases oxidative stress. It exhibits neurotoxic effects, particularly on dopamine-producing neurons, and is associated with the etiology of Parkinson’s disease. To better understand the impact of rotenone on neural development and function, we examined the effect of rotenone on gene expression using human induced pluripotent stem (iPS) cells-derived neural organoids. Cells were treated with rotenone as well as the controls at varying concentrations (0.3 μM, 1 μM, and 25 μM) for 48 hours. RNA was subsequently extracted, and RNA sequencing (RNA-seq) was performed to analyze gene expression profiles. The results revealed that rotenone exposure potentially suppresses critical ligand-receptor interactions involved in neural development. Network interaction analysis of KEGG signaling pathways highlighted the involvement of the focal adhesion pathway and the neuroactive ligand-receptor interaction pathway in the neurotoxic effects of rotenone.

overall_design: To evaluate the effects of rotenone exposure on the expression of genes related to neurodevelopment and synaptic transmission, undifferentiated hiPS cells were exposed to rotenone (0.3 μM, 1 μM, 25 μM) for 48 hours on the second day of differentiation. On day 4, total RNA was collected, RNA-seq data was obtained, and gene expression profiling analysis was performed.

first: Hideko

last: Sone

first: XianYang

last: Qin


title: liver GR epigenomic changes with rs6190 SNP genocopy

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: this dataset encompasses the liver GR epigenomic changes elicited in 4-month-old mice by the rs6190 genocopy allele

overall_design: We compared 4 months-old mice (C57BL/6J background) homozygous for the rs6190 SNP genocopy allele (R24K-homo) vs homozygous for the reference allele (R24K-WT). Livers were collected at ~ZT4 and immediately flash frozen for further processing.

first: Hima

last: Durumutla


title: Plasma DNA Methylation-Based Biomarkers for MPNST Detection in Patients with Neurofibromatosis Type 1

city: Houston

first: Keila

middle: E.

last: Torres

state: TX

address: 1515 Holcombe Blvd

department: Surgical Oncology

institute: The University of Texas MD Anderson Cancer Center

type: Methylation profiling by high throughput sequencing

summary: Malignant peripheral nerve sheath tumor (MPNST) development is characterized by an altered DNA methylation landscape, which presents a promising area for developing MPNST-specific biomarkers for screening patients with NF1. Genome-wide DNA methylation profiling of a cohort of 13 patients with MPNST (29 samples of tumor and adjacent neurofibroma tissues) and of NF1-MPNST cell lines was performed to identify and validate candidate MPNST-specific CpG sites (CpGs). A logistic regression prediction model was constructed to select MPNST-specific CpGs distinct from adjacent neurofibromas and normal tissues. To test if hypermethylation at selected CpGs can also be detected in plasma from patients with MPNST, cfMBD-seq was applied to profile the cfDNA methylome of blood from patients with MPNST and NF1. Based on stringent feature-selection criteria and predictive modeling, we identified 73 candidate MPNST-specific CpGs (67 with unique CpG island locations) that reliably discriminated MPNSTs from neurofibromas. Validation of five candidate biomarkers confirmed successful MPNST detection (sensitivity: > 88%, specificity: > 91%) in tissues. In plasma samples, 63 of 67 selected genomic regions had greater than 1.2-fold higher methylation in patients with MPNST than those with NF1. Further, we identified 15 CpG islands that consistently separated plasma from patients with confirmed MPNST diagnosis from plasma of individuals with NF1 without a diagnosis of malignant transformation (FDR < 0.1). Our findings confirmed a unique hypermethylation pattern present during malignant transformation. This study highlights the potential to be further investigated as biomarkers in clinical settings for early MPNST detection in patients with NF1.

overall_design:
We used plasma samples collected from 5 MPNST and 7 NF1 patients to compare the differences in methylation profile of 73 CpGs.
cfMBD-seq was applied to profile the cfDNA methylome of blood from patients with MPNST and NF1

first: Katarzyna

last: Tomczak

first: Manishkumar

middle: S

last: Patel

first: Angela

last: Bhalla

first: Christine

last: Peterson

first: Sharon

last: Landers

first: S

last: Callahan

first: Di

last: Zhang

first: Justin

last: Wong

first: Jace

middle: P

last: Landry

first: Alexander

last: Lazar

first: J

last: Livingston

first: B

last: Guadagnolo

first: Heather

middle: G

last: Lyu

last: Lillemoe

first: Christina

last: Roland

first: Emily

middle: Z

last: Keung

first: Christopher

last: Scally

first: Kelly

middle: K

last: Hunt

first: Ian

last: McCutcheon

first: John

last: Slopis

last: Gu

first: Paul

last: Scheet

first: Liang

last: Wang

first: Kunal

last: Rai


title: liver transcriptional changes with rs6190 SNP genotype (R24K in GR protein)

first: Mattia

last: Quattrocelli

summary: this dataset encompasses the transcriptomic changes elicited in liver tissues of 4-months-old mice with either the artificially-knock-in rs6190 genotype, or the control non-mutant (WT) genotype.

overall_design: Mice were obtained and interbred from the CCHMC Transgenic Core through CRISPR-mediated genomic engineering. Analyses were performed at ~16 weeks of age, comparing livers from littermate female mice homozygous for the SNP or homozygous for the reference allele. Tissues were harvested at ~ZT4.

first: Hima

last: Durumutla


title: Ex vivo-generated human CD1c+ regulatory B cells by a chemically defined system suppress immune responses and alleviate graft-versus-host disease

city: Guangzhou

first: yueming

last: sun

state: Guangdong

address: Zhongshan secand street 74

department: basic medicine

institute: Sun Yat-sen University

summary: IL-10+ regulatory B cells (Bregs) show great promise in treating graft versus host disease (GVHD), a life-threatening complication of post-hematopoietic stem cell transplantation. However, obtaining high-quality human IL-10+ Bregs in vitro remains a challenge due to the lack of unique specific marker and the triggering of pro-inflammatory cytokines expression. Here, by uncovering the critical signaling pathways in Bregs induction by mesenchymal stromal cells (MSCs), we firstly established an efficient Bregs induction system based on MSCs and GSK-3β blockage (CHIR-99021), which had a robust capacity to induce IL-10+ Bregs while suppress TNF-α expression. Furthermore, these Bregs population could be identified and enriched by CD1c+. Mechanistically, MSCs induced the expansion of Bregs through the PKA-mediated phosphorylation of cAMP response element binding protein (CREB). Thus, we developed a chemical-defined inducing protocol by PKA-CREB agonist, instead of MSCs, which can also effectively induce CD1c+ Bregs with lower TNF-α expression. Importantly, induced CD1c+ Bregs suppressed the proliferation of PBMC and the inflammatory cytokines secretion of T cells. When adoptive transferred to a humanized mouse model of GVHD, induced CD1c+ Bregs effectively alleviated GVHD. Overall, we establish an efficient ex vivo induction system for human Bregs, which has implications in developing novel Bregs-based therapies for GVHD.

overall_design:
To investigate alterations of B cells after induction with MSCs, we first analyzed the RNA-seq data of total B cells cocultured with MSCs.
We then uncover the relevant pathways by which MSCs regulated CD1c+ B cells.

first: Yingying

last: Bao

first: Xiaoyong

last: Chen

first: Andy Peng

last: Xiang


title: VCPIP1 facilitates pancreatic cancer progression via Hippo/YAP signaling

city: Shenyang

first: Zhihao

last: Liu

address: No.36 in sanhao street

institute: China Medical University

summary: The dys-regulation of Hippo signaling was observed in pancreatic adenocarcinoma (PAAD), while the over-activation of YAP was crucial for tumor progression. It is unclear why YAP was hyper-activated in PAAD, although the inhibitory phospho-cascade was still functional. Recently studies revealed that the ubiquitin modification of YAP also play important roles in Hippo/YAP axis and cancer progression. In order to understand the potential mechanisms of ubiquitination and deubiquitination process in YAP function, we carried out siRNA screening for critical deubiquitinases in PAAD. Via the deubiquitinases (DUB) library, we identified Valosin Containing Protein Interacting Protein 1 (VCPIP1) as an important effector in YAP function and PAAD progression. Inhibition of VCPIP1 hampered PAAD progression via Hippo signaling. Clinical data revealed that VCPIP1 was elevated in PAAD and correlated with poor survival in PAAD patients. Biochemical assays showed that VCPIP1 could interact with YAP and inhibit K48-linked poly-ubiquitination, which subsequently increased YAP stability. Interestingly, YAP could direct bind to VCPIP1 promoter region and facilitate its transcription in PAAD. Our study revealed a forward feedback loop between VCPIP1 and Hippo signaling in PAAD, indicating VCPIP1 as a potential therapeutic drug targets in PAAD.

overall_design: RNA-seq profiling of AsPC-1 cells transfected with siControl or siVCPIP1 for 48h


title: Examining the role of ER ⍺ and β in ovarian granulosa cell transdifferentiation in aged ovaries

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: To examine the role of estrogen receptors (ERs) on ovarian function in aged animals and indentify genes that may contribute to ovarian transdifferentation in ovaries lacking both ER⍺ and Erβ. Gene expression was examined in single knockout and double knockout ovaries and identified genes that were different in each. Among the three knockout animals examined, only 43 genes were shared among the Ex3⍺ERKO, Ex3βERKO and Ex3⍺βERKO compared to the control. The Ex3⍺ERKO ovaries had 645 genes differentially expressed, the Ex3βERKO had 94 genes differentailly expressed and the Ex3⍺βERKO had the most differentially expressed with 2,193 genes compared to control ovaries which had one allele of each ER.

overall_design: Ovaries were collected from year old mice and homogenized in TRIzol. Total RNA was isolated following manufacturers procedures.

first: April

last: Binder

first: Katerine

last: Burns

first: Karina

last: Rodriguez

first: Katerhine

last: Hamilton

first: Fernando

last: Pardo-Manuel de Villena

first: Kenneth

last: Korach


title: The Romboutsia ilealis and derived 2-oxindole-3-aceic acid regulate obesity-associated lipid accumulation via PSMD3-mediated YTHDF2 deubiquitination

city: Hangzhou

first: Luoyi

last: Zhu

state: Zhejiang

address: 866 Yuhang Tang Road

institute: Zhejiang University

summary: Specific gut microbiota is critically involved in metabolic diseases, including obesity. Through analysis of gut microbiota in diabetic patients and animal models, it was found that Romboutsia ilealis is closely associated with obesity. Here, our findings show that oral administration of Romboutsia ilealis significantly alleviates diet-induced obesity and metabolic dysfunction. Interestingly, this effect occurs not through modulation of food intake or energy expenditure, but by regulating lipid absorption and metabolism in the gut. Additionally, metabolomics analysis identified 2-oxindole-3-acetic acid (OAA) as the key metabolite involved in the regulation of obesity by Romboutsia ilealis. Its regulatory effect on intestinal lipid absorption was further validated both in vitro and in vivo. Mechanistically, using biotin-labeled OAA combined with proteomic analysis, we found that OAA directly interacts with the deubiquitin enzyme PSMD3, increasing the ubiquitination level of m6A binding protein YTHDF2 and reducing its protein stability, thereby enhancing intestinal lipid absorption. Furtherly, through m6A-seq, we discovered that YTHDF2 negatively regulates the expression of RXRB by recognizing the m6A sites on its mRNA, which in turn downregulates the expression of lipid absorption and transport proteins CD36 and FABP2, ultimately inhibiting intestinal lipid absorption. In summary, our findings reveal that Romboutsia ilealis and OAA regulate obesity-associated lipid accumulation through PSMD3-mediated deubiquitination of YTHDF2, suggesting that they represent novel prebiotics and probiotics with potential as therapeutic agents against obesity.

overall_design: MeRIP-seq analysis of IPEC-J2 cells after treatment with 0 μM and 25 μM OAA for 24h

last: Huang

first: Shuqi

first: Shiqi

last: Luo

first: Yige

last: Li

first: Yizhen

first: Xin

last: Zong


title: Very Low-Calorie Ketogenic Diet (VLCKD) and molecular liver cells modification mediated by Small Extracellular Vesicles (sEVs)

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

summary: The very low-calorie ketogenic diet (VLCKD) has emerged as an effective weight loss strategy for obese patients. It significantly reduces visceral adipose tissue (VAT), which is cardinal for mitigating metabolic complications associated with obesity. By promoting rapid weight loss, VLCKD helps to decrease insulin resistance and alleviate inflammation. Chronic liver inflammation can progress to severe conditions like non-alcoholic steatohepatitis and fibrosis, potentially resulting in liver failure and hepatocellular carcinoma. Transient elastography (FibroScan) is a known technique for assessing hepatic steatosis, with FIB E levels below 8kPa indicating low fibrosis risk (LR), while levels above 8kPa suggest a higher risk of chronic liver disease (IHR). Prevention of fibrosis includes lifestyle changes such as a healthy diet and increased physical activity. Traditional low-calorie diets often fail to achieve significant weight loss; hence, the very low-calorie ketogenic diet (VLCKD) is proposed as an effective strategy to decrease VAT and insulin resistance. Recent studies indicate extracellular vesicles (EVs), particularly small EVs (sEVs), play a crucial role in liver fibrosis by activating hepatic stellate cells. Our group identified that sEVs, to be involved in liver degeneration binded to the fibrosis. The aim of this study is to investigate the role of sEVs in 60 obese adults classified as LR and IHR based on FIB E score, enrolled in an 8-week VLCKD weight loss program. Remarkably, the cellular reactivity to sEVs derived from these patients in the early production and modulation of certain fibrosis markers, such as MMPs, and stress fibres Vimentin, and α-Actin was studied.

overall_design: We used RNA sequencing technology to understand the molecular changes of HEPA-RG after stimulation with patient-derived EXOs before (T0) and after (T1) treatment with a VLCKD, using samples from both IHR and LR patients

first: Emanuele

last: Piccinno

first: Francesco

last: Balestra

first: Maria

last: Scavo


title: Differential Gene Expression in oxaliplatin-resistant versus unteated PANC1 cells

city: Boston

first: Jonathan

last: Celli

state: MA

address: 100 Morrissey Blvd

institute: University of Massachusetts Boston

summary: We sought to examine changes in gene expression of PANC1 cells with acquired resistance to oxaliplatin chemotherapy. Cultures of PANC1 cells, an established pancreatic cancer cell line, were exposed to oxaliplatin chemotherapy over multiple passages and acquired a stable drug-resistant phenotype labeled as PANC1OR. Previously reported immunofluorescence and western blots indicate that PANC1OR exhibit increased EMT (increased cytoskeletal vimentin, decreased E-cadherin and fibroblast-like morphology). Here we sought to examine more broadly the differential expression of genes associated with acquired drug resistance in these cells.

overall_design: As reported in Cramer et al Mol Cancer Res (2017) PANC1 cells were grown with increasing concentrations of oxaliplatin (Tocris) in regular complete media over successive passages until a stable proliferative phenotype (PANC1OR) without chemotherapy was observed and maintained following cryopreservation and thawing. Drug resistance was confirmed by comparative dose response and measurement of a statistically significant increase in IC50. RNA was extracted from triplicate cell cultures of PANC1 and PANC1OR cells using the TRIzol reagent (Life Technologies Corporation, Carlsbad, CA). RNAseq was performed by the Center for Personalized Therapy Genomics Core at University of Massachusetts Boston. The quality of the raw fastq files were assessed using FastQC (v.0.11.5). Adaptor sequences, “AGATCGGAAGAGCACACGTCTGAACTCCAGTCA”, and “AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" were trimmed from the 3’ end of the reads using Cutadapt commandline tool form the Trime Galore package (v.0.4.2). The trimmed reads were mapped against the human reference genome (Ensemble, GRCh38) using STAR/2.5 using default parameters25. The average alignment rate was 96%. The sorted BAM files generated by STAR were used to estimate the transcript abundance per sample using featureCount from the Subread package (v.1.6.2)26. Gene expression analysis was performed using the edgR Bioconductor R package (v.3.24.3)27. The edgeR TMM method (trimmed mean of M values) was applied to the filtered genes utilizing the DGElist(), calcNormFactors(), estimateGLMCommonDisp(), estimateGLMTrendedDisp(), estimateGLMTagwiseDisp() functions. The glmFit and glmLRT functions from edgeR were used to fit a negative binomial generalized log-linear model to the read counts. The expression of the genes was ranked by logFoldChange (logFC) and false discovery rate (FDR). Differentially expressed genes (DEGs) were determined using abs(logFC) > 2 and FDR < 0.01 cutoffs, resulting in 1342 protein coding DEGs.

first: Eric

last: Struth

first: Maryam

last: Labaf

first: Vida

last: Karimnia

first: Yiran

last: Liu

first: Gwendolyn

last: Cramer

first: Joanna

last: Dahl

first: Frank

last: Slack

first: Kourosh

last: Zarringhalam


title: Elevation of Granulocyte colony stimulating factor (G-CSF) in human AMD donor RPE-choroid

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

summary: Single nuclei RNA sequencing identified choroidal endothelial cells and fibroblasts as the primary cell types responsible for increasing G-CSF expression in response to mCRP in RPE-choroid organ cultures.

overall_design: RPE and choroid were obtained from a single human donor and incubated in DMEM containing mCRP (treated) or PBS (control). Nuclei from both isolates were evaluated with single-nucleus RNA-seq.

first: Robert

middle: F

last: Mullins

first: Kelly

last: Mulfaul

middle: E


title: Gene expression data of NMDAR-E Associated with Ovarian Teratoma

city: Shanghai

first: Hexia

last: Xia

state: --- Select One ---

address: No.419 Fangxie Rd. Shanghai

institute: Obstetrics and Gynecology Hospital of Fudan University

summary: Purpose: To identify significantly differentially expressed genes and to investigate the intricate molecular regulatory network underlying anti-NMDA receptor encephalitis associated with ovarian teratoma. Methods: This retrospective study analyzed ovarian teratoma samples from patients with and without NMDAR-E. We employed RNA sequencing  for gene expression profiling. qPCR and Western blotting were used for gene and protein expression validation. Results: We identified 2524 significantly differentially expressed genes. The changes were notable in mRNA  levels in ovarian teratomas associated with NMDAR-E. Functional enrichment analysis highlighted extracellular matrix and immune activation pathways. Key genes and proteins involved in ferroptosis and immune activation, including SLC40A1, GGH, FKBP11, CCDC80, and ANK3, showed significant expression differences.Conclusions: Our findings offer deeper insights into the pathophysiology of NMDAR-encephalitis associated with ovarian teratomas. The identified biomarkers, particularly in ferroptosis and immune activation pathways, provide potential targets for diagnosis and treatment.

overall_design: To identify significantly differentially expressed genes and to investigate the intricate molecular regulatory network underlying anti-NMDA receptor encephalitis associated with ovarian teratoma, four ovarian teratoma samples from patients with NMDAR-E and three samples without NMDAR-E were collected. We then performed gene expresssion analysis of RNA-seq data of these samples.

first: Lingwei

last: Ma

first: Xinmen

last: Sun

first: Wei

last: Zhang


title: Only infant MLL rearranged leukemia is susceptible to an inhibition of PLK-1 by volasertib

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

summary: MLL rearranged (MLLr) leukemia is in general characterized by a poor prognosis. Depending on the cell of origin, it can differ in the aggressiveness and the therapy response. For instance, in adults, volasertib blocking Polo-like-Kinase 1 (PLK-1), was well-tolerated, but only with limited success. On the other site, PLK-1 characterizes an infant MLLr signature indicating a potential specific sensitivity. By using our CRISPR/Cas9 MLLr model in hematopoietic stem and progenitor cells (HSPCs), derived from both human cord blood (huCB) and bone marrow (huBM), mimicking exactly the infant and adult patient diseases, we were able to shed light on this phenomenon. PLK-1 was significantly increased in our huCB compared to huBM model and healthy HPSCs, that was underpinned by analyzing infant and adult MLLr leukemia patients. Importantly, the expression height correlated with a functional response. Volasertib induced a significant dose-dependent decrease of proliferation and cell cycle arrest most pronounced in the infant model. Mechanistically, upon volasertib treatment, we uncovered a negative feedback only in the huBM model by compensatory upregulation of PLK-1. Our study emphasizes the importance of the cell of origin in leukemogenesis and provides the rationale to further evaluate volasertib as new therapeutic strategy in infant MLLr leukemia.

overall_design: Human CD34+ cells derived from cord blood and bone marrow, modified by using CRISPR/Cas9 to carry an endogenous t(9;11) translocation were treated with volasertib for determining differential gene expression.

first: Corina

last: Schneidawind

first: Jacqueline

last: Fischer

first: Thomas

last: Hentrich


title: The circadian clock gene BMAL1 modulates autoimmunity features in lupus

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: An important pathogenic role for neutrophils in systemic lupus erythematosus (SLE) has been proposed. Neutrophils that lack brain and muscle aryl hydrocarbon receptor nuclear translocator-like 1 (Bmal1), one of the clock genes, are defective in aging and proinflammatory responses. We assessed the role of Bmal1 in clinical and immunologic manifestations of murine lupus and in human SLE neutrophils. We used myeloid-conditional Bmal1 knockout mice (Bmal1Mye−/−) and wild type (WT) that were treated with epicutaneous TLR7/8 agonist (imiquimod; IMQ) for 6 weeks to induce a lupus phenotype. Upon euthanasia, immune responses, autoantibodies and renal manifestations were evaluated. NET formation and gene expression of bone marrow (BM)-derived murine neutrophils were evaluated. BMAL1 expression was quantified in SLE neutrophils and compared with clinical disease. IMQ-treated Bmal1Mye−/− and WT displayed comparable systemic inflammation. While renal function did not differ, serum anti-dsDNA levels and renal immune complex deposition were significantly increased in Bmal1Mye−/−. While no differences were observed in NET formation, expression levels of April in BM neutrophils were significantly higher in Bmal1Mye−/−. Bulk RNA-sequence data showed that BM neutrophils in IMQ-treated Bmal1Mye−/− were relatively immature when compared to IMQ-treated WT. BM showed enhanced April protein expression in Bmal1Mye−/− mice. BMAL1 levels in human SLE peripheral blood neutrophils correlated positively with serum C3 and negatively with serum anti-dsDNA levels. Taken toghether, Bmal1 is associated with lower disease activity in SLE. These results indicate that perturbation in the circadian rhythm of neutrophils can have pathogenic consequences in SLE.

overall_design: To investigate the role of Bmal1 in mouse neutrophils, we obtained bone marrow neutrophils from untreated or imiquimod-treated Bmal1 Mye-/- or WT mice by negative selection. We then performed RNA sequensing with 5 samples in each group. Then comparison was made between untreated and imiquimod-treated animals and between Bmal1 Mye-/- and WT.

first: Shuichiro

last: Nakabo

first: Donavon

last: Sandoval-Heglund

first: Norio

last: Hanata

first: Victoria

last: Hoffmann

first: Mingzeng

first: William

last: Ambler

first: Zerai

last: Manna

first: Elaine

last: Poncio

first: Sarfaraz

last: Hasni

first: Shamima

last: Islam

first: Stefania

last: Dell'Orso

first: Mariana

middle: J

last: Kaplan