title: Transcriptomic analysis reveals that Rho GTPases regulate trap development and lifestyle transition of the nematode-trapping fungus Arthrobotrys oligospora

status: Public on Dec 24 2021

city: Kunming

first: yang

last: le

address: No.2 of Cuihubeilu

institute: Yunnan university

summary: Nematode-trapping (NT) fungi can form unique infection structures (traps) to capture and kill free-living nematodes, thus play a potential role in the biocontrol of nematodes. Arthrobotrys oligospora is a representative species of the NT fungi. Here we performed dual RNA-seq to understand the interaction between A. oligospora and Caenorhabditis elegans. We identified 5752 unique differentially expressed genes during trap formation and predation, and the rac gene was significantly upregulated. Alternative splicing events occurred in 896 2012 genes, including the rac and rho2 gene. Further, we characterized three Rho GTPases (Rho2, Rac, and Cdc42) in A. oligospora using gene disruption and multi-phenotypic analysis. The analyses showed that AoRac and AoCdc42 play an important role in mycelium growth, lipid accumulation, DNA damage, sporulation, trap formation, pathogenicity, and stress response in A. oligospora. Furthermore, AoCdc42 and AoRac specifically interacted with components of the Nox complex, thus regulating the production of reactive oxygen species. Furthermore, the transcript levels of several genes associated with the protein kinase A, mitogen-activated protein kinase, and p21-activated kinase were also altered in the mutants, suggesting that Rho GTPases might function upstream of these kinases. This study highlights the important role of Rho GTPases in A. oligospora and provides insights into the regulatory mechanism of signaling pathways in trap morphogenesis and lifestyle transition of NT fungi.

overall_design: To obtain real-time information, we used RNA-seq technology to sequence the transcriptome profiles between A. oligospora and nematode C. elegans at different time points (0 h, 12 h, 24 h, 36 h, and 48 h). After sequencing a mixed sample (A. oligospora and C. elegans), fungal reads were extracted by searching the RNA-seq reads in the A. oligospora genome.

first: Le

last: Yang

first: Jinkui


title: Transcriptome of human neuroblastoma SH-SY5Y cells in response to 2B protein of enterovirus-A71

status: Public on Dec 23 2021

city: Klong-luang

first: Jeeraphong

last: Thanongsaksrikul

state: Patumthani

country: Thailand

institute: Thammasat University

type: Expression profiling by high throughput sequencing

summary: Non-structural 2B protein of enterovirus-A71 has reported involving in intracellular Ca2+ manipulation and altering cellular homeostasis such as inducing cell death in human SH-SY5Y cells. The aim of the study is to profile transcriptomic signature of human neuroblastoma SH-SY5Y cells altered by EV-A71 2B protein using RNA-sequencing analysis. We generated mRNA expression profiles of SH-SY5Y cells transfected with EV-A71 2B protein fused with mCherry and FLAG tag protein (2BmCherry) and mCherry as well as parental SH-SY5Y cells. We find that 7 genes including CCL2, RELB, IL32, PLAT, PTGES, PHLDA1, and TNFRSF9 are uniquely overexpressed in 2BmCherry comparing to mCherry. Moreover, there were 333 upregulated and 333 downregulated genes showed significant different expression level in 2BmCherry transcriptome in comparison with SHSY5Y transcriptome but not in mCherry vs SHSY5Y comparison. Functional analysis showed that EV-A71 2B upregulated genes involved Ca2+-related signaling pathways participating gene expression, immune response, apoptosis, and long-term potentiation (synaptic adaptation) of neuron in the transfected SH-SY5Y cells.

overall_design: mRNA profiles of SH-SY5Y cells expressing EV-A71 2B protein fused with mCherry and FLAG tag protein, mCherry and parantal SH-SY5Y cells

first: Kittisak

last: Suanpan

first: Potjanee

last: Srimanote

first: Pongsri

last: Tongtawe


title: ADAR1 RNA editing quenches innate immune activation in endothelial cells

status: Public on Dec 27 2021

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

country: USA

institute: University of Pittsburgh

summary: RNA editing has been shown to implicate in cardiovascular diseases, including dysregulated RNA editing in endothelial cell (EC) that involves Adenosine Deaminase Acting on RNA1 (ADAR1). However, the specific function of ADAR1 in EC at physiologic condition has not been established and the mechanism remains to be defined. This study is to determine the specific physiologic role of ADAR1 in EC and reveal its molecular and cellular mechanisms.

overall_design:
A mouse model carrying an EC-specific deletion of ADAR1 gene was established through breeding Cdh-5 Cre transgenic and floxed ADAR1 mice. Deletion of ADAR1 in ECs resulted in newborn death with multiple organ injuries. Genome-wide gene expression analysis revealed an obvious innate immune activation with dramatic elevation of Interferon Stimulated Genes (ISGs) expression. ADAR1 deficiency impacted the proliferation, migration and tube-formation capacities of EC. Genome-wide analysis of EC RNA transcript found extensive RNA editing in EC and ADAR1 deficiency dramatically reduced RNA editing on SINE transcripts that modifies the corresponding dsRNA structures. Notably, we demonstrated that the altered cellular RNA activates the RNA sensing signaling pathway and deletion of the cellular RNA receptor Melanoma Differentiation-Associated protein 5 (MDA-5) prevented the immune activation in EC, and completely rescued the EC ADAR1 deficient mice from death. Gene expression analysis confirmed that the rescue was associated with the blockage of RNA sensing pathway as shown by the restored ISG expression levels in EC.
Two inducible ADAR1 knockout mice from two independent litters were used for EC isolation (annotated as EC1 and EC2). RNA samples were isolated from 4-OH-Tamoxifen treated (TM) and nontreated control (CON) cells for sequencing.

first: Xinfeng

last: Guo

first: Silvia

first: Rose

last: Yan

first: Vy

last: Nguyen

first: Liyong

last: Zhang

first: Tony

last: Wang

first: Mazen

last: Zenatai

first: Timothy

middle: R

last: Billiar

first: Qingde


title: Long non-coding RNA expression profile of primary melanoma versus nevi

city: Xi'an

first: Jingjing

last: Ma

address: No. 127 Changlexi Road

country: China

institute: Fourth Military Medical University

summary: To explore the role of long non-coding RNAs (lncRNAs) in melanoma progression, we performed lncRNAs microarray to identify differentially expressed lncRNAs between primary melanoma and nevus.

overall_design: 3 paired primary melanoma and nevi were analyzed. Nevi are as control groups.

first: Qiong

last: Shi

first: Sen

first: Weigang

first: Rui

last: Ge

first: Weinan

first: Chunying

last: Li


title: Prenatal cadmium exposure alters proliferation in mouse CD4+ T cells via LncRNA Snhg7

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Prenatal cadmium (Cd) exposure leads to immunotoxic phenotypes in the offspring. Long non-coding RNAs (lncRNAs) are integral to T cell regulation. Here, we identified genes and pathways altered in CD4+ T cell by prenatal Cd exposure. We investigated the role of long non-coding RNA small nucleolar RNA hostgene 7 (lncSnhg7) in T cell proliferation: LncSnhg7 expression increases in CD4+ T cells following stimulation with anti-CD3/CD28 beads. LngSnhg7 and a downstream protein, GALNT7, are upregulated in T cells from offspring exposed to Cd during gestation. Overexpression of miR-34a, a regulator of lnhcSnhg7 and GALNT7, suppresses GALNT7 protein levels in primary T cells, but not in a mouse T lymphocyte cell line. The T cells isolated from Cd-exposed offspring exhibit increased proliferation after activation in vitro, but Treg suppression and CD4+ T cell apoptosis are not affected by prenatal Cd exposure. In conclusion, prenatal Cd exposure alters the expression of lncRNAs during T cell activation. The induction of lncSnhg7 is enhanced in splenic T cells from Cd offspring resulting in the upregulation of GALNT7 protein and increased proliferation following activation. miR-34a overexpression decreased GALNT7 expression suggesting that the lncSnhg7/miR-34a/GALNT7 is an important pathway in primary CD4+ T cells. These data highlight the need to understand the consequences of environmental exposures on lncRNA functions in non-cancerous cells.

overall_design: Male and female C.Cg-Foxp3tm2Tch/J mice were mated with continuous exposure to 10 ppm CdCl2 (or unspiked water for the controls) via their drinking water. Female mice were exposed throughout pregnancy. Spiked water was replaced with normal water within 12 hours of the birth of the pups. Control and Cd-exposed offspring were aged to 8 weeks. CD4 T Cells were isolated from the splenocytes using negative selection. CD4 T cells were stimulated in vitro with anti-CD3/CD28 beads for 16h. RNA were purified from the unstimulated and stimulated cells. Gene expression was analyzed by RNA-Sequencing.

first: Jamie

last: McCall

first: Melinda

last: Varney

first: Sebastian

last: Dziadowicz

first: Casey

last: Hall

first: Kathryn

last: Blethen

first: John

last: Barnett

first: Ivan

last: Martinez


title: SP7 mutant S309W genomic binding in MC3T3 cells

city: Bethesda

first: James

last: Iben

state: MD

address: 10 CENTER DR

department: NICHD

institute: NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: S309W mutation of SP7 is found in a patient with craniosynostosis, cranial hyperostosis, and long bone fragility. In this experiment we aimed to compare the effect of the mutation on SP7 genomic binding in the presence of DLX5

overall_design: MC3T3 cells were transfected with DLX5 and wild-type or S309W mutant of FLAG-tagged SP7, followed by ChIP-Seq using anti-FLAG M2 antibody

first: Julian

last: Lui

first: Jeffrey

last: Baron


title: CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells (bulk cells)

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

summary: Conventional reprogramming methods rely on the ectopic expression of transcription factors to reprogram somatic cells into induced pluripotent stem cells (iPSC). Forced expression of transcription factors might lead to off-target gene activation and heterogeneous reprogramming, resulting in the emergence of alternative cell types and aberrant iPSC. Activation of endogenous pluripotency factors by CRISPR activation (CRISPRa) can potentially reduce this heterogeneity. Here we describe a high efficiency reprogramming of human somatic cells into iPSC using optimized CRISPRa. Efficient reprogramming was dependent on the additional targeting of the embryo genome activation-enriched Alu-motif and the miR-302/367 locus. Single-cell transcriptome analysis revealed that the optimized CRISPRa reprogrammed cells with more directly and specifically into the pluripotent state when compared to the conventional reprogramming method. These findings support the use of CRISPRa for high quality reprogramming of human iPSC.

overall_design: Transcriptomic analysis of ten LCL and five fibroblast derived human iPSC lines generated by CRISPR activation method

first: Joonas

last: Sokka

first: Masahito

last: Yoshihara

first: Laura

last: Laiho

first: Andrew

last: Warren

first: Christian

last: Stadelmann

first: Helena

last: Kilpinen

first: Eeva-Mari

last: Jouhilahti

first: Diego

last: Balboa

first: Shintaro

last: Katayama

first: Aija

last: Kyttälä

first: Juha

last: Kere

first: Timo

last: Otonkoski

first: Jere

last: Weltner

first: Ras

last: Trokovic


title: Antibacterial mechanism of peptide Asp-Tyr-Asp-Asp based on multiomics and molecular dynamics  [E. coli]

city: Guangzhou

first: shanshan

last: Zhuang

state: Guangdong

address: Guangzhou, Guangdong, 510225, China

department: College of Light Industry and Food

institute: Zhongkai College of Agriculture and Engineering

summary: In this study, the mechanism of action of the small molecular peptide (DYDD) exhibiting antibacterial properties the application of the peptide in the field of food preservation have been presented. Metabolomics and transcriptomic techniques were used to analyze the metabolic effects of DYDD on E. coli. The differential metabolite screening and cluster analysis techniques were used for analyzing the data. It was found that DYDD could up-regulate 44 metabolites, down-regulate 105 metabolites and DYDD primarily affected 35 metabolic pathways in E. coli. Combined with transcriptome analysis, DYDD primarily influenced the metabolic pathways of E. coli by regulating the genes participating in the amino acid metabolic pathways and sulfur metabolic pathways. Then, the effects of DYDD on POPC-, POPE-, and POPG-based membranes were analyzed using the molecular dynamics simulation. The results showed that DYDD had the strongest binding with Pope membrane, and the insertion of DYDD not only led to the disorder of phospholipid head groups, but also increased the surface area and permeability of the membrane. Finally, DYDD was applied to chestnut kernel infected by E. coli. The results showed that DYDD had good antibacterial effect, could delay the decay and browning of chestnut kernel, and had fresh-keeping effect.

overall_design: Escherichia coli was incubated in TSB at 37 C for 8 h. During the logarithmic phase, 200 μL of bacterial solution was added to 200 mL of liquid medium, 200 μL of sterile water (control group; E_CK), or 50 mg/mL of DYDD solution (treatment group; P_DDDY). The bacteria were then cultured on a shaking table at 150 R/min and 37 C for 24 h, centrifuged at 6000 R/min and 4 C for 10 min, washed with PBS three times, and then collected and stored at -80 C.

first: Yao

last: Bao

first: Huangyou

last: Zhang

first: Jianliang

last: Liu

first: Huifan


title: CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells

first: Jouni

last: Kvist

summary:
Conventional reprogramming methods rely on the ectopic expression of transcription factors to reprogram somatic cells into induced pluripotent stem cells (iPSC). Forced expression of transcription factors might lead to off-target gene activation and heterogeneous reprogramming, resulting in the emergence of alternative cell types and aberrant iPSC. Activation of endogenous pluripotency factors by CRISPR activation (CRISPRa) can potentially reduce this heterogeneity. Here we describe a high efficiency reprogramming of human somatic cells into iPSC using optimized CRISPRa. Efficient reprogramming was dependent on the additional targeting of the embryo genome activation-enriched Alu-motif and the miR-302/367 locus. Single-cell transcriptome analysis revealed that the optimized CRISPRa reprogrammed cells with more directly and specifically into the pluripotent state when compared to the conventional reprogramming method. These findings support the use of CRISPRa for high quality reprogramming of human iPSC.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: UV-induced DNA lesion mapping in retinoblastoma 1 (RB1) knock out cells

status: Public on Dec 29 2021

city: Stanford

first: Ashby

middle: J

last: Morrison

state: CA

address: 371 Serra Mall Gilbert Bldg, Room 326

department: Biology

institute: Stanford University

summary: In this study, we generated a human genome-wide map of DNA lesions induced by ultraviolet (UV) radiation in retinoblastoma knockout (RB1 KO) cells. Interestingly, we observed increased carcinogen susceptibility in closed HI-C domainS, pericentric and subtelomeric regions in RB1 KO. We also observed increased susceptibility at cancer driver loci such as TERT and TPTE. These loci are highly mutated in melanoma. Finally, we proposed that loss of tumor suppressor function can alter carcinogen susceptibility, and subsequently the mutation frequency of the genome.

overall_design: IP of CPD lesions, followed by in-vitro repair and next-generation sequencing

first: Ka

middle: M

last: Wong

first: Devin

middle: A

last: King

first: Erin

middle: K

last: Schwartz

first: Rafael

middle: E

last: Herrera


title: CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells (single cells)

overall_design: Single cell transcriptomic analysis from four different time-points during human LCL reprogramming using four different reprogramming conditions

first: Joonas

last: Sokka

first: Masahito

last: Yoshihara

first: Laura

last: Laiho

first: Andrew

last: Warren

first: Christian

last: Stadelmann

first: Helena

last: Kilpinen

first: Eeva-Mari

last: Jouhilahti

first: Diego

last: Balboa

first: Shintaro


title: Phospho-antibody microarray analyses for wild-type and Pak1-deficient breast cancer cells

city: Tlalnepantla de Baz

first: Luis

middle: E.

last: Arias-Romero

email: larias@unam.mx, lear1607@hotmail.com

address: Av. de los Barrios #1

department: UBIMED

country: Mexico

institute: FES-Iztacala, UNAM

summary: To identify differentially phosphorylated proteins between wild-type and Pak1-deficient mouse breast cancer cells, we performed a comparative study by using phospho-antibody arrays.

overall_design: We compared the phosphorylation profiles of murine Pak1-deficient breast cancer cells vs. Pak1 wild type breast cancer cells. All the experiments were performed in duplicate using tumor derived cells.

first: Olga

last: Villamar-Cruz

first: Héctor

middle: I

last: Saldivar-Cerón


title: Spt5 histone binding activity preserves chromatin during transcription by RNA polymerase II

status: Public on Dec 22 2021

city: New York

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: Nucleosomes are disrupted transiently during eukaryotic transcription, yet the displaced histones must be retained and redeposited onto upstream DNA, to preserve nucleosome density and associated histone modifications.  Here we show that the essential Spt5 processivity factor of RNA polymerase II (Pol II) plays a direct role in this process in budding yeast.  Functional orthologues of eukaryotic Spt5 are present in archaea and bacteria, reflecting its universal role in RNA polymerase processivity.  However, eukaryotic Spt5 is unique in having an acidic amino terminal tail (Spt5N) that is sandwiched between the downstream nucleosome and the upstream DNA that emerges from Pol II.  We show that Spt5N contains a histone-binding motif that is required for viability in yeast cells and prevents loss of nucleosomal histones within actively transcribed regions.  These findings indicate that eukaryotic Spt5 combines two essential activities, which together couple processive transcription to the efficient capture and re-deposition of nucleosomal histones.

overall_design: 24 samples; ChIP-Seq

first: Shoufu

last: Duan


title: Mutant p53 elicits context-dependent pro-tumorigenic phenotypes

city: Philadelphia

first: Christopher

last: McNair

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

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


title: Mutant p53 elicits context-dependent pro-tumorigenic phenotypes (ChIP-Seq)

summary: These studies characterized R273C-p53 and R273H-p53 in prostate cancer cells

overall_design: Binding of p53 was assessed in hormone proficient conditions through ChIP-seq of p53 in LNCaP-derived cells lines

first: Karen

last: Knudsen

first: Jennifer

last: McCann

first: Irina

last: Vasilevskaya


title: Mutant p53 elicits context-dependent pro-tumorigenic phenotypes (microarray)

overall_design: Gene expression changes in cells expressing R273C-p53 and R273H-p53 were assessed in LNCaP-derived prostate cancer cells


title: Genome-wide knockout screen of OC43/SARS-CoV2-infected Vero E6 cells

city: Zurich

first: Moritz

last: Schaefer

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: Genome-wide CRISPR screens identified host factors that promote human coronavirus infection, revealing novel antiviral drug targets.

overall_design: The objectives of this study were to identify host factors that promote HCoV replication and to determine whether these host factors can be targeted with commercially available drugs to block viral infection in vitro.  To achieve this goal, we performed genome-wide CRISPR knockout screens in Vero E6 cells using a newly generated Vervet sgRNA library and in HEK293T-hACE2 cells using the commercially available human Brunello sgRNA library. In brief, cells transduced with sgRNA libraries were infected with HCoVs, SARS-CoV-2 and OC43, using various MOIs. Cells surviving infection were expanded and re-infected, and the sgRNAs enriched in resistant clones was determined bvy sequencing.

first: M

last: Grodzki

first: A

middle: P

last: Bluhm

last: Tagmount

last: Russo

first: R

last: Rafiee

first: C

middle: D

last: Vulpe

first: S

last: Karst

middle: H

last: Norris


title: Genome-wide knockout screen of OC43/SARS-CoV2-infected HEK293-hACE2 cells I


title: The effect of S309W mutation on SP7 genomic binding in chondrocytes

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

country: Japan

institute: The University of Tokyo

summary: SP7/Osterix is a transcription factor critical for osteoblast maturation and bone formation. We identidied a missense variant (c.926C>G:p.S309W) in SP7 in a patient with a unique high turnover bone disease. Mice with the corresponding variant similarly showed a complex skeletal phenotype distinct from that of Sp7-null mice. We therefore performed ChIP-Seq in primary chondrocytes to study how the mutation alters the genomic binding of SP7.

overall_design: Primary mouse chondrocytes isolated from proximal tibia and distal femur of 7 day old male mice cardiomyocytes were cultured in DMEM/F12 media supplemented with 10% FBS, P/S, and 50 μg/mL ascorbic acid. Retrovirus expressing either wild-type SP7 or S309W variant of SP7 were produced with HEK-derived ECO cells and used for infecting primary chondrocytes. About 5 days post-infection, chondrocytes were harvested and cross-linked with 1% formaldehyde for genomic DNA isolation.

first: Julian

middle: C

last: Lui

first: Jeffrey

last: Baron


title: CRISPR interference reveals that all-trans-retinoic acid promotes macrophage control of Mycobacterium tuberculosis by limiting bacterial access to cholesterol and propionyl-CoA

status: Public on Dec 21 2021

city: Boston

first: Gregory

middle: Hunter

last: Babunovic

state: MA

address: 665 Huntington Ave., SPH 1, Room 802

department: Immunology and Infectious Diseases

institute: Harvard T.H. Chan School of Public Health

summary: Macrophages are a protective replicative niche for Mycobacterium tuberculosis (Mtb) but can kill the infecting bacterium when appropriately activated. To identify mechanisms of clearance, we compared bacterial restriction by human macrophages after treatment with 26 compounds, including some currently in clinical trials for tuberculosis. All-trans-retinoic acid (ATRA), an active metabolite of vitamin A, drove the greatest increase in Mtb control. Bacterial clearance was transcriptionally and functionally associated with changes in macrophage cholesterol trafficking and lipid metabolism. To determine how these macrophage changes affected bacterial control, we performed the first Mtb CRISPR interference screen in an infection model, identifying Mtb genes specifically required to survive in ATRA-activated macrophages.  These data showed that ATRA treatment starves Mtb of cholesterol and the downstream metabolite propionyl-CoA. Supplementation with sources of propionyl-CoA, including cholesterol, abrogated the restrictive effect of ATRA.  This work demonstrates that targeting the coupled metabolism of Mtb and the macrophage improves control of infection, and that it is possible to genetically map the mode of bacterial death using CRISPR interference.

overall_design: RNA-seq of human primary macrophages, uninfected or infected with Mycobacterium tuberculosis, treated with vehicle control or different retinoic acid receptor agonists.

first: Michael

last: Chase

first: Sarah

last: Fortune


title: Genome-wide knockout screen of OC43/SARS-CoV2-infected HEK293-hACE2 and Vero E6 cells

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus


title: Genome-wide knockout screen of OC43/SARS-CoV2-infected HEK293-hACE2 cells II


title: Human cortical organoids with engineered microglia-like cells [scRNA-Seq]  Apr 05, 2024   pending   None

city: NEW HAVEN

first: Bilal

last: Cakir

state: Connecticut

address: 10 Amistad Street, Ste 214J

institute: Yale University


title: Human cortical organoids with engineered microglia-like cells [CROP-seq]

summary: Microglia play vital roles in the emergence and preservation of a healthy brain microenvironment with their impaired functions highlighted in neurodevelopmental and neurodegenerative disorders. However, investigating the microglia function in health and disease states has been challenging due to the lack of easily accessible human models. Here, we develop a method to generate functional microglia inside human cortical organoids (hCOs) from human embryonic stem cells (hESCs) and apply this system to dissect the role of microglia under inflammation induced by amyloid- (A). The overexpression of the myeloid-specific transcription factor PU.1 generated microglia-like cells in hCOs, producing mhCOs (microglia-containing hCOs) and engrafted in the mouse brain. Single-cell transcriptomics reveals that mhCOs acquire a microglia cell cluster with an intact complement/chemokine system. Functionally, microglia in mhCOs protect parenchyma from cellular and molecular damage caused by A.  A-induced expression of genes associated with apoptosis, ferroptosis, and Alzheimer’s disease (AD) stage III genes was attenuated in mhCOs. Finally, we determined the function of AD-associated genes highly expressed in microglia in response to A by using pooled CRISPRi coupled with single-cell RNA sequencing in mhCOs. Together, mhCOs represent an innovative platform to investigate neurodegenerative disorders and serve to develop therapeutics in the future.

overall_design: Single-cell CRISPRi Screening of microglia-like cells containing cortical organoids

first: Yoshiaki

last: Tanaka

first: Benjamin

last: Patterson

first: In-Hyun

last: Park


title: Transcriptomic analysis of differentiated myoblasts

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: Adult skeletal muscle is a plastic tissue that can adapt its size to workload. Here, we show that RhoA within myofibers is needed for overload-induced hypertrophy by controlling satellite cell fusion to the growing myofibers without affecting protein synthesis. At the molecular level, we demonstrate that, in response to increased workload, RhoA controls in a cell autonomous manner Erk1/2 activation and the expressions of extracellular matrix (ECM) regulators such as Mmp9/Mmp13/Adam8 and of macrophage chemo-attractants such as Ccl3/Cx3cl1. Their decreased expression in RhoA mutant is associated with ECM and fibrillar collagen disorganization and lower macrophage infiltration. Moreover, Mmps inhibition and macrophage depletion in controls phenocopied the lack of growth of RhoA mutants. These findings unravel the implication of RhoA within myofibers, in response to increase load, in the building of a permissive microenvironment for muscle growth and for satellite cell accretion through ECM remodeling and inflammatory cell recruitment.

overall_design: The aim of the analysis is to compare myotubes controls and myotubes lacking RhoA. Primary myoblast were isolated by RhoAfloxed mice by FACS. The cells isolated by FACS,  proliferate and differentiate in culture. The differentiated myotubes were transduced with Adeno-mcherry or Adeno-cre-mcherry adenoviruses in order to delete RhoA ex vivo. RhoA deletion occurs ex vivo once that the myotubes are formed in order to mimic the deletion that occurs in vivo in adult myofibers. RNA was isolated from primary differentiated myoblasts transduced with Adeno-mcherry or Adeno-cre-mcherry adenovirus. Microarray analysis will help to understand the molecular pathways involved in fusion defect observed in vivo. Isolated RNA from 4 myotubes transduced with Adeno mcherry and from 4 myotubes transduced with Adeno-cre-mcherry were used to perform trasncriptomic arrays.

first: Chiara

last: Noviello

first: Athanassia

last: Sotiropoulos


title: Impaired KDM2B-mediated PRC1 recruitment to chromatin causes defective neural stem cell self-renewal and ASD/ID-like behaviors [ChIP-Seq]

status: Public on Dec 20 2021

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

summary: Autism spectrum disorder (ASD) and intellectual disability (ID) are neurodevelopmental diseases associated with various genetic mutations. Recent clinical studies report that chromosomal 12q24.31 microdeletions are associated with human ASD/ID. However, the causality and underlying mechanisms linking 12q24.31 microdeletions to ASD/ID pathogenesis remain undetermined.  Here we show Kdm2b, one of the genes located in chromosomal 12q24.31, plays a critical role in maintaining neural stem cells (NSCs) in the developing mouse brain. Loss of the CxxC-ZF domain of KDM2B impairs its function in recruiting Polycomb repressive complex 1 (PRC1) to chromatin, resulting in de-repression of genes involved in cell apoptosis, cell cycle arrest, NSC premature senescence, and leading to the loss of NSC populations in the brain. Importantly, the Kdm2b mutation is sufficient to induce ASD/ID-like social and memory deficits in adult mice. Thus, our study reveals a critical role of an epigenetic factor KDM2B in normal brain development, a causality between the Kdm2b mutation and genesis of ASD/ID-like phenotypes in mice, and potential molecular mechanisms linking the function of KDM2B-PRC1 in transcriptional regulation and NSC self-renewal to the12q24.31 microdeletion-associated ASD/ID.

overall_design: Examine the KDM2B and RING1B occuapncy and gene expression in wild-type and heterozygous Kdm2b mutant neural progenitor cells.


title: Impaired KDM2B-mediated PRC1 recruitment to chromatin causes defective neural stem cell self-renewal and ASD/ID-like behaviors [RNA-Seq]


title: Impaired KDM2B-mediated PRC1 recruitment to chromatin causes defective neural stem cell self-renewal and ASD/ID-like behaviors


title: Human cortical organoids with engineered microglia-like cells [scRNA-Seq]

overall_design: Single-cell transcriptome profiles of microglia-like cells containing cortical organoids


title: Geminiviruses employ host DNA glycosylases to subvert DNA methylation-mediated defense

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an epigenetic mechanism that plays important roles in gene regulation and transposon silencing. Active DNA demethylation has evolved to counterbalance DNA methylation at many endogenous loci. Here, we report that active DNA demethylation also targets viral DNAs, tomato yellow leaf curl China virus (TYLCCNV) and its satellite tomato yellow leaf curl China betasatellite (TYLCCNB), to promote their virulence. We demonstrate that the βC1 protein, encoded by TYLCCNB, interacts with a ROS1-like DNA glycosylase in Nicotiana benthamiana and with the DEMETER (DME) DNA glycosylase in Arabidopsis thaliana. The interaction between βC1 and DME facilitates the DNA glycosylase activity to decrease viral DNA methylation and promote viral virulence. These findings reveal that active DNA demethylation can be regulated by a viral protein to subvert DNA methylation-mediated defense.

sample_organism:
Arabidopsis thaliana
Nicotiana benthamiana

overall_design: To detected methylatuion levels of intergenic region of TYLCCNV and BSCTV, we delvelop a locus specifical bisulfite sequencing in this study.

first: Xiaojian

last: Gui

first: Chang

last: Liu

first: Xueping

last: Zhou


title: The interaction between the Spt6-tSH2 domain and Rpb1 affects multiple functions of RNA Polymerase II

city: Salt Lake City

first: Tim

last: Formosa

state: UT

address: 15 N Medical Dr East RM 4100

department: Biochemistry

institute: University of Utah School of Medicine

summary: The conserved transcription elongation factor Spt6 makes several contacts with the RNA Polymerase II (RNAPII) complex, including a high-affinity interaction between the Spt6 tandem SH2 domain (Spt6-tSH2) and phosphorylated residues of the Rpb1 subunit in a region linking the catalytic core and the heptad repeats at the C-terminal domain (CTD). This interaction contributes to generic localization of Spt6, but we show here that it also has gene-specific roles. Disrupting the interface affected transcription start site selection at a subset of genes whose expression is regulated by this choice, and this was accompanied by changes in the distinct pattern of Spt6 occupancy at these sites. Splicing efficiency was also impacted, as was apparent progression through introns that encode snoRNAs. Expression of genes that are particularly sensitive to efficient restoration of chromatin after transcription were affected, and a distinct role in maintaining +1 nucleosomes was identified, especially at ribosomal protein genes. The Spt6-tSH2:Rpb1 interface therefore has both genome-wide functions and local roles at subsets of genes where dynamic decisions regarding initiation, transcript processing, or termination are made. We propose that the Spt6-tSH2:Rpb1 interaction participates in coordinating appropriate responses to the varying local conditions encountered RNAPII at each gene, perhaps by modulating the elongation rate to allow reconfiguration of accessory factor activity or availability.

overall_design: 21 samples (3 replicates each of 7 yeast strains) were grown to logarithmic phase (final OD ~0.8) in rich medium at 30° C. Cells were crosslinked with 1% formaldehyde for 20 minutes, collected by centrifugation, spheroplasted, digested with Micrococcal nuclease, then DNA was extracted.

first: Zaily

last: Connell

first: Laura

middle: L

last: McCullough

first: Timothy

last: Parnell


title: Spt6-tSH2 domain and Rpb1


title: Single-cell genomics profiling of the endoderm of the mouse embryonic pharynx [scRNA-seq]

city: Worcester

first: René

last: Maehr

address: 368 Plantation St

department: Program in Molecular Medicine/Diabetes Center of Excellence

institute: UMass Medical School

summary: Maldevelopment of the pharyngeal endoderm, an embryonic tissue critical for patterning of the pharyngeal region and ensuing organogenesis, ultimately contributes to several classes of human developmental syndromes and disorders. Such syndromes are characterized by a spectrum of phenotypes that currently cannot be fully explained by known mutations or genetic variants due to gaps in characterization of critical drivers of normal and dysfunctional development. Despite the disease-relevance of pharyngeal endoderm, we still lack a comprehensive and integrative view of the molecular basis and gene regulatory networks (GRNs) driving pharyngeal endoderm development. To close this gap, we applied transcriptomic and chromatin accessibility single-cell sequencing technologies to generate a multi-omic developmental resource spanning pharyngeal endoderm patterning to the emergence of organ-specific epithelia in the developing mouse embryo. We identify novel cell-type specific gene regulation, distill GRN models that define developing organ domains, and characterize the role of an immunodeficiency-associated forkhead box transcription factor.

overall_design: Single-cell RNA profiling of the pharyngeal endoderm of the mouse embryo. On embryonic days 9.5, 10.5, 11.5, and 12.5, pharyngeal endoderm was isolated by a combination of dissection (mechanical isolation of the whole pharynx) and cell sorting (purification of viable, Pax9+ epithelia). Data include two or three samples per timepoint (biological replicates).

first: Margaret

last: Magaletta

first: Macrina

last: Lobo

first: Eric

last: Kernfeld

first: Hananeh

last: Aliee

first: Jack

last: Huey

first: Teagan

last: Parsons

first: Fabian

last: Theis


title: Single-cell genomics profiling of the endoderm of the mouse embryonic pharynx [sc-ATAC-seq]

overall_design: Single-cell chromatin profiling of a developing pharyngeal endoderm. On embryonic days 11.5 and 12.5, pharyngeal endoderm was isolated by a combination of dissection (mechanical isolation of the whole pharynx) and cell sorting (purification of viable, Pax9+ epithelia). Data include two samples per genotype (biological replicates).


title: Single-cell genomics profiling of the endoderm of the mouse embryonic pharynx

overall_design: Single-cell RNA profiling of Foxn1 knockout and heterozygous control mouse embryonic pharyngeal endoderm. On embryonic day 12.5, pharyngeal endoderm was isolated by a combination of dissection (mechanical isolation of the whole pharynx) and cell sorting (purification of viable, Pax9+ epithelia). Data include two samples per genotype (biological replicates).


title: The interaction between the Spt6-tSH2 domain and Rpb1 affects multiple functions of RNA Polymerase II [MNase-seq]

summary: The conserved transcription elongation factor Spt6 makes several contacts with the RNA Polymerase II (RNAPII) complex, including a high-affinity interaction between the Spt6 tandem SH2 domain (Spt6-tSH2) and phosphorylated residues of the Rpb1 subunit in the linker between the catalytic core and the C-terminal domain (CTD) heptad repeats. This interaction contributes to generic localization of Spt6, but we show here that it also has gene-specific roles. Disrupting the interface affected transcription start site selection at a subset of genes whose expression is regulated by this choice, and this was accompanied by changes in a distinct pattern of Spt6 accumulation at these sites. Splicing efficiency was also diminished, as was apparent progression through introns that encode snoRNAs. Chromatin-mediated repression was impaired, and a distinct role in maintaining +1 nucleosomes was identified, especially at ribosomal protein genes. The Spt6-tSH2:Rpb1 interface therefore has both genome-wide functions and local roles at subsets of genes where dynamic decisions regarding initiation, transcript processing, or termination are made. We propose that the interaction modulates the availability or activity of the core elongation and histone chaperone functions of Spt6, contributing to coordination between RNAPII and its accessory factors as varying local conditions call for dynamic responses.

overall_design: 6 samples (3 replicates each of 2 yeast strains) were grown to logarithmic phase (final OD ~0.8) in rich medium at 30° C. Cells were crosslinked with 1% formaldehyde for 20 minutes, collected by centrifugation, spheroplasted, digested with Micrococcal nuclease, then DNA was extracted.


title: Transcriptional profiling of estrogen receptor fusion genes in breast cancer cell lines

status: Public on Dec 19 2021

city: Houston

first: Jonathan

middle: Thomas

last: Lei

state: TX

address: 1 Baylor Plaza

department: Medicine - Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: Genomic analysis has recently identified multiple ESR1 gene translocations in estrogen receptor-alpha positive (ERα+) metastatic breast cancer (MBC) that encode chimeric proteins whereby the ESR1 ligand binding domain (LBD) is replaced by C-terminal sequences from many different gene partners. Here we functionally screened 15 ESR1 fusions and identified 10 that promoted estradiol-independent cell growth, motility, invasion, EMT and resistance to fulvestrant. RNA sequencing identified a gene expression pattern specific to functionally active ESR1 gene fusions that was subsequently reduced to a diagnostic 24-gene signature. This signature was further examined in 20 ERα+ patient-derived xenografts (PDXs) and in 55 ERα+ MBC samples. The 24-gene signature successfully identified cases harboring ESR1 gene fusions and also accurately diagnosed the presence of activating ESR1 LBD point mutations. Therefore, the 24-gene signature represents an efficient approach to screening samples for the presence of diverse somaticESR1 mutations and translocations that drive endocrine treatment failure in MBC.

overall_design: RNA-seq of stable T47D breast cancer cells expressing HA-tagged ESR1 constructs and YFP control in hormone deprived media, -/+ E2. (ESR1-e6 denotes ESR1 fusion containing the first 6 exons of ESR1)

first: Matthew

last: Ellis

middle: T

first: Xuxu

last: Gou

first: Meenakshi

last: Anurag


title: Epigenetic aging of the demographically non-aging naked mole-rat [RRBS]

first: Vadim

middle: N.

last: Gladyshev

address: 77 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital and Harvard Medical School

summary: The naked mole-rat (NMR) is an exceptionally long-lived rodent that does not show increased mortality with age, uniquely defining NMR as a demographically non-aging mammal. Here, we performed bisulfite sequencing on over one hundred NMR blood samples differing in age, assessing more than 3 million common CpG sites. We observed an information loss of the NMR methylome during aging suggesting that NMR ages. Unsupervised clustering based on the 758 CpG sites whose methylation level strongly correlate with age suggests an age-related shift of the NMR methylome. We also developed an epigenetic aging clock that accurately predicts the NMR age spread across the genome. Based on the clock, NMRs age much slower than mice and much faster than humans, consistent with their known maximum lifespans. We further found that patterns of age-related methylation changes of aging clock sites in Tert and Prpf19 showed differences between NMRs and mice. Together, the data indicate that NMRs, like other mammals, epigenetically age even in the absence of demographic aging of this species.

overall_design: Examination of DNA methylation (RRBS) of naked mole-rat blood samples ranging in age from 0.01 years to 11.63 years.

first: Csaba

last: Kerepesi

first: Margarita

middle: V

last: Meer

first: Julia

last: Ablaeva

first: Vince

middle: G

last: Amoroso

first: Sang-Goo

last: Lee

first: Bohan

last: Zhang

first: Maxim

last: Gerashchenko

first: Alexandre

last: Trapp

first: Sun

last: Yim

first: Ake

last: Lu

first: Morgan

last: Levine

first: Andrei

last: Seluanov

first: Steve

last: Horvath

first: Thomas

last: Park

first: Vera

last: Gorbunova

middle: N


title: The Spt6-tSH2 domain coordinates functional transitions of the RNA Polymerase II CTD during initiation and elongation.

first: Tim

last: Formosa

summary: The conserved transcription elongation factor Spt6 makes several contacts with the RNA Polymerase II (RNAPII) complex, including a high-affinity interaction between the Spt6 tandem SH2 domain (Spt6-tSH2) and phosphorylated residues in Rpb1 in a region between the catalytic core and the heptad repeats of its C-terminal domain (CTD). This interaction contributes to the global occupancy of Spt6 within transcription units, suggesting that it has a general role in tethering Spt6 to the elongation complex. However, we show here that disrupting this binding caused increases in some transcripts, revealing specific functional roles in regulating the expression of subsets of genes. These included loci whose regulation involves differential transcription start site selection, early termination of transcription, or efficient restoration of chromatin integrity after transcription. Loss of this interaction also caused a defect in splicing, and apparent pausing of RNAPII progression in regions requiring more complex processing of excised introns. The results support a global role for the Spt6-tSH2:Rpb1 interaction as one of several means of stabilizing the association of Spt6 with RNAPII, but they also reveal local functions at specific sites, especially those where dynamic decisions regarding initiation or termination are made, or where changes in the configuration of associated factors occur. We therefore propose that the Spt6-tSH2:Rpb1 interaction can provide a conduit for communication between RNAPII and the elongation factor function of Spt6, or with other factors associated with the Rpb1 CTD, supporting appropriate elongation through challenging templates and efficient co-transcriptional processing.

overall_design: 21 samples (3 replicates each of 7 yeast strains) were grown to logarithmic phase in rich medium at 30C. Cells were collected by centrifugation, RNA was extracted, and RNA-seq was performed.

first: Zaily

last: Connell

first: Laura

last: McCullough

first: Timothy

middle: J

last: Parnell


title: Transcriptome results in hippocampus and cortex of KCNMA1-/- (BK KO) mice.

status: Public on Dec 18 2021

city: 上海

first: yu

last: yao

address: 上海市宝山区南陈路333号

institute: 上海大学

summary: In this study, we used RNA-Seq to analyze the transcriptome of BK KO/WT mice hippocampus and cortex, and performed transcriptome profiling to characterize the differentially expressed genes. A total of 652 genes were screened with the threshold of significance at P < 0.05 and |log2foldchange| > 0.58, among which 382 genes were down-regulated and 270 genes were up-regulated in hippocampus tissues. In cortex tissues, we detected a total of 561 differentially expressed genes with the threshold of significance at P < 0.05 and |log2foldchange| > 0.58, including 162 up-regulated genes and 399 down-regulated genes. In order to better understand the potential functions of differentially expressed genes, Gene Ontology (GO) enrichment analysis was carried out to assess the involved pathways. Biological process pathway in GO analysis results showed that development process and biological adhesion were enriched. The results of kyoto encyclopedia of genes and genomes (KEGG) showed that insulin secretion, axon guidance, p53 signaling pathway, HIF-1 signaling pathway and calcium signaling pathway were enriched in hippocampus. On the other hand, cortical KEGG results showed that cell adhesion molecules (CAMs), ECM-receptor interaction, phagosome and calcium signaling pathway were enriched. Dysregulation of gene expression, especially astrocyte activation, neuroinflammation and autophagy, might be the molecular mechanism of BK-LOF meditated epilepsy. This study explores the possible mechanism of epilepsy by transcriptome, reveals the relationship between KCNMA1-LOF and epilepsy, and provides a possible molecular template for individualized treatment of epilepsy.

overall_design: Hippocampus and cortex mRNA profiles of  WT and BK KO mice.

first: Yu

last: Yao

first: Jie

last: Tao


title: Transcriptome comparison of small and large intestine-derived monolayers and murine intestinal crypts

city: San Francisco

first: jake

last: bieber

address: 1700 4th Street

institute: University of California, San Francisco

summary: Gastrointestinal toxicity is a major concern in the development of drugs. Here, we establish the ability to use murine small and large intestine-derived monolayers to screen drugs for toxicity. As a proof-of-concept, we applied this system to assess gastrointestinal toxicity of ~50 clinically used oncology drugs, encompassing diverse mechanisms of action. Nearly all tested drugs had a deleterious effect on the gut, with increased sensitivity in the small intestine. The identification of differential toxicity between the small and large intestine enabled us to pinpoint differences in drug uptake (antifolates), drug metabolism (cyclophosphamide) and cell signaling (EGFR inhibitors) across the gut. These results highlight an under-appreciated distinction between small and large intestine toxicity and suggest distinct tissue properties important for modulating drug-induced gastrointestinal toxicity. The ability to accurately predict where and how drugs affect the murine gut will accelerate preclinical drug development.

overall_design: Included three biological replicates per condition. Small and large intestine-derived monolayers were cultured for 24 hours before RNA harvest.

first: Jake

last: Bieber

first: Steven

last: Altschuler

first: Lani

last: Wu


title: Integrative approach for precise genotyping and transcriptomics of a salt tolerant introgression line in rice

city: Barcelona

first: Mireia

last: Bundó

state: Barcelona

address: C/ de la vall moronta, edifici CRAG, campus UAB

country: Spain

institute: CRAG-Centre for research in agricultural genomics

summary: Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar  PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. Equally, the impact of introgressions from a Saltol donor parent on the global transcriptome of ILs is largely unknown. Here, genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASP) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL line (IL22). A total of 1,595 genes were identified in indica regions in IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes potentially contributing to salt stress tolerance were identified in indica segments of IL22. Comparative transcript profiling also revealed important transcriptional reprograming in IL22 plants both under non-stress and salt-stress conditions, indicating an impact on the transcriptome of the japonica background by the indica introgressed genes and vice versa. Interactions among indica and japonica genes would provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines.

overall_design: Transcriptomics of a parental and introgressed line in response to a 24h 80mM NaCl treatment

first: Héctor

last: Martín-Cardoso

first: Michele

last: Pesenti

first: Jorge

last: Gómez-Ariza

first: Laia

last: Castillo

first: Julien

last: Frouin

first: Xavier

last: Serrat

first: Salvador

last: Nogués

first: Brigitte

last: Courtois

first: Cecile

last: Grenier

first: Gian

last: Sacchi

first: Blanca

last: San Segundo


title: RNAseq transcriptome analysis of A. baumannnii MS14413 treated with PBT2, zinc and tetracycline

status: Public on Dec 17 2021

city: Brisbane

first: David

middle: Manuel Pereira

last: De Oliveira

state: QLD

address: St Lucia

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

summary: Acinetobacter baumannii causes high mortality in ventilator-associated pneumonia patients and antibiotic treatment is compromised in multi-drug resistant strains resistant to beta-lactams, carbapenems, cephalosporins, polymyxins and tetracyclines. Among COVID-19 patients receiving ventilator support, multi-drug resistant A. baumannii secondary infection is associated with a two-fold increase in mortality. Here we investigated the use of the 8-hydroxyquinoline ionophore PBT2 to break resistance of A. baumannii to tetracycline class antibiotics.

overall_design: For A. baumannii MS14413, 3 sample conditions in triplicate were analyzed. Sample conditions included: 1) bacterial treatment with cation-adjusted Muller Hinton broth (CA-MHB; reference sample); or 2)  CA-MHB + 64 µM PBT2 + 8 µM ZnSO4; or 3)  CA-MHB + 64 µM PBT2 + 8 µM ZnSO4 + 1 µg/mL tetracycline

middle: M

first: Minh-Duy

last: Phan

first: Mark

last: Walker

middle: A

last: Schembri


title: Maternal high-fat diet alters the characteristics of astrocytes and worsens the outcome of stroke in rat offspring, which improves after FGF21 administration

city: Wenzhou

first: Yanxuan

last: Li

address: Chashan

institute: Wenzhou Medical University

summary: Background: Maternal high-fat diet (MHFD) has been shown to increase susceptibility to neurological disease in later offspring, but the underlying mechanism is not clear. Fibroblast growth factor 21 (FGF21) has been reported to have a neuroprotective effect in stroke, but its mechanism of action remains unknown. In this study, we investigated the mechanism of the effect of MHFD on stroke in offspring in adulthood and the mechanism by which FGF21 acts on stroke and restores neurological function. Methods: We performed transcriptome sequencing analysis on D21 neonatal rats. Bodyweight and blood indicators were recorded in the adult rats after MHFD. FGF21 was administered 7 h after photochemical modeling twice a day for three consecutive days. Results: We found numerous mRNA changes between the MHFD group and a normal maternal diet (MND) group at D21, including genes related to astrocyte and PI3K/Akt pathways. The body weight, blood glucose, and triglycerides of the MHFD offspring were higher, ischemic lesions were larger, the number of activated astrocytes was lower, and the neurological function score was worse than that of the MND group. After FGF21 administration, WB and qPCR analyses showed that astrocytes and the PI3K/Akt pathway were upregulated, while NF-κB and inflammatory cytokines expression were inhibited in stroke and peri-stroke regions. Conclusion: Taken together, we conclude that MHFD alters the characteristics of astrocytes and other transcriptome changes in their offspring, leading to a worse prognosis of stroke, while FGF21 plays a neuroprotective role by inhibiting NF-κB and inflammatory factors and activating the PI3K/Akt pathway and activating more astrocytes in the MND group than the MHFD group.

overall_design: examine mouse brains' differences between MHFD and MND.

first: Mengqi

last: Lin

first: Li

first: Yunjun

last: Yang


title: Epigenetic and Transcriptional Analysis of human ASC populations

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

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

overall_design: Refer to individual Series


title: Transcriptome analysis using RNA-seq in human mammary epithelial cells

city: San Antonio

first: Meena

last: Kusi

address: 7703 Floyd Curl Dr

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary: Epigenome delineates lineage-specific transcriptional programs and restricts cell plasticity to prevent non-physiological cell fate transitions. Although cell diversification fosters tumor evolution and therapy resistance, upstream mechanisms that regulate the stability and plasticity of cancer epigenome remain elusive. Here, we show that 2-hydroxyglutarate (2HG) not only suppresses DNA repair but also mediates high-plasticity chromatin landscape. A combination of single-cell epigenomic and multi-omic approaches demonstrates that 2HG disarranges otherwise well-preserved stable nucleosome positioning and promotes cell-to-cell variability. 2HG induces loss of motif accessibility to luminal-defining transcriptional factors FOXA1, FOXP1 and GATA3 and a shift from luminal to basal-like gene expression. Breast tumors with high 2HG exhibit enhanced heterogeneity with undifferentiated epigenomic signatures linked to adverse patient prognosis. Further, ascorbate-2-phosphate (A2P) eradicates heterogeneity and impairs growth of high 2HG-producing breast cancer cells. These findings suggest 2HG as a key determinant of cancer plasticity and provide a rational strategy to counteract tumor cell evolution.

overall_design: Single cell chromatin accessibility was assessed by using scATAC-seq. Transcriptome analysis was performed by bulk RNA-seq.

first: Kohzoh

last: Mitsuya

first: Tim

last: Huang


title: Immune Gene Expression in Monocytes from Autism Spectrum Disorders

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

summary: To examine how activation of different toll-like receptors (TLR) impacts gene expression in Autism Spectrum Disorder (ASD), we cultured peripheral blood monocytes from children with ASD, Pervasive Developmental Disorder Not Otherwise Specified (PDDNOS) or Asperger and  typically developing children and treated them with either lipoteichoic acid (LTA) or lipopolysaccharide (LPS) to activate LTR2 or 4 respectively. Following 24 hours of stimulation, we then performed RNA sequencing to profile mRNA responses between non-treated (NT), LTA and LPS treated samples for each diagnosis (control or ASD).

overall_design: 3'QuantSeq on mRNA from PBMCs from children with ASD, PDDNOS or Typical development. Cells were cultured with no treatment (NT) or immune stimulation (LPS or LTA).

first: Paul

last: Ashwood

first: Megan

last: Rowland

first: Heather

last: Hughes


title: Arginine methyltransferase regulates monocyte extravasation and function

status: Public on Dec 16 2021

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

summary: Extravasation of monocytes into tissue and to the site of injury is a fundamental immunological process underlying a variety of innate inflammatory responses across multiple organ systems, which requires rapid responses via post translational modifications (PTM) of proteins. Specifically, methylation of protein by arginine methyltransferases (PRMTs) is an epigenetic PTM implicated in inflammatory responses. However, how methyltransferases drive immune regulation particularly in the lung, the resultant tissue injury and whether this might be of therapeutic value has remained unclear. Here, we demonstrate that PRMT7 was increased in the lung of chronic obstructive pulmonary disease (COPD) patients and positively correlated with tissue injury. Accordingly, in clinically relevant models of COPD, lung fibrosis and skin injury, mice with reduced expression of PRMT7 were protected against disease development, due to decreased recruitment of pro-inflammatory monocytes to the site of injury. Mechanistically, we discovered in monocytes activation of NF-κB/RelA induces PRMT7, promoting mono-methylation of histones, which crucially regulates RAP1A and subsequent adhesion and migration ability. Furthermore, in pro-inflammatory monocytes, ALOX5 derived LTB4 induced ACSL4 expression in lung epithelial cells and consequently sensitized towards ferroptosis, thus aggravating tissue injury. Conclusively, specific targeting of arginine mono-methylation offers yet-unappreciated therapeutic potential against monocyte-driven inflammatory conditions.

overall_design: Single-cell transcriptomics experiment after prolonged cigarette smoke exposure

first: Thomas

last: Conlon

first: Gizem

last: Günsel

first: Aicha

last: Jeridi

first: Niklas

last: Lang

first: Maximilian

last: Strunz

first: Ilias

last: Angelidis

first: Herbert

middle: B

last: Schiller

first: Ali

last: Yildirim


title: RNA seq analysis of BL/6C57 or BL/6NZB mice

status: Public on Dec 15 2021

city: New York

first: Edmund

last: Jenkins

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

summary: RNA seq analysis was done on the  liver samples of BL/6C57 or BL/6NZB male and female mice at 50 weeks

first: Doris

last: Germain

first: Mrittika

last: Chattopadhyay


title: Expression analysis of Huh-7 cells treated with LNA gapmer targeting glucocorticoid receptor (GR) RNA

city: Kawasaki

first: Takao

last: Inoue

state: Kanagawa

address: 3-25-26, Tonomachi

department: Division of Molecular Target and Gene Therapy Products

institute: National Institute of Health Sciences

summary:
Antisense oligonucleotide (ASO) has the potential to induce off-target effects due by inadvertent binding of ASOs to unintended RNAs that   have a sequence similar to the target RNA. In the present study, we focused on the effects of oligonucleotide extension of gapmer ASOs on off-target effects.
We performed microarray analysis using Huh-7 cells (human liver-derived cells) treated with a 14-mer LNA gapmer ASO and the extended 18-mer derivatives with the same core 14-mer region.

overall_design: The  Huh-7 cells were seeded in 12-well plates (n = 4/group) and transfected with the LNA-gapmer ASOs using Lipofectamine® 2000 according to the manufacturer’s protocol.Cells treated with transfection reagent in the absence of ASO were used as a control. After a further 24 h,  total RNA was isolated.

first: Hidenori

last: Yasuhara

first: Tokuyuki

last: Yoshida


title: Hemochromatosis drives acute lethal intestinal responses to hyper-yersiniabactin-producing Yersinia pseudotuberculosis

city: Rensselaer

first: Sridar

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Hemachromatosis (iron-overload) increases host susceptibility to siderophilic bacterial infections that cause serious complications, but the underlying mechanisms remain elusive. The present study demonstrates that oral infection with hyper-yersiniabactin (Ybt) producing Yersinia pseudotuberculosis Δfur mutant (termed Δfur) results in severe systemic infection and acute mortality to hemochromatotic mice due to rapid disruption of the intestinal barrier. Transcriptome analysis of Δfur infected intestine revealed upregulation in cytokine-cytokine receptor interactions, the complement and coagulation cascade, the NF-κB signaling pathway, and chemokine signaling pathways, and downregulation in cell adhesion molecules and TLR signaling pathways. Further studies indicate that dysregulated IL-1b signaling triggered in hemachromatotic mice infected with Δfur damages the intestinal barrier by activation of myosin light chain kinases (MLCK) and excessive neutrophilia. Inhibiting MLCK activity or depleting neutrophil infiltration reduces barrier disruption, largely ameliorates immunopathology, and substantially rescues hemochromatotic mice from lethal Δfur infection. Moreover, early intervention of IL-1b overproduction can completely rescue hemochromatotic mice from the lethal infection.

overall_design: Transcriptome analysis of Yersinia pseudotuberculosis PB1 or Δfur  infected intestine tissues at 3 days post infection

first: Shreya

last: Das

first: Mohd

last: Saqib

first: Meng

last: Ryan

first: Fengyi

last: Wan

first: Wei

last: Sun


title: CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy

city: Mexico City

first: Ernesto

last: Soto-Reyes

state: Mexico City

address: Av. Vasco de Quiroga

department: Departamento de Ciencias Naturales

institute: Universidad Autónoma Metropolitana

summary: High-grade serous ovarian carcinoma (HGSC) is the most lethal gynecologic malignancy due to the lack of reliable biomarkers, effective treatment and chemoresistance. Improving the diagnosis and the development of targeted therapies is still needed. The molecular pathomechanisms driving HGSC progression are not fully understood though crucial for effective diagnosis and identification of novel targeted therapy options. The oncogene CTCFL (BORIS), the paralog of CTCF, is a transcriptional factor highly expressed in ovarian cancer (but in rarely any other tissue in females) with cancer-specific characteristics and therapeutic potential. In this work, we seek to understand the regulatory functions of CTCFL to unravel new target genes with clinical relevance. We used in vitro models to evaluate the transcriptional changes due to the presence of CTCFL, followed by a selection of gene candidates using de novo network enrichment analysis. The resulting mechanistic candidates were further assessed regarding their prognostic potential and druggability. We show that CTCFL-driven genes are involved in cytoplasmic membrane functions; in particular, the Pi3K-AKT initiators EGFR1 and VEGFA, as well as ITGB3 and ITGB6 are potential drug targets. Finally, we identified the CTCFL targets ACTBL2, MALT1 and PCDH7 as mechanistic biomarkers to predict survival in HGSC. Finally, we elucidated the value of CTCFL in combination with its targets as a prognostic marker profile for HGSC progression and as putative drug targets.

overall_design: In OVCAR3 ovarian cancer cell line, CTCFL was overexpressed (OVCAR3_BORIS_OE) and decreased (OVCAR3_BORIS_KD) with plasmid transfections or siRNAS, respectively. Three technical replicates were pooled to generate individual biological replicates, which were further analyzed with paired-end RNA-seq. Three biological replicates for each condition and control samples (OVCAR3_CONTROL) were evaluated.

first: Marisol

last: Salgado-Albarrán


title: IFNγ sensitizes macrophages to pathogen ligand killing via a unique caspase-8 and mitochondrial cell death pathway licensed by nitric oxide

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Caspase-8 modulates TLR-induced gene transcription, which is only partially dependent on caspase-8 catalytic activity. Moreover, The slow kinetics of IFNγ and LPS-induced BMDM killing offers the possibility that transcriptional responses may contribute to cell death activation. We performed 3' mRNA-sequencing to examine whether caspase-8 might contribute, at least in part, to IFNγ and LPS-triggered macrophage death via its transcriptional role. We found that caspase-8-mediated transcriptional re-programming of BMDMs. Importantly, caspase-8 modulates expression of Bcl-2 family members and inducible nitric oxide synthase (iNOS) to promote activation of the mitochondrial apoptotic effectors, BAX and BAK.

overall_design: BMDMs derived from Mlkl-/- and Mlkl-/-Caspase-8-/- mice (n =3 mice of each genotype) were primed with IFNγ (50 ng/ml) overnight then stimulated with LPS (50 ng/ml) for 7 hours. 3' mRNA sequencing was performed on the samples.

first: Daniel

middle: S

last: Simpson

middle: Y

first: Edwin

middle: D

last: Hawkins

first: James

middle: E

last: Vince

first: Rebecca

last: Feltham


title: Expression data for LGG exposure to C. elegnas

status: Public on Dec 12 2021

city: Seoul

first: Sangdon

last: Ryu

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science

summary:
LGG exposure of C. elegans protects C. elegans against pathogen infection and prolongs lifespan. In particular, it prolongs lifespan by up-regulating specific genes to pathogenic microorganisms.
We used microarrays to elucidate miRNA expression to determine how LGG exposure in C. elegans affected miRNAs and identified miRNAs that were significantly regulated in this process.

overall_design: Microarray experiments were performed to compare the expression of miRNA with OP50 when C. elegans was exposed to LGG for 24 h. Nematodes were collected through M9 buffer after 24 h exposure to LGG or OP50.

first: Bohyun

last: Yun


title: The effects of physical exercise training and / or human neural progenitor cell transplantation on the infarct area environment of stroke rats

city: Guangzhou

first: Rui

last: Wu

state: GuangDong

address: NO.600 Tianhe Road, Tianhe District

department: Department of Rehabilitation Medicine

institute: The Third Affiliated Hospital, Sun Yat-sen University,

summary: To detect the effects of physical exercise training and / or human neural progenitor cell transplantation on the infarct area environment of stroke rats, we conducted a genome-wide RNA sequencing and a gene ontology (GO) enrichment analysis of differentially expressed mRNAs in each group was performed.

overall_design: The storke rats were divided into four group: physical exercise group, culture medium injection group, neural progenitor transplantation group and physical exercise combine neural progenitor transplantation group. Each group has three or four replicates.

first: Yiping

last: Guo

first: Guangjing

last: Pan

first: Xiquan

last: Hu


title: Longitudinal single-cell RNA-sequencing (scRNAseq) of broncho-alaveolar compartment of rhesus macaque model of  COVID-19

status: Public on Dec 13 2021

city: St Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St.Louis

summary: To gain insights into the early immune dynamics of transcriptional changes during SARS-CoV-2 infection in airways,  we performed longitudinal scRNA-Seq of the broncho-alveolar lavage (BAL) cells isolated from SARS-CoV-2 infected rhesus macaques. We found early induction of innate type-1 interferon responses with accumulation of a distinct macrophage population that possesses an interferon-driven innate anti-viral gene signature early during infection.

overall_design: BAL cells isolated from young rhesus macaques infected with SARS-CoV-2 WA1 strain at longitudinal timepoints representing pre-infection, acute and post-acute phases of COVID-19  were cryopreserved and analyzed by scRNAseq to reveal early innate immune  dynamics.

first: Dhiraj

middle: K

last: Singh

first: Ekaterina

last: Aladyeva

first: Shibali

last: Das

first: Bindu

last: Esaulova

first: Amanda

last: Swain

first: Mushtaq

last: Ahmed

first: Journey

last: Cole

first: Chivonne

last: Moodley

first: Smriti

last: Mehra

first: Larry

last: Schlesinger

first: Shabaana

last: Khader

first: Deepak

last: Kaushal


title: Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos [Hi-C]

city: Beijing

first: Chen

last: Li

state: Beijing

address: Yihe Yuan Road No.5

department: Institute of Molecular Medicine

institute: Peking University

summary: We performed multi-omics exploration of early aorta endothelial cells (AECs), hemogenic endothelial cells (HECs), pre-HSCs and long-term HSCs (LT-HSCs) along definitive HSC emergence in mouse embryos. Globally, we find that most hematopoiesis related enhancers were already pre-activated at the beginning, followed by strengthened looping structure of enhancers and promoters. After the stronger interactions forming, enhancers can be further activated to promote hematopoiesis gene expressions. Specifically, the important hematopoietic transcription factor (TF) RUNX1 can mediate enhancer-promoter interactions, which starts from a subset of early AECs, prior to appearance of HECs. Thus, the stepwise and asynchrony cooperation of multi-omics and TFs in definitive hematopoiesis has been revealed holistically in vivo. It may also reflect general epigenetic regulation models of developmental processes.

overall_design: Datasets: 1) Hi-C data of early AECs (E10.0 AGM), HECs (E10.0 AGM), pre-HSCs (E11.0 AGM) and LT-HSCs (E14.5 fetal liver), with replicates. 2) H3K27ac, H3K27me3, H3K4me3, H3K4me1 and RUNX1 ChIP-seq data of early AECs (E10.0 AGM), HECs (E10.0 AGM), pre-HSCs (E11.0 AGM) and LT-HSCs (E14.5 fetal liver), with replicates.

middle: C

first: Guangyu

last: Zhang

first: Di

last: Liu

first: Junjie

last: Du

first: Lan

last: Yu

first: Aibin

last: He

first: Bing


title: Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos [ChIP-seq]

overall_design: Datasets: 1) Hi-C data of early AECs (E10.0 AGM), HECs (E10.0 AGM), pre-HSCs (E11.0 AGM) and LT-HSCs (E14.5 fetal liver), with replicates. 2) H3K27ac, H3K27me3, H3K4me1, H3K4me3 and RUNX1 ChIP-seq data of early AECs (E10.0 AGM), HECs (E10.0 AGM), pre-HSCs (E11.0 AGM) and LT-HSCs (E14.5 fetal liver), with replicates.


title: Mesenchymal cell-derived septoclasts resorb cartilage during endochondral ossification and fracture healing

status: Public on Dec 11 2021

city: Muenster

first: Kishor Kumar

last: Sivaraj

address: Roentgenstrasse 20

department: Department of Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

overall_design: Examination of Pdgfra-GFP+ mouse long bone stromal cells and metaphyseal mesenchymal stromal cells

first: Kishor

first: Paul-Georg

last: Majev

first: Ralf

middle: H

last: Adams


title: A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis [RMRP_SHAPE]

status: Public on Dec 14 2021

city: Edinburgh

first: Nic

last: Robertson

address: Swann Building, Max Born Crescent

department: Tollervey Lab

country: United Kingdom

institute: University of Edinburgh

summary: Mutations in the human RMRP gene cause Cartilage Hair Hypoplasia (CHH), an autosomal recessive disorder characterized by skeletal abnormalities and impaired T-cell activation. RMRP encodes a non-coding RNA, which forms the core of the RNase MRP ribonucleoprotein complex. In budding yeast, RMRP cleaves a specific site in the pre-ribosomal RNA (pre-rRNA) during ribosome synthesis. CRISPR-mediated disruption of RMRP in human cells lines caused growth arrest, with pre-rRNA accumulation. Here, we analyzed disease-relevant primary cells, showing that mutations in RMRP impair mouse T cell activation and delay pre-rRNA processing. Analysis of pre-rRNA processing in patient-derived human fibroblasts with CHH-linked mutations showed a similar pattern of processing delay. Human cells engineered with the most common CHH mutation (70AG in RMRP) show specifically impaired pre-rRNA processing, resulting in reduced mature rRNA and a reduced ratio of cytosolic to mitochondrial ribosomes. Moreover, the 70AG mutation caused a reduction in intact RNase MRP complexes. Together, these results indicate that CHH is a ribosomopathy, and the first human disorder of rRNA processing to be described.

overall_design: Wildtype or RMRP 70A->G mutant cells were grown to log phase in RPMI. The SHAPE reagent 1M7 (or DMSO for untreated samples) was added to a final concentration of 10 mM and in-cell acylation reaction left to proceed for 15 minutes at 37 degrees. RNA was extracted and reverse transcribed using an RMRP-specific primer. Sites of RNA modification are represented as mutations or deletions in the sequencing, and were analysed with the ShapeMapper 2 tool.

first: Vadim

last: Shchepachev

first: David

last: Wright

first: Tomasz

middle: W

last: Turowski

first: Christos

last: Spanos

first: Aleksandra

last: Helwak

first: Rose

last: Zamoyska

last: Tollervey


title: Single cell RNA sequencing and TCR repertoire analysis of MIS-C affected patients versus healthy controls and severe adult COVID-19

status: Public on Dec 09 2021

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: In rare instances, pediatric SARS-CoV2 infection results in a novel immunodysregulation syndrome termed multisystem inflammatory syndrome in children (MIS-C). We compared MIS-C immunopathology with that of severe COVID-19.  MIS-C does not result in pneumocyte damage but is associated with vascular endothelitis, gastrointestinal epithelial injury and endotoxemia. In MIS-C, IFN dominates the inflammatory signature  in contrast to type I interferons in severe COVID-19. While HLA-DRlo classical monocytes dominate severe COVID-19,  patrolling monocyte activation characterize MIS-C. TIM-3 expression on activated CD4/CD8  T cells and on CD57+ NK cells is a distinctive MIS-C feature. In all MIS-C patients, single cell TCR profiling demonstrates a skewed TCR repertoire enriched for TRBV11-2 and a superantigenic signature which is absent in severe COVID-19. Using NicheNet, we confirm IFN as a central cytokine in the communication between activated T cells, NK cells and patrolling monocytes. Rapid normalization of IFN, TIM-3 loss on T cells and patrolling monocytes contraction upon treatment highlight their potential role in MIS-C immunopathogenesis.

overall_design: Single cell RNA sequencing of 7 pediatric patients suffering from MIS-C, compared with 5 healthy siblings that did not experience MIS-C, and 4 adult patients with severe COVID-19. Patient samples were obtained during hospitalisation and at maximal inflammation. Samples from siblings were acquired ambulatory in the absence of inflammation. We compared transcriptomic data in leukocytes between these three cohorts and used additional computational modelling tools (GSEA, IPA and Nichenet) to characterize the immunodysregulation that is observed in MIS-C and is distinct from baseline conditions in their healthy siblings and adult COVID-19. In addition, we specifically analyzed the TCR repertoire within the T cells of these patients.

first: Levi

last: Hoste

first: Lisa

last: Roels

first: Leslie

last: Naesens

first: Victor

last: Bosteels

first: Stijn

last: Vanhee

first: Sam

last: Dupont

first: Cedric

first: Robin

last: Browaeys

first: Niels

last: Vandamme

first: Kevin

last: Verstaen

first: Jana

first: Karel

middle: F

last: Van Damme

first: Bastiaan

last: Maes

first: Elisabeth

last: De Leeuw

first: Jozefien

last: Declercq

first: Helena

last: Aegerter

first: Leen

last: Seys

first: Ursula

last: Smole

first: Sofie

last: De Prijck

first: Manon

last: Vanheerswynghels

first: Karlien

last: Claes

first: Veronique

last: Debacker

first: Gert

last: Van Isterdael

first: Lynn

last: Backers

first: Kathleen

first: Paul

last: Bastard

first: Emmanuelle

last: Jouanguy

first: Seng-Ying

first: Gilles

last: Mets

first: Joke

last: Dehoorne

first: Kristof

last: Vandekerckhove

first: Petra

last: Schelstraete

first: Jef

last: Willems

first: Patrick

last: Stordeur

first: Sophie

last: Janssens

first: Rrudi

last: Beyaert

first: Yvan

last: Saeys

first: Jean

middle: L

last: Casanova

first: Bart

last: Lambrecht

first: Filomeen

last: Haerynck

first: Simon

last: Tavernier


title: Pre-configuring chromatin architecture with histone modifications guide hematopoietic stem cell formation in mouse embryos.

first: Chen

last: Li


title: Next Generation Sequencing Facilitates Quantitative Analysis of HIV Elite controller, HIV ART, HIV ART-naive and healthy control Transcriptomes

city: Charleston

first: Zhenwu

last: Luo

state: SC

address: 173 Ashley Ave

department: Immunology & Microbiology

institute: Medical University of South Carolina

summary: A small group of HIV-1-infected individuals, termed elite controllers (ECs), display control of HIV replication in the absence of antiretroviral therapy (ART). However, the mechanisms of resistance to HIV in ECs remains largely unknown. To identify host factors specific to the ECs that might be involved in controlling HIV infection, we performed RNA-seq transcriptome analysis, and a total of 44 samples were included. The monocytes from each sample were enriched, sequenced, and subjected to comparative transcriptome analysis to screen candidate genes that might affect resistance to HIV infection. we found several candidate genes with highly divergent expression  that might contribute to the different outcomes of HIV infection in ECs and non-ECs. This finding will help elucidate the mechanisms by which ECs restrict HIV replication and represents a new approach for treatment of HIV.

overall_design: mRNA profiles of from HIV+ Elite controller, HIV+ antiretroviral therapy (ART), HIV+ ART-naïve (or treatment-Naïve) and healthy control

first: Wei

last: Jiang


title: The landscape of H3K4me3 associated interactions between chromatin and RNAs in rice.

status: Public on Dec 10 2021

city: Hangzhou

first: Xingyu

last: Huang

state: Zhejiang

address: 866 Yuhangtang Road, Hangzhou, Zhejiang Province

institute: Life Sciences Institute (LSI), Zhejiang University (ZJU)

overall_design: Refer to individual Series


title: SPX domain proteins are agents of inositol pyrophosphate toxicosis in fission yeast

status: Public on Dec 08 2021

first: Angad

last: Garg

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: This RNA-Seq analysis compares gene expression of spx1∆ mutant contrasting to the WT fission yeast S. pombe

overall_design: 1 test sample and 1 control sample was processed (each sample has 3 replicate experiments). WT samples cultured at the same time and sequenced in the same run were previously deposited in GEO dataset GSE164616

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus

city: Madison

first: Brent

last: Anderson

state: WI

address: 1550 Linden Dr.

department: Bacteriology

institute: University of Wisconsin-Madison

summary: The nucleotide messenger (p)ppGpp allows bacteria to adapt to fluctuating environments by reprogramming the transcriptome. Despite its well-recognized role in gene regulation, (p)ppGpp is only known to directly affect transcription in Proteobacteria by binding to the RNA polymerase. Here we reveal a different mechanism of gene regulation by (p)ppGpp in Firmicutes from soil bacteria to pathogens: (p)ppGpp directly binds to the transcription factor PurR to downregulate purine biosynthesis. We identified PurR as a receptor of (p)ppGpp in Bacillus anthracis and revealed that (p)ppGpp strongly enhances PurR binding to its regulon in the Bacillus subtilis genome. A co-structure reveals that (p)ppGpp binds to a PurR pocket reminiscent of the active site of PRT enzymes that has been repurposed to serve a purely regulatory role, where the effectors (p)ppGpp and PRPP compete to allosterically control transcription. PRPP inhibits PurR DNA binding to induce transcription of purine synthesis genes, whereas (p)ppGpp antagonizes PRPP to enhance PurR DNA binding and repress transcription. A (p)ppGpp-refractory purR mutant fails to downregulate purine synthesis genes upon starvation. Our work establishes the precedent of (p)ppGpp as a classical effector of transcription repressors and reveals the key function of (p)ppGpp in regulating nucleotide synthesis through gene regulation, from the human intestinal tract to host-pathogen interfaces.

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: Comparing PurR ChIP enrichment in the Bacillus subtilis genome before and after treatment with arginine hydroxamate (RHX) to induce (p)ppGpp. This study used 25 total samples. Five samples (3 ChIP replicates and 2 input replicates) were from B. subtilis grown in a medium with nucleobases to enhance PurR repression and identify PurR binding sites genome-wide. Five samples (3 ChIP replicates and 2 input) were from B. subtilis before RHX treatment and five samples (3 ChIP replicates and 2 input) were from B. subtilis after RHX treatment. Lastly, the same RHX treatment was performed on a (p)ppGpp-null B. subtilis strain, producing ten samples (five before RHX, 3 ChIP replicates and 2 input; five after RHX, 3 ChIP replicates and 2 input).

first: Jeremy

last: Schroeder

first: Jue

last: Wang


title: Genome-wide maps of LADs distribution in control and Dam-WT/Dam-R527C LMNA stabilized Hela cells

status: Public on Dec 07 2021

first: Ming

last: Kuang

address: Xueyuan Road 38 #, Haidian District

summary: To determine if LMNA R527C mutation affect the arrangement and function of LADs, we performed Lamin A DamID-seq in wild type and mutant LMNA-stablized Hela cells. Reads of Lamin A ChIP-seq in LADs were decreased in mutant cells compared with wild type. These data suggested that the binding affinity of Lamin A to LADs was reduced after R527C mutation

overall_design:
To determine if R527C mutation affects the arrangement and function of LADs, we performed Lamin A DamID-seq in control and Dam-WT/Dam-R527C LMNA stabilized Hela cells.
Examination of  LADs distribution in control and Dam-WT/Dam-R527C LMNA stabilized Hela cells.

first: Yingchi

last: Zhao


title: Single-cell RNA sequencing to identify 51248 single cells from periodontal tissues of healthy humans and periodontitis patients with or without treatment

city: Nanjing

first: Wen

last: Sun

address: 140 Hanzhong Road

institute: Nanjing Medical University

summary: Single-cell transcriptomics were used to comprehensively resolve the osteoimmunology microenvironment that are involved in periodontal tissues from human chronic periodontitis before and after nonsurgical periodontal therapy, as well as clinically healthy controls. This allows unbiased assessment of many heterogeneous cells at the single-cell level, hence revealing complexities of the molecular components and differences with counterparts residing in periodontal tissues.

overall_design: Single-cell mRNA profiles of periodontal tissues of healthy humans and periodontitis patients with or without treatment were generated by Single-cell RNA sequencing, using BD Rhapsody system.

first: Yue

last: Chen


city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

summary: The effects of Candida albicans on the metastatic activity of oral squamous cell carcinoma was observed in vitro and in vivo. In the in vitro experimental setup HO-1-N-1 and HSC-2 human oral squamous cell carcinoma cell lines were treated with zymosan, heat-killed Candida albicans, heat-killed C. parapsilosis, live C. albicans and live C. parapsilosis. Whole transcriptomics was performed of the human tumor cells. In the in vivo experiment human HSC-2 tumor cells were injected to the tongue of mice. Whole transcriptomic analysis was performed of the human HSC-2 derived tumor cells comparing control tumor and oral candidiasis treated tumor.

overall_design:
in vitro: 2 OSCC cell lines untreated or treated with 5 different treatments.
in vivo: 4 control tumors, 4 oral candidiasis-treated tumors.

first: Máté

last: Vadovics

last: Gácser

last: Szücs

first: Márton

last: Horváth


title: Genome-wide maps of Lamin A-LADs binding affinity in control and LMNA R527C mutant MSCs

summary: To determine if LMNA R527C mutation affect the arrangement and function of LADs, we performed Lamin A ChIP-seq in wild type and mutant MSCs. Reads of Lamin A ChIP-seq in LADs were decreased in mutant cells compared with wild type. These data suggested that the binding affinity of Lamin A to LADs was reduced after R527C mutation

overall_design:
To determine if R527C mutation affects the arrangement and function of LADs, we performed Lamin A ChIP-seq in  control and LMNA R527C mutant MSCs.
Examination of  Lamin A-LADs binding affinity in control and LMNA R527C mutant MSCs.


title: MYC Amplifies Gene Expression through Global Changes in Transcription Factor Dynamics

city: Bethesda

first: Daniel

middle: R

last: Larson

address: 41 Medlar Dr.

institute: NIH

summary: The MYC oncogene has been studied for decades, yet there is still intense debate over how this transcription factor controls gene expression. Here, we seek to answer these questions with an in vivo readout of discrete events of gene expression in single cells. We engineered an optogenetic variant of MYC (Pi-MYC) and combined this tool with single-molecule RNA and protein imaging techniques to investigate the role of MYC in modulating transcriptional bursting and transcription factor binding dynamics in human cells. We find that the immediate consequence of MYC overexpression is to increase the duration rather than frequency of bursts, a functional role which is different from the majority of human transcription factors. We further propose that the mechanism by which MYC exerts global effects on the active period of genes is by altering the binding dynamics of transcription factors involved in RNA Polymerase II complex assembly and productive elongation.

overall_design: SLAM-Seq profiles of human bronchial epithelial cell lines (HBEC3-KT) stably expressing photo-inducible MYC-mCherry (Pi-MYC) or a photo-inducible mCherry control (Pi-mCherry),  cultured for 180min in the dark or under blue light. Data provided includes 2 biological replicates of each condition.

first: Yihan

last: Wan

first: Simona

last: Patange

first: Dan


title: Genome-wide maps of chromatin openness in control and LMNA R527C mutant MSCs

summary: We performed ATAC-seq to examine to chromatin of openness of coding genes in healthy control and LMNA R527C patient-derived MSCs. The reduction of LADs did not increase the accessibility of the promoters flanking coding genes. The genome wide analysis of ATAC-seq showed that openness of coding genes related chromatin was decreased in mutant MSCs.Thus, R527C mutant Lamin A led to dysfunction of LADs and dysregulation of gene transcription, probably, leading to slow down or arrest of cell proliferation and differentiation.

overall_design:
LADs were distributed across heterochromatic, promoter, and actively transcribed regions of the genome and were associated with DNA methylation and suppressed gene expression. We thus performed ATAC-seq to examine to chromatin of openness of coding genes in control and LMNA R527C mutant MSCs as Lamin A-LADS binding affinity were changed during LMNA R527C mutation.
Examination of chromatin openness in control and LMNA R527C mutant MSCs.


title: Transcriptome responses to defined insecticide selection pressures in the German cockroach

city: West lafayette

first: Michael

last: Scharf

state: IN

address: 901 W State St

department: Entomology

institute: Purdue University

summary:
Purpose: Next-generation transcriptome sequencing was done to understand host and eukaryotic microbiome changes in gene expression in association with defined insecticide selection pressures. The specific goal of this research was to understand whole-body physiological responses in German cockroaches and associated microbiota, at the metatranscriptome level, to defined insecticide selection pressures.
Methods:  We used the insecticide indoxacarb as the selecting insecticide, which is an important bait active ingredient for cockroach control.  Six generations of selection with indoxacarb bait produced a strain with substantial (>20x) resistance relative to inbred control lines originating from the same parental stock.
Results: Metatranscriptome sequencing revealed 1123 significantly differentially expressed genes in > two of three statistical models (81 upregulated and 1042 downregulated; FDR p<0.001; log2FC of +/- 1). The majority of upreglated genes were from the host cockroach while the majority of downregulated genes were from associated viruses and the eukaryotic microbiome.
Conclusions: We show here significant impacts by insecticide selection on not only host stress-respnses like detoxification, but also on clearace of microbial parasites, pathogens, commensals and/or symbionts.

overall_design: Whole-body mRNA expression profiles in cockroaches subjected to six generations of insecticide selection in comparison to identical genetic lines that inbred without selection (three replicates each; 6 replicate samples total).

first: Ameya

last: Gondhalekar


title: An instructive role for Interleukin-7 receptor α in the development of human B-cell precursor leukemia

status: Public on Dec 06 2021

city: Rehovot

last: Ben-Avraham

address: Hertzel 234

department: Grand Israel National Center for Personalized Medicine

country: Israel

institute: Weizmann Institute of Science

summary: Bulk RNAseq for transplanted transduced (CRLF2-IL7RAins or BB control)CB cells

overall_design: Total RNA was purified from 5000-20000 transduced (CRLF2+ or GFP+) CD45+CD3- cells that were sorted from spleens of transplanted mice. cDNA libraries were prepared using SMARTer v3 kit (Clontech Laboratories, Inc. A Takara Bio Company, Mountain View, CA, USA) followed by the Nextera-XT indexing protocols (Illumina, CA, USA). Genome-wide expression profiles were obtained by sequencing of the samples on Illumina NextSeq 500 using NextSeq 500/550 High Output v2 kit.

first: Ifat

last: Geron

first: John

last: Brown

first: Shai

last: Izraeli

first: Tariq

last: Enver


title: Circadian key component CLOCK/BMAL1 interferes with segmentation clock in mouse embryonic organoids

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: In mammals, circadian clocks are strictly suppressed during early embryonic stages as well as pluripotent stem cells, by the lack of CLOCK/BMAL1 mediated circadian feedback loops. During ontogenesis, the innate circadian clocks emerge gradually at a late developmental stage, then, with which the circadian temporal order is invested in each cell level throughout a body. Meanwhile, in the early developmental stage, a segmented body plan is essential for an intact developmental process and somitogenesis is controlled by another cell-autonomous oscillator, the segmentation clock, in the posterior presomitic mesoderm (PSM). In the present study, focusing upon the interaction between circadian key components and the segmentation clock, we investigated the effect of the CLOCK/BMAL1 on the segmentation clock Hes7 oscillation, revealing that the expression of functional CLOCK/BMAL1 severely interferes with the ultradian rhythm of segmentation clock in induced PSM and gastruloids. RNA sequencing analysis showed that the premature expression of CLOCK/BMAL1 affects the Hes7 transcription and its regulatory pathways. These results suggest that the suppression of CLOCK/BMAL1-mediated transcriptional regulation during the somitogenesis may be inevitable for intact mammalian development.

overall_design: Examination of total RNA in CLOCK/BMAL1-overexpressing mouse embryonic stem cells (ESCs) and induced presomitic mesoderm (iPSM) colonies

first: Yasuhiro

last: Umemura

first: Nobuya

last: Koike


title: TLR4 is a regulator of trained immunity in a murine model of Duchennemuscular dystorphy

city: Montral

first: Jun

last: Ding

state: Quebec

address: 1001 Decarie Blvd.

department: Medicine

institute: McGill University

summary: The main purpose of our study is to investigate if muscle damage in mdx mice alters the phenotype of macropahges at precursor level in the bone marrow. Here we show major remodeling of the epigenetic, metabolic and functional inflammatory profiles of monocyte-derived macrophages from the bone marrow of mdx mice is TLR4-dependent. This altered phenotype of mdx BMDM demonstrates the hallmark features of trained immunity, including being transmissible and long-lasting after bone marrow transplantation to non-dystrophic mice.

overall_design: Examination of 2 different histone modifications in Bone marrow derived macrophages.

first: Salyan

last: Bhattarai

first: Basil

last: Petrof


title: Differential roles for DNAJ isoforms in HTT-polyQ and mutant FUS aggregation modulation revealed by chaperone network screens

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

institute: Technion

summary: Protein aggregation is a hallmark of many neurodegenerative diseases. In order to cope with misfolding and aggregation, cells have evolved an elaborate network of molecular chaperones, composed of different families. But while chaperoning mechanisms for different families are well established, functional and regulatory diversification within chaperone families is still largely a mystery. Here we decided to explore chaperone functional diversity, through the lens of pathological aggregation. We revealed that different naturally-occurring isoforms of DNAJ chaperones showed differential effects on different types of aggregates. We performed a chaperone screen for modulators of two neurodegeneration-related aggregating proteins, the Huntington’s disease-related HTT-polyQ, and the ALS-related mutant FUS (mutFUS). The screen identified known modulators of HTT-polyQ aggregation, confirming the validity of our approach.  Surprisingly, modulators of mutFUS aggregation were completely different than those of HTT-polyQ. Interestingly, different naturally-occurring isoforms of DNAJ chaperones had opposing effects on HTT-polyQ vs. mutFUS aggregation. We identified a complex of the full length (FL) DNAJB14 and DNAJB12 isoforms which substantially alleviated mutFUS aggregation, in an HSP70-dependent manner. Their naturally occurring short isoforms were unable to form the complex, nor to interact with HSP70, and lost their ability to reduce mutFUS aggregation. In contrast, the short isoform of DNAJB12 significantly alleviated HTT-polyQ aggregation, while DNAJB12-FL aggravated HTT-polyQ aggregation. Finally, we demonstrated that full-length DNAJB14 ameliorated mutFUS aggregation compared to DNAJB14-short in primary neurons. Together, our data unraveled distinct molecular properties required for aggregation protection in different neurodegenerative diseases, and revealed a new layer of complexity of the chaperone network elicited by naturally occurring J-protein isoforms, highlighting functional diversity among the DNAJ family.

overall_design: Expression of wild-type and aggregating variants of HTT and FUS proteins in human cell line (HEK293T) followed by separation of diffused and aggregate expression populations using PulsA protocol, followed by transcriptome analysis.

first: Anatoly

last: Meller

first: Amal

last: Younis


title: Genetic screen for suppression of transcriptional interference reveals fission yeast 14-3-3 protein Rad24 as an antagonist of precocious Pol2 transcription termination

city: New York

first: Angad

last: Garg

summary: This RNA-Seq analysis compares gene expression of rad24∆ mutant contrasting to the WT fission yeast S. pombe

overall_design: 1 test sample and 1 control sample was processed (each sample has 3 replicate experiments)

first: Beate

last: Schwer

first: Stewart

last: Shuman