title: Transcriptomic study of NR8383 rat macrophages cells following exposure to TiO2 (NM105, p25 anatase/rutile)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 3 cm²/cm² of TiO2 (NM105, p25 anatase/rutile). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (3 cm²/cm²) of TiO2 (NM105, p25 anatase/rutile) for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to  NM403 carbon nanotubes

status: Public on Aug 18 2023

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

country: France

institute: Université de lorraine

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 0.8 cm²/cm² of NM403. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (0.8 cm²/cm²) of NM403 for 4 h were measured. For each condition, four biological replicates were performed.

first: Sara

last: Nahlé

first: Romain

last: Schmitt

first: Bertrand

middle: H

last: Rihn

first: Luc

last: Ferrari


title: Transcriptomic study of NR8383 rat macrophages cells in control condition (DMEM culture medium supplemented with 10% of fetal bovine serum)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages: here is the control for Air Liquid Interface (ALI) in DMEM culture medium supplemented with fetal bovine serum (FBS). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated in DMEM culture medium supplemented with 10% FBS, ALI, for 4 h were measured. For each condition, four biological replicates were performed.

first: Mélanie

middle: M

last: Leroux

last: Hocquel

first: Zahra

last: Doumandji


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to  Printex90 (ALI)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 0.9 cm²/cm² through an Air Liquid Interface (ALI) of Printex90 (ALI). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (0.9 cm²/cm²) of Printex90 (ALI) for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptomic study of NR8383 rat macrophages cells in submerged condition (control)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages: here is the control for submerged condition. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated in submerged condition, for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptomic study of NR8383 rat macrophages cells in control condition (water, H2O)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages: here is the control for Air Liquid Interface (ALI) in water (H2O). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated in water (H2O), ALI, for 4 h were measured. For each condition, four biological replicates were performed.


title: Optimized Infra-red photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells

status: Public on Aug 17 2023

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

summary: We report the PAR-CLIP data for endogenous IGF2BP3 protein in colorectal carcinoma cell line (HCT116). In this study, we established an immunoprecipitation protocol to obtain highly pure endogenous IGF2BP3-RNA complexes and compared RNase cleavage conditions. The PAR-CLIP protocol was modified to use single adapter circular ligation approach to increase the efficiency in library preparation and reduce sequence bias. Moreover, we implemented the use of highly-sensitive infra-red (IR) fluorescent dyes instead of radioactive probes to visualize IGF2BP3-crosslinked RNAs. We named the modified method “IR-PAR-CLIP”.

overall_design: Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of IGF2BP3 in HCT116 cells

first: G

middle: E

last: Karagöz


title: High CO2- and pathogen-driven expression of carbonic anhydrase βCA3 confers basal immunity in tomato

city: Hangzhou

first: Zhangjian

last: Hu

state: Zhejiang province

address: yuhangtang road 886

country: China

institute: zhejiang university

type: Expression profiling by high throughput sequencing

summary: The goals of the study are to compare the influence of CO2 concentration and Pseudomonas syringae pv. tomato DC3000 (Pst)  in wild type and βca3 mutant plants to cover the mechanism of βCA3-mediated basal immunity.

overall_design: Examination of 2 plant types（WT and βca3） in a combined treatment of CO2 concentration and Pst

first: Kai

last: Shi

first: Qiaomei

last: Ma


title: Sphingomyelin synthase–related protein SMSr is a phosphatidylethanolamine phospholipase C protein that promotes nonalcoholic fatty liver disease

city: Brooklyn

first: Mulin

last: He

state: New York

address: 310 Clarkson Avenue, Apt.615

country: USA

institute: SUNY Downstate Health Sciences Univ

summary: Sphingomyelin synthase (SMS)–related protein (SMSr) is a phosphatidylethanolamine phospholipase C (PE-PLC) molecule that is conserved and ubiquitous in mammals. However, its biological function is still not clear. We previously observed that SMS1 deficiency–mediated glucosylceramide accumulation caused nonalcoholic fatty liver diseases (NAFLD), including nonalcoholic steatohepatitis (NASH) and liver fibrosis. Here, first, we evaluated high-fat diet/fructose-induced NAFLD in Smsr knock out (KO) and WT mice. Second, we evaluated whether SMSr deficiency can reverse SMS1 deficiency-mediated  NAFLD, using Sms1/Sms2 double and Sms1/Sms2/Smsr triple KO mice. We found that SMSr/PE-PLC deficiency attenuated high-fat diet/fructoseinduced fatty liver and NASH,  and attenuated glucosylceramide accumulation-induced NASH, fibrosis, and tumor formation. Further, we found that SMSr/PE-PLC deficiency reduced the expression of many inflammatory cytokines and fibrosis-related factors, and PE supplementation in vitro or in vivo mimicked the condition of SMSr/PE-PLC deficiency. Furthermore, we demonstrated that SMSr/PEPLC deficiency or PE supplementation effectively prevented membrane-bound βcatenin transfer to the nucleus, thereby preventing tumor-related gene expression. Finally, we observed that patients with NASH had higher SMSr protein levels in the liver, lower plasma PE levels, and lower plasma PE/phosphatidylcholine (PC) ratios, and that human plasma PE levels are negatively associated with TNF-α and TGFβ1 levels. In conclusion, SMSr/PE-PLC deficiency causes PE accumulation, which can attenuate fatty liver, NASH, and fibrosis. These results suggest that SMSr/PE-PLC inhibition therapy may mitigate NAFLD.

overall_design: We collected liver isolated from wild-type and SMSrKO mice high-fat diet with fructose (in drinking water) for 16 weeks, and we isolated hepatocytes from two months old WT, Sms1/Sms2-dKO, and Sms1/Sms2/Smsr-tKO mice for RNA sequencing.

first: Zhiqiang

last: Li

first: Xian-Cheng

last: Jiang


title: Effects of HLA DRB1*15:01 interactions with ⍺-syn32-46 on gene expression in the ileum

city: New York

first: Connor

last: Monahan

state: NY

institute: Columbia University

summary: HLA DRB1*15:01 is overrepresentated in Parkinson's disease patients and binds with high affinity to the ⍺-synuclein peptide, 32-46. Immunization of humanized mice expressing HLA DRB1*15:01 with ⍺-syn32-46 induces enteric phenotypes similar to those of prodromal Parkinson's disease. We collected the ileum from HLA mice immunized with either Complete Freund's Adjuvant (CFA) with ⍺-syn32-46 or CFA alone, and sequenced the tissue with bulk RNA sequencing at 21 days post immunization to determine changes in gene expression.

overall_design: 10-12 week old HLA DRB1*15:01 expressing MHC-II (-/-) mice were immunized with ⍺-syn32-46 (100ug) in CFA (200ug) or CFA alone. At 14 days post immunization (DPI), mice were boosted again with the same emulsion followed by an injection of pertussis toxin (400ng), then an additional pertussis toxin injection at 16 DPI. At 21 DPI, the ileum was collected into TRIzol reagent for bulk RNA sequencing

first: Francesca

last: Garretti

first: David

last: Sulzer

first: Dritan

last: Agalliu


title: Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

country: Italy

institute: Stazione Zoologica Anton Dohrn

summary: Identifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. We use single-cell RNA sequencing (scRNA-seq) to survey the cell types of the sea urchin early pluteus larva.

overall_design: Generation, analysis and integration of single cell RNA-seq data of 3 dpf Strongylocentrotus purpuratus larva.

first: Periklis

last: Paganos

first: Danila

last: Voronov

first: Jacob

last: Musser

first: Detlev

last: Arendt

first: Maria

middle: I


title: Vitamin K1 induced cytotoxic effects and transcriptomic analysis in acute T-cell lymphocytic leukemia Jurkat cells

city: Beijing

first: Ying

last: Shang

address: Anxiangbeili Street

institute: Strategic Support Force Medical Center

summary: Vitamin K1 (VK1), an essential nutrient related to coagulation, has been proved to have anticancer properties in various cancer cells. However, little is known about the effects of VK1 on hematologic malignancies. The aim of the study was to evaluate the cytotoxic effects of VK1 on acute T-cell lymphocytic leukemia Jurkat cells (Jurkat T cells). In addition, VK1 induced changes of gene expression in Jurkat T cells were also observed.

overall_design: Differentially expressed genes (DEGs) of Jurkat T cells induced by VK1 were analyzed by RNA sequencing on the Illumina Novaseq6000 sequencer.

first: Shaoyan

last: Si

first: Shujun

last: Song

first: Xiaotong

last: Lou


title: The 3’ Untranslated Region (3’UTR) Coding Sequence of PHO84, Rather Than the Antisense RNA, Promotes Gene Repression

city: West Lafayette

first: Elizabeth

middle: J

last: Tran

state: IN

address: 175 S. University Street

department: Biochemistry

institute: Purdue University

summary: We provide evidence that the model of antisense-mediated repression of PHO84 gene is not correct, and that the 3’UTR of PHO84 exhibits a repressive effect on the sense transcript. We also provide a list of trans-acting elements promoting 3’UTR-dependent repression. Such information can be taken further to possibly identify key players in human diseases arising from gene expression dysregulation.

overall_design: Comparative gene expression profiling analysis of Transient transcriptome sequencing (TT-seq) data was performed for wild-type and dbp2 KO S. cerevisiae strains

first: Youssef

middle: A

last: Hegazy

first: Sara

middle: C

last: Cloutier

first: Sagar

last: Utturkar

first: Subhadeep

last: Das


title: Canagliflozin mediates tumor suppression alone and in combination with radiotherapy in non-small cell lung cancer (NSCLC) through inhibition of HIF-1a

city: Hamilton

first: Theodoros

last: Tsakiridis

address: 699 Concession St

country: Canada

institute: McMaster University

summary: Non-small cell lung cancer (NSCLC) has a poor prognosis and effective therapeutic strategies are lacking. The diabetes drug canagliflozin inhibits NSCLC cell proliferation and the mammalian target of rapamycin (mTOR) pathway, which mediates cell growth and survival, but it is unclear whether this drug can enhance response rates when combined with cytotoxic therapy. Here, we evaluated the effects of canagliflozin on human NSCLC response to cytotoxic therapy in tissue cultures and xenografts. Ribonucleic acid sequencing (RNA-seq), real-time quantitative PCR (RT-qPCR), metabolic function, small interfering ribonucleic acid (siRNA) knockdown and protein expression assays were used in mechanistic analyses. We found that canagliflozin inhibited proliferation and clonogenic survival of NSCLC cells, and augmented the efficacy of radiotherapy to mediate these effects and inhibit NSCLC xenograft growth. Canagliflozin treatment alone moderately inhibited mitochondrial oxidative phosphorylation and exhibited greater anti-proliferative capacity than specific mitochondrial complex-I inhibitors. The treament downregulated genes mediating hypoxia-inducible factor (HIF)-1a stability, metabolism and survival, activated adenosine monophosphate-activated protein kinase (AMPK) and inhibited mTOR, a critical activator of HIF-1a signaling. HIF-1a knockdown and stabilization experiments suggested that canagliflozin mediates anti-proliferative effects, in part, through suppression of HIF-1a. Transcriptional regulatory network analysis pinpointed histone deacetylase 2 (HDAC2), a gene suppressed by canagliflozin, as a key mediator of canagliflozin’s transcriptional reprogramming. HDAC2 knockdown eliminated HIF-1a levels and enhanced the anti-proliferative effects of canagliflozin. HDAC2-regulated genes suppressed by canagliflozin are associated with poor prognosis in several clinical NSCLC datasets. In addition, we include evidence that canagliflozin also improves NSCLC response to chemotherapy. In summary, canagliflozin may be a promising therapy to develop in combination with cytotoxic therapy in NSCLC.

overall_design: Total RNA was isolated from 3 replicates of A549 cells treated with either 10 uM canagliflozin, 5 Gy radiotherapy (RT) or vehicle (DMSO) for 24h. A total of 9 samples were analyzed.

first: Olga-Demetra

last: Biziotis

first: Evangelia

first: Amr

last: Ali

first: Elham

last: Ahmadi

first: Jianhan

last: Wu

first: Simon

last: Wang

first: Bassem

last: Mekhaeil

first: Kanwaldeep

last: Singh

first: Gabe

last: Menjolian

first: Thomas

last: Farrell

first: Bassam

last: Abdulkarim

first: Ranjan

middle: K

last: Sur

first: Aruz

last: Mesci

first: Peter

last: Ellis

first: Tobias

last: Berg

first: Jonathan

middle: L

last: Bramson

first: Paola

last: Muti

first: Gregory

middle: R

last: Steinberg


title: Effects of HLA DRB1*15:01 interactions with ⍺-syn32-46 on gene expression in intestinal immune cells in mice

first: Connor

last: Monahan

summary: HLA DRB1*15:01 is overrepresentated in Parkinson's disease patients and binds with high affinity to the ⍺-synuclein peptide, 32-46. Immunization of humanized mice expressing HLA DRB1*15:01 with ⍺-syn32-46 induces enteric phenotypes similar to those of prodromal Parkinson's disease. We collected the small intestines from HLA mice immunized with either Complete Freund's Adjuvant (CFA) with ⍺-syn32-46 or CFA alone, sorted the CD45+ immune cells, then performed single-cell RNA sequencing to evaluate gene expression at single cell resolution.

overall_design: 10-12 week old HLA DRB1*15:01 expressing MHC-II (-/-) mice were immunized with ⍺-syn32-46 (100ug) in CFA (200ug) or CFA alone. At 14 days post immunization (DPI), mice were boosted again with the same emulsion followed by an injection of pertussis toxin (400ng), then an additional pertussis toxin injection at 16 DPI. At 21 DPI, the small intestine was collected and dissociated to single cells. The cells were sorted, and CD45+ cells were collected for single-cell RNA sequencing.

first: Francesca

last: Garretti

first: David

last: Sulzer

first: Dritan

last: Agalliu


title: TRAP-based allelic translation efficiency imbalance analysis to identify genetic regulation of ribosome occupancy in specific cell types in vivo

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: The alteration of gene expression due to variations in the sequences of transcriptional regulatory elements has been a focus of substantial inquiry in humans and model organisms. However, less is known about the extent to which natural variation contributes to post-transcriptional regulation. Allelic Expression Imbalance(AEI) is a classical approach for studying the association of specific haplotypes with relative changes in transcript abundance. Here, we benchmarked a new TRAP based approach to associate genetic variation with transcript occupancy on ribosomes in specific cell types, to determine if it will allow examination of Allelic Translation Imbalance(ATI), and Allelic Translation Efficiency Imbalance, using as a test case mouse astrocytes in vivo. We show that most changes of the mRNA levels on ribosomes were reflected in transcript abundance, though ~1.5% of transcripts have variants that clearly alter loading onto ribosomes orthogonally to transcript levels. These variants were often in conserved residues and altered sequences known to regulate translation such as upstream ORFs, PolyA sites, and predicted miRNA binding sites. Such variants were also common in transcripts showing altered abundance, suggesting some genetic regulation of gene expression may function through post-transcriptional mechanisms. Overall, our work shows that naturally occurring genetic variants can impact ribosome occupancy in astrocytes in vivo and suggests that mechanisms may also play a role in genetic contributions to disease.

overall_design: 4 TRAP and 4 input samples from an astrocyte trap line, derived from an FVB/C57BL6 F1 cross

first: Yating

last: Liu

first: Anthony

last: Fischer

first: Celine

last: St. Pierre

first: Juan

middle: F

last: Macias-Velasco

first: Heather

last: Lawson


title: APLNR marks a multipotent human cardiac progenitor derived with induced pluripotent stem cells

city: Hong Kong

first: Yin Yu

last: Lam

address: 102 Pokfulam Road

department: Department of Paediatrics and Adolescent Medicine

institute: The University of Hong Kong

summary: We identified APLNR as a surface marker for in vitro cardiac progenitors derived from human induced pluripotent stem cells (hiPSC). To gain further insight on the differentiation trajectory and its relevance with in vivo cardiac development, we performed polyA mRNA-sequencing on APLNR+ in vitro cardiac progenitors derived from 3 hiPSC lines at 0, 24, 48 and 72 hours post-immunomagnetic isolation. Our study revealed APLNR+ in vitro cardiac progenitors differentiate via a transient progenitor stage before further differentiation into cardiomyocytes and cardiac mesenchyme.

overall_design: Poly-A mRNA from APLNR+ in vitro cardiac progenitors at 0, 24, 48 and 72 hours post-isolation were taken for sequencing.

first: Chun Ho

last: Chan

first: Wendy

last: Keung

first: Yiu Fai

last: Cheung


title: Transplantation of wild-type hematopoietic stem and progenitor cells rescue Alzheimer’s disease in a mouse model and highlights the central role of microglia in disease pathogenesis

city: La Jolla

first: Stephanie

last: Cherqui

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Alzheimer’s disease (AD) is the most prevalent cause of dementia, but still no effective treatment exists. Microglia have been implicated in AD pathogenesis, but their role is still matter of debate. Our study represents direct evidence that microglia play a key role in disease progression, and that replacing diseased APP/PSEN1 microglia via single systemic wild-type (WT) hematopoietic stem and progenitor cell (HSPC) transplantation rescue AD phenotype in the 5xFAD mice. Cell replacement led to complete prevention of memory loss and neurocognitive impairment, and significant decrease of β-amyloid plaques in the hippocampus and cortex. Neuroinflammation was also significantly reduced. Transcriptomic analysis revealed significant decrease in gene expression related to “disease-associated microglia” in the cortex, and “neurodegeneration-associated endothelial cells” in the hippocampus of the WT HSPC-transplanted 5xFAD mice compared to diseased controls. This work shows the importance of microglia in AD and that HSPC transplant represents a promising therapeutic avenue.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT mice, 5xFAD mice, 5xFAD mice transplanted with 5xFAD HSPCs, or 5xFAD mice transplanted with WT HSPCs 4 months post transplantation.

first: Priyanka

last: Mishra

first: Alexander

last: Silva

first: Jay

last: Sharma

first: Jacqueline

last: Nguyen

first: Donald

middle: P

last: Pizzo

first: Denise

last: Hinz

first: Debashis

last: Sahoo


title: Augmenting CAR T Cell Function with LIGHT

status: Public on Aug 16 2023

first: Jahan

last: Rahman

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: Chimeric antigen receptor (CAR) T cell therapy has shown remarkable clinical success in the treatment of B-cell acute lymphoblastic leukemia (B-ALL), non-Hodgkin lymphoma (NHL), and multiple myeloma (MM), but its clinical efficacy in other hematologic tumors and solid tumors has been modest. Some of the major challenges that diminish the efficacy of CAR T cells against solid tumors are tumor-associated antigen heterogeneity and the immunosuppressive tumor microenvironment (TME). To overcome these problems, we developed CAR T cells overexpress with LIGHT (TNFSF14), which is a ligand of both LtβR (lymphotoxin beta receptor) on cancer cells and HVEM (herpes virus entry mediator) on immune cells. In addition to the cancer cell-directed cytotoxicity mediated by the CAR T cells themselves, the interaction of LIGHT with LTβR on tumor cells led to antigen-independent killing; moreover, LIGHT also provided immunostimulatory properties to the T cells. Hence, LIGHT-CAR T cells promoted, through multimodal and orthogonal mechanisms, an improved antitumor response through enhanced tumor killing and costimulatory potential. The antigen-independent killing of heterogeneous cancer cells was widely applicable across various cancer cell lines and was mediated by LIGHT CAR T cells in an LTβR-dependent manner. In addition, LIGHT-CAR T cells demonstrated higher proliferative capacity and proinflammatory cytokine secretion than non-LIGHT expressing CAR T cells. Furthermore, LIGHT-CAR T cells conferred significant tumor control and concomitant survival benefit as compared to non-LIGHT CAR T cells in xenograft models of solid tumors with a heterogeneous expression of the target antigen. The application of LIGHT-CAR T cell therapies may provide a novel therapeutic approach to the treatment of solid tumors in the context of antigen-heterogeneous disease thereby preventing outgrowth of antigen-negative populations leading to disease relapse.

overall_design: To further elucidate mechanisms of the enhanced cytotoxicity of LIGHT CAR T cells compared to standard second-generation CAR T cells, we performed Cellular Indexing of Transcriptomes and Epitopes (CITE-seq) to evaluate the transcriptional state and surface protein expression of individual CAR T cells before and after co-culture with cancer cells. We generated mesothelin-directed CAR T cells with and without LIGHT (Meso_28z-LT and Meso_28z, respectively) from four healthy human donors (A-D) and sequenced them post-sorting at baseline (t=0) and 48 hours after co-culture with cancer cells (t=48h). We performed cell hashing (32) to combine samples of the same condition (construct + timepoint) from different donors and used an extensive panel of 130 antibody-derived tags (ADTs) to stain cell surface proteins

first: Winson

last: Cai

first: Kento

last: Tanaka

first: Xiaoli

last: Mi

first: Vinagolu

last: Rajasekhar

first: Jonathan

last: Khan

first: Sarah

last: Yoo

first: Serena

last: Mathew

first: Sydney

last: Souness

first: Terence

last: Purdon

first: James

last: McDowell

first: Takeshi

last: Fujino

first: John

last: Healey

first: Omar

last: Abdel-Wahab

first: David

last: Scheinberg

first: Renier

last: Brentjens

last: Daniyan


title: Patient-derived Enteroids provide a Platform for the Development of Therapeutic Approaches in Microvillus Inclusion Disease

city: Boston

first: Jay

last: Thiagarajah

state: MA

address: 300 Longwood Avenue, EN620

department: Gastroenterology

institute: Boston Children's Hospital

summary: Microvillus Inclusion Disease (MVID), caused by loss-of-function mutations in the motor protein Myosin Vb (MYO5B), is a severe infantile disease characterized by diarrhea, malabsorption, and acid-base instability, requiring intensive parenteral support for nutritional and fluid management. Human patient-derived enteroids represent a model for investigation of monogenic epithelial disorders but are a rare resource from MVID patients. We developed human enteroids with different loss-of function MYO5B variants and showed that they recapitulated the structural changes found in native MVID enterocytes. Multiplex Immunofluorescence imaging of patient duodenal tissues revealed patient-specific changes in localization of brush border transporters. Functional analysis of electrolyte transport revealed profound loss of Na+/H+ exchange (NHE) activity in MVID patient enteroids with near-normal chloride secretion. The chloride channel-blocking anti-diarrheal drug, Crofelemer, dose-dependently inhibited agonist-mediated fluid secretion. MVID enteroids exhibited altered differentiation and maturation versus healthy enteroids. Gamma-secretase inhibition with DAPT recovered apical brush border structure and functional Na+/H+ exchange activity in MVID enteroids. Transcriptomic analysis revealed potential pathways involved in the rescue of MVID cells including serum- and glucocorticoid-induced protein kinase 2 (SGK2), and NHE regulatory factor 3 (NHERF3). These results demonstrate the utility of patient-derived enteroids for developing therapeutic approaches to MVID.

overall_design:
Experiments showed that the gamma secretase inhibitor DAPT is able to morphologically and functionally rescue patient-derived epithelial cells from patients with microvillus inclusion disease. To investigate the effect of the gamma-secretase inhibitor DAPT on the transcriptome and identify potential  mechanistic targets for this effect we treated duodenal enteroids with DAPT.
Duodenal enteroid derived from 2 healthy patients and 2 patients with MVID were either treated with vehicle (dmso) or DAPT for 4 days. We then performed gene expression profiling using data obtained from RNA sequencing.
Comparative gene expression profiling of healthy untreated, treated and MVID treated, untreated.

first: Krishnan

last: Raghunathan


title: In vitro cardiac differentiation is analogous to its in vivo counterpart

first: Yin Yu

last: Lam

summary: In vitro cardiac differentiation can be readily achieved in human induced pluripotent stem cells (hiPSCs) via temporal modulation of Wnt signalling. However, its differentiation trajectory and the in vivo counterpart of intermediate progenitor populations has yet to be elucidated. This study aims to capture the most diverse amount of distinct cell populations during in vitro cardiac differentiation by performing single cell RNA-sequencing at day 2, 4, 5 and 9 cells undergoing in vitro cardiac differentiation. Our study has revealed in vitro cardiac differentiation is analogous with in vivo second heart field cell specification.

overall_design: Day 2, 4, 5 and 9 cells undergoing in vitro cardiac differentiation derived from 2 hiPSC lines.

first: Chun Ho

last: Chan

first: Wendy

last: Keung

first: Yiu Fai

last: Cheung


title: Distinct Epithelial-Innate Immune Cell Transcriptional Circuits Underlie Airway Hyperresponsiveness in Asthma

city: Seattle

first: Ryan

last: Murphy

state: WA

address: 850 Republican St.

department: Division of Pulmonary, Critical Care, and Sleep Medicine

institute: University of Washington

summary:
Indirect airway hyperresponsiveness (AHR) is a highly specific feature of asthma but the underlying mechanisms responsible for driving indirect AHR remain incompletely understood. We aimed to identify differences in gene expression in epithelial brushings obtained from individuals with asthma who were characterized for indirect AHR in the form of exercise-induced bronchoconstriction (EIB).
RNA-sequencing (RNA-seq) analysis was performed on epithelial brushings obtained from individuals with asthma with (n=11) and without EIB (n = 9).

overall_design: Bulk RNA-seq analysis comparing gene expression from epithelial brushing samples in individuals with asthma and EIB (n=11) and individual with asthma without EIB (n=9)

first: Murphy

last: Ryan


title: The Transcriptomic Consequences of Zika Virus Infection on Porcine Induced Neural Stem Cells and Associated Gene Regulatory Networks

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

summary: The aim of this study was to investigatethe potential susceptibility, cell tropism, and neurogenesis of porcine induced neural stem cells (piNSCs) after infection with ZIKV.

overall_design: Transcriptome data of porcine induced neural stem cells that were infected with different strains of the Zika virus

first: Warunya

last: Chakritbudsabong

first: Wasinee

last: Rungsarityotin

first: Ladawan

last: Sariya

first: Somjit

last: Chaiwattanarungruengpaisan

first: Jarupha

last: Taowan

first: Wanvisa

last: Surarith

first: Phakhin

last: Juntahirun

first: Nattarun

last: Chaisilp

first: Sasitorn

last: Rungarunlert


title: A Cleavage Product METTL3a-(238-580) Mediates m6A Methyltransferase Complex Assembly and mTOR Activation

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

summary: N6-methyladenosine (m6A) methylation of mRNA by the methyltransferase complex (MTC), with core components including METTL3-METTL14 heterodimers and Wilms’ tumor 1-associated protein (WTAP), contributes to breast tumorigenesis, but the mechanism of MTC assembly remains elusive. Here, we identify a novel cleaved form METTL3a (residues 239-580 of METTL3), that is highly expressed in breast cancer. Furthermore, we find that both METTL3a and full-length METTL3 are required for MTC assembly, RNA m6A deposition, as well as cancer cell proliferation. Mechanistically, we find that METTL3a is required for METTL3-METTL3 interaction, which is a prerequisite step for recruitment of WTAP in MTC assembly. Analysis of m6A sequencing data shows that depletion of METTL3a globally disrupts m6A methylation, and METTL3a mediates mTOR activation via m6A-mediated suppression of TMEM127 expression. Consequently, we find that METTL3 cleavage is mediated by proteasome in an mTOR-dependent manner, revealing positive regulatory feedback between METTL3a and mTOR signaling. Our findings reveal METTL3a as an important component for MTC assembly, and suggest the METTL3a-mTOR axis as a potential therapeutic target for breast cancer.

overall_design: m6A-modified sites in T47D cells infected with retrovirus encoding sgMETTL3 resistant METTL3-WT, METTL3-Δ198, METTL3-Δ238 or control vector (Vec) followed by another infection with sgMETTL3 or sgControl (sgCtrl).

first: Jing

last: Zhang


title: Effect of mir-210-3p on The Function of c-kit+ Cardiac Progenitor Cells under Ischemia and Hypoxia

city: Nanning

first: Louyi

last: Shen

address: No. 6 Shuangyong Road

institute: The First Affiliated Hospital of Guangxi Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: C-kit+ cardiac progenitor cells (CPCs) play an important role in improving the prognosis of ischemic heart disease. MicroRNAs have been shown to have a protective role in the cardiac repair process, but their specific functional mechanisms are still unclear. The aim of this study was to screen for differentially expressed miRNAs in c-kit+ CPCs under hypoxia and explore their effects on the function of c-kit+ CPCs. We found that miR-210-3p was significantly upregulated in hypoxia-treated c-kit+ CPCs through second-generation sequencing. Protein chip detection revealed that c-kit+ CPCs could express cytokines such as FGF basic, Angiogenin, and VEGF, and that hypoxia could enhance the secretion of some angiogenesis-related factors. Silencing miR-210-3p, on the other hand, resulted in a reduction in the secretion of these angiogenesis-related factors. In addition, we found that the conditioned medium of hypoxia-treated c-kit+ CPCs could promote the proliferation, migration, and tube formation ability of mouse cardiac microvascular endothelial cells (CMECs). Conversely, the conditioned medium of c-kit+ CPCs with silenced miR-210-3p after hypoxia inhibited the proliferation, migration, and tube formation ability of CMECs. These results suggest that c-kit+ CPCs may exert their pro-angiogenic effects through paracrine mechanisms, which are regulated by miR-210-3p. The upregulation of miR-210-3p in hypoxia-treated c-kit+ CPCs may enhance their paracrine function by regulating the secretion of angiogenic factors, thereby promoting angiogenesis in ischemic heart disease. Therefore, miR-210-3p plays a key role in regulating the paracrine function of c-kit+ CPCs and can affect the process of angiogenesis. The role of miR-210-3p has potential application value for the treatment of ischemic heart disease, and may become one of the important targets for future treatment of ischemic heart disease.

overall_design: Take healthy adult male C57BL/6 mice aged 4-6 weeks, digest their hearts using trypsin and collagenase, and use anti-c-kit-coupled magnetic beads for magnetic-activated cell sorting (MACS) to isolate c-kit cells. Culture the cells under hypoxia for 12 hours to establish the hypoxia model. Randomly divide the cultured cells into a normal control group and a hypoxia group, and extract cellular RNA for miRNA sequencing.

first: Guan

last: Fan

first: Guoliang

last: Yang

first: Zhijie

first: Chun

last: Gui


title: Hedyotis diffusa-Sculellaria barbata (HD-SB) suppresses the progression of colorectal cancer cells via the hsa_circ_0039933/hsa-miR-204-5p/wnt11 axis

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

summary: Our previous study confirmed that the combination of Hedyotis diffusa (HD) and Scutellaria barbata (SB) significantly inhibited colorectal cancer cells proliferation and the WNT signaling pathway. However, the exact molecular modulation remains unclear. In this study, colorectal cancer cells (SW620) were treated with 1 mg/mL HD-SB for 24 h, and high-throughput sequencing of circRNAs was performed. The level of hsa_circ_0039933 in three colorectal cancer cell lines (HT-29, SW620, and HCT116) was verified by qPCR. After transfection of hsa_circ_0039933 overexpression plasmids or small interfering RNAs, CCK8, apoptosis, cell migration, and cell invasion were utilized to evaluate the function of hsa_circ_0039933 in the progression of colorectal cancer cells. We identified hsa_circ_0039933, which was downregulated in HD-SB-induced colorectal cancer cells and positively related to colorectal cancer progression. In SW620 cells with relatively high expression of hsa_circ_0039933, interfering with the expression of hsa_circ_0039933 inhibited the proliferation, invasion, and migration of SW620 cells. In HCT116 cells with relatively low expression of hsa_circ_0039933, overexpression of hsa_circ_0039933 promoted the proliferation and invasion and migration ability of HCT116. Mechanistically, hsa_circ_0039933 targeted hsa-miR-204-5p to increase the expression of wnt11, leading to the activation of the Wnt pathway, thereby promoting the proliferation of colorectal cancer cells. This work revealed the potential molecular mechanism of HD-SB for the treatment of colorectal cancer, which was to inhibit the Wnt signaling pathway through the hsa_circ_0039933/hsa-miR-204-5p/wnt11 axis, then suppressing proliferation, migration, and invasion in colorectal cancer cell.

overall_design: In our study, we investigated the influence of HD-SB on CRC development and the mechanism of related pathways by high-throughput sequencing of circRNAs. A novel down-regulated circRNA, hsa_circ_0039933, was identified as a pro-oncogene and related to CRC proliferation, invasion, and migration, and to promote CRC progression by acting as ceRNA that regulates wnt11. This study showed that HD-SB reduced the progression of colorectal cancer cells by mediating the hsa-miR-204-5p/wnt11 by downregulating the expression of hsa_circ_0039933.

first: Danye

last: Zhu

first: Shanmin

last: Yuan

first: Cong

last: Chen


title: Islr regulates satellite cells asymmetric division through Sparc/p-ERK1/2 signaling pathway

city: 北京市

first: Fan

last: Liu

state: 北京市

address: 北京市海淀区中国农业大学西校区

institute: 中国农业大学

summary: Satellite cells are adult muscle stem cells responsible for muscle regeneration after acute or chronic injuries. The balance between stem cell self-renewal and differentiation impacts the kinetics and efficiency of skeletal muscle regeneration. This study elucidated the function of Islr in satellite cell asymmetric division. Satellite cell specific deletion of Islr compromises muscle regeneration in adult mice by impairing the satellite cell pool. Islr is pivotal for satellite cell proliferation and its deletion promotes asymmetric cell fate segregation of satellite cells. A mechanistic search revealed that Islr interacts and stabilizes the Sparc protein, which activates p-ERK1/2 signaling required for asymmetric division. In combination, the findings have identified Islr as a key regulator of satellite cell asymmetric division through the Sparc/p-ERK1/2 signaling pathway, which provides a new insight into satellite cell biology and open avenues for the treatment of myopathy.

overall_design: Satellite cells were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of Islr and analyzed using RNAseq.

first: Xiong

last: Wang

first: Kuo

first: Yang

last: Su


title: single-cell RNA and TCR sequencing of sorted CD4+CD26- T cells sorted from 7 CTCL peripheral blood samples

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: Purpose: Characterization of the gene expression profile and TCR profile of CD4+CD26- T cells from CTCL to understand the cell of origin

overall_design: We bead-sorted CD4+CD26- T cells from 7 CTCL peripheral blood samples and performed 10X single-cell RNA and TCR sequencing

first: Carly

last: Harro

first: Xiaoqing

last: Yu

first: Jose

last: Conejo-Garcia


title: Novel Roles for the Transcriptional Repressor E4BP4 in Both Cardiac Physiology and Pathophysiology [4 mouse lines]

city: Birmingham

first: Lamario

last: Williams

state: AL

address: 1825 University Boulevard, Room 121

department: Medicine

institute: University of Alabama at Birmingham

summary: Circadian clocks temporally orchestrate biological processes critical for cellular/organ function. For example, the cardiomyocyte circadian clock modulates cardiac metabolism, signaling, and electrophysiology over the course of the day, such that, disruption of the clock leads to age-onset cardiomyopathy (through unknown mechanisms). Here, we report that genetic disruption of the cardiomyocyte clock results in chronic induction of the transcriptional repressor E4BP4. Importantly, E4BP4 deletion prevents age-onset cardiomyopathy following clock disruption. These studies also indicate that E4BP4 regulates both cardiac metabolism (eg, fatty acid oxidation) and electrophysiology (eg, QT interval). Collectively, these studies reveal that E4BP4 is a novel regulator of both cardiac physiology and pathophysiology.

overall_design: Comparative gene expression profiling analysis of  RNA-seq data for biventricular heart tissue isolated from 4 mouse lines: 1) cardiomyocyte-specific Bmal1 knockout (CBK; Bmal1flox/flox/MHCαCre+/-) and littermate control (Bmal1flox/flox/MHCαCre-/-) mice; 2) cardiomyocyte-specific E4bp4 knockout (CEK; E4bp4flox/flox/MHCαCre+/-) and littermate control (E4bp4flox/flox/MHCαCre-/-) mice; 3) cardiomyocyte-specific Bmal1/E4bp4 double knockout (CBK/CEK; Bmal1flox/flox/E4bp4flox/flox/MHCαCre+/-) and littermate control (Bmal1flox/flox/E4bp4flox/flox/MHCαCre-/-) mice; and 4) Cre recombinase control (MHCαCre+/-) and littermate wild-type mice. Individual Bmal1flox/flox, E4bp4flox/flox, and MHCαCre+/- mouse lines

first: Sobuj

last: Mia

first: Ravi

last: Sonkar

first: Mary

last: Latimer

first: David

last: Rawnsley

first: Samir

last: Rana

first: Jin

last: He

first: Pieterjan

last: Dierickx

first: Teayoun

last: Kim

first: Min

last: Xie

first: Kirk

last: Habegger

first: Masato

last: Kubo

first: Lufang

last: Zhou

first: Morten

last: Thomsen

first: Sumanth

last: Prabhu

first: Stuart

last: Frank

first: Paul

last: Brookes

first: Mitchell

last: Lazar

first: Abhinav

last: Diwan

first: Martin

last: Young


title: Mouse inbred strain-derived ES cells in low temperature

city: Kobe

first: Genshiro

middle: A.

last: Sunagawa

state: Hyogo

address: 2-2-3, Minatojimaminamimachi, Chuo-ku, Kobe

country: Japan

institute: RIKEN Center for Biosystems Dynamics Research

summary: To evaluate the transcriptome of ES cells at cold temperatures.

overall_design: Three mouse ES cell lines were cultured in two temperatures (37 °C and 31 °C), and the transcriptome was compared.

first: Koukyou

last: Suita

first: Kiyomi

last: Ishikawa


title: MEK5-mediated gene expression changes in PC3 human prostate cancer cells

city: New York

first: Constantinos

last: Broustas

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

summary: Mitogen/extracellular signal-regulated kinase kinase-5 (MEK5) belongs to the family of MAP kinases. It is activated by the upstream kinases MEKK2 and MEKK3. MEK5, in turn, phosphorylates and activates extracellular signal-regulated kinase 5 (ERK5) at Thr218/Tyr220. MEK5/ERK5 pathway plays a pivotal role in tumor initiation and progression, including prostate cancer. MEK5 protein is overexpressed in prostate cancer cells compared with normal cells and MEK5 levels are correlated with prostate cancer metastasis. Global gene expression was determined in PC3 cells stably expressing a scrambled (control) shRNA or MEK5 shRNA using the Agilent Mouse Whole Genome microarrays. Gene ontology and pathway analysis of differentially expressed genes using Ingenuity Pathway Analysis and gene set enrichment analysis (GSEA) revealed MEK5 knockdown attenuates a number or critical signaling pathways required for prostate tumor growth and progression.

overall_design: Gene expression was measured in PC3 human prostate cancer cells stably expressing a scrambled shRNA (shControl) or MEK5 shRNA. Three replicates/condition were used.

middle: G


title: MEK5-mediated gene expression changes in DU145 human prostate cancer cells

summary: Mitogen/extracellular signal-regulated kinase kinase-5 (MEK5) belongs to the family of MAP kinases. It is activated by the upstream kinases MEKK2 and MEKK3. MEK5, in turn, phosphorylates and activates extracellular signal-regulated kinase 5 (ERK5) at Thr218/Tyr220. MEK5/ERK5 pathway plays a pivotal role in tumor initiation and progression, including prostate cancer. MEK5 protein is overexpressed in prostate cancer cells compared with normal cells and MEK5 levels are correlated with prostate cancer metastasis. Global gene expression was determined in DU145 cells stably expressing a scrambled (control) shRNA or MEK5 shRNA using the Agilent Mouse Whole Genome microarrays. Gene ontology and pathway analysis of differentially expressed genes using Ingenuity Pathway Analysis and gene set enrichment analysis (GSEA) revealed MEK5 knockdown attenuates a number or critical signaling pathways required for prostate tumor growth and progression.

overall_design: Gene expression was measured in DU145 human prostate cancer cells stably expressing a scrambled shRNA (shControl) or MEK5 shRNA. Three replicates/condition were used.


title: Transformer 2β regulates alternative splicing of cell cycle regulator genes to promote ovarian cancer cell progression

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Poor prognosis of late stage ovarian cancer patients is observed with high metastasis rate, but the underlying molecular mechanism is ambiguous. RNA binding proteins (RBPs) play important roles in post-transcriptional regulation in tumor neoplasia and metastasis. In this study, we dedicated to explore the molecular functions of a canonical RBP, TRA2B, in cancer cells. By knocking TRA2B expression in HeLa cells and performing whole transcriptome sequencing experiment (RNA-seq), we found TRA2B-regulated alternative splicing profile was tightly associated with mitotic cell cycle, apoptosis, and several cancer pathways. Meanwhile, hundreds of genes were regulated by TRA2B at expression level, and their functions were enriched in cell proliferation, cell adhesion and angiogenesis, which were also related to cancer progression. We also observed the AS regulation and expression regulation were independent by integrating AS genes and expression changed genes. We then explored and validated the carcinogenic functions of TRA2B by knocking down its expression in ovarian cancer cells. In vivo, higher expression level of TRA2B was associated with poor prognosis in ovarian cancer patients. In conclusion, we demonstrated the important roles of TRA2B in ovarian cancer neoplasia and progression, and identified the underlying molecular mechanisms, making a contribution to molecular targeting treatment of ovarian cancer in the future.

overall_design: In this study, using next-generation RNA sequencing (RNA-seq) technology, we systematically investigated the global TRA2B-regulated AS events and the global gene expression change by silencing the expression of Tra2β in cancer cells. We found TRA2B could extensively regulate gene expression and AS in HeLa cells, which was highly related to its carcinogenic functions. Silencing experiment of TRA2B in ovarian cells validated its functions in cell proliferation, cell invasion and cell apoptosis in ovarian cancer cells. In summary, we extensively confirmed the carcinogenic functions of TRA2B in ovarian cancer cells, which were completed by regulating the expression and alternative splicing of associated genes.

first: Ronghua

last: Liu


title: Regulatory Enhancer Profiling of Mesenchymal-type Gastric Cancer Reveals Subtype-Specific Epigenomic Landscapes and Targetable Vulnerabilities

city: Singapore

first: Shamaine

last: Ho

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Recent studies have highlighted mesenchymal-subtype GC (Mes-GC) as a clinically aggressive subtype with few treatment options. Genome-wide chromatin profiles of primary GCs and GC cell lines were generated to identify Mes-GC-specific enhancer landscapes. Computational analysis uncovered TEAD1 as a master regulator of Mes-GC enhancers. TEAD1 ChIP-seq and RNA-seq/H3K27ac ChIP-seq following TEAD1 knockdown was performed as validation experiments.

overall_design:
Genome-wide chromatin profiles of 49 primary GCs and GC cell lines were analyzed. TEAD1 ChIP-seq in 3 GC cell lines and RNA-seq/H3K27ac ChIP-seq following TEAD1 knockdown in 2 GC cell lines were also performed.

Raw files for primary tissue RNA-seq were not submitted due to patient privacy concerns.

first: Patrick

last: Tan


title: Gene expression of 61 FFPE tissues of DLBCL patients at high-risk (aaIPI 2 or 3)

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: Current staging classifications do not accurately predict the benefit of high-dose chemotherapy (HDC) with autologous stem-cell transplantation (ASCT) for patients with diffuse large B-cell lymphoma (DLBCL) at high risk (age-adjusted International Index [aaIPI] score 2 or 3), who have achieved first complete remission after R-CHOP (rituximab, cyclophosphamide, vincristine, doxorubicin, and prednisone) treatment. We aim to construct a genetic prognostic model for improving individualized risk stratification and response prediction for HDC/ASCT therapy. We identified differentially expressed mRNAs associated with relapse of DLBCL.

overall_design: Affymetrix Human U133 Plus 2.0 microarrays (ThermoFisher Scientific, Waltham, MA, USA) identified differentially expressed mRNAs between 34 relapse and 27 relapse-free DLBCL patients.

first: Xiaopeng


title: Effect of blocking A2aR in sepsis on the splenic transcriptome

status: Public on Aug 15 2023

city: tianjin

first: Teng

last: Zhang

address: nanjing road

institute: Tianjin Medical University General Hospital

summary: Using C57BL/J mice, we constructed a septic cecum ligation perforation model with altered survival after blocking A2aR. Therefore, we wished to observe the transcriptome changes in the spleen.

overall_design: Using C57BL/J mice, a sepsis cecum ligation perforation model was constructed, ZM241385 was given to the experimental group, and saline was given to the control group. 24 hours after the operation, the spleens of the mice were obtained, preserved using liquid nitrogen, and analysed by transcriptome sequencing.

first: Tao

last: Ma


title: A CRISPR screen of HIV dependency factors reveals CCNT1 is non-essential in T cells but required for HIV-1 reactivation from latency [CRISPR]

first: Terry

last: Hafer

email: tjhafe@gmail.com, thafer@fredhutch.org

state: Washington

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency reactivation. We identified several HIV- 1 dependency factors that play a key role in HIV-1 latency reactivation including ELL, UBE2M, TBL1XR1, HDAC3, AMBRA1, and ALYREF. Knockout of Cyclin T1 (CCNT1), a component of the P-TEFb complex important for transcription elongation, was the top hit in the screen and had the largest effect on HIV latency reversal with a wide variety of latency reversal agents. Moreover, CCNT1 knockout prevents latency reactivation in a primary CD4+ T cell model of HIV latency without affecting activation of these cells. RNA sequencing data showed that CCNT1 regulates HIV-1 proviral genes to a larger extent than any other host gene and had no significant effects on RNA transcripts in primary T cells after activation. We conclude that CCNT1 function is redundant in T cells but is absolutely required for HIV latency reversal.

overall_design: We performed a CRISPR screen to understand the host genes involved in latency reversal, by targeting a library of putative HIV Dependency Factors previously described using latently infected Jurkat T cells (J-Lats) as a model. In this screen, we transduced a library containing guides targeting 527 genes (8 guides per gene, and 210 non-targeting controls), used puromycin to select for cells which have the vector and treated cells with either a DMSO control or an LRA (latency reversal agent). We are interested in understanding the genes which are depleted in the viral supernatant relative to the genomic DNA pool.

first: Hafer

last: Terry

first: Emerman

last: Michael


title: A CRISPR screen of HIV dependency factors reveals CCNT1 is non-essential in T cells but required for HIV-1 reactivation from latency

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

overall_design: Refer to individual Series


title: Activity of the GHRH Antagonist MIA-602 and its Underlying Mechanisms of Action in sarcoidosis

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: Growth hormone releasing hormone (GHRH) is a potent stimulator of growth hormone secretion from pituitary gland. Although GHRH is essential for growth of immune cells, the regulatory effects of its antagonist in granulomatous disease remains unknown. The goal is to evaluate the expression of GHRH receptor in human tissue with sarcoidosis granuloma and demonstrate the anti-inflammatory effects of MIA-602 (a GHRH antagonist) in in vitro and in vivo studies. Granulomatous reaction in the mouse lung was developed as previously described (PMID: 31921151). Mice were treated with 5 micrograms of MIA-602 (an GHRH antagonist) daily subcutanously. RNA from mouse lungs were extracted and RNASeq was perfomed.

overall_design: We selected 3 mice for MIA 602 treatment. They all were challenged with microparticles generated from Mycobacterium abscessus for granuloma development. MIA-602 was given daily via under skin injection. Mice were sacrificed after 3 weeks and lungs were extracted for analysis.

first: Mehdi

last: Mirsaeidi


title: A CRISPR screen of HIV dependency factors reveals CCNT1 is non-essential in T cells but required for HIV-1 reactivation from latency [RNA-Seq]

overall_design: To investigate the role of CCNT1 in host gene regulation as well as its effect on HIV-1 transcripts, we performed bulk RNA sequencing of J-Lat 10.6 cells that were either wild-type for CCNT1 or knocked out for CCNT1. We performed the RNA sequencing on two clonal knockouts of CCNT1. J-Lat cells were either unstimulated or treated with TNFα.  We also wanted to investigate the role of CCNT1 in host gene regulation by knocking out CCNT1 or AAVS1 (control) in primary CD4+ T cells, assessing whether knockout affects T cell activation, and performing bulk RNA sequencing. In this case, we isolated CD4+ T cells from three healthy donors, activated T cells, then performed CRISPR/Cas9 knockout by electroporating Cas9 ribonucleoproteins containing guide RNAs targeting CCNT1 or AAVS1. Cells were then activated with CD3/CD28 antibody co-stimulation and RNA was harvested after 24 hours.


title: Epigenetic changes and an extensive rewiring of the transcriptome underlie worker size distribution in the Florida carpenter ant [miRNA-seq]

city: Montreal

first: Moshe

last: Szyf

state: QC Quebec

address: 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology & Therapeutics

institute: McGill University

summary: Variation in continuous traits, such as height, is a complex output of genetic and environmental factors. In the Florida carpenter ant, workers are 75% genetically related but exhibit a wide range of lengths that broadly categorizes them into minor or major subcastes with specific roles within the colony. While initial studies have suggested that epigenetic changes can mediate the influence of the environment in the differential development of minor and major ants, no study has comprehensively studied ant size as a continuous phenotype with genome-wide approaches. Here, we exploit the entire continuous spectrum of ant size, mRNA expression, microRNA expression, and DNA methylation – in combination with genomic sequencing – to identify the molecular and epigenetic factors driving the determination of body size. We report dramatic changes in gene expression in key genes linked to sugar metabolism as well as the correlation of expression of a large proportion of the transcriptome to size, involving pathways related to DNA replication, muscle growth, and neuronal development. We further identify  and investigate the correlation of the expression of microRNAs and levels of DNA methylation with size, as well as their link to histone modifications, which together, might sculpt differential gene expression profiles. Together, this study unveils a coordinated molecular and epigenetic regulatory network determining body size, offering valuable insights into developmental biology and the molecular contributions to body size in the context of C. floridanus and beyond.

overall_design: Here, we applied a comprehensive multimodal omics approach to evaluate the molecular contributors to C. floridanus worker size by constructing combined genome-wide DNA sequence variation, DNA methylation, gene expression, and microRNA expression profiles, each from every individual ant across 48 terminal-stage larvae whose sizes span the complete range of larval lengths

first: Daniel

last: Sapozhnikov

first: Travis

first: Xinyu

last: Zhao

first: Ehab

last: Abouheif


title: Epigenetic changes and an extensive rewiring of the transcriptome underlie worker size distribution in the Florida carpenter ant [EM-seq]

type: Methylation profiling by high throughput sequencing


title: Epigenetic changes and an extensive rewiring of the transcriptome underlie worker size distribution in the Florida carpenter ant [BiSulfite-seq]


title: Epigenetic changes and an extensive rewiring of the transcriptome underlie worker size distribution in the Florida carpenter ant [RNA-seq]


title: KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [RNA-seq]

city: Los Angeles

first: Valerie

last: Arboleda

address: 615 Charles E. Young Drive South

department: Department of Pathology and Laboratory Medicine

institute: UCLA

summary: Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo truncating mutations in the gene KAT6A (Lysine(K) acetyltransferase 6A). ARTHS is clinically heterogeneous but characterized by several common features including intellectual disability, developmental and speech delay, hypotonia, congenital heart defects and gastrointestinal problems. KAT6A mRNA is highly expressed throughout early development and the levels of expression are lower levels in differentiated tissues, suggesting a key role maintenance of the stem cell characteristics. Across these cell types, the gene-regulatory mechanisms controlled by KAT6A and the histone-acetylation complex in which it works remain unknown. In this study, we created ARTHS patient-derived (n=7) and control (n=13) dermal fibroblasts from skin punch biopsies. KAT6A is expressed at moderate levels in human fibroblast cells and we performed a comprehensive profiling of the epigenomic and transcriptomic changes in ARTHS.

overall_design: In this study, we created ARTHS patient-derived (n=7) and control (n=13) dermal fibroblasts from skin punch biopsies and performed multiomic profiling of these samples.

first: Meghna

last: Singh

first: Sarah

last: Spendlove

first: Angela

last: Wei

first: Leroy

last: Bondhus

first: Aileen

last: Nava

first: Ben

last: Garcia


title: KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [ATAC-seq]


title: KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes.


title: Transcriptome analysis reveals key genes and pathways that the antagonist NOX_6_18 acts on GPR132 in macrophages of WAT or Liver

city: Jinan

first: Jin-Peng

last: Sun

address: 44 West Wenhua Road

institute: Shandong University

summary: Our research is helpful to understand the physiological and pathological level changes caused by the antagonist NOX_6_18 acting on the receptor GPR132 on the macrophages of WAT or Liver, to find the mechanism of the signaling pathway downstream of GPR132 under the action of the antagonist NOX_6_18.

overall_design: In this study, we isolated macrophages in WAT or Liver from GPR132fl/fl or Lyz2_cre+/_GPR132fl/fl mice fed HFD  that were treated with control vehicle or the antagonist NOX_6_18. The control group and the antagonist stimulation group (2 samples each) were subjected to RNA sequencing.

first: J

first: M

middle: X

last: Gao


title: Epigenetic changes and an extensive rewiring of the transcriptome underlie worker size distribution in the Florida carpenter ant


title: Expression data of plasma cell from MGUS patients

city: Little Rock

first: Fumou

state: Arkansas

address: 4301 W. Markham, Slot 508

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

summary:
Multiple myeloma is preceded by monoclonal gammopathy of undetermined significance (MGUS). Serum markers are currently used to stratify MGUS patients into clinical risk groups. A molecular signature predicting MGUS progression has not been produced. We have explored the use of gene expression profiling to risk-stratify MGUS and developed an optimized signature based on large samples with long-term follow-up.
Microarray analysis of mRNA from MGUS patients with stable disease and MGUS patients that progressed to MM within 10 years, was used to define a molecular signature of MGUS risk.

overall_design: Bone marrow plasma cells from MGUS patients were enriched by anti-CD138 immunomagnetic beads for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify genetic differences in the bone marrow plasma cells of stable and progressive MGUS patients. Patients who progressed to MM within 10 years after diagnosis of MGUS were considered Progressing (P), while the other 334 MGUS had not progressed called Stable (S).

first: Fenghuang

last: Zhan

first: John

last: Shaughnessy


title: KAT6A mutations in Arboleda-Tham syndrome affect regulation and expression of HOXC genes [ChIP-seq]


title: The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

summary: Deregulated DNA replication is a major contributor to human developmental disorders and cancer, yet our understanding of how replication is coordinated with changes in transcription and chromatin structure is limited. Our lab has employed the zebrafish model to investigate the mechanisms driving changes in the replication timing program during development. Previous studies have identified changes in replication timing patterns from the onset of zygotic transcription through gastrulation in zebrafish embryos. The protein Rif1 is crucial for replication timing in a wide range of eukaryotes, yet its role in establishing the replication timing program and chromatin structure during early vertebrate development is not well understood. Using Rif1 mutant zebrafish and performing RNA sequencing and whole-genome replication timing analysis, we found that Rif1 mutants were viable but had a defect in female sex determination. Interestingly, Rif1 loss primarily affected DNA replication timing after gastrulation, while its impact on transcription was more pronounced during zygotic genome activation. Our results indicate that Rif1 has distinct roles in regulating DNA replication and transcription at different stages of development.

overall_design: Quantseq 3' mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages (one-cell, 256-cell, Dome, Shield, Bud and 24 hpf).

first: Emily

last: Masser

first: Tyler

last: Noble

first: Joseph

last: Siefert

first: Duane

last: Goins

first: Courtney


title: The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development [SLAM-seq]

overall_design: SlamSeq 3' mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages (256-cell and Dome).


title: TET1 regulates skeletal stem cell (SSC) mediated cartilage regeneration in osteoarthritis

city: Stanford

first: Nidhi

last: Bhutani

address: 240 Pasteur drive

department: Orthopaedic Surgery

institute: Stanford School of Medicine

summary: Objective: Skeletal stem cells are known to be regulated by their local self-regulating niche, that is comprised mainly of their progeny and secreted paracrine factors. What cell intrinsic factors govern the maintenance and function of the SSC remains elusive. Methods: Using the previously characterized Tet1-/- mice we investigated the differences in skeletal stem cell lineage tree. Further we examined the ability of these cells to differentiate into osteogenic and chondrogenic lineages, both with and without injury. Transcriptomic differences and inflammatory cytokines were investigated for differences in cartilage development pathways.  Results: Loss of Tet1 skews the SSC lineage tree by expanding the SSC pool at the expense of its progeny as well as by enhancing the chondrogenic differentiation of SSC and the multilineage bone cartilage stromal progenitors (BCSP). Tet1 inhibition leads to enhanced chondrogenesis in mouse BCSP upon injury, in human SSC and chondroprogenitors (CP) isolated from osteoarthritic (OA) human cartilage and in late stages of OA in a mouse model. Transcriptomic analyses of SSC and BCSP lacking Tet1 revealed dysregulated pathways including alterations in Tgfb signaling, melatonin degradation and cartilage development associated genes.  Conclusion: Tet1 was identified as critical regulator of SSC fate. Loss of Tet1 selectively enhances chondrogenic ability of skeletal stem cells. Supplementation of melatonin can dampen inflammation and lead to better cartilage health.

overall_design: SSC and BCSP Wildtype v/s Tet1 KO

first: Akshay

last: Pandey


title: Decoding the Replication Timing Program in Zebrafish: The Role of Rif1

overall_design: Replication timing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages (preMBT, Shield, Bud, and 24 hpf) using our RepliTimer pipeline (https://github.com/SansamLab/RepliTimer/tree/v1.0.11; DOI 10.5281/zenodo.6426313). The data was based on the copy-number variations between filtered G1 and S-phase whole-genome sequencing read counts.


title: Tissue-resident, extravascular Ly6c- monocytes are critical for inflammation in the synovium Figure 3 & 7

city: Chicago

first: Deborah

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

summary: Identification of intra- and extra- vascular Syn Ly6c- cells

overall_design: CITE-seq and scATAC-seq on CD45+CD11b+Ly6g-SiglecF-Cd64- cells from the joint synovium

first: Harris

last: Perlman


title: Tissue-resident, extravascular Ly6c- monocytes are critical for inflammation in the synovium Figure 4

summary: Extra-vascular tissue location confers phenotype of TR-MC

overall_design: Bulk RNA-seq on sorted CD45+CD11b+Ly6g-SiglecF-Cd64- populations from joint synovium


title: Tissue-resident, extravascular Ly6c- monocytes are critical for inflammation in the synovium Figure 2 & 7

summary: scRNA-seq analysis of joint myeloid niche identifies tissue Syn Ly6c- cells.

overall_design: Single-cell RNA-seq on CD45+CD11b+Ly6g-SiglecF-Cd64-Ly6c- cells from the joint synovium


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells [H3K27ac ChIP-seq PB and RA]

city: Cambridge

first: Sarah

last: Gillen

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: We have used H3K27ac ChIP-seq to assess the global impact of the combination of palbociclib and retinoic acid on the epigenetic H3K27ac landscape in three neuroblastoma cell lines.

overall_design: H3K27ac ChIP-seq in SK-N-BE(2)C cells following DMSO, RA, PB or PB+RA treatment for 5 days

first: Roshna

last: Gomez

first: Fahad

last: Ali

first: Anna

last: Philpott


title: Tissue-resident, extravascular Ly6c- monocytes are critical for inflammation in the synovium Figure 1

summary: Synovial Ly6c- cells are phenotypically distinct from circulating NCM

overall_design: Bulk RNA-seq on sorted myeloid cell populations from blood and joint synovium


title: Effect of growth temperature on gene expression of Lentilactobacillus kefiri and Lactobacillus kefiranofaciens co-culture

city: Lincoln

first: Hasan

last: Otu

state: NE

address: 430F NH

department: Electrical and Computer Engineering

institute: University of Nebraska-Lincoln

summary: We obtained L. kefiri (JCM5818) and L. kefiranofaciens (JCM6985) from the Japan Collection of Microorganisms (JCM). Bacteria were grown together at two different temperatures of 30C and 37C profiled for transcriptomics, metabolomics, and proteomics.

sample_organism:
Lentilactobacillus kefiri
Lactobacillus kefiranofaciens

overall_design: Comparative gene expression profiling analysis of RNA-seq data for L. kefiri and L. kefiranofaciens co-culture at 30C and 37C with 10 biological replicates at each temperature point.

middle: H

first: Handan

last: Can

first: Sree

last: Chanumolu


title: Whole transcriptome analysis of Lingual Sensory Neurons in Naïve and Tongue-Tumor Bearing Male and Female Mice

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Using RNA sequencing of FACS sorted retro-labeled sensory neurons innervating tongue tissue, we determined changes in transcriptomic profiles in males and female mice under naïve as well as tongue-tumor bearing conditions Our data revealed the following interesting findings:  1) Naïve female neurons innervating the tongue exclusively expressed immune cell markers such as Csf1R, C1qa and others, that weren’t expressed in males.  2) Male neurons were more tightly regulated than female neurons upon tumor growth; 3) While very few differentially expressed genes (DEGs) overlapped between males and females post-tumor growth, several biological processes (BPs) were similar between two sexes. However, additional distinct processes were sex-specific; 4) Post-tumor growth, male DEGs contained an equal mix of transcription factors, ligands, growth factors, receptors and channels, whereas female DEGs predominantly contained channels/receptors, enzymes, cytokines and chemokines.

overall_design: Neurons were isolated by preparation of single-cell suspensions of TG tissues followed by flow sorting. Each sample was prepared by pooling 4 TGs from 2 animals for normal sample and 4 animals for tumor-bearing samples. Total of 12 samples (independent triplicate samples derived from normal and tumor tissues, both from male and female mice) were submitted for RNA-sequencing.

first: Tarek

last: Ibrahim

first: Ping

last: Wu

first: Shivani

last: Ruparel

first: Zhao

last: Lai


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells

overall_design: Refer to individual Series


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells [RNA-seq PB and RA]

summary: We have used RNA-seq to assess the global impact of palbociclib, retinoic acid and the combined treatment on the transcriptome.

overall_design: RNA-seq in SK-N-BE(2)C treated with DMSO, 10uM retinoic acid, 1uM palbociclib or 1uM palbociclib + 10uM retinoic acid

first: Kirsty

middle: M

last: Ferguson


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells [H3K27ac ChIP-seq palbociclib]

summary: We have used H3K27ac ChIP-seq to assess the global impact of palbociclib on the epigenetic H3K27ac landscape in three neuroblastoma cell lines.

overall_design: H3K27ac ChIP-seq in SK-N-BE(2)C, IMR-32 and SH-SY5Y following PB treatment for 5/7 days

first: Lewis

last: Chaytor

first: Laura

last: Woods


title: Boswellic acid formulations are not suitable for additive treatment of pediatric high-grade glioma

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Introduction: Pediatric high-grade gliomas (pedHGG) comprise a very poor prognosis. Thus, parents of affected children are increasingly resorting to complementary and alternative medicine (CAM). Among others, one of the most frequently used CAM are boswellic acids (BA).   Methods: The therapeutic effectiveness of the three main BA, alpha-boswellic acid (α-BA), beta-boswellic acid (β-BA) and 3-acetyl-11-keto-beta-boswellic acid (AKBA) was analyzed in a histone 3 (H3)-wildtype and a H3.3K27M-mutant pedHGG cell line, either alone or in combination with radiotherapy and/or temozolomide chemotherapy. Cell viability, stemness properties and apoptosis as well as mRNA sequencing and in ovo tumor growth was investigated upon BA treatment.   Results: Whereas α-BA and β-BA exert only mild anti-tumor effects in H3WT and H3.3K27M-mutated pedHGG cells, AKBA treatment reduced cell viability and stemness potential especially in H3.3K27M-mutant pedHGG cells. In addition, slight anti-inflammatory effects were observed after AKBA treatment of H3.3K27M-mutant pedHGG cells. However, no effects on apoptosis and in ovo tumor growth were found. Of note, α-BA and β-BA treatment even resulted in tumor promoting effects in both pedHGG cells.

overall_design: RNA was isolated from three independent biological replicates of HSJD-DIPG-007 cells after treatment with AKBA or DMSO for 48h

first: Maria

last: Wiese

first: Bente

last: Pohlmeier

first: Klaudia

last: Kubiak

first: Fatma

middle: E

last: El-Khouly

first: Maren

last: Sitte

first: Angel

last: Carcaboso

first: Josh

middle: N

last: Baugh

first: Thomas

last: Perwein

first: Gunther

last: Nussbaumer

first: Michael

last: Karremann

first: Gerrit

last: Gielen

first: Christof

last: Kramm


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells [RNA-seq PB]

first: Sarah

last: Gillen

summary: We have used RNA-seq to assess the global impact of palbociclib on the transcriptome at early and late time points in three neuroblastoma cell lines.

overall_design: RNA-seq in SK-N-BE(2)C, IMR-32 and SH-SY5Y following PB treatment for 24 hours and 5/7 days

first: Anna

last: Philpott


title: Bcl6 mediates CD8+ T cell fate decision in cancer

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

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


title: Bcl6 regulates CD8+ T cell fate decision in cancer [RNA-Seq]

summary: Overcoming CD8+ T cell "exhaustion" is critical in cancer immunotherapy. Intra-tumor CD8+ T cells contain stem-like (Texprog) and terminally differentiated (Texterm) subpopulations that mediate the persistence and potency of anti-tumor responses, respectively. How extrinsic signals via transcription factors control these two subsets are unclear. Previously, Bcl6 was shown to be selectively expressed by Texprog cells and promote their generation in chronic infection. Here, we found that in cancer, Bcl6 deficiency impacted, not the generation, but rather the persistence of Texprog cells, thus abrogating long-term tumor control. Bcl6 expression in CD8+ T cells is reciprocally regulated by TGF-?-SMAD2 and IL-2-STAT5 signaling pathways. Blimp1, regulated by IL-2 signaling, potently inhibited Bcl6 expression and its transcriptional activities; Prdm1 deficiency greatly improved the efficacy of anti-PD-1 therapy. Thus, we identified the TGF-?-Bcl6 and IL-2-Blimp1 antagonistic pathways in regulation of anti-tumor CD8+ T cells, which benefits cancer immunotherapy.

overall_design:
RNA-seq of Bcl6+, DN, TIM-3+ CD8+ TILs isolated from tumors in E.G7-bearing Bcl6-RFP mice.
RNA-seq of control and Prdm1-overexpressing OT-I cells from E.G7 tumors on about day 8 post transfer.
RNA-seq of control and Bcl6-overexpressing OT-I cells from E.G7 tumors on about day 8 post transfer.

first: Qinli

last: Sun

first: Xiaohong

last: Zhao


title: RNA sequencing of spermatogonia with different m6a methylation

city: Nanning

first: dandan

last: zhong

state: Guangxi

address: state Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University

institute: Guangxi university

summary: we knocked down the expression level of METTL3 in spermatogonia to reduce the total m6A methylation in the cells, and mapped the RNA expression profile of spermatogonia after the total m6A methylation level was reduced，and  we after the m6A methylation was reduced, many lncRNA and mRNA were differently expressed

overall_design: Check the RNA expression of two different m6a methylation modified spermatogonia.

first: Dandan

last: Zhong

first: Hui

last: Li


title: small RNA sequencing of spermatogonia with different m6a methylation

summary: we knocked down the expression level of METTL3 in spermatogonia to reduce the total m6A methylation in the cells, and mapped the small RNA expression profile of spermatogonia after the total m6A methylation level was reduced，and  we after the m6A methylation was reduced, many miRNA and circRNA were differently expressed

overall_design: Check the small RNA expression of two different m6a methylation modified spermatogonia.


title: Bcl6 regulates CD8+ T cell fate decision in cancer [ChIP-Seq]

overall_design: We constructed Bcl6-HA-ires-GFP expressing plasmid, and performed ChIP-seq using transfected in vitro cultured CD8+ T cells.


title: Using Genomic Signatures to Elucidate Individual and Mixture Effects of Inorganic Arsenic and Manganese in Placental Trophoblasts

status: Public on Aug 14 2023

city: Chapel Hill

first: Anastasia

middle: Natalie

last: Freedman

state: NC

address: 135 Dauer Dr

department: Environmental Sciences and Engineering

institute: University of North Carolina at Chapel Hill

summary:
HTR-8/SVneo human placental trophoblast cells were exposed to low-level environmentally relevant concentrations of iAs, Mn, and iAs-Mn mixtures.
A microarray assay was performed to understand the changes and differences in gene expression in relation to  single-metal and metal-mixtures

overall_design: Placental trophoblasts were seeded and exposed to iAs (0.3µM, 1µM, 1.5µM), Mn (5µM, 10µM, 20µM), or an iAs-Mn mixture (0.3µM iAs+5µM Mn, 1µM iAs + 10µM Mn, 1.5µM iAs + 20µM Mn). Samples were developed in triplicate, and unexposed controlls were included as well. Cells were exposed for 24 hrs prior to RNA extraction.

first: Rebecca

last: Fry

first: Mike

last: Vernon


title: HOTAIRM1 suppresses Estrogen Receptor activity in breast cancer by restricting chromatin accessibility of pioneer factor FOXA1

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

summary: Although a majority of breast cancers (BrCa) are Estrogen receptor-alpha (ERa)-positive, existing endocrine therapies that target ERa can lead to hormone-resistant disease. The mechanisms of how normal breast epithelium is transformed into malignant remain poorly defined, and a deeper understanding is needed to design novel therapeutics. Several epigenetic regulators including long non-coding RNAs (lncRNAs) are aberrantly expressed in BrCa, resulting in abnormal gene expression patterns and tumor growth. Here, we show that HOTAIRM1, which we previously defined as a p53-regulated lncRNA in human stem cells, acts as a tumor suppressor to counteract ERa-activity in BrCa. Global expression analyses uncovered a significant correlation between reduced HOTAIRM1 expression and poor survival of ER+ BrCa patients. Promoter DNA methylation and histone mark enrichment revealed that HOTAIRM1 is epigenetically silenced in BrCa patients and cell lines. We found that HOTAIRM1 depletion promotes, whereas exogenous HOTAIRM1 reduces survival and proliferation of BrCa cells. Guilt by association analysis in BrCa patients, combined with HOTAIRM1-dependent transcriptome profiling in BrCa cells reveal that HOTAIRM1 expression negatively correlates with proteins involved in ERa-activity and estrogen response. An unbiased profiling of HOTAIRM1-interactome show that HOTAIRM1 interacts with pioneer factor FOXA1 in ER+ BrCa cells. Further, our global ER/FOXA1 chromatin enrichment profiling in response to estrogen demonstrate increased enrichment of ER and FOXA1 to estrogen response elements (EREs) that results in significantly higher expression of ERa-targets in absence of HOTAIRM1. Thus, HOTAIRM1 suppresses ERa-activity in BrCa by restricting chromatin accessibility of pioneer factor FOXA1. To our knowledge, our results are the first to define a non-proteomic component that disrupts the activity of a pioneer factor in order to achieve tumor suppression

overall_design: mRNA-Seq from siControl and siHOTAIRM1 MCF7 cells; ChIP-Seq of ER-alpha and FOXA1 in shControl and shHOTAIRM1 MCF7 cells deprived of hormones (-E2) or treated with Estrogen (+E2) for 1 hr

first: Abhinav

last: Jain

first: Michelle

last: Barton


title: Impact of spaceflight and artificial gravity on sulfur metabolism in mouse liver: sulfur metabolomic and transcriptomic analysis

city: Yokohama

first: Ryo

last: Kurosawa

state: Kanagawa

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

institute: RIKEN

summary: Spaceflight induces hepatic damage, partially owing to oxidative stress caused by the space environment such as microgravity and space radiation. We examined the roles of anti-oxidative sulfur-containing compounds on hepatic damage after spaceflight. We analyzed the livers of mice on board the International Space Station for 30 days. During spaceflight, half of the mice were exposed to artificial earth gravity (1 g) using centrifugation cages. Sulfur-metabolomics of the livers of mice after spaceflight revealed a decrease in sulfur antioxidants (ergothioneine, glutathione, cysteine, taurine, thiamine, etc.) and their intermediates (cysteine sulfonic acid, hercynine, N-acethylserine, serine, etc.) compared to the controls on the ground. Furthermore, RNA-sequencing showed upregulation of gene sets related to oxidative stress and sulfur metabolism, and downregulation of gene sets related to glutathione reducibility in the livers of mice after spaceflight, compared to controls on the ground. These changes were partially mitigated by exposure to 1 g centrifugation. For the first time, we observed a decrease in sulfur antioxidants based on a comprehensive analysis of the livers of mice after spaceflight. Our data suggest that a decrease in sulfur-containing compounds owing to both microgravity and other spaceflight environments (radiation and stressors) contributes to liver damage after spaceflight.

overall_design: To examine the roles of anti-oxidative sulfur-containing compounds on hepatic damage after spaceflight, we performed transcriptome analysis of the livers of mice on board the International Space Station for 30 days.

first: Iwao

last: Ohtsu

first: Kengo

last: Suzuki


title: Activation of Thousands of Genes in the Lungs and Kidneys by Sepsis is Countered by the Selective Nuclear Blockade

city: Nashville

first: Jozef

last: Zienkiewicz

state: TN

address: 1161 21st Ave. South, T2220, MCN

institute: Vanderbilt University

summary: The steady rise of sepsis globally has reached almost 49 million cases in 2017, and 11 million sepsis-related deaths. The genomic response to sepsis comprising multi-system stage of raging microbial inflammation has been reported in the whole blood, while effective treatment is lacking besides anti-microbial therapy and supportive measures. Here we show that, astoundingly, 6,237 significantly expressed genes in sepsis are increased or decreased in the lungs, the site of acute respiratory distress syndrome (ARDS). Moreover, 5,483 significantly expressed genes in sepsis are increased or decreased in the kidneys, the site of acute injury (AKI). This massive genomic response to polymicrobial sepsis is countered by the selective nuclear blockade with the cell-penetrating Nuclear Transport Checkpoint Inhibitor (NTCI). It controlled 3,735 sepsis-induced genes in the lungs and 1,951 sepsis-induced genes in the kidneys. The NTCI also reduced without antimicrobial therapy the bacterial dissemination: 18-fold in the blood, 11-fold in the lungs, and 9-fold in the spleen. This enhancement of bacterial clearance was not significant in the kidneys. Cumulatively, identification of the sepsis-responsive host’s genes and their control by the selective nuclear blockade advances a better understanding of the multi-system mechanism of sepsis. Moreover, it spurs much-needed new diagnostic, therapeutic, and preventive approaches.

overall_design: We investigated the lungs' and kidneys' genome response to polymicrobial sepsis. We also established an impact of nuclear import blockade on gene expression in sepsis. Polymicrobial sepsis was induced in 8-10-week-old female C57BL/6 mice (Jackson Laboratories, Bar Harbor, ME) by a single intraperitoneal injection of cecal microbiome (CM) stock solution. Mice were treated with saline or with cell-penetrating nuclear transport checkpoint inhibitor (NTCI), cSN50.1 peptide. A control group of mice were challenged with sham (5% dextrose) and treated with saline. A gene expression profiling (RNA-seq) was performed using NGS of lungs and kidneys total RNA samples from mice euthanized at 6 hours post CM challenge. The comparative gene expression profiling analysis (DESeq2) was performed using RNA-seq data for groups: CM + saline vs. Sham + saline and CM + NTCI vs CM + saline in both organs.

first: Huan

last: Qiao

first: Yan

last: Liu

first: Jacek

last: Hawiger


title: Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity [ATAC-seq]

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

institute: University of Oxford

summary: Mucosal-associated invariant T (MAIT) cells are innate-like T cells that recognize microbial metabolites through a semi-invariant T cell receptor (TCR). Major questions remain regarding the extent of human MAIT cell functional and clonal diversity. To address these, we analyzed the single-cell transcriptome and TCR repertoire of blood and liver MAIT cells and developed functional RNA sequencing, a method to integrate function and TCR clonotype at single-cell resolution. MAIT cell clonal diversity was comparable to conventional memory T cells, with private TCR repertoires shared across matched tissues. Baseline functional diversity was low and largely related to tissue site. MAIT cells showed stimulus-specific transcriptional responses in vitro, with cells positioned along gradients of activation. Clonal identity influenced resting and activated transcriptional profiles but intriguingly was not associated with the capacity to produce IL- 17. Overall, MAIT cells show phenotypic and functional diversity according to tissue localization, stimulation environment and clonotype.

overall_design: ATAC-seq on sorted blood CD8+ naïve T, MAIT and memory T (Tmem) cells.

middle: C

first: Paul

last: Klenerman

first: Nicholas

last: Provine


title: Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity [Exp 4]

overall_design: Isolated blood T cells were left unstimulated or stimulated for 20 h with MR1/5-OP-RU (TCR), IL-12 + IL-18 (cytokine) or both, before MAIT cell (CD3+CD26+CD161hiVα7.2+) sorting. Additionally, isolated T cells were left unstimulated or stimulated for 68 h with both MR1/5-OP-RU and IL-12 + IL-18 (TCR+cytokine), before MAIT cell sorting. Single-cell gene, surface protein and TCR repertoire analysis was performed using 10x Genomics technology.


title: Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity [Exp 2]

overall_design: MAIT (CD3+MR1/5-OP-RU+) and Tmem (CD3+MR1/5-OP-RU-CCR7-) cells were sorted from human blood (n = 8) and liver (n = 3) samples for single-cell gene, surface protein and TCR repertoire analysis using 10x Genomics technology.


title: MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine


title: 16S rRNA sequencing data of ileal contents samples  in goats infusion of three short-chain fatty acids

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

summary: Emerging data has highlighted the importance of short-chain fatty acids (SCFAs) on ruminal microbiome and derived metabolism profiling, and ruminal epithelial health and nutritional absorption in ruminants. However, little is known about the roles of SCFAs on ileal microbiome profiles. Here, we combined infusion of three SCFAs, to study their different roles in ileal microbiome succession  profiling using a in vivo goat model.

overall_design: A total of 24 healthy female goats (47.44 ± 3.38 kg, 1.5 years old)  were selected in our study. All goats were commenced on a standard diet and were fed 2 times a day1. Goats were housed individually in their tie stalls and had free access to water and feed. After ad libitum for 14 days continuous stable feeding, goats were randomly assigned to 4 groups (n = 6/group) to receive different infusion treatments. Goats in CON group received normal saline infusion at 0.8 g/kg body weight (BW) as normal control group, while in SA group received sodium acetate infusion at 0.8 g/kg BW, in SP group received sodium propionate infusion at 0.8 kg/kg BW, and in SB group received sodium butyrate infusion at 0.5 kg/kg BW. Total volume of 1 L infusion solutions was slowly perfused through oral daily before morning feeding of each goat, and the infusion lasted for 12 days. After slaughter, the ileal contents samples were immediately collected and stored at -80 °C for microbiome analysis.


title: Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

summary: RNA-binding proteins (RBPs) target RNA in a context-dependent manner to regulate gene expression. Protein-protein interaction (PPI) maps of RBP complexes and networks are critical for defining RBP function and RNA targeting. Yet, PPI networks under-represent RBP baits and need more information about RNA-driven interactions. Therefore, we generated an RNA-aware, RBP-interactome map combining two strategies that use systematic proteomic methods to identify 1) protein interactions using co-immunoprecipitation in the presence or absence of RNase treatment of a ~100 RBPs across the RNA life-cycle and 2) RNA-dependent complexes using Size Exclusion Chromatography. Together, this dataset provides proteome-wide, cell-type specific, and quantitative identification of RNA-protein interactions across multiple RNA processing events. In the resulting PPI network, several hundred database-supported interactions establish many complexes operating at each of these mRNA life-cycle stages. Nearly a thousand novel interactions imply new functions for RBPs across multiple steps of the RNA life cycle. Overlapping our network with eCLIP data, we find RNA targets between interactors and uncover complex-driven binding signatures. Betweenness-centrality scores identify multi-functional RBPs that participate across multiple mRNA life-cycle steps. We characterize the novel interactions and functions of different classes of multi-functional proteins. We find the scaffolding protein, ERH, interacts with numerous nuclear speckle proteins and facilitates splicing and mRNA export. Finally, we show that the splicing factor, SNRNP200, interacts with nuclear export, localization, and translation proteins and is an essential factor of RNA granule formation during stress. Our large-scale RBP interaction network provides new insights and a valuable resource for exploring new RBP complexes operating to control gene expression.

overall_design:
eCLIP-seq of human SNRNP200, CAPRIN, and G3BP1
eCLIP of RBP of interest. Each sample has an input and IP sample

first: Katherine

last: Rothamel

first: Lena

last: Street

first: Ahmed

last: Abdou

first: Wenhao

last: Jin

first: Kevin

last: Dong

last: Rhine

first: Assa

last: Madrigal

first: Norah

last: Al-Azzam

first: Kris

last: Brannan

first: Marko

last: Jovanovic

first: Gene

last: Yeo


title: Gene regulatory networks underlying human microglia maturation [ATAC-seq]

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

summary: Microglia, the tissue resident macrophages of the brain, are observed as early as the fourth week of human gestation and engage in a variety of processes essential for brain development and homeostasis. Microglia phenotypes are highly regulated by the brain environment but the transcriptional networks that specify their maturation remain poorly understood and the extent to which fetal or postnatal phenotypes can be modeled using iPSC-derived cells has not been systematically investigated. Here, we characterized stage-specific transcriptomes and epigenetic landscapes of fetal and postnatal human microglia ex vivo and acquired corresponding data in iPSC-derived microglia in vitro, in cerebral organoids, and as a function of time following engraftment into humanized mice.  By developing new computational approaches that integrate these data to predict state-specific transcription factor networks, we provide evidence that MiTF/TFE and MEF2 factors are key nodes in transcription factor networks associated with fetal microglia phenotypes, whereas MAFB, KLFs and IRF transcription factors are key nodes in the networks associated with postnatal phenotypes.  We further demonstrate that many features of the human fetal to postnatal transition in microglia gene expression are recapitulated in a time-dependent manner following the engraftment of iPSC-derived hematopoietic progenitor cells into humanized mice.  These studies thereby provide new computational and data resources enabling the elucidation of transcription factor networks underlying stage-specific human microglia phenotypes.

overall_design: Poly-A RNA-seq and ATAC-seq of iPSC-derived microglia, iPSC-derived microglia co-cultured with cerebral organoids, and iHPC xenografted into humanized mice and isolated at various time points.

first: Claudia

middle: Z

last: Han

first: Rick

last: Li

first: Emily

last: Hansen

first: Samantha

last: Trescott

first: Bethany

last: Fixsen

first: Celina

middle: T

last: Nguyen

first: Hunter

last: Bennett

first: Nathanael

middle: J

last: Spann

first: Cristina

last: Mora

first: Olivier

last: Poirion

first: Justin

last: Buchanan

first: Anna

last: Warden

first: Bing

last: Xia

first: Johannes

last: Schlachetzki

first: Martina

last: Pasillas

first: Sebastian

last: Preissl

first: Gabriela

last: Ramirez

first: Jean

last: Challacombe

first: Samuel

last: Anavim

first: Avalon

last: Johnsonn

first: Mihir

last: Gupta

first: Michael

middle: L

last: Levt

first: Sharona

middle: B

last: Haim

first: David

last: Gonda

first: Louise

last: Laurent

first: Mathew

last: Blurton-Jones

first: Nicole

last: Coufal

middle: K


title: Gene regulatory networks underlying human microglia maturation [RNA-seq]

first: Christopher

last: Glass

first: Claudia

last: Han

first: Rick

last: Li

first: Emily

last: Hansen

first: Samantha

last: Trescott

first: Bethany

middle: R

last: Fixsen

first: Celina

last: Nguyen

first: Hunter

last: Bennett

first: Nathanael

last: Spann

first: Cristina

last: Mora

first: Olivier

last: Poirion

first: Justin

last: Buchanan

middle: P

middle: D