title: Human Adult Glial Progenitors Are Transcriptionally Distinct from Their Fetal Counterparts [bulk RNA-seq]

city: Rochester

first: Steven

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Glial progenitor cells (GPCs), the primary source of oligodendrocytes and astrocytes in the human CNS, emerge during the 2nd trimester of human development and subsequently colonize the brain, where a pool remains throughout adulthood.  While fetal GPCs are highly migratory and proliferative, there is evidence that their capacities diminish throughout aging or as a result of demyelination-induced exhaustion, thus compromising their ability to mobilize, remyelinate, and self-renew.  To investigate this mechanism, we first utilized bulk and scRNA-Sequencing to characterize the human fetal GPC pool and leveraged these data to elucidate transcriptional discrepancies in adult human GPCs.  This revealed age-induced transcriptional shifts towards loss of proliferative competency and the potential onset of senescence. Further, we inferred adult networks of direct repressive transcription factor activity that may drive functional decline during GPC aging.  Finally, we coupled these data with miRNA profiling of both populations to establish both upstream and parallel arms of repression that may stifle the functional aptitude of aged GPCs.  These identified upstream regulators may be ideal therapeutic targets toward rejuvenating GPCs crippled by mitotic exhaustion or aging.

overall_design:
Human brain samples were obtained under approved Institutional Review Board protocols from consenting patients at Strong Memorial Hospital at the University of Rochester.  Brain tissue was obtained from normal GW 18-24 cortical and/or VZ/SVZ dissections or adult white matter/cortex epileptic resections (18,19, and 27 years old for mRNA, 8, 20, 43, and 54 years old for miRNA).  Fetal GPC acquisition, dissociation and immunomagnetic sorting of A2B5+/PSA-NCAM- cells were as described (Windrem et al., 2004). GPCs were isolated from dissociated tissue using a dual immunomagnetic sorting strategy: depleting mouse anti-PSA-NCAM+ (Millipore, DSHB) cells, using microbead tagged rat anti-mouse IgM (Miltenyi Biotech), then selecting A2B5+ (clone 105; ATCC, Manassas, VA) cells from the PSA-NCAM- pool, as described (Windrem et al., 2004; Windrem et al., 2008). After sorting, cells were maintained for 1-14 days in DMEM-F12/N1 with 10 ng/ml bFGF and 20 ng/ml PDGF-AA. Alternatively  CD140a/PDGFRA-defined GPCs were isolated and sorted using MACS as described (Sim et al., 2011b), yielding an enriched population of CD140+ glial progenitor cells.

Please note that the 'bulkRNA_counts.txt' contains the processed data for both GSE165994 and GSE142306 samples.

first: John

middle: N

last: Mariani

first: Erin

last: Kesel

first: Nguyen

last: Huynh

first: Devin

last: Chandler-Militello

middle: A


title: Halofuginone is a potent inhibitor of SARS-CoV-2 Infection and Replication [Exp3]

status: Public on Aug 28 2023

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

type: Expression profiling by high throughput sequencing

summary: Here we identify halofuginone, a Prolyl-tRNA Synthetase (PRS) inhibitors as a potent inhibitors of SARS-CoV-2 cellular entry and viral replication. To infect the host cell, the SARS-CoV-2 spike protein interacts with cell surface heparan sulfate (HS) and angiotensin-converting enzyme 2 (ACE2) through its Receptor Binding Domain. Removal of cell surface HS or blockade of HS biosynthesis represents a promising clinical target for treatment of SARS-CoV-2. In vitro studies confirm that halofuginone and PRS inhibitors prevent HS biosynthesis and thereby HS cell surface presentation and Spike protein binding. Halofuginone also suppresses authentic SARS-CoV-2 infection by inhibiting PRS activity, which decreases the translation efficiency of proline-rich HS biosynthetic enzymes and essential SARS-CoV-2 proteins after infection. Thus, halofuginone inhibits SARS-CoV-2 at both attachment and post-entry steps and blocks SARS-CoV-2 infection of human lung airway epithelial cells at low nanomolar concentrations. These findings support the use of halofuginone, an orally bioavailable anti-fibrotic and anti-inflammatory compound with encouraging clinical phase 1 safety data, as an antiviral drug to prevent SARS-CoV-2 infection.

overall_design: Examination of the effect of Halofuginone, Borrelidin, ProSA, SerSA VeroE6 cells

middle: P

first: Philip

middle: L

last: Gordts


title: Regulation of Endogenous Retroviruses and Cellular Genes by HIV-1 Rev

city: Charlottesville

first: Lou

last: Hammarskjold

state: VA

address: 1340 Jefferson Park Avenue

country: USA

institute: University of Virginia

summary: A combination of bioinformatics, RNAseq, and cell-based functional assays were used to study the changes in host cell gene expression when HIV-1 Rev was expressed. These results suggest that HIV Rev is capable of modulating gene and mRNA isoform expression, during HIV-1 infection.

overall_design: Investigation into host cell gene expression when HIV-1 Rev is expressed in T-lymphocyte cells.

first: Laurie

middle: R

last: Gray

first: David

last: Rekosh


title: Halofuginone is a potent inhibitor of SARS-CoV-2 Infection and Replication [Exp2]

summary: Here we identify halofuginone, a Prolyl-tRNA Synthetase (PRS) inhibitors as a potent inhibitors of SARS-CoV-2 cellular entry and viral replication. To infect the host cell, the SARS-CoV-2 spike protein interacts with cell surface heparan sulfate (HS) and angiotensin-converting enzyme 2 (ACE2) through its Receptor Binding Domain. Removal of cell surface HS or blockade of HS biosynthesis represents a promising clinical target for treatment of SARS-CoV-2. In vitro studies confirm that halofuginone and PRS inhibitors prevent HS biosynthesis and thereby HS cell surface presentation and Spike protein binding. Halofuginone also suppresses authentic SARS-CoV-2 infection by inhibiting PRS activity, which decreases the translation efficiency of proline-rich HS biosynthetic enzymes and essential SARS-CoV-2 proteins after infection (data not provided here). Thus, halofuginone inhibits SARS-CoV-2 at both attachment and post-entry steps and blocks SARS-CoV-2 infection of human lung airway epithelial cells at low nanomolar concentrations. These findings support the use of halofuginone, an orally bioavailable anti-fibrotic and anti-inflammatory compound with encouraging clinical phase 1 safety data, as an antiviral drug to prevent SARS-CoV-2 infection.

overall_design: Examination of the effect of ISRIB on halofuginone response in Hep3B cells


title: Halofuginone is a potent inhibitor of SARS-CoV-2 Infection and Replication [Exp1]

overall_design:
Examination of the effect of Halofuginone vs DMSO on Hep3B cells
Examination of the effect of Halofuginone, Borrelidin, ProSA, SerSA on VeroE6 cells


title: Halofuginone is a potent inhibitor of SARS-CoV-2 Infection and Replication

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

overall_design: Refer to individual Series


title: Tbx1 promotes neo-lymphangiogenesis and constraints the immune response to facilitate repair.

city: Shanghai

first: Min

last: Zhang

state: Shanghai

address: 1678 Dongfang Road

department: Shanghai Children's Medical Center

country: China

institute: Shanghai Jiao Tong University School of Medicine


title: Transcription profiling of Tbx1 function in adult myocardial infarction hearts [bulk RNA-seq]

summary: Post-myocardial infarction (Post-MI) heart failure is an unanswered clinical challenge. Current immunological intervention trials to reduce MI damage are unsatisfactory. Tbx1, the major 22q11.2 deletion syndrome (22q11.2DS) disease gene, reactivated in cardiac lymphatic endothelial cells (LECs) to promote post-MI repair. Endothelial deletion of Tbx1 deteriorated post-MI cardiac function. To identify the initial endothelial-derived gene expression changes that are responsible for lymphangiogenesis and cell non-autonomous functions towards immune cells after MI, we enriched CD31+ endothelial cells from 5 dpMI Ctrl and Tbx1cko hearts and performed RNA-seq. In conclusion, our findings revealed that Tbx1 can promote lymphangiogenesis and alleviate excessive cardiac inflammation in post MI hearts.

overall_design: Transcriptomic analysis on Ctrl and Tbx1 endothelial knockout hearts after myocardial infarction.

first: Wenfeng

last: Wang

first: Zhen


title: Defective Branched-Chain Amino Acid Catabolism in Dorsal Root Ganglia Contributes to Mechanical Pain

status: Public on Aug 27 2023

city: chengdu

first: huijing

last: xie

state: Please select an option

address: china

institute: westchina

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Impaired branched-chain amino acid (BCAA) catabolism has recently been implicated in the development of mechanical pain, but the underlying molecular mechanisms are unclear. Here we report that defective BCAA catabolism in dorsal root ganglion (DRG) neurons sensitizes mice to mechanical pain by increasing lactate production and expression of the mechanotransduction channel Piezo2. In high-fat diet-fed obese mice, we observe downregulation of PP2Cm, a key regulator of the BCAA catabolic pathway, in DRG neurons. Mice with conditional knockout of PP2Cm in DRG neurons exhibit mechanical allodynia under normal or SNI-induced neuropathic injury conditions. Furthermore, the VAS scores in the plasma of patients with peripheral neuropathic pain are positively correlated with BCAA contents. Mechanistically, defective BCAA catabolism in DRG neurons promotes lactate production through glycolysis, which increases H3K18la modification and drives Piezo2 expression. Inhibition of lactate production or Piezo2 silencing attenuates the pain phenotype of knockout mice in response to mechanical stimuli. Therefore, our study demonstrates a causal role of defective BCAA catabolism in mechanical pain by enhancing metabolite-mediated epigenetic regulation.

overall_design: Cut-tag for H3K18la in mouse DRG neurons

first: Huijing

last: Xie

first: Ju

last: Li

last: Lian


title: Single cell RNAseq profiling of Tbx1 function in adult post myocardial infarction hearts [scRNA-seq]

summary: Post-myocardial infarction (Post-MI) heart failure is an unanswered clinical challenge. Current immunological intervention trials to reduce MI damage are unsatisfactory. Thus a thorough understanding of post-MI immune response is imperative. Tbx1, the major 22q11.2 deletion syndrome (22q11.2DS) disease gene, reactivated in cardiac lymphatic endothelial cells (LECs) to promote post-MI repair. Endothelial deletion of Tbx1 deteriorated post-MI cardiac function through a dual approach, impaired lymphangiogenesis and weakened immunosuppression. To characterize cell autonous function of Tbx1 in endothelial population and cell non-autonous effect in immune cells, we set to performed scRNA-seq on Ctrl (Tbx1flox/flox) and Tbx1cko (Fabp4-Cre;Tbx1flox/flox) hearts. The dataset is comprised of total 55,106 single cells transcriptomes. We identified eight principal non-myocyte types with their known markers, including CD31-expressing vascular endothelial cell (VEC), LEC, pericyte, as well as CD45-expressing monocyte/macrophage, dendritic cell (DC), neutrophil, T/innate lymphoid cell (ILC), and B cell. Interestingly, we found that the relative percentage of monocyte/macrophage population, which is most abundant among all immune cells, was significantly decreased in Tbx1cko hearts, whereas T/ILC population was increased. Taken together, single cell transcriptomic analyses suggest a potential cell non-autonomous effect that Tbx1 deficiency in endothelium may cause imbalance in immune response.

overall_design: We set to performed scRNA-seq on enriched CD31+ endothelial cells and CD45+ leucocytes from Ctrl and Tbx1cko hearts. We collected samples at 4, 5, 6, and 7 dpMI, reasoning that the the most significant cellular and transcriptional distincts between Ctrl and Tbx1cko would occur during the initial 4-day window of Tbx1 reactivation.

first: Xiao


title: Characterization of distinct types of open chromatin and their impacts on gene transcription in maize

city: Nanjing City

first: Wenli

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: Nanjing Agricultural University

sample_organism:
Arabidopsis thaliana
Zea mays

platform_organism:
Arabidopsis thaliana
Zea mays


title: Characterization of distinct types of open chromatin and their impacts on gene transcription in maize [ChIP-seq]

summary: Open chromatin plays key roles in regulating gene expression in eukaryotic genomes. However, functional implications of fragile nucleosome overlapping open chromatin are still largely unknown, especially in plants. Here, through simultaneous measurement of MHSs and nucleosomes, we detected two distinct types of open chromatin, one with nucleosome-free (type-I MHSs) and the other with fragile nucleosomes (type-II MHSs) in maize and Arabidopsis. Both types of MHSs can function as cis-regulatory elements and have similar TF binding motifs. Furthermore, fragile nucleosomes with MHSs have unique DNA sequence features with less AT and more GC dinucleotides, whereas other fragile nucleosomes without overlapping MHSs have more AT and less GC dinucleotides. In particular, we observed distinct fragile nucleosome positioning patterns occurred around the summit of type-I and type-II MHSs, phased fragile nucleosome arrays and only two well-phased fragile nucleosomes surrounding the summit of type-I and type-II MHSs, respectively. We finally found that type-II MHS-related genes with BCTSS or SCTSS express more than type-I-related genes with the corresponding CTSS, which is mediated by combined actions of MHSs with TFs, fragile nucleosomes, Pol II and epigenetic marks.

first: K

last: Lin

first: J

last: Gao

first: W


title: Estrogen-mediated regulation of Fam3d in mouse uterus during the estrous cycle

city: Seoul

first: Hyukjung

last: Kim

address: 120, Neungdong-ro

department: Stem cell and regeneration biotechnology

country: South Korea

institute: Konkuk University

summary: The uterus, a female reproductive organ regulated by the sex hormones estrogen and progesterone, undergoes periodic cyclical changes. The estrous cycle refers to the reproductive cycle in non-primate mammalian females. During the mouse estrous cycle, the uterus undergoes various physiological changes as a result of dynamic hormonal changes. Accurate regulation of these changes is crucial for the establishment of a successful pregnancy. Notably, estrogen plays an important role in the regulation of the proestrus and estrus stages of the estrous cycle. Family with sequence similarity 3 (Fam3) is a cytokine-like gene family with four members: Fam3a, Fam3b, Fam3c, and Fam3d. Expression and regulation of the Fam3 family members in mouse uterine physiology remain largely unknown. Therefore, this study aimed to investigate the expression of Fam family members in the uterus during the estrous cycle and evaluate its regulation by estrogen using a mouse model. Analysis of mouse uterine RNA sequencing data revealed upregulated expression of Fam3b, Fam3c, and Fam3d during the proestrus and estrus stages. Fam3d expression was dynamically regulated during the estrous cycle, with high expression levels during the proestrus and estrus stages. To investigate whether Fam3d expression is regulated by estrogen, we administered estradiol (E2) to ovariectomized mice at different time points. Fam3d expression was highest 24 h after E2 injection, suggesting that estrogen plays a crucial role in regulating Fam3d expression. Furthermore, inhibition experiments using the estrogen receptor alpha (ERα) antagonist ICI revealed that estrogen regulates Fam3d expression through the ERα-mediated pathway. Immunofluorescence staining demonstrated that FAM3D was exclusively expressed in the luminal and glandular epithelia but not in the stroma. Additionally, FAM3D was predominantly localized in the cytoplasm, particularly in the apical region, and not in the nucleus. These findings provide valuable insights into the potential role of Fam3d in the uterus and lay the groundwork for future research on its function and significance in uterine physiology.

overall_design: To study the genes that depend on the estrous cycle, we determined the estrous cycle in mice using a vaginal smear assay.

first: Byeongseok

first: Giwan

last: Lee

first: Minju

last: Kang

first: Joohee

first: Youngsok

last: Choi


title: Characterization of distinct types of open chromatin and their impacts on gene transcription in maize [MNase-seq]

overall_design: Low-MNase-seq, High-MNase-seq.


title: Characterization of distinct types of open chromatin and their impacts on gene transcription in maize [MH-seq]

overall_design: MH-seq


title: Expression data of 5-FU and Rapamycin treated wild type and DDIT4-deficient human gastric cancer BGC-803 cell line

city: Shenyang City

first: Zhenning

address: 155 North Nanjing Street

department: Department of Surgical Oncology and General Surgery

institute: The First Affiliated Hospital of China Medical University

summary:
We used mircoarray to identify the potential regulation on the gene level between DDIT4+/+ and DDIT4−/− cells treated with 5-FU at 24h.
Genes related to protein secretion, androgen response, mitotic spindle, hypoxia, TNFa signaling via NFKB, apoptosis, glycolysis, mTORC1 signaling, G2M checkpoint, KRAS signaling up are enriched in the DDIT4KO gastric cancer cell treated with 5-FU.

overall_design: RNA from gastric cancer cells was isolated from DDIT4KO and NC MGC-803 cells that were treated with 5-FU 24 hours. DDIT4KO cells treated with 5-FU have significantly increased proliferation compared with NC cells. DDIT4KO and NC MGC-803 gastric cancer cells treated with 5-FU was compared to determine DDIT4 tragets under stimulation in gastric cancer.

first: Zhi-Feng

last: Miao

first: Jing-Xu

last: Sun

first: Jason

middle: C

last: Mills

first: Zhen-Ning


title: Serum microRNA panel to differentiate malignant pulmonary nodules from benign pulmonary nodules

city: Zhengzhou

first: Liping

last: Dai

state: Henan

address: 40 Daxue Road

institute: Zhengzhou University

summary: A serum miRNA combination could be a favourable classifier to differentiate malignant pulmonary nodules from benign pulmonary nodules.

overall_design: Serum miRNA profiles of 30 samples, which consist of 10 samples from patients with malignant pulmonary nodules, 10 samples from patients with benign pulmonary nodules, and 10 samples from healthy individuals. Aim to reduce bias caused by sample heterogeneity, each serum sample as a pool included two participants.

first: Man

last: Liu

first: Qiufang

last: Si

first: Ting

last: Yang


title: Neutrophil Death Medicates Alveolar Macrophage Proliferation and Phagocytosis

status: Public on Aug 26 2023

city: ROCHESTER

first: Xiaochen

state: MN

address: 200 first street SW

department: Immunology

institute: Mayo Clinic

summary: In this report, we performed bulk RNA sequencing of AMs from AMs (alone), AM: BAL neutrophils (BAL), and AM: PR8 neutrophils (PR8) (1:1 ratio).

overall_design: AMs from mono-cultured AMs and co-cultured AMs with BAL and PR8 neutrophils

first: Min

last: Cui


title: Group 1 metabotropic glutamate receptor expression defines a T cell memory population during chronic Toxoplasma infection that enhances IFN-gamma and perforin production in the CNS

city: Riverside

first: Edward

last: Vizcarra

state: California

address: 900 University Ave

institute: UC Riverside

summary: Within the brain, a pro-inflammatory response is essential to prevent clinical disease due to Toxoplasma gondii reactivation. Infection in the immunocompromised leads to lethal Toxoplasmic encephalitis while in the immunocompetent, there is persistent low-grade inflammation which is devoid of clinical symptoms. T cells are the dominant immune cell that prevent clinical disease, and this is mediated through the secretion of effector molecules such as perforins and IFNγ. However, other extrinsic signals that promote protection and the formation of memory T cells within tissue are poorly understood. During chronic infection, there is an increase in extracellular glutamate that, due to its function as an excitatory neurotransmitter, is normally tightly controlled in the brain. To investigate glutamate’s influence of CD8 T cells, single cell RNA-sequencing (scRNA-seq) was performed on brain CD8 T cells that were cell-sorted for CD3+CD8+mGluR1-mGluR5- or CD3+CD8+mGluR1+mGluR5+ expression. In addition, we also sorted on splenic CD8 T cells isolated from 3wpi mice with the aforementioned genotype for comparative analysis

overall_design: We sequenced 27497 sorted CD8 T cells from Toxoplasma-infected brain (8904) or spleen (18593), 3-weeks post infection (wpi). This dataset is composed of one sorted population of CD3+CD8+mGluR1-mGluR5- brain T cells (7676), and three replicates of CD3+CD8+mGluR1+mGluR5+ brain T cells (324, 570, 334). Additionally,  splenic T cells were also sorted for CD3+CD8+mGluR1-mGluR5- (16091) or CD3+CD8+mGluR1+mGluR5+ (2502) expression.

first: Emma

middle: H

last: Wilson


title: Integrated analysis of dysregulated long non-coding RNA and mRNA expression profiles and function prediction in SH-SY5Y cells exposed to manganese

city: Beijing

first: Piye

last: Niu

state: Beijing

address: You An Men Wai Xi Tou Tiao 10#

department: Department of Occupational and Environmental Health,School of Public Health

institute: Capital Medical University

summary: To investigate whether lncRNAs and mRNAs expression changes in human neuroblastoma cells (SH-SY5Y) following excessive Mn treatment, we have employed whole genome microarray expression profiling.

overall_design: Manganese induced expression profiles of lncRNAs and mRNAs in dopaminergic SH-SY5Y cells were measured at 6 hours after exposed to doses of 0 and 500μM MnCl2. Three independent experiments were performed at each time using different donors for each experiment.

first: Li

last: Chen

first: Dongmei

last: Song

first: Yuanyuan

last: Zhang


title: Morphine addiction-NAc_RNA sequencing

city: Shijiazhuang

first: Hongyu

address: Tiyu

institute: Hebei Medical University

summary: The current study aimed at addressing a question: How the expression of key lncRNAs is altered in the NAc during the formation of morphine addiction memory? To answer these two questions, the mice were trained by using the conditioned place preference (CPP) paradigm. Then, the aberrant expression of lncRNAs was identified in the NAc tissue of the mice by RNA-sequencing.

overall_design: The NAc tissues from C57BL/6N mice from the two groups that were subjected to morphine or saline training CPP model were harvested; three samples (6 mice) from each group were used for total RNA isolation. RNA-seq was performed by BioMarker (Beijing, China). In short, following RNA quantification and qualification, RNA integrity was examined with the RNA Nano 6000 Assay Kit and the Agilent Bioanalyzer 2100 library preparation for RNA sequencing system (Agilent Technologies, CA, USA). Any library preparations in this study were sequenced on an an Illumina platform. The known lncRNAs were differentiated from the assembled transcripts if the sequencing species has known lncRNA annotations. The remaining transcripts(unknown transcripts) were used to screen for putative lncRNAs.Three computational approaches include CPC/CNCI/Pfam/CPAT were combined to sort non-protein codingRNA candidates from putative protein-coding RNAs in the unknown transcripts. Putative protein-coding RNAs were filtered out using aminimum length and exon number threshold. Transcripts with lengths more than 200 nt and have more than two exons were selected as lncRNA candidates and further screened using CPC/CNCI/Pfam/CPAT that have the power to distinguish the protein-coding genes from the non-coding genes. As well as the different types of lncRNAs include lincRNA, intronic lncRNA, anti-sense lncRNA ,sense lncRNA were selected using gffcompare.

first: Di

last: Wen

first: Chunling

last: Ma

first: Bing

last: Xie


title: NRF2 is a spatiotemporal metabolic hub driving the polyfunctionality of Th2 cells in allergic asthma

status: Public on Aug 25 2023

city: Incheon

first: Hye-Yeon

last: Ju

address: 119 Academy-ro Yeonsu-gu, Incheon Republic of Korea

institute: Incheon National University

summary: Polyfunctional Th2 cells play a crucial role in triggering diverse pathogenic responses in allergic diseases by producing multiple cytokines. However, the precise mechanism underlying their polyfunctionality remains elusive. In this study, we elucidate the pivotal role of Nrf2 in polyfunctional Th2 cells during allergic asthma. We found that an increase in reactive oxygen species (ROS) in immune cells infiltrating the lungs is necessary for the development of eosinophilic asthma. Deletion of the ROS sensor Nrf2 specifically in T cells, but not in dendritic cells, significantly abolished eosinophilia and polyfunctional Th2 cells in the airway. Mechanistically, Nrf2 intrinsic to T cells is essential for inducing optimal oxidative phosphorylation and glycolysis capacity, thereby driving Th2 cell polyfunctionality, partially by inducing PPARγ, independently of IL-33. Treatment with an Nrf2 inhibitor leads to a substantial decrease in polyfunctional Th2 cells and subsequent eosinophilia in mice, and a reduction in the production of Th2 cytokines from peripheral blood mononuclear cells (PBMCs) in asthmatic patients. These findings highlight the critical role of Nrf2 as a spatial and temporal metabolic hub that is essential for polyfunctional Th2 cells, suggesting potential therapeutic implications for allergic diseases.

overall_design: We employed murine models of allergic asthma to study the role of Nrf2 in helper T cell immunity and allergic disorders. We disrupted the Nrf2 activity with a small molecule inhibitor or a conditional deletion of Nfe2l2 in T cells (CD4∆Nrf2). Single cell RNA-seq was performed to screen for potential target pathways of Nrf2.

first: Garam

last: Choi

first: Jahyun

last: Bok

first: Jungseo

first: Jae

middle: W

last: Shin

first: Hansol

last: Oh

first: Yeojin

last: Jeon

first: Jiyeon

last: Kim

first: Daehong

first: Heesu

last: Moon

first: Jeong-Eun

last: Lee

first: Young-Sam

last: Keum

first: You-Me

first: Hye

middle: Y

first: Sung

last: Park

first: Mi-Ryung

last: Han

first: Yeonseok

last: Chung


title: Mammalian mitochondrial translation infidelity leads to oxidative stress-induced cell cycle arrest and cardiomyopathy

first: Wenqiang

last: Zheng

address: No. 320 Yueyang Road, Shanghai

institute: SIBCB

summary: Editing of mischarged tRNAs by cytoplasmic aminoacyl-tRNA synthetases (aaRSs) is of high significance for protein homeostasis, whose impairment causes neurodegeneration. However, whether mitochondrial translation needs fidelity and the significance of proofreading (editing) by mitochondrial aaRSs are long-term mysteries. Here, we showed that NIH-3T3 cell line critically depend on the editing of mitochondrial threonyl-tRNA synthetase (Tars2) editing, the disruption of which accumulated Ser-tRNAThr and generated a large abundance of Thr-to-Ser misincorporated peptides. Such infidelity impaired mitochondrial translation and oxidative phosphorylation, causing oxidative stress and cell cycle arrest at G0/G1 phase. ROS removal by N-acetylcysteine relieved abnormal cell proliferation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NIH-3T3 cells and its mutate derivative (NIH-3T3-MU).

first: Wen-Qiang

first: Jian-Hui

last: Zhang

first: Zi-Han

last: Li

first: Xiuxiu

last: Liu

first: Yong

first: Shuo

last: Huang

first: Jingsong

first: Bin

last: Zhou

first: Gilbert

last: Eriani

first: En-Duo

last: Wang

first: Xiao-Long


title: RUNX1 loss renders hematopoietic and leukemic cells dependent on interleukin-3 and sensitive to JAK inhibition [ATAC-seq]

city: San Francisco

first: Amy

last: Fan

state: CA

address: 769 25th Ave

department: Pathology

institute: UCSF

summary: Disease-initiating mutations in the transcription factor RUNX1 occur as germline and somatic events that cause leukemias with particularly poor prognosis. However, the role of RUNX1 in leukemogenesis is not fully understood and effective therapies for RUNX1-mutant leukemias remain elusive. Here, we use primary patient samples and a RUNX1 knockout model in primary human hematopoietic cells to investigate how RUNX1 loss contributes to leukemic progression and to identify targetable vulnerabilities. Surprisingly, we found that RUNX1 loss decreased proliferative capacity and stem cell function. However, RUNX1-deficient cells selectively upregulated the interleukin-3 (IL-3) receptor. Exposure to IL-3, but not other JAK/STAT cytokines, rescued RUNX1 KO proliferative and competitive defects. Further, we demonstrated that RUNX1 loss repressed JAK/STAT signaling and rendered RUNX1-deficient cells sensitive to JAK inhibitors. Our study identifies a dependency of RUNX1-mutant leukemias on IL-3/JAK/STAT signaling, which may enable these aggressive blood cancers to be targeted with existing agents.

overall_design: Comparative chromatin accessibility analysis of cord blood derived CD34+ gene edited at the AAVS1 or RUNX1 locus. 4 biological replicates.


title: Uncovering transcriptomic landscape alterations of CAN-2409 in in vitro and in vivo glioma models

city: Boston

first: Sean

last: Lawler

state: MA

address: 75 Francis St

institute: Brigham and Women's Hospital

summary: Rationale: CAN-2409 is a locally delivered oncolytic therapy, which results in vaccination against the injected tumor. CAN-2409  consists of a non-replicating adenovirus armed with the Herpes virus thymidine kinase, which metabolizes ganciclovir into a phosphorylated nucleotide that is incorporated into the tumor cell’s genome, thereby inflicting immunogenic cancer cell death. While CAN-2409’s immunological impact has been well characterized, its effects on the tumor cells transcriptome remains unknown. We compared the transcriptomic landscape after treatment of glioblastoma models with CAN-2409 in vitro and in vivo to assess how the interplay with the tumor microenvironment influences CAN-2409-mediated transcriptome alterations.  Methods: We performed RNA-Seq with CAN-2409 treated patient-derived glioma stem-like cells and tumors of C57/BL6 mice and compared KEGG pathway usage and differential gene expression focusing on immune cell and cytokine profiles. T-cell -killing assays were performed to assess candidate effectors.  Results: PCA analysis showed distinct clustering of control and CAN-2409 samples under both conditions. KEGG pathway analysis revealed significant enrichment for p53 signaling and cell cycle pathway, with similar dynamics for key regulators of both pathways in vitro and in vivo, including MYC, CCNB1, PLK1 and CDC20. Cytokine expression analysis revealed upregulation of pro-inflammatory IL12a under both conditions; immune cell gene profiling showed reduction of myeloid associated genes. T-cell- killing assays showed increased killing in the presence of IL-12.  Conclusion: CAN-2409 significantly alters the transcriptome both in vitro and in vivo. Comparison of pathway enrichment revealed mutual and differential utilization of pathways under both conditions, suggesting a modulating influence on the cell cycle in tumor cells, and of the tumor microenvironment on the transcriptome in vivo. IL-12 synthesis likely depends on interactions with the tumor microenvironment, and it facilitates CAN-2409 cell killing. This dataset provides potential to understand resistance mechanisms and identify potential biomarkers for future studies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For in vitro experiments, cells were treated with CAN-2409 (MOI 100) and 10g/ml ganciclovir, for in vivo experiments, 3 μl of AdV-tk with 2×108 vector particles [vp]/μl were injected intracranially and animals treated with 20 mg/kg bodyweight ganciclovir intraperitoneally 2x/day for 7 days. Both AdV-tk and ganciclovir were kindly provided by Candel Therapeutics Inc. (Needham, MA, USA). For generation of in vivo samples, 100,000 GL261fluc cells were injected intracranially in 2 μl HBSS 2mm right lateral, 1mm frontal to the bregma, and 3mm deep in the brains of albino C57/BL6 mice. Tumor growth was monitored by bioluminescence imaging with the Perkin-Elmer IVIS Lumina 3 after intraperitoneal of injection of D-Luciferin (#LUCK-1G, Gold Biotechnology).  14 days post-tumor implantation, CAN-2409 (treatment group) or HBSS (control) was stereotactically injected intratumorally by, followed by 7 days treatment with ganciclovir in the treatment group as described above. All animal experiments were performed according to BWH Center for Comparative Medicine IACUC guidelines. Animals were euthanized on the third day after end of therapy.

first: Marilin

middle: S

last: Koch

first: Mykola

last: Zdioruk

first: Michal

middle: O

last: Nowicki

first: Michael

last: Hoetker

first: Zachary

middle: T

last: Herbert

first: Francesca

last: Barone

first: Paul

last: Tak

first: E

last: Chiocca

first: Ghazaleh

last: Tabatabai

middle: E


title: Rapid TCR:Epitope Ranker (RAPTER): A primary human T cell reactivity screening assay pairing epitope and TCR at single cell resolution

city: Tarrytown

first: Lili

last: Blumenberg

state: NY

address: 777 Old Saw Mill River Road

department: VI Next

institute: Regeneron Pharmaceuticals

summary: Identifying epitopes that T cells respond to is critical to understanding T cell-mediated immunity. Traditional multimer and other single cell assays often require large blood volumes and/or expensive HLA-specific reagents and provide limited phenotypic and functional information. Here, we present the Rapid TCR:Epitope Ranker (RAPTER) assay, a single cell RNA sequencing (scRNA-SEQ) method that uses primary human T cells and antigen presenting cells (APCs) to assess functional T cell reactivity at single cell resolution. Using hash-tag oligonucleotide (HTO) coding and T cell activation-induced markers (AIM), RAPTER defines paired epitope specificity and TCR sequence and can include RNA- and protein-level T cell phenotype information.  We demonstrate that RAPTER identified specific reactivities to viral and tumor antigens at sensitivities as low as 0.15% of total CD8+ T cells, and deconvoluted low-frequency circulating HPV16-specific T cell clones from a cervical cancer patient. The specificities of TCRs identified by RAPTER for MART1, EBV, and influenza epitopes were functionally confirmed in vitro. In summary, RAPTER identifies low-frequency T cell reactivities using primary cells from low blood volumes, and the resulting paired TCR: ligand information can directly enable immunogenic antigen selection for vaccine epitope inclusion, antigen-specific TCR tracking, and TCR cloning for further therapeutic development.

overall_design: Human PBMCs were put through the RAPTER assay described in the manuscript then measured via scRNAseq

first: Raquel

last: Deering

first: Lianjie

last: Li

first: Ankur

last: Dhanik

first: Se

last: Jeong

first: Stephane

last: Pourpe

first: Hang

last: Song

first: Lauren

last: Boucher

first: Shoba

last: Ragunathan

first: Yanxia

first: Maggie

last: Zhong

first: Jessica

last: Kuhnert

first: Christina

last: Adler

first: Peter

last: Hawins

first: Namita

last: Gupta

last: Moore

first: Min

last: Ni

first: Johanna

last: Hansen

first: Yi

last: Wei

first: Gavin

last: Thurston


title: The effect of a BCCA-free, with 1% propionate, diet on 1W pressure overload-induced H3K23-propionyl [BCAA-free-1W-TAC with propionate-ChIP-Seq]

city: Newark

first: Maha

last: Abdellatif

state: NJ

address: 185 S. Orange Ave., MSB

department: Cell Biology and Molecular Medicine

institute: Rutgers University

summary: Identifying branched-chain amino acid (BCAA) oxidation enzymes in the nucleus led us to predict that they are a source of propionyl-CoA that could be utilized for histone propionylation and, thereby, regulate gene expression. To investigate this and its effect on the development of cardiac hypertrophy and failure, we applied pressure overload on the heart in mice maintained on a diet with standard levels of BCAA (BCAA-control) versus a BCAA-free diet. The former was associated with an increase in H3K23-propionyl (H3K23Pr) at the promoters of upregulated genes [e.g., cell signaling and extracellular matrix (ECM) genes] and a decrease at the promoters of downregulated genes [e.g., electron transfer complex (ETC I-V) and metabolic genes]. Intriguingly, the BCAA-free diet diminished the increase in promoter-H3K23Pr and significantly reduced ECM gene expression and collagen deposition. Conversely, the BCAA-free diet abolished the downregulation of ETC I-V subunits, enhanced mitochondrial respiration, and curbed cardiac hypertrophy. Thus, lowering the intake of BCAA reduces histone propionylation, which moderates the effects of stress on the heart.

overall_design:
Mice were fed a BCAA-free diet or a BCAA-control diet, with 1% propionate supplement, for 4 days. Mice were then subjected to a sham or transverse aortic constriction (TAC) surgery for 1-week (1W), while being maintained on the same diets.  The heart function and structure was asssessed by echocardiography, the heart isolated, chromatin extracted and analyzed by ChIP-Seq, each sample is a pool of 3 hearts (Active Motif).
The antibody used for the ChIP-seq is anti-H3K23-propionyl (Abcam, ab2414466).


title: RUNX1 loss renders hematopoietic and leukemic cells dependent on interleukin-3 and sensitive to JAK inhibition

first: Amy

last: Fan

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

overall_design: Refer to individual Series


title: The effect of a BCCA-free diet on 1W pressure overload-induced H3K23-propionyl [BCAA-free-1W-TAC-ChIP-Seq]

overall_design:
Mice were fed a BCAA-free diet or a BCAA-control diet for 4 days. Mice were then subjected to a sham or transverse aortic constriction (TAC) surgery for 1-week (1W), while being maintained on the same diets.  The heart function and structure was asssessed by echocardiography, the heart isolated, chromatin extracted and analyzed by ChIP-Seq, each sample is a pool of 3 hearts (Active Motif).
The antibody used for the ChIP-seq is anti-H3K23-propionyl (Abcam, ab2414466).


title: The effect of a BCCA-free diet on 2W pressure overload-induced H3K23-propionyl [BCAA-free-2W-TAC-ChIP-Seq]

overall_design:
Mice were fed a BCAA-free diet or a BCAA-control diet for 4 days. Mice were then subjected to a sham or transverse aortic constriction (TAC) surgery for 2-week (2W), while being maintained on the same diets.  The heart function and structure was asssessed by echocardiography, the heart isolated, chromatin extracted and analyzed by ChIP-Seq, each sample is a pool of 3 hearts (Active Motif).
The antibody used for the ChIP-seq is anti-H3K23-propionyl (Abcam, ab2414466).


title: The effect of a BCCA-free diet on 2W pressure overload-induced cardiac gene expression [BCAA-free-2W-TAC-RNA-Seq]

overall_design: Mice were fed a BCAA-free diet or a BCAA-control diet for 4 days. Mice were then subjected to a sham or transverse aortic constriction (TAC) surgery for 2-week (2W), while being maintained on the same diets.  The heart function and structure was asssessed by echocardiography, the heart isolated, RNA extracted and analyzed by RNA-Seq (Azenta).


title: Transcriptional maintenance of cortical somatostatin interneuron subtype identity during migration

city: Stockholm

first: Kasra

last: Nikouei

address: Solnav. 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Cortical interneuron diversity arises from the interplay of intrinsic developmental patterning and local extrinsic cues. While individual genetic programs underlying cardinal cell type identity are established in immature neurons prior to integration into cortical circuits, it remains unclear whether distinct interneuron subtype identities are pre-established, and if so, how their identity is maintained prior to circuit integration. Sox6 is a transcription factor with an established role in the maturation of interneurons derived from the medial ganglionic eminence and cell-type specification in other neuronal and non-neuronal cells. To determine a possible role in maintaining cortical somatostatin-expressing (Sst+) interneuron subtype identity, we conditionally removed Sox6 (Sox6-cKO) in migrating Sst+ interneurons and assessed the effects on their mature identity. In adolescent animals, five of eight molecular Sst+ subtypes were nearly absent in the cortex of Sox6-cKO mice. This reduced subtype diversity was not due to a decrease in the overall number of Sst+ interneurons and cells displayed electrophysiological maturity and expressed genes enriched within the broad class of Sst+ interneurons. Furthermore, we show that at embryonic day 18.5, prior to cortical integration, mature Sst+ cell subtype identity could already be inferred in both control and Sox6-cKO cortices, suggesting that the loss in subtype diversity observed in the mature cortex is due to a disrupted subtype maintenance. Importantly, Sox6 removal at postnatal day 7, after Sst+ interneurons have finished migrating and begun integration into the network, did not disrupt marker expression of Sst+ subtypes in the mature cortex. Therefore, Sox6 is necessary during this migratory phase for maintenance of Sst+ subtypes identity, indicating that subtype maintenance requires active transcriptional programs during migration.

overall_design: Single-cell RNA sequencing on cortical somatostatin interneurons (SstCre::fluorescent reporter) from Sox6 control and Sox6 conditional knock-out mice. Cells were collected at two different time points, 1) after tangential migration but before neuronal network integration from neocortex of pups at embryonic day 18.5 and 2) mature somatostatin interneurons from primary somatosensory cortex of mice at postnatal day 21-28. We have also included a dataset of cortical parvalbumin expressing interneurons from control mice at postnatal day 21-28.

first: Hermany

last: Munguba

first: Hannah

last: Hochgerner

first: Sten

last: Linnarsson

first: Jens

last: Hjerling-Leffler


title: Early milk-feeding regimes in calves exert long-term influence on the development of ovarian granulosa cells

city: Dummerstorf

first: Anja

last: Baufeld

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Research Institute for Farm Animal Biology

summary:
We analysed effects of different feeding regimes of milk replacer (MR) during rearing on ovarian physiology with specific emphasis on the numbers of granulosa cells (GCs) as well as gene expression characteristics in GCs at the age of puberty onset.  Animals of the 20% feeding group had a significantly higher body weight, but the proportion of animals having a corpus luteum at the time of slaughter was not different between groups, suggesting a similar onset of puberty. Calves of the 10% group showed a constant granulosa cell count regardless of the number of follicles (r = 0.23) whereas in the 20% group increasing numbers of GCs were detected with a higher follicle count (r = 0.71). The mRNA microarray analysis revealed a total of 557 differentially expressed genes in GCs (fold change > |1.5| and p<0.05). Among the top downregulated genes were OAS1X, MX2 and OAS1Z, whereas the top upregulated genes were BOLA, XCL1 and MT1E, which are known to be regulated by interferon. Subsequent signaling pathway analysis revealed the involvement of several immune response mechanisms in accordance with a number of interferons as upstream regulators.
The results indicate that the plane of MR feeding in early life have an impact on the number and physiology of GCs later in life. This might influence the overall reproductive life initiated by the onset of puberty in cattle. In addition, the observed alterations in GCs of calves fed less MR might be a consequence of interferon regulated immunological pathways.

overall_design: Overall 10 samples were analyzed. Different feeding regimes (10% vs. 20% MR) in early life were compared with n=5 for each feeding group. Two groups of calves received either 10% or 20% of bodyweight MR per day during their first 8 weeks. After weaning, both groups were fed the same mixed ration ad libitum until slaughter at 8 months of age.

first: Volker

last: Röttgen

first: Lisa-Marie

last: Tümmler

first: Dirk

last: Koczan

first: Alexander

last: Rebl

first: Björn

last: Kuhla

last: Vanselow


title: The effect of a BCCA-free diet on 1W pressure overload-induced cardiac gene expression

overall_design: Mice were fed a BCAA-free diet or a BCAA-control diet for 4 days. Mice were then subjected to a sham or transverse aortic constriction (TAC) surgery for 1-week (1W), while being maintained on the same diets.  The heart function and structure was asssessed by echocardiography, the heart isolated, RNA extracted and analyzed by RNA-Seq (Azenta).

first: Abdellatif

last: Maha


title: RUNX1 loss renders hematopoietic and leukemic cells dependent on interleukin-3 and sensitive to JAK inhibition [RNA-seq]

overall_design: Comparative gene expression analysis of cord blood derived CD34+ gene edited at the AAVS1 or RUNX1 locus. 4 biological replicates.


title: Intratibial Osteosarcoma Growth and Pulmonary Metastasis Inhibition by HIPPO Signaling Pathway-Induced Photodynamic Therapy

city: shanghai

first: Junli

last: Chang

address: Wanping South Road 725

institute: Long hua Hospital

summary: Cancer is a global leading cause of death, with nearly 10 million people dying from cancer in 2020. Photodynamic therapy (PDT) has emerged as a promising cancer treatment modality; however, the potential molecular mechanisms remain obscure. Herein, we designed a near-infrared (NIR) light-activated nanoplatform (TPBC-PEG) to explore the therapeutic effects and mechanisms of PDT by using a model of intratibial primary and pulmonary metastasis osteosarcoma. Under laser irradiation, TPBC-PEG photosensitizer dose-dependently inhibited proliferative and metastatic capability while promoting apoptosis of osteosarcoma cells in vitro, and also effectively suppressed carcinogenesis and pulmonary metastasis in osteosarcoma xenograft mouse model. Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis after high-throughput mRNA-seq indicated that the HIPPO signaling pathway was one of the 20 most significantly related signaling pathways. And a series of experiments for determining the HIPPO signaling activity were conducted to reconfirm the specificity. Collectively, PDT of TPBC-PEG micelles against carcinogenesis and pulmonary metastasis of deep-seated intratibial osteosarcoma was achieved by activating HIPPO signaling pathway. Our study identified a hitherto uncharacterized molecular mechanism of PDT, which may provide new insights to understand and design promising nanoplatforms for future cancer therapies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 143B cells and TPBC-PEG and PDT treated 143B cells.

first: Yanping

last: Yang


title: Evaluation of somatic copy number variation detection by NGS techonologies and bioinformatics tools

city: Silver Spring

first: Wenming

last: Xiao

state: MD

address: 10903 New Hampshire Avenue

department: Office of New Drugs

institute: Center for Drug Evaluation and Research, FDA

summary: We have benchmarked the performance of cancer CNV calling by six most recent software tools on their detection accuracy, sensitivity, and reproducibility.  We also explored the consistency of CNV calling across different orthogonal technologies, including optical mapping and microarrays.  Using consensus results from six CNV callers and confirmation from three orthogonal methods, we established a high-confidence CNV call set for the reference sample.

overall_design: Three replicate preparations of the tumor cell line HCC1395 were compared to three replicate preparations of its matched normal control cell line HCC1395BL using the Illumina Infinium CytoSNP-850K BeadChip.

first: Erich

last: Jaeger


title: Changes in Flk1-positive endothelial cells in hypoxia [GFP]

city: tsukuba

first: akiyama

last: tatsuya

address: amakubo

country: Japan

institute: university of tsukuba

summary:
To investigate the role of Flk1 in pulmonary arterial hypertension, we observed the behavior of Flk1 in a disease model using Flk1-GFP mice.
Gene expression profiling analysis was performed using data obtained from RNA-seq of Flk1-positive cells on days 1 and 8 of hypoxia exposure, when Flk1 changes were greatest.

overall_design: mRNA profiles of Flk1-positive cells from Flk1-GFP mice exposed to hypoxia (0, 1, and 8 days) were generated by FACS-sorting and RNA-sequencing, using MoFlo XDP (Beckman coulter)and NextSeq500 (Illumina).

first: Akiyama

first: Sadahiro

last: taketaro

first: Ieda

last: masaki


title: Next-generation sequencing reveals the regulatory mechanism of transcription factor HOXD9 in gastric cancer

city: GUAGNZHOU

first: JIAYING

last: LI

state: GUAGNDONG

address: No. 1063, No. 1023, Shatai South Road, Baiyun District, Guangzhou

department: Gastrointerology

institute: Soutern Medical University

summary: HOXD9 is a transcription factor reported to facilitate metastasis in gastric cancer. In our study, we tried to figure out the role HOXD9 played in gastric cancer metastasis by obtaining its expression profiling.

overall_design: mRNA and lncRNA profiles of LV-HOXD9 and LV-vector MKN-74 cells in triplicate with Illumina HiSeq 4000

first: Jide

last: WANG

first: Jiaying

last: Li


title: Molecular subphenotyping using placental transcriptomics in early-onset preeclampsia and fetal growth restriction

city: Chicago

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

summary: Placental disorders contribute to pregnancy complications including preeclampsia (PE) and fetal growth restriction (FGR), but debate regarding their specific pathobiology persists. Our objective was to apply transcriptomics with weighted gene correlation network analysis (WGCNA) to further clarify the placental dysfunction in these conditions.

overall_design: We performed RNA sequencing (RNA-seq) with WGNCA using 30 human placental samples, separated into villous tissue (VT) and decidua basalis (DB) and clinically grouped as follows: (1) early-onset PE (EOPE, n=8); (2) EOPE+FGR (n=7); normotensive, nonanomalous preterm FGR (n=5); idiopathic preterm birth (iPTB, n=5); and uncomplicated term births (TB, n=5).

first: Irina

last: Buhimschi

first: Catalin


title: Role of Flk1 in pulmonary arterial hypertension [Flox]

summary:
To investigate the role of Flk1 in pulmonary arterial hypertension, we generated mice lacking Flk1 specifically in vascular endothelial cells.
We exposed these mice to hypoxia and collected Flk1-KO endothelial cells by FACS for RNA-seq.

overall_design: The mRNA profiles of Flk1-KO endothelial cells in Normoxia or Hypoxia were generated by FACS-sorting and RNA-sequencing using MoFlo XDP (Beckman coulter) and NextSeq500 (Illumina).


title: Tumor-intrinsic expression of the autophagy gene Atg16l1 suppresses anti-tumor immunity in colorectal cancer

city: South San Francisco

first: Yasin

last: Senbabaoglu

address: 1 DNA Way

institute: Genentech


title: Effect of depletion of HMOX1 on gene expression of AsPC-1 cells.

status: Public on Aug 24 2023

city: Shenzhen

first: Qianying

last: Hu

state: State...

address: 3025 Shennanzhong Road,Shenzhen

institute: Sun Yat-sen University

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant tumors. Endoplasmic reticulum stress plays an essential role in PDAC progression. Here, we aim to identify the ERS-related genes in PDAC and build reliable risk models for diagnosis, prognosis and immunotherapy response of PDAC patients. We report HMOX1 as an important gene of ER stress related-signature we established in PDAC. The depletion of HMOX1 results in tumor growth inhibition. Our data lay the foundation for further investigating the potential mechanism.

overall_design: To investigate the potential mechanism of HMOX1 in the regulation of proliferation in PDAC, we conducted transcription sequencing of the AsPC-1 cells expressing RNAi against HMOX1 and scramble siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq.

first: Shuguang

last: Liu

first: Kaimeng

last: Huang

first: Riqing

first: Lishan

last: Fang


title: The effect of a BCCA-free diet, with 1% propionate, on 1W pressure overload-induced cardiac gene expression [BCAA-free w propionate-1W-TAC-RNA-Seq]

first: Maha

last: Abdellatif

overall_design: Mice were fed a BCAA-free dietwith 1% propionate supplement or a BCAA-control diet with 1% propionate supplement for 4 days. Mice were then subjected to a sham or transverse aortic constriction (TAC) surgery for 1-week (1W), while being maintained on the same diets.  The heart function and structure was asssessed by echocardiography, the heart isolated, RNA extracted and analyzed by RNA-Seq (Azenta).


title: Elucidating the Role of Flk1 in Pulmonary arterial Hypertension

first: akiyama


title: The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [scRNA-seq]

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

summary: Direct reprogramming of fibroblasts into induced cardiomyocytes (iCMs) holds great promise for heart regeneration. Although great progress has been made in understanding the transcriptional and epigenetic mechanisms of iCM reprogramming, its translational regulation remains largely unexplored. Here we characterized the translational landscape of iCM reprogramming using integrative ribosome and transcriptomic profiling, and showed extensive translatome re-patterning during fibroblast conversion into iCM. Loss of function screening for translational regulators uncovered Ybx1 as a critical barrier to iCM induction. Knockdown of Ybx1 dramatically improved the efficiency and quality of iCM reprogramming. Mechanistically, Ybx1 directly bound the transcripts of Srf and Baf60c, both of which mediated, at least partially, the repressive effect of Ybx1 on iCM generation.and Depletion of Ybx1 de-repressed the translation of its targets including SRF and Baf60c. Interestingly, upon removing Ybx1, Tbx5 alone could reprogram fibroblasts into iCMs that exhibit classic iCM molecular features and reprogramming trajectories revealed by our single cell dual-omics. In sum, we presented here a global view of translatome dynamics of cardiac reprogramming and identified a novel translational barrier, Ybx1, to iCM generation. Removing this barrier allowed the single factor mediated iCM reprogramming.

overall_design: Single-cell RNA-seq profiles of T+shNT and T+shYbx1 infected  fibroblast were generated at day 12 post infection by 10x Genomics Chromium System.

first: Yifang

last: Xie

first: Marazzano

last: Colon

first: Jiandong

first: Li

last: Qian


title: Histone H3K36me3 regulates E2F transcription as part of the DNA replication stress checkpoint response

city: Oxford

first: Linda

last: van Bijsterveldt

state: non-US Resident

address: Old Road Campus

institute: Oxford Institute for Radiation Oncology

summary: DNA replication stress drives genomic instability, thus contributing to the rapid evolution of tumours. Sustained E2F-dependent transcription, which is actively maintained in a checkpoint-dependent manner, is required for replication stress tolerance and is a key mechanism preventing the generation of DNA damage under these conditions. However, the activation and regulation of the E2F response remains poorly understood. Here, we establish a role for SETD2-dependent H3K36 trimethylation in facilitating E2F target gene expression in S-phase and promoting efficient DNA replication under both normal and replication stress conditions in human cells. Loss of SETD2 results in reduced E2F1-binding to its target genes, causing expression defects in almost all E2F transcripts, including CDT1, CDC6, and MCM2-7. Further, we find that E2F target gene expression following hydroxyurea-induced replication fork stalling requires ATR-dependent H3K36 trimethylation. Accordingly, SETD2 loss results in reduced replication fork progression and increased levels of replication stress-induced DNA damage, indicative of reduced replication stress tolerance. Together, these findings establish a central role for SETD2-dependent H3K36me3 in the replication stress checkpoint, thereby ensuring genomic integrity.

overall_design: RNA-seq of U2OS cell lines treated with either non-targeting control siRNA or SETD2 siRNA, followed by control, hydroxyurea (HU), ATR inhibitor (VE-822), or HU+VE-822 48 hours post-transfection (n=2)

first: Lee

last: Armfield

first: Michael

last: Tellier

first: Gwendal

last: Dujardin

first: Cosetta

last: Bertoli

first: Kirsten

last: Lopez

first: Kok-Lung

last: Chan

first: Shona

last: Murphy

first: Nicholas

last: Proudfoot

first: Robertus

last: de Bruin

first: Timothy

last: Humphrey


title: Akkermansia muciniphila Membrane Protein Improves Cognitive Function in Aged Mice by Reducing IL-6 Expression

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: We implemented transcriptomic analyses of blood and hippocampus of old mice treated with Akkermansia muciniphila Membrane Protein for 8 weeks.

overall_design: These mice with the treatment of Akkermansia muciniphila Membrane Protein for 6 weeks.


title: NRF2 is a spatiotemporal metabolic hub driving the polyfunctionality of Th2 cells in allergic asthma

city: ulsan

first: hansol

last: oh

address: 50, UNIST-gil, Ulsan 44919

institute: UNIST

summary: Polyfunctional T cell responses are detrimental in immune disorders; however, it is unclear how effector T cell subsets acquire polyfunctionality in tissues.  Here, we demonstrate that the activation of Nrf2 is necessary for the differentiation polyfunctional Th2 cells in vivo. Reactive oxygen species (ROS) levels are significantly  elevated in lung-infiltrating immune cells during allergic asthma, and inhibiting either ROS or Nrf2 significantly decreases eosinophilia and polyfunctional Th2 cells in the lung.  In vivo studies using multiple cell-type specific Nrf2-deficient mice and mixed bone marrow chimeras revealed that cell-intrinsic Nrf2 drives IL-5 and IL-13 expression  in Th2 cells independently of IL-33. Mechanistically, Nrf2 promotes optimal OXPHOS and glycolysis capacity by inducing PPARg expression and glucose uptake to drive  polyfunctionality of Th2 cells. Blocking Nrf2 reduces IL-5 and IL-13 production from house dust mite allergen-specific Th2 cells obtained from asthma patients.  These findings demonstrate that Nrf2 acts as a spatiotemporal metabolic hub driving the differentiation of polyfunctional Th2 cells,  which may have therapeutic implications for controlling allergic lung inflammation.

overall_design: To investigate the mechanisms by which effector Th2 cells acquire polyfunctionality,  we utilized animal models of allergic asthma. Our hypothesis was that if a cell-intrinsic factor plays a critical role  in the polyfunctional program of T cells, its levels would be significantly altered in the lung-infiltrating immune cells  compared to those in the draining lymph nodes.  We performed RNA-seq and ATAC-seq to obtain epigenetics data of WT and cKO.


title: The ecdysone receptor promotes or suppresses proliferation according to ligand level

city: London

first: Gantas

last: Perez Mockus

address: 1 Brill Place

institute: Francis Crick Institute

summary: Steroid hormones control various cellular activities in a context-dependent manner. For example, ecdysone, which acts through a type II nuclear receptor, has seemingly opposite effects in Drosophila wing precursors, promoting proliferation during larval stages, and triggering proliferation arrest at pupariation. We find that wing precursors proliferate normally in the complete absence of the ecdysone receptor (EcR), whether ecdysone is present or not, suggesting that ecdysone overrides a default anti-proliferative activity of the receptor. By contrast, termination of proliferation by high concentration of 20E at the end of larval life requires ligand-induced transcriptional activation by the receptor. The switch from one mode of regulation to the other is determined by ligand level, as measured with a calibrated EcR transcriptional reporter and ex vivo proliferation assays. Accordingly, RNA Seq analysis uncovers distinct transcriptional responses to different doses of ecdysone. Some genes are only activated at high doses (high threshold targets) and likely to comprise genes that stop proliferation at pupariation, when ecdysone titres are high. We find that other target genes respond to all physiological concentrations of ecdysone. Some of these genes are known to promote proliferation and could therefore contribute to the pro-proliferation activity of low-level ecdysone. Finally, we show mathematically and with synthetic reporters that relatively simple combinations of regulatory elements can recapitulate the behaviour of both types of target genes.

overall_design: Total-RNAseq from 24h AL2-L3 wing imaginal discs incubated for 2.5h at 25°C in Dye medium supplemented with different concentrations of 20E.

last: Perez-Mockus


title: SIRPa agonist antibody treatment ameliorates experimental arthritis and colitis

first: Jason

last: Hackney

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

overall_design: Refer to individual Series


title: SIRPa agonist antibody treatment ameliorates experimental arthritis and colitis [sequencing]

summary: The innate immune system is finely tuned to enable rapid response to pathogenic stimuli but keep quiescent during tissue homeostasis.Balance of activating and inhibitory signaling sets a threshold for immune activation. Signal regulatory protein (SIRPa) is an immune inhibitory receptor expressed by myeloid cells and interacts with CD47 to inhibit immune cell phagocytosis, migration, and activation. Despite the progress of SIRPa and CD47 antagonist antibodies to promote anti-cancer immunity, it is not yet known whether therapeutic SIRPa receptor agonism could restrain excessive autoimmune inflammation in the context of autoimmunity. Here, we reported that increased neutrophil- and monocyte-associated genes including SIRPA in inflamed tissues biopsies of rheumatoid arthritis and inflammatory bowel diseases, and elevated SIRPA in colonic biopsies is associated with treatment refractory ulcerative colitis patients. We next identified a novel agonistic anti-SIRPa antibody that exhibited potent anti-inflammatory effects in reducing neutrophil and monocytes chemotaxis and tissue infiltration. In preclinical models of arthritis and colitis, anti-SIRPa agonistic antibody ameliorates autoimmune joint inflammation and inflammatory colitis through reducing neutrophils and monocytes in tissues. Our work provides a proof-of-concept for SIRPa receptor agonism for suppressing excessive innate immune activation and autoimmune inflammatory therapeutic treatment

overall_design: Comparison of non-disease control, disease mice with a negative control antibody, and disease mice treated with anti-SIRPa antibody. Total paw tissues (each from 4 individual mice) of naïve, isotype control, agonistic anti-SIRPa treated mice 7 days post K/BxN serum transfer. Joint samples were isolated for RNA sequencing and each sample is from one individual animal.

first: Markus

last: Xie


title: Co-effects of m6A dynamics and chromatin accessibility changes regulate cardiomyocyte differentiation

first: Xuehong

state: Guangdong Province

address: Haizhuqu, No.135 Xingangxi lu

institute: Sun Yat-Sen University

type: Methylation profiling by high throughput sequencing

summary: The growth and differentiation of cardiomyocytes are primarily driven by gene expression dynamics, with various epigenetic modifications playing a crucial role in this process. One of the most common modifications on mRNA, m6A, influences the regulation of mRNA metabolism; however, its function remains enigmatic. In this study, we identified a correlation between m6A modification and cardiomyocyte differentiation by profiling m6A dynamics during the transition of pluripotent stem cells into cardiomyocytes. Although the overall m6A modification level remains relatively stable, most genes exhibit changes in their m6A levels as cardiomyocyte differentiation progresses. We observed that alterations in chromatin accessibility can impact the binding capabilities of m6A writers, erasers, and readers, consequently affecting m6A levels. Furthermore, the coordinated changes of m6A and chromatin accessibility are closely associated with early-stage cardiomyocyte differentiation. These findings suggest that m6A is a significant factor in determining the fate of cardiomyocyte differentiation, shedding light on its role in this critical process.

overall_design: Comparative m6A profiling analysis of Pooling MeRIP-seq data for hESC, mesoderm, cardiac progenitor and cardiomyocytes.

first: Guanzheng

last: Luo

last: Cao

first: Zhang

last: Zhang

first: Zhun


title: Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [CUT-RUN]

city: Houston

first: Junwoo

last: Lee

state: Texas

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

summary: The RNA transcribed from enhancer regions, referred to as eRNA, has been suggested to directly activate transcription by helping to recruit transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find the AT-hook of SWI/SNF alone binds preferentially RNA and as part of the esBAF complexes associates with eRNA transcribed from intronic and intergenic regions. SWI/SNF is globally recruited in cis by eRNA to cell-type specific enhancers at two distinct stages in early mammalian development and not at promoters or enhancers that are shared between the two stages. SWI/SNF recruited by eRNA facilitates recruitment and/or activation of MLL3/4, p300/CBP and Mediator co-activators to stage-specific super-enhancers that in the primed embryonic stage activate cell lineage priming related genes. We find a strong connection between ATP-dependent chromatin remodeling and eRNA in cell identity and super-enhancer activation.

overall_design: Immunoprecipitated samples (Brg1, H3K27ac, Med1, H3K4me1 and MLL3/4) and mock control samples (IgG) were prepared for biological duplicates of wild type (WT) and two AT hook domain deletion mutants (dAT1, dAT2) in naïve and primed conditions. These samples were sequenced by 75bp paired-end, Illumina HiSeq3000.

first: Srinivas

last: Animireddy

first: Dhurjhoti

last: Saha

first: Yue

last: Lu


title: SIRPa agonist antibody treatment ameliorates experimental arthritis and colitis [array]

summary: The innate immune system is finely tuned to enable. rapid response to pathogenic stimuli but keep quiescent during tissue homeostasis. Balance of activating and inhibitory signaling sets a threshold for immune activation. Signal regulatory protein (SIRPa) is an immune inhibitory receptor expressed by myeloid cells and interacts with CD47 to inhibit immune cell phagocytosis, migration, and activation. Despite the progress of SIRPa and CD47 antagonist antibodies to promote anti-cancer immunity, it is not yet known whether therapeutic SIRPa receptor agonism could restrain excessive autoimmune inflammation in the context of autoimmunity. Here, we reported that increased neutrophil- and monocyte-associated genes including SIRPA in inflamed tissues biopsies of rheumatoid arthritis and inflammatory bowel diseases, and elevated SIRPA in colonic biopsies is associated with treatment refractory ulcerative colitis patients. We next identified a novel agonistic anti-SIRPa antibody that exhibited potent anti-inflammatory effects in reducing neutrophil and monocytes chemotaxis and tissue infiltration. In preclinical models of arthritis and colitis, anti-SIRPa agonistic antibody ameliorates autoimmune joint inflammation and inflammatory colitis through reducing neutrophils and monocytes in tissues. Our work provides a proof-of-concept for SIRPa receptor agonism for suppressing excessive innate immune activation and autoimmune inflammatory therapeutic treatment

overall_design: Comparison of non-disease joint tissue to tissue samples from osteoarthritis and rheumatoid arthritis


title: Comparison of ESC-derived and Primary-derived Tip-like Cell Transplants

city: Boston

first: Feiya

last: Wang

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

summary: The goal of this experiment was to determine whether transcriptionally similar ESC-derived and primary donor cells give rise to similar donor-derived cells following transplantation into bleomycin injured lungs.

overall_design: Adult 129X1/S1 mice were given 1.5U/kg bleomycin intratracheally. 10 days later mice received either 4e6 mCh+ ESC-derived tip-like cells (no lentiviral label) or 4e6 primary tip-like cells (labeled with a DsRed lentivirus). At 59 days post-transplantation the lungs of these mice were digested and sorted using FACS. Donor-derived cells were isolated based on the expression of mCherry or DsRed and endogenous cells were collected from the same lungs. 2 separate mice were pooled for both transplant conditions.

first: Michael

last: Herriges

first: Pushpinder

last: Bawa

first: Darrell

last: Kotton


title: The dual lipid desaturase/hydroxylase DEGS2 controls phytoceramide levels necessary to counter intestinal inflammation

city: Dallas

first: Jin Huk

last: Choi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Intestinal immunity is dependent on barrier function to maintain quiescence.  The mechanisms for the maintenance of this barrier are not fully understood.  Delta 4-desaturase, Sphingolipid 2 (DEGS2) is a lipid desaturase and hydroxylase, which catalyzes the synthesis of ceramide and phytoceramide from dihydroceramide. Using a forward genetic approach, we found and validated a mutation in Degs2 as causative in increasing susceptibility to colitis and altering the phytoceramide balance in the colon. DEGS2 is expressed in the intestinal epithelium, and the colitis phenotype is dependent on the non-hematopoietic compartment of the mouse. In the absence of DEGS2, the colon lacks phytoceramides and accumulates large amounts of the precursor lipid dihydroceramide. In response to DSS induced colitis, colonic epithelial cells in DEGS2-deficient mice had increased cell death and decreased proliferation compared to those in wildtype mice. These findings demonstrate that DEGS2 is needed to maintain epithelial integrity, protect against DSS-induced colitis and maintain lipid balances in vivo.

overall_design: Transcriptome analysis of the colonic epithelial cells from control and Degs2 deficient mice

first: Emre

last: Turer


title: A low-complexity domain of Tet3 dioxygenase shields the oocyte methylome from oxidative erosion [BiSulfite-seq]

city: Beijing

first: Fan

last: Guo

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Dynamic DNA methylation and demethylation regulate gene expression during development. While DNA methyltransferases (DNMTs) establish and maintain cytosine methylation patterns, Ten-eleven translocation (Tet) dioxygenases catalyze sequential oxidation of 5-methylcytosine (5mC) to promote demethylation. Target-specific 5mC oxidation requires precise regulation of the Tet enzymatic activity. However, the mechanism underlying their activity control remains largely unexplored. Here we show a large low-complexity domain (LCD), present within the catalytic domain of Tet3, functions to repress the dioxygenase activity. Recombinant LCD-deleted Tet3 exhibits enhanced activity to convert 5mC into oxidized species. Deletion of the Tet3 LCD in mouse oocytes renders 5mC oxidation indiscriminately across the genome, leading to most prominently the derepression of ERVK retrotransposons and upregulation of adjacent genes. The extensive 5mC oxidation is associated with impairments in oocyte development. These findings suggest an intrinsic auto-regulatory mechanism of Tet3 dioxygenase operating to ensure a tight regulation of its enzymatic activity to achieve spatiotemporal specificity of methylome reprogramming during oocyte development.

overall_design: Methylation profiling by high throughput sequencing in WT and Tet3 LCD KO GV oocytes.

first: Rui

last: Yan

first: Zhen-Yu

last: Shao

first: Xiao-Jie

first: Ya-Rui

last: Du


title: A low-complexity domain of Tet3 dioxygenase shields the oocyte methylome from oxidative erosion [RNA-seq]

overall_design: Expression profiling by high throughput sequencing in WT, Tet3 LCD KO, Dnmt3a KO, Dnmt3a, Tet3 LCD DKO,  Tet3 LCD KO HD Mut, Tet3 KO and Tet1,2,3 TKO GV oocytes.


title: The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [scRNA-seq and scATAC-seq]

first: Yuchen

last: Yang

overall_design: Single-cell RNA-seq and ATAC-seq profiles of T+shYbx1 infected  fibroblast were generated at day 3 post infection by 10x Genomics Chromium System.

first: Yifang

last: Xie

first: Jiandong

last: Liu

first: Li

last: Qian


title: The impact of ESC-derived tip-like cell transplantation on non-epithelial lineages

summary: The goal of this experiment was to determine whether transplantation of ESC-derived tip-like cells had any discernable impact on gene expression or clustering in non-epithelial cells.

overall_design: Adult 129X1/S1 mie were given 1.5U/kg bleomycin intratracheally. 10 days later mice received either 4e6 mCh+ ESC-derived tip-like cells (GFP lentiviral label) or vehicle only (LPM media). At 48 days post-transplantation the lungs of these mice were digested and sorted using FACS. Lungs were dissected down to regions surrounding GFP+ cell transplants (or comparable regions in controls) to enrich for cells potentially impacted by the localized injury and cell transplantation. DRAQ7-/EpCAM-/CD45+ and DRAQ7-/EpCAM-/CD45- cells were mixed at a 1:2 ratio in an attempt to get roughly even mix of immune, endothelial, and other non-epithelial lineages. For each condition, cells were pooled equally from 3 seperate mice in the same cohort.


title: A low-complexity domain of Tet3 dioxygenase shields the oocyte methylome from oxidative erosion [ ACE-seq]

overall_design: 5hmC profiling by high throughput sequencing in WT and Tet3 LCD KO GV oocytes.

last: Zhang


title: The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition

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


title: A low-complexity domain of Tet3 dioxygenase shields the oocyte methylome from oxidative erosion


title: Effect of ApoE deficiency on microRNA expression in bone marrow derived macrophages (BMDM)

status: Public on Aug 23 2023

city: San Francisco

first: Robert

last: Raffai

address: 4150 Clement St

department: Surgery

institute: University of California San Francisco

type: Non-coding RNA profiling by high throughput sequencing

summary: ApoE exerts pleiotropic properties in controlling inflammation and myeloid cell activation. We here uncover microRNA regulation as yet another mechanism that ApoE acts upon to control immune cell activity and inflammatory response. We compared the expression of microRNAs in BMDM derived from ApoE-KO (EKO) or WIldtype (WT) mice and identified 78 microRNAs to be differentially expressed between these two groups. Among these microRNAs, we identified miR-146a-5p to be highly upregulated in WT BMDM as compared to EKO BMDM. This is consistent with our prior study that reports a role of ApoE in promoting the biogenesis of this microRNA via the transcription of its host gene PU.1 (Spi1) in monocytes/macrophages. Of note, miR-146a-5p is recognized as a potent inhibitor of the NF-κB signaling pathway via the inactivation of IRAK1 and TRAF6. Furthermore, we identified mIR-142a-3p as downregulated in WT BMDM as compared to EKO BMDM. This microRNA has been reported to control important metabolic functions in myeloid cells by targeting the long chain fatty acid transporter CPT1A, thereby inhibiting fatty acid oxidation. Our data thus uncovers another novel of ApoE in controlling lipid metabolism in myeloid cells by suppressing the expression of miR-142a-3p. Taken together, our data provide a novel framework for the microRNA signatures regulated by ApoE in myeloid cells. Moreover, we uncovered an important mechanism of which ApoE can regulate myeloid cell immunometabolism via the regulation of miR-146a-5p and miR-142a-3p.

overall_design: To investigate the differential expression of microRNAs in ApoE-KO (EKO) BMDM versus Wildtype (WT) BMDM. Bone marrow cells are taken from age-matched male mice that are 6- to 12-week-old and cultured into BMDM. We then collected the total RNA and performed microRNA expression profiling analysis using data obtained from small RNA-seq of the two different cell groups. Three biological replicates (n = 3) were used for each group.

first: Tuan

last: Phu


title: Uncovering the phenotypic consequences of multi-locus imprinting disturbances using genome-wide methylation analysis in genomic imprinting disorders

city: Seongnam-si

first: Hwa Young

last: Kim

state: Gyeonggi-do

address: 82, Gumi-ro 173 Beon-gil

institute: Seoul National University Bundang Hospital

summary: Genome wide DNA methylation analysis using blood leukocyte DNA was performed on 15 patients with genomic imprinting disorders (13 Beckwith–Wiedemann syndrome [BWS], two Silver–Russell syndrome [SRS]), and four controls. The Illumina HumanMethylation850 BeadChip was used to obtain DNA methylation profiles at a more than 850,000 CpGs.

overall_design: Bisulphite converted DNA from the 19 samples were hybridised to the Illumina HumanMethylation850 BeadChip

first: Hwa

first: Jung

last: Ko


title: CLCF1 signaling restrains thermogenesis and disrupts metabolic homeostasis by inhibiting mitochondrial biogenesis in brown adipocytes

city: Baltimore

first: Meng

last: Ding

state: Maryland

address: 733 n broadway

institute: Johns Hopkins University

summary: Great progress has been made in identifying positive regulators that activate adipocyte thermogenesis, but negative regulatory signaling of thermogenesis remains poorly understood. Here, we found that cardiotrophin-like cytokine factor 1 (CLCF1) signaling led to loss of brown fat identity, which impaired thermogenic capacity. CLCF1 levels decreased during thermogenic stimulation but were considerably increased in obesity. Adipocyte-specific CLCF1 transgenic (CLCF1-ATG) mice showed impaired energy expenditure and severe cold intolerance. Elevated CLCF1 triggered whitening of brown adipose tissue by suppressing mitochondrial biogenesis. Mechanistically, CLCF1 bound and activated ciliary neurotrophic factor receptor (CNTFR) and augmented signal transducer and activator of transcription 3 (STAT3) signaling. STAT3 transcriptionally inhibited both peroxisome proliferator-activated receptor-γ coactivator (PGC) 1α and 1β, which thereafter restrained mitochondrial biogenesis in adipocytes. Inhibition of CNTFR or STAT3 could diminish the inhibitory effects of CLCF1 on mitochondrial biogenesis and thermogenesis. As a result, CLCF1-TG mice were predisposed to develop metabolic dysfunction even without external metabolic stress. Our findings revealed a previously unknown brake signal on nonshivering thermogenesis and suggested that targeting this pathway could be used to restore brown fat activity and systemic metabolic homeostasis in obesity.

overall_design: To understand the mechanism of CLCF1-mediated BAT dysfunction, we performed RNA sequencing (RNA-seq) on BAT from WT and CLCF1-ATG mice. Total RNA was isolated from BAT of WT and CLCF1-ATG mouse (n =4/group) using TRIzol reagent.

first: Qiqun

last: Tang

first: Yang


title: Sequencing data analysis and circRNA analysis of biliary atresia (BA) and choledochal cyst (CC) liver tissues

first: Bin

last: Wang

address: Department of General Surgery, Shenzhen Children’s Hospital, 7019 Yitian Road, Futian District, Shenzhen 518000, Guangdong, China

institute: Shenzhen Children’s Hospital

summary: We obtained a circRNA map of BA liver tissue based on RNA high-throughput sequencing and identified 78 significant DECs.

overall_design: We extracted RNA from liver tissues from 3 cases of biliary atresia and 3 cases of choledochal cyst, and compared the differentially expressed circRNAs through high-throughput sequencing. We ensured the accuracy of the sequencing results by filtering the sequencing data.

first: Dong

first: Yinghui

last: Dong

first: Jiahui

last: Gao

first: Zhouguang

last: Wu


title: Effect of ApoE in communicating CD4+ T cell activation and proliferation

state: California

summary: While ApoE expression by myeloid cells is recognized to control inflammation, whether such benefits can be communicated via extracellular vesicles including exosomes is not known. Through the study of exosomes produced by macrophages derived from the bone marrow of Wildtype (WT-BMDM-exo) and ApoE deficient (EKO-BMDM-exo) mice, we uncover a critical role of ApoE in regulating cell signaling properties. We treated splenic CD4+ T cells with EKO-BMDM-exo, WT-BMDM-exo, or PBS and performed gene expression profiling analysis. We found that CD4+ T cells treated with EKO-BMDM-exo show elevations in genes involved in the T-cell receptor complex (Cd3e, Cd247, & Cd4) and Il2rg, a key component of cytokine receptors on CD4+ T cells. Taken together, our data unveil a novel property of macrophage ApoE in controlling adaptive immunity by their secreted exosomes.

overall_design: To investigate the differential expression of mRNAs in splenic CD4+ T cells treated with exosomes derived from the bone marrow of Wildtype (WT-BMDM-exo) and ApoE deficient (EKO-BMDM-exo) mice, or PBS as control. Splenic CD4+ T cells are taken from male mice that are 6- to 12-week-old and stimulated with anti-CD3/anti-CD28 beads and murine IL-2. Cells are then treated with EKO-BMDM-exo, or WT-BMDM-exo, or PBS for 18 hours. We then collected the total RNA and performed gene expression profiling analysis using data obtained from RNA-seq of the three different cell groups. Three biological replicates (n = 3) were used for each group.


title: Sophoridine derivative 6j inhibits liver cancer cell proliferation via ATF3 mediated ferroptosis

city: Nanning

first: Lichuan

state: China

address: N0. 100, Daxue East Road

department: School of Medicine

institute: Guangxi University

summary: Liver cancer is one of the most lethal malignancies with an annual death of over 830,000 cases. Although targeted therapeutic drugs have achieved certain clinical efficacy, only sorafenib and lenvatinib are currently marketed as first-line targeted drugs to treat patients with advanced liver cancer. Therefore, developing more drugs are urgently needed. Ferroptosis is an iron-dependent programmed cell death (PCD) distinct from known PCDs including apoptosis, necrosis, and autophagy. Targeting ferroptosis is recognized as a promising potential therapeutic modality for liver cancer. Activating transcription factor 3 (ATF3) is an important ferroptosis inducer and targeting ATF3 offers a potential means to cancer therapy. In the present study, we reported for the first time a sophoridine derivative 6j with promising anti-liver cancer effects in vitro and in vivo. Compound 6j could induce liver cancer cells ferroptosis by promoting the accumulation of intracellular Fe2+, reactive oxygen species (ROS), and MDA. Inhibition of ferroptosis by ferrostatin-1 alleviated 6j induced accumulation of Fe2+, ROS, and MDA and restored cell viability. Further study revealed that compound 6j upregulated the expression of ATF3 via ER stress and knockdown of ATF3 by RNA interference attenuated 6j induced ferroptosis and cell proliferation inhibition. This study would provide new insights for the design of ferroptosis inducers and the development of anti-liver cancer drugs.

overall_design: To investigate compound 6j induced expression profiling, liver cancer  cells MHCC-97H were treated with 6j or vehicle


title: Evaluating the therapeutic potential of different sources of mesenchymal stem cells in acute respiratory distress syndrome

city: Palo Alto

first: Avnesh

last: Thakor

state: Default

address: 3155 Porter Drive

institute: Stanford University

summary: In different preclinical studies, different sources of MSCs derived from adipose tissue, bone marrow, placenta, umbilical cord have shown effectiveness in treating ARDS. However, their clinical translation has not been effective as demonstrated by variable outcomes from clinical trials. One reason for this could be the MSC source chosen for clinical translation as there is lack of study comparing the different sources of MSCs. In previous work, we performed a “head-to-head” comparison between different sources of MSCs and showed that each source had a unique genomic and proteomic “signature”. Hence, in this current study, we investigated the choice of MSC source best suited for therapy in an LPS-induced mouse model of ARDS.  We compare the 3 most commonly used MSC sources: bone marrow derived-MSCs (BM-MSCs), adipose tissue derived-MSCs (AD-MSCs) and umbilical cord derived-MSCs (UC-MSCs) therapy in LPS-induced ARDS model where we did bulk RNA sequencing of the lungs to validate the efficacy of therapy in terms of different changes in gene label and different pathways involved.

overall_design: ARDS was induced via an intra-tracheal injection of lipopolysaccharide (LPS)at the dose of 5mg/kg in phosphate buffered saline (PBS). After 4h following LPS injection, mice were randomized to receive a single intravenous injection of 1x10^6 MSCs (of a single source) or PBS. After 48 hours, whole lung tissue was collected and homogenized in trizol (Thermofisher Scientific, USA). RNA extraction was then done using RNA mini kit (Qiagen, Germany) according to the manufacturer’s guidelines with the quality of RNA evaluated using an Agilent bioanlyzer 2100 system. Samples with RNA integrity number (RIN) ≥ 6.8 were considered for library preparation.

first: Shobha

last: Regmi

first: Abantika

last: Ganguly

first: Shiva

last: Pathak

first: Rosita

last: Primevera

first: Shashank

last: Chetty

first: Everett

last: Meyer


title: A Method for Temporal-Spatial Multivariate Genomic Analysis of Acute Wound Healing via Tissue Stratification: A Porcine Negative Pressure Therapy Pilot Study

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: (ACUP Abstract) Evaluating the effect of negative pressure therapy on wound healing. The current study will physically and systematically characterize the wound site through the healing process, and provide valuable new information on how bacteria interacts with Granufoam, Surgicel, Owen's Rayon, Fibrin Glue, and the wound site during the healing process, and may lead to the development of new materials and dressings to be used for wound healing applications. (Manuscript Abstract) Wound therapies are capable of modulating the complex molecular signaling profile of tissue regeneration. However traditional, bulk tissue analysis results in nonspecific expressional profiles and diluted signaling that lacks temporal-spatial information. In this study, an acute incisional porcine wound model was developed in the context of negative pressure wound therapy (NPWT). Dressing materials were inserted into wounds with or without NPWT exposure and evaluated over 8-hours. Upon wound explantation, tissue was stratified and dissected into the epidermis, dermis, or subcutaneous layer, or  left undissected as a bulk sample and all groups processed for RNAseq. RNAseq of stratified layers provided spatial localization of expressional changes within defined tissue regions, including angiogenesis, inflammation, and matrix remodeling. Different expressional profiles were observed between individual tissue layers relative to each other within a single wound group and between each individual layer relative to bulk analysis. Tissue stratification identified unique differentially expressed genes within specific layers of tissue that were hidden during bulk analysis, as well as amplification of weak signals and/or inversion of signaling between two layers of the same wound, suggesting that two layers of skin can cancel out signaling within bulk analytical approaches. The unique wound stratification and spatial RNAseq approach in this study provides a new methodology to observe expressional patterns more precisely within tissue that may have otherwise not been detectable. Together these experimental data offer novel insight into early expressional patterns and genomic profiles, within and between tissue layers, in wound healing pathways that could potentially help guide clinical decisions and improve wound outcomes.

overall_design: Acute porcine (sus scorfa) incisional wound model. Multiple dressing material insert were placed within wound tissue interface and exposed to +/- negative pressure therapy for 0, 2, 4, or 8 hours. Control include baseline wounds immediately process upon wounding at time 0-hour, biopsy punch of non-wound tissue, and control (untreated) wounds for each timepoint.

first: Jacob

last: Hodge

first: David

last: Zamierowski

first: Jennifer

last: Robinson

first: Adam

last: Mellott


title: The translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition [Ribo-seq and RNA-seq]

first: Yuchen

last: Yang

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary: Direct reprogramming of fibroblasts into induced cardiomyocytes (iCMs) holds great promise for heart regeneration. Although great progress has been made in understanding the transcriptional and epigenetic mechanisms of iCM reprogramming, its translational regulation remains largely unexplored. Here we characterized the translational landscape of iCM reprogramming using integrative ribosome and transcriptomic profiling, and showed extensive translatome re-patterning during fibroblast conversion into iCM. Loss of function screening for translational regulators uncovered Ybx1 as a critical barrier to iCM induction. Knockdown of Ybx1 dramatically improved the efficiency and quality of iCM reprogramming. Mechanistically, Ybx1 directly bound the transcripts of Srf and Baf60c, both of which mediated, at least partially, the repressive effect of Ybx1 on iCM generation.and Depletion of Ybx1 de-repressed the translation of its targets including SRF and Baf60c. Interestingly, upon removing Ybx1, Tbx5 alone could reprogram fibroblasts into iCMs that exhibit classic iCM molecular features and reprogramming trajectories revealed by our single cell dual-omics. In sum, we presented here a global view of translatome dynamics of cardiac reprogramming and identified a novel translational barrier, Ybx1, to iCM generation. Removing this barrier allowed the single factor mediated iCM reprogramming.

overall_design: Ribo-seq and RNA-seq libraries were generated on day 5 cardiac fibroblasts (CFs) infected with viral vector encoding the polycistronic Mef2c/Gata4/Tbx5 (MGT) and control cells, namely, the primary CFs

first: Yifang

last: Xie

first: Jiandong

last: Liu

first: Li

last: Qian


title: RNA N6-methyladenosine methyltransferase METTL3 drives NAFLD-HCC and is a therapeutic target for boosting immunotherapy [m6A-seq]

city: hongkong

first: Yasi

last: PAN

address: Rm701, LiKS Med Sci Bldg, PWH, Shatin

country: Hong Kong

institute: the Chinese University of Hong Kong

summary: Non-alcoholic fatty liver disease (NAFLD) is an emerging risk factor of hepatocellular carcinoma (HCC). However, the mechanism and target therapy on NAFLD-HCC are still unclear. Here, we identify that the N6-methyladenosine (m6A) methyltransferase METTL3 promotes NAFLD-HCC. Hepatocyte-specific Mettl3 knockin exacerbated NAFLD-HCC formation while Mettl3 knockout exerted an opposite effect in mice. Single-cell RNA-seq revealed that METTL3 suppressed antitumor immune response by reducing infiltration of Gzmb+ and IFN-γ+ CD8+ T-cell, thereby facilitating immune escape. Mechanistically, METTL3 mediates SCAP mRNA m6A to promote its translation, leading to the activation of cholesterol biosynthesis. This enhanced secretion of cholesterol and cholesteryl esters, lipotoxins that impaired CD8+ T cell function in tumor microenvironment. Targeting of METTL3 by sgRNA, nanoparticle-siRNA, or pharmacological inhibitor (STM2457) in combination with anti-PD1 synergized to reinvigorate cytotoxic CD8+ T cells and mediate tumor regression. Together, METTL3 is a therapeutic target in NAFLD-HCC, especially in conjunction with immune checkpoint blockade (ICB) therapy.

overall_design: To investigate the function of METTL3 in NAFLD-HCC, we established shMETTL3 in HKCI2 cell line, then performed RNA-seq, m6A-seq and ribo-seq


title: RNA N6-methyladenosine methyltransferase METTL3 drives NAFLD-HCC and is a therapeutic target for boosting immunotherapy [RNA-Seq]


title: Gallic Acid Pretreatment Mitigates Parathyroid Ischemia-Reperfusion Injury through Signaling Pathway Modulation

city: Kunming

first: Nianqiu

state: China/Yunnan

address: 519 Kunzhou Road, Xishan

department: Breast Surgery

institute: The Third Affiliated Hospital of Kunming Medical University: Yunnan Cancer Center, Kunming, 650000, Yunnan

summary: As a polyphenolic herbal extract, Gallic acid (GA) is known for its antioxidant and anti-inflammatory properties. However, its application in parathyroid ischemia-reperfusion injury (IRI) has not been well examined. This study aimed to elucidate the protective effects of GA pretreatment in a parathyroid IRI model and explore the underlying mechanisms.Hypoxia and hypoxia/reoxygenation models were established with primary parathyroid cells to explore the protective effect of GA.The results from sequencing and bioinformatic analyses indicated that GA might regulate MMP1, MMP9, FOSB, GSY2, DUSP5, TRPV1/3, TIAM1 and multiple signaling pathways in this process such as IL-17, AMPK, MAPK, Transient Receptor Potential (TRP) channels, cAMP and Rap1.

overall_design: mRNA-seq was collected from control untreated parathyroid cells (Negative Control group, NC), hypoxia/reoxygenation cells  (IRI (6H-6H) cell (Model group, M)), and GA-pretreated hypoxia/reoxygenation cells (IRI (6H-6H) cells that were pretreated with1200 uM GA (Treatment group, T) ) to unravel the potential underlying mechanism.

first: Weihan

last: Cao


title: RNA N6-methyladenosine methyltransferase METTL3 drives NAFLD-HCC and is a therapeutic target for boosting immunotherapy

overall_design: Refer to individual Series


title: PAMPS and Innate Immune Memory

city: Nashville

first: Margaret

middle: Ann

last: Mcbride

state: Tennessee

address: 1211 Medical Center Drive

department: Anesthesiology

institute: Vanderbilt University Medical Center

summary: Exposure to pathogen-associated molecular patterns (PAMPs) induces an augmented, broad-spectrum antimicrobial response to subsequent infection, a phenomenon termed innate immune memory. This study examined the effects of treatment with β-glucan, a fungus-derived Dectin-1 ligand, and monophosphoryl lipid A (MPLA), a bacteria-derived TNS4 ligand, on innate immune memory with a focus on identifying common cellular and molecular pathways. Treatment with either PAMP prepared the innate immune system to respond more robustly to Pseudomonas aeruginosa infection in vivo by facilitating mobilization of innate leukocytes into blood, their recruitment to the site of infection, augmentation of microbial clearance and attenuation of cytokine production. Examination of macrophages ex vivo showed that metabolism, phagocytosis and respiratory burst were amplified by treatment with either agent, although MPLA more robustly augmented these activities and more effectively facilitated killing of bacteria. Both agents activated gene expression pathways in macrophages that control inflammation, antimicrobial functions and protein synthesis and suppressed pathways regulating cell division with MPLA more potently inducing global gene transcription. β-glucan treatment minimally modified macrophage differential gene expression in response to LPS challenge compared to control whereas MPLA attenuated the magnitude of the LPS-induced transcriptional response. These results show that b-glucan and MPLA similarly augment the innate response to infection in vivo. Yet, MPLA more potently induces alterations in macrophage metabolism, antimicrobial functions, gene transcription and the response to LPS.

overall_design: Bone marrow-derived macrophages from WT C57BL/6 mice were treated with β-glucan, monophosphoyl lipid A (MPLA), lipopolysaccaride (LPS), vehicle (DMSO or normal saline (NS)), or multiple treatments in sequence. We then performed gene expression profile analysis from 2-3 biological replicates per treatment at multiple timepoints. The effects on the transciptome were compared between groups. This data comes from 3 batches of RNA sequencing, and analysis of each batch was perfomed relative to its own vehicle controls. Samples 1-18 are a batch, as are samples 19-30, and 31-36.

last: McBride

first: Edward

last: Sherwood