title: A divergent and complementary transcriptional response in poxvirus-infected and bystander inflammatory monocytes is partly dictated by interferon [iMO_Bcells_ECTV]

summary: Inflammatory monocytes (iMO) and B-cells are the main targets of the poxvirus ectromelia virus (ECTV) in the lymph nodes of mice and play distinct roles in surviving the infection. Infected and bystander iMO control ECTV’s systemic spread, preventing early death, while B-cells make antibodies that eliminate ECTV. Our work demonstrates that within an infected animal that survives ECTV infection, intrinsic and bystander infection of iMO and B-cells differentially control the transcription of genes important for immune cell function and, perhaps, cell identity. Bystander cells upregulate metabolism, antigen presentation, and interferon-stimulated genes. Infected cells downregulate many cell-type-specific genes and upregulate transcripts typical of non-immune cells. Bys and Inf iMO non-redundantly contribute to the cytokine milieu and the interferon response. Furthermore, we uncovered how IFN-I or IFN-γ signaling differentially regulates immune pathways in Inf and Bys iMO and, that at steady state, IFN-I primes iMO for rapid IFN-I production and antigen presentation.

overall_design: Bystander and infected iMO and B-cells were sorted from popliteal draining lymph nodes of ectromelia virus-infected mice at 3 days post-infection. GFP-expressing ectromelia virus was used for sorting Bystander and Infected cells. As controls, Naïve iMO were sorted from spleen and Naïve B-cells sorted from lymph node of uninfected animals. 3 biological replicates were sequenced for all groups, except for Inf iMO for which only 2 biological replicates were sequenced.

middle: R

last: Melo-Silva

first: Marisa

middle: I

last: Roman

first: Cory

last: Knudson

first: Lingjuan

last: Tang

first: Ren-Huan

last: Xu

first: Michel

last: Tassetto

first: Patrick

last: Dolan

first: Raul

last: Andino

first: Luis

last: Sigal


title: A divergent and complementary transcriptional response in poxvirus-infected and bystander inflammatory monocytes is partly dictated by interferon [iMO IFN ECTV]

status: Public on Oct 18 2022

city: Huntingdon Valley

first: Carolina

last: Rezende Melo da Silva

state: Pennsylvania

address: 2527 Morgan run

department: Microbiology and Immunology

country: USA

institute: Thomas Jefferson University

type: Expression profiling by high throughput sequencing

overall_design: Bystander and infected iMO were sorted from popliteal draining lymph nodes of ectromelia virus-infected mixed bone marrow chimeric mice at 3 days post-infection. GFP-expressing ectromelia virus was used for sorting Bystander and Infected cells. As controls, Naïve iMO were sorted from spleens of uninfected bone marrow chimeras. 4 biological replicates were sequenced for WT bystander and infected iMO. 2 biological replicates were sequenced for Naive iMO and for knockout bystander and infected iMO.

middle: J


title: Early life exercise primes the neural epigenome to facilitate gene expression and hippocampal memory consolidation [CUT&RUN]

city: Irvine

first: Autumn

middle: Skye

last: Ivy

state: CA

address: 825 Health Sciences, Medical Sciences D330

institute: Universtity of California, Irvine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Aerobic exercise is well known to promote neuroplasticity and hippocampal memory. In the developing brain, early-life exercise (ELE) can lead to lasting improvements in hippocampal function, yet molecular mechanisms underlying this phenomenon have not been fully explored. In this study, adolescent transgenic mice harboring the “NuTRAP” (Nuclear tagging and Translating Ribosome Affinity Purification) cassette in Emx1 expressing neurons (“Emx1-NuTRAP” mice) undergo ELE followed by a hippocampal learning task, in order to determine the molecular underpinnings of exercise contributing to improved hippocampal memory performance. We simultaneously isolate and sequence translating mRNA and nuclear chromatin from a single hippocampus in a cell-type specific manner (excitatory neurons), demonstrate validity of our new technical approach, and couple multi-omics sequencing data to evaluate histone modifications H4K8ac and H3K27me3 and their influence on gene expression after ELE. We then evaluate new gene expression – histone modification relationships specifically during hippocampal memory consolidation that may play a critical role in facilitated memory after ELE. Our data reveal novel candidate gene-histone modification interactions and implicate gene regulatory pathways involved in ELE’s impact on hippocampal learning and memory.

overall_design: Comparative gene expression between mice allowed to exercise in early life and those not allowed to do so either with object location memory (OLM) training or without. For those without OLM training H4K8ac and H3K27me3 presence was compared and correlated with differential gene expession using CUT&RUN-seq.

first: Anthony

middle: M

last: Raus

first: Tyson

middle: D

last: Fuller

first: Nellie

middle: E

last: Nelson

first: Samuel

middle: A

last: Valientes

first: Anita

last: Bayat

middle: S


title: Analysis of sequences downstream of the polyadenylation signal and their influence on gene expression

city: Novosibirsk

first: Alexey

last: Pindyurin

address: Acad. Lavrentiev Ave. 8/2

country: Russia

institute: IMCB SB RAS

summary: Using massively parallel reporter assay (MPRA) we study influence of multiple variants of sequences located downstream of the polyadenylation signal (PAS) on the reporter gene transcription in human HEK293T cells. We have found that consensus sequence located downstream of the PAS and providing the strong increase in the reporter gene transcription is extremely T-rich. Since HEK293T cell culture is one of the most prominent host cell lines for recombinant antibody expression, we believe that our results may be useful for improving the efficiency of producing biotherapeutics including therapeutic antibody.

overall_design: Massively parallel reporter assay (MPRA) of the reporter gene transcription depending on the multiple variants of sequences located downstream of the polyadenylation signal (PAS) in human HEK293T cells

middle: V

first: Evgeniya

last: Omelina

first: Anna

last: Letiagina

last: Ogienko

first: Lidiya

last: Boldyreva

first: Yuliya

last: Galimova

first: Lyubov

last: Yarinich

middle: N

last: Andreeva


title: HCV infection increases the expression of ACE2 receptor, leading to enhanced entry of both HCV and SARS-CoV-2 into hepatocytes and a coinfection state

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: this study provides the first experimental evidence for the SARS-CoV-2-HCV coinfection of liver cells, suggesting that HCV infection may be a potential risk factor for enhanced liver disease in coinfected patients. Although this outcome is supported by recent clinical findings, the specific effects of the enhanced infection SARS-CoV-2 and replication of HCV in coinfection states on liver pathology remains to be evaluated in clinical settings. In a broader view, this study emphasizes the importance of identifying coinfecting pathogens that increase the risk of SARS-CoV-2 infection and that may accelerate COVID-19-related co-morbidities.

overall_design: RNA-seq analysis was performed on data from SARS-CoV-2-infected cells (n=3) and HCV+SARS-CoV-2 coinfected cells (n=3) obtained in this study, and on data from HCV-infected cells (n=6) and uninfected cells obtained from Perez et al. 2019

first: Domovitz

last: Tom

first: Ayoub

last: Samer

first: Werbner

last: Michal

first: Alter

last: Joel

first: Izhaki

middle: T

last: Lee

first: Yahalom-Ronen

last: Yfat

first: Tikhonov

last: Evgeny

first: Meirson

last: Tomer

first: Maman

last: Yaakov

first: Paran

last: Nir

first: Israely

first: Dessau

last: Moshe

first: Gal-Tanamy

last: Meital


title: Extracellular galectin 4 drives immune evasion and promotes T-cell apoptosis in pancreatic cancer [RNA-Seq]

city: Umea

first: Cedric

last: Patthey

address: Analysvägen 1,

country: Sweden

institute: Umeå University

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by rich deposits of extracellular matrix (ECM), affecting the pathophysiology of the disease. Here, we identified galectin 4 (gal 4) as a cancer cell produced protein deposited into the ECM of PDAC tumors and detected high circulating levels of gal 4 in PDAC patients. In orthotopic transplantation experiments we observed increased infiltration of T-cells and prolonged survival in immunocompetent mice transplanted with cancer cells with reduced expression of gal 4. Increased survival was not observed in immunodeficient RAG1-/- mice, demonstrating that the effect was mediated by the adaptive immune system. Furthermore, by performing single-cell RNA-sequencing we found that the myeloid compartment and cancer-associated fibroblast (CAF) subtypes were altered in the transplanted tumors. Reduced gal 4 expression was associated with higher proportion of myofibroblastic CAFs and reduced numbers of inflammatory CAFs. We also found higher proportions of M1 macrophages, T-cells and antigen presenting dendritic cells in tumors with reduced gal 4 expression. Using a co-culture system, we observed that extracellular gal 4 induced apoptosis in T-cells by binding CD3, resulting in anergy or induction of apoptosis. Hence, we show that gal 4 is involved in immune evasion and identify gal 4 as a promising drug target for overcoming immunosuppression in PDAC.

overall_design: Bulk RNA-seq analysis of two murine pancreatic cancer organoid lines derived from the mT5 line described in Boj et al, 2015 (PMID: 25557080). A Galectin 4 shRNA knock-down organoid line (Gal4KD) was compared to a scramble control line in paired technical triplicates. Epcam+/Cd45-/Pdpn- cells were FACS sorted and sequencing libraries were made on 500 cells per sample.

first: Lidström

last: Tommy

first: Öhlund

last: Daniel

first: Patthey

last: Cedric


title: Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

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: Background: Ductal carcinoma in situ (DCIS) is the most common type of in situ premalignant breast cancers. What drives DCIS to invasive breast cancer is unclear.  Basal-like invasive breast cancers are aggressive.  We have previously shown that N-Ras is highly expressed selectively in basal-like subtypes of invasive breast cancers and can promote their growth and progression. In this study, we investigated whether NRAS expression at the DCIS stage can control transition from luminal DCIS to basal-like invasive breast cancers.   Methods: Wilcoxon rank-sum test was performed to assess expression of NRAS in DCIS compared to invasive breast tumors in patients.  NRAS levels were also determined by fluorescence in situ hybridization in patient tumor microarrays (TMAs) with concurrent normal, DCIS, and invasive breast cancer, and association of NRAS mRNA levels with DCIS and invasive breast cancer was assessed by paired Wilcoxon signed-rank test.  Pearson’s correlation was calculated between NRAS mRNA levels and basal biomarkers in the TMAs, as well as in patient datasets.  RNA-seq data was generated in cell lines and unsupervised hierarchical clustering was performed after combining with RNA-seq data from a previously published patient cohort.   Results: Invasive breast cancers showed higher NRAS mRNA levels compared to DCIS samples. These NRAShigh lesions were also enriched with basal-like features, such as basal gene expression signatures, lower ER, and higher p53 protein and Ki67 levels.  We have shown previously that N-Ras drives aggressive features in DCIS-like and basal-like SUM102PT cells.  Here, we found that NRAS-silencing induced a shift to a luminal gene expression pattern.  Conversely, NRAS overexpression in the luminal DCIS SUM225 cells induced a basal-like gene expression pattern, as well as an epithelial-to-mesenchymal transition signature.  Furthermore, these cells formed disorganized mammospheres containing cell masses with an apparent reduction in adhesion.    Conclusions: These data suggest that elevated NRAS levels in DCIS is not only a marker but can also control the emergence of basal-like features leading to more aggressive tumor activity, thus supporting the therapeutic hypothesis that targeting N-Ras and/or downstream pathways may block disease progression for a subset of DCIS patients with high NRAS.

overall_design: RNA-seq of doxycycline inducible knockdown of NRAS in SUM102PT cells; RNA-seq of SUM225 cells overexpressing NRAS

first: Eric

middle: C

last: Chang

first: Ze-Yi

last: Zheng

first: Meenakshi

last: Anurag


title: Extracellular galectin 4 drives immune evasion and promotes T-cell apoptosis in pancreatic cancer

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

overall_design: Refer to individual Series


title: Context-dependent function of long noncoding RNA PURPL in transcriptome regulation during p53 activation

city: Bethesda

first: Ashish

last: Lal

state: Maryland

address: 37 Convent Drive, Room 6134

department: NCI

institute: NIH


title: Context-dependent function of long noncoding RNA PURPL in transcriptome regulation during p53 activation (Iso-Seq)

summary:
The goal of our study is to investigate the role of the p53-induced lncRNA PURPL in the context of liver cancer.
To achieve this, we identified transcript variants of PURPL expressed in liver cancer cells and assayed for the transcriptome changes caused by PURPL knockdown after p53 induction.

overall_design: 1. Transcriptome profiling using Illumina and isoform profiling using PacBio of SKHEP1 and HepG2 liver cancer cell lines to check the expression of PURPL and identify transcript variants. 2. mRNAseq profile of established SKHEP1 PURPL CRISPRi cell lines.

first: Corrine

last: Hartford

first: Lorinc

last: Pongor

first: Yongmei

last: Zhao

first: Xiongfong

last: Chen

first: Caroline

last: Fromont

first: Ritu

last: Chaudhary

first: Xiao

middle: L

last: Li

first: Katherine

last: Pasterczyk

first: Ravi

last: Kumar

first: Bruna

last: Muys

first: Dimitrios

last: Tsitsipatis

first: Raj

last: Chari

first: Myriam

last: Gorospe

first: Mirit

last: Aladjem

first: Ioannis

last: Grammatikakis


title: RNA-seq, ChIP-seq and Mnase-Seq analysis of CHD6-silenced prostate cancer cells C4-2

first: Dongyu

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

type: Methylation profiling by high throughput sequencing

summary:
Purpose: Study of the role of CHD6 linking nucleosome ejection in castration-resistant prostate cancer(CRPC)
Method: The expression of CHD6 or E2F1 was silenced by 2 shRNAs (3 replicates) targeted at CHD6 or E2F1 in C4-2 cells, scramble RNA as control. mRNA profiles and genome-wide chromatin-state maps were generated by deep sequencing. CHD6 and IgG ChIP was conducted in C4-2 cells. MNase before and after CHD6-silenced was conducted in C4-2 cells.
Results: E2F1 and E2F1 downstream  genes were significantly down regulated by CHD6 knockdown. The binding of CHD6 on chromatin is required for nucleosome eviction in transcriptional activation of oncogenic pathways.

overall_design: Expression profiling by RNA-seq, profiling of CHD6 and E2F1 (wildtype and knockdown) from C4-2 cell lines. DNA was purified from chromatin immunoprecipitates for CHD6 or IgG using the phenol/chloroform extraction. IgG was used as a negative control for ChIP. Then, DNA was amplified by quantitative PCR and normalized to input. Micrococcal nuclease digestion was performed (Nuclei were incubated for 15 min and 60 min) followed by high-throughput sequencing (MNase-Seq) in both C4-2 control cells and CHD6 knockdown cells.

first: D

first: M

last: Zhang

first: Q

last: Cao

first: K


title: Extracellular galectin 4 drives immune evasion and promotes T-cell apoptosis in pancreatic cancer [scRNA-Seq]

first: Cedric

last: Patthey

overall_design: Single cell RNA-seq analysis of two mouse pancreatic tumours collected 6.5 weeks after orthotopic transplantation of tumour organoid lines (Gal4KD vs scramble control). The two tumour organoid lines were derived from the mT5 line described in Boj et al, 2015 (PMID: 25557080). A tumour from the Galectin 4 shRNA knock-down organoid line (Gal4KD) was compared to a tumour from the scramble control organoid line. Epcam-/Cd45-/Pdpn+ fibroblastic cells and Epcam-/Cd45+/Pdpn- immune cells were sorted into different tubes by flow cytometry, and ~5*10^4 immune cells were pooled with ~5*10^4 immune cells from the same tumour.  A total of 7500 cells per sample was used.

first: Lidström

last: Tommy

first: Öhlund

last: Daniel

first: Patthey

last: Cedric


title: Unraveling capsule biosynthesis and signaling networks in Cryptococcus neoformans

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

summary: Cryptococcus neoformans is an opportunistic basidiomycete pathogen that is a major etiological agent of fungal meningoencephalitis leading to more than 180,000 deaths worldwide annually. For this pathogen, the polysaccharide capsule is a key virulence factor, which interferes with the phagocytosis by host innate immune cells, but its complex signaling networks remain elusive. In this study, we systematically analyzed capsule biosynthesis and signaling networks by using C. neoformans transcription factor (TF) and kinase mutant libraries under diverse capsule-inducing conditions, such as Dulbecco’s Modified Eagle’s (DME), Littman’s medium (LIT) and fetal bovine serum (FBS) medium. We found that deletion of GAT201, YAP1, BZP4, and ADA2 consistently causes capsule production defects in all tested media, indicating that they are capsule-regulating core TFs. Epistatic and expression analysis showed that Yap1 and Ada2 control Gat201 upstream, whereas Bzp4 and Gat201 regulate capsule production independently. We next searched for potential upstream kinases and found that mutants deleted of PKA1, BUD32, POS5, IRE1 or CDC2801 showed reduced capsule production under all three capsule induction conditions, whereas mutants deleted of HOG1 and IRK5 displayed enhanced capsule production. Notably, Pka1 and Irk5 controls induction of GAT201 and BZP4, respectively, under capsule induction condition. Finally, we monitored transcriptome profiles governed by Bzp4,  Gat201, and Ada2 under capsule-inducing condition and demonstrated that these TFs regulate redundant and unique sets of downstream target genes. In conclusion, this study provides further insight into the complex regulatory mechanism of capsule production related signaling pathways in C. neoformans.

overall_design: Transcriptome patterns of H99S, bzp4Δ, ada2Δ and gat201Δ strains were comparatively analyzed by RNA-sequencing. Cryptococcus neoformans strains were grown at 30°C for 16hr in a YPD medium and transferred to 50 mL of fresh YPD medium and incubated at 30°C until the OD600 reached 0.8. Half of the cells were further incubated in an LIT liquid medium for 2hr. Then the cells were harvested by centrifugation and lyophilized. Total RNAs were prepared as described above and purified with RNeasy Mini Kit (QIAGEN). The concentration was measured by Quant-IT RiboGreen (Invitrogen). The quality of the RNA was verified by the TapeStation RNA screentape (Agilent). Cultured samples were prepared independently three times, and the cDNA library was constructed with the 1 µg of total RNAs for each sample by Illumina TruSeq mRNA library kit (Illumina) and sequenced by the Illumina platform. The adapter sequences were trimmed from the sequencing reads by using Cutadpat v3.4 with Python 3.7.4. The reference genome sequence of C. neoformans H99 and annotation data were downloaded from the NCBI FTP server, derived from Broad Insitute. The reads were aligned to the C. neoformans H99 genome sequence using Hisat2 v2.2.1 with the HISAT and Bowtie2 algorithm and processed as previously reported. Hisat2 was performed with “-p 30” and “– dta -1” options and other parameters set as default. Aligned reads were converted and then sorted by Samtools v1.9 with the “-Sb -@ 8” option for converting, and “-@ 20 –m 2000000000” option for sorting, and the other parameters were set as default. Transcript assembly and abundance estimation were performed using Stringtie v2.1.1 by using the “-p 12” option, and also the “-B” option to run the Ballgown analysis. Assembled transcripts were merged to a single GTF ﬁle, and the relative transcript abundances were calculated via Fragments Per Kilobase of exon per Million fragments mapped (FPKM). The FPKM and read count matrix were generated by the R package “isoformswitchanalyzerR” and analyzed by DESeq2. Differentially expressed genes (DEG) analysis was performed using DESeq2 v1.24.0 with default sets with the Ballgown. The volcano plot was illustrated by using R v4.1.0 and R package "EnhancedVolcano", with the cutoff (more than two-fold changes with p< 0.05). PCA plot was generated by R package "DeBrowser" and heatmap was also generated by following R package. KEGG pathway analysis was performed using the R package "Cluster profiler", after changing H99S gene locus ID to JEC21 orthologue locus ID.

first: Eun-Ha

last: Jang

first: Ji-Seok

last: Kim

first: Seong-Ryong

last: Yu


title: Context-dependent function of long noncoding RNA PURPL in transcriptome regulation during p53 activation (RNA-Seq I)

first: Ashish

last: Lal

overall_design: 1. Transcriptome profiling using Illumina and isoform profiling using PacBio of SKHEP1 and HepG2 liver cancer cell lines to check the expression of PURPL and identify transcript variants. 2. mRNAseq profile of established PURPL CRISPRi cell lines.

first: Corrine

last: Hartford

first: Lorinc

last: Pongor

first: Yongmei

last: Zhao

first: Xiongfong

last: Chen

first: Caroline

last: Fromont

first: Ritu

last: Chaudhary

first: Xiao

last: Li

first: Katherine

last: Pasterczyk

first: Ravi

last: Kumar

first: Bruna

first: Dimitrios

first: Raj


title: Early life exercise primes the neural epigenome to facilitate gene expression and hippocampal memory consolidation [RNA-seq]

first: Autumn

last: Ivy

first: Anthony

last: Raus

first: Tyson

last: Fuller

first: Nellie

last: Nelson

first: Samuel

last: Valientes

first: Anita

last: Bayat


title: Piperaquine-resistant PfCRT mutations differentially impact drug transport, hemoglobin catabolism and parasite physiology in Plasmodium falciparum asexual blood stages

city: University Park

first: Manuel

last: Llinas

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: The emergence of multidrug resistance in Plasmodium falciparum parasites presents a significant obstacle to the malaria elimination agenda. Resistance to piperaquine (PPQ), an important first-line partner drug, has spread across Southeast Asia where it has contributed to widespread treatment failures. The genetic cause of resistance to PPQ is attributable to a novel set of amino acid substitutions in the P. falciparum chloroquine resistance transporter (PfCRT). The objective of our study is to characterize gene expression signatures associated with PPQ-resistance associated PfCRT mutations by comparing transcriptional profiles of PPQ-resistant PfCRT mutants (F145I, G353V, M343L) and isogenic PPQ-sensitive lines that were generated by zinc finger nuclease (ZFN) based editing in a long-term adapted (Dd2).

overall_design: We employed microarray technology to establish the global gene expression profiles of these four PfCRT-edited parasite lines (Dd2, Dd2+F145I, Dd2+G353V, Dd2+M343L) and unedited Dd2 at the trophpzoite stage of the intra-erythrocytic developmental cycle. The RNA expression profiles of the PfCRT mutant and isogenic parasites were compared to identify changes at basal levels. Two to three independent experiments were performed for each parasite strain.

first: Sachel

last: Mok

first: David

last: Fidock

first: Lindsey

last: Orchard

last: Llinás


title: Effect of Cyclohexidmide treatment on early transcription of HSV-1 ΔICP22 and repaired virus

city: Ithaca

first: Joel

last: Baines

state: NY

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

summary: Study was performed to assess the requirement for HSV-1 IE protein, ICP22, to be expressed to regulate early HSV-1 transcription

overall_design: PRO-Seq was performed on nuclei extracted at 1.5 hpi from HEp-2 cells infected with ΔICP22 HSV-1 mutant and its genetically restored repair. Infections occurred at an MOI of 5 in the presence or absence of the protein synthesis inhibitor cycloheximide (CHX)

first: Laura

last: Dunn

first: Claire

last: Birkenheuer

first: Rachel

last: Dufour


title: Unravelling the pathobiological role of the fungal KEOPS complex in Cryptococcus neoformans

first: Yong-Sun

last: Bahn

summary: The kinase, putative endopeptidase and other peptides of small size (KEOPS) complex plays critical cellular functions in eukaryotes, but its pathobiological roles remains elusive in fungal pathogens. Here we comprehensively analyze the pathobiological functions of the KEOPS complex in fungal meningoencephalitis pathogen Cryptococcus neoformans. The cryptococcal KEOPS complex appears to have a linear arrangement of Pcc1-Kae1-Bud32-Cgi121, supported by physical interaction between Pcc1-Kae1, Kae1-Bud32, and Bud32-Cgi121, but does not have Gon7 ortholog, which is the part of the S. cerevisiae KEOPS complex. Deletion of PCC1, KAE1, and BUD32 causes severe growth defects with perturbed cell cycle control.

overall_design: C. neoformans strains grown overnight in YPD medium weretransferred to 50 mL of fresh YPD medium and incubated at 30°C until the OD600 reached 0.6. The cells were then harvested by centrifugation and lyophilized. Total RNAs were isolated by Easy-BLUE (iNtRON), treated with DNase I (Qiagen), and puriﬁed with RNeasy MiniElute clean up kit (Qiagen) following the manufacturer’s instruction. Cultured samples were prepared independently three times for each strain, the cDNA library was constructed with the 1 µg of total RNAs for each sample by Illumina TruSeq mRNA library kit (Illumina) and sequenced by Illumina platform. The adapter sequences were trimmed from the sequencing reads by using Cutadpat v3.4 with Python 3.7.4. (1). The reference genome sequence of Cryptococcus neoformans H99 and annotation data were downloaded from the NCBI ftp server. The reads were aligned to the Cryptococcus neoformans H99 genome sequence using Hisat2 v2.2.1 with the Hisat and Bowtie2 algorithm and processed as previously reported (2). Hisat2 was performed with “-p 30”and “– dta -1”option and other parameters set as default. Aligned reads were converted and then sorted by Samtools v1.9 (3) with “-Sb -@ 8”option for converting, and “-@ 20 –m 2000000000” option for sorting and the other parameters set as default. Transcript assembly and abundance estimation were performed using Stringtie v2.1.1 by using “-p 12” option, and also “-B” option to run the Ballgown analysis (4). Assembled transcripts were merged to single GTF ﬁle, and the relative transcript abundances were calculated via Fragments Per Kilobase ofexon per Million fragments mapped (FPKM). The FPKM and readcount matrix was generated by R package “isoformswitchanalyzerR” and analyzed by DESeq2. Differentially expressed genes (DEG) analysis was performed using DESeq2 v1.24.0 with default sets with the Ballgown. Volcano plot was illustrated by using R v4.1.0, with the cutoff (more than two-fold changes with p< 0.05).

first: Yeseul

last: Choi

first: Eunji

last: Jeong

first: Dong-Gi

last: Lee

first: Jae-Hyung

last: Jin

first: Yee-Seul

last: So

first: Seong-Ryong

last: Yu

first: Kyung-Jo

first: Yoonjie

last: Ha

first: Chi-Jan

last: Lin

first: Ying-Lien

last: Chen

first: Jun Bae

last: Park

first: Hyun-Soo

last: Cho

first: Anna

middle: F

last: Averette

first: Joseph

last: Heitman

first: Kyu-Ho

first: Kangseok


title: Early life exercise primes the neural epigenome to facilitate gene expression and hippocampal memory consolidation

first: Autumn

last: Ivy


title: Immediate early proteins of herpes simplex virus transiently repress viral transcription before subsequent activation.

first: Joel

last: Baines

summary: This study was undertaken to further clarify the roles of HSV-1 immediately early (IE) genes ICP4, ICP0, and ICP22 in early viral transcription. Precision nuclear Run On followed by deep Sequencing (PRO-Seq) was used to identify sites of Pol activity to high resolution on the genomes of HSV-1 viruses bearing mutations in a0, a4 or a22/US1, and corresponding viruses in which these loci were genetically restored. The results indicated that prior to initiating activation of transcription, IE genes first mediate transcriptional repression.

overall_design: PRO-Seq was performed on nuclei extracted at either 1.5, 3 or 6 hpi from HEp-2 or HFF cells infected with HSV-1 mutant viruses: n12 (ICP4-null), n212, (ICP0-null), DICP22 and their genetically restored repairs at an MOI of 5. Infection experiments with n12 and repair were also performed in the presence of cycloheximide (CHX). Drosophila melanogaster nuclei were spiked-in before the run-on to normalise for sequencing depth across samples.

first: Laura

last: Dunn

first: Claire

last: Birkenheuer


title: Effect of high-fat and chow diets on satellite cell transcriptome

city: Créteil

first: Fred

last: Relaix

address: 8 rue du Général Sarrail

country: France

institute: INSERM U955 Université Paris-Est Créteil

summary: To study the satellite cell transcriptome in obese and lean mice, we FACS-sorted satellite cells from the muscles of mice on high fat and chow diets, extracted RNA and performed RNA sequencing

overall_design: Comparative gene expression profiling analysis of RNA-seq data for satellite cells isolated from obese and lean mouse muscle

first: Sergio

last: Perez-Diaz

first: Zeynab

last: Koumaiha

first: Matthew

last: Borok

first: Frederic

last: Aurade

first: Maria

last: Pini

first: Baptiste

last: Periou

first: Christine

last: Rouault

first: Yasmine

last: Baba-Amer

first: Karine

last: Clement

first: Genevieve

last: Derumeaux

first: Francois

last: Authier

first: Peggy

last: Lafuste


title: Robust induction of primordial germ cells of white rhinoceros on the brink of extinction

city: Osaka

first: Masafumi

last: Hayashi

address: 2-2 Yamada-oka, Suita

department: Department of Genome Biology

country: Japan

institute: Osaka University

summary: In vitro gametogenesis, the process of generating gametes from pluripotent cells in culture, is a powerful tool for improving our understanding of germ cell development as well as an alternative source of gametes.(1) Conservation of the northern white rhinoceros (NWR), a species for which only two females remain, would be a compelling application of in vitro gametogenesis as a gametes source. Here, we established a culture system that induces a robust number of primordial germ cell-like cells (PGCLCs) from pluripotent stem cells of the NWR and southern white rhinoceros (SWR), the closest species to the NWR. PGCLC differentiation from SWR embryonic stem cells is highly reliant on BMP and WNT signals, as observed in mice and humans, though the timing and duration of these signals need to be optimized for each species. Genetic analysis revealed that SOX17 is essential for SWR-PGCLC induction, as it is in humans. Under the defined condition, NWR induced pluripotent stem cells differentiated into PGCLCs whose transcriptome was highly similar to that of SWR-PGCLCs. We also identified cell surface markers, CD9 and ITGA6, that enabled us to isolate PGCLCs without genetic alteration in pluripotent stem cells. This study provides a first step toward production of NWR gametes in culture and understanding of the basic mechanism of PGC specification in a large animal.

sample_organism:
Ceratotherium simum simum
Ceratotherium simum cottoni

overall_design: Transcriptomes of embryonic stem cells, pre-induced cells, and primordial germ cell like cells of southern white rhinoceros and induced pluripotent stem cells, pre-induced cells, and primordial germ cell like cells of northern white rhinoceros.

first: Vera

last: Zywitza

first: Yuki

last: Naitou

first: Nobuhiko

last: Hamazaki

first: Frank

last: Goeritz

first: Robert

last: Hermes

first: Susanne

last: Holtze

first: Giovanna

last: Lazzari

first: Cesare

last: Galli

first: Jan

last: Stejskal

first: Sebastian

last: Diecke

first: Thomas

middle: B

last: Hildebrandt

first: Katsuhiko


title: Hypoxia promotes osteonesis via regulation of the mito-nuclear communication [ATAC-seq]

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

country: Germany

institute: Max Planck Institute

summary: Bone marrow mesenchymal stem cells (MSCs) reside in a hypoxic niche that maintains their differentiation potential. Several studies have highlighted the critical role of hypoxia (low oxygen concentration) in the regulation of stem cell function, reporting differentiation defects following a switch to normoxia (high oxygen concentration). However, the molecular events triggering changes in stem cell fate decisions in response to high oxygen remain elusive. Here, we study the impact of normoxia in the mito-nuclear communication, with regards to stem cell differentiation. We show that normoxia-cultured MSCs undergo profound transcriptional alterations which cause irreversible osteogenesis defects. Mechanistically, high oxygen promotes chromatin compaction and histone hypo-acetylation, particularly on promoters and enhancers of osteogenic genes. Although normoxia induces rewiring of metabolism, resulting in high acetyl-CoA levels, histone hypo-acetylation occurs due to trapping of acetyl-CoA inside mitochondria, likely due to lower CiC activity. Strikingly, restoring the cytosolic acetyl-CoA pool via acetate supplementation remodels the chromatin landscape and rescues the osteogenic defects. Collectively, our results demonstrate that the metabolism-chromatin-osteogenesis axis is heavily perturbed in response to high oxygen and identify CiC as a novel, oxygen-sensitive regulator of MSC function.

overall_design: Study the impact of long-term exposure to normoxia on the chromatin-metabolism-stem cell fate axis.

first: Andromachi

last: Pouikli

first: Swati

last: Parekh


title: Context-dependent function of long noncoding RNA PURPL in transcriptome regulation during p53 activation (RNA-Seq II)

first: Ashish

last: Lal

first: Corrine

middle: R

last: Hartford

first: Lorinc

last: Pongor

first: Yongmei

last: Zhao

first: Xiongfong

last: Chen

first: Caroline

last: Fromont

first: Ritu

last: Chaudhary

first: Xiao

last: Li

first: Katherine

last: Pasterczyk

first: Ravi

last: Kumar

first: Bruna

last: Muys

first: Dimitrios

last: Tsitsipatis

first: Raj

last: Chari

first: Myriam

last: Gorospe

first: Mirit

last: Aladjem

first: Ioannis

last: Grammatikakis


title: Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP

city: LA JOLLA

first: Hsuan-Lin

last: Her

address: 9500 Gilman Dr,

institute: UCSD

summary: UV cross-linking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the current enhanced CLIP (eCLIP) protocol still requires ~4 days of hands-on time and lacks the ability to scale. We present a new method termed antibody barcode CLIP (ABC) that utilizes DNA-barcoded antibodies to multiplex CLIP detection methods. We demonstrate the scalability and simplicity of ABC by performing CLIP on multiple RBPs simultaneously, minimizing sample-to-sample variation, and maintaining the same material requirement for a single eCLIP experiment.

overall_design: ABC(Antibody barcoded eCLIP) is perform as singleplex (RBFOX2, SLBP) or multiplex (for 10 RBPs)

first: Daniel

last: Lorenz

first: Kylie

last: Shen

first: Kasey

last: Hutt

first: Allan

last: Nojadera

first: Stephanie

last: Bruns

first: Sergei

last: Manakov

first: Karen

last: Chapman

first: Gene

middle: W

last: Yeo


title: The Xbp1-regulated transcription factor Mist1 restricts antibody secretion by restraining Blimp1 expression in plasma cells

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Antibody secretion by plasma cells provides acute and long-term protection against pathogens. The high secretion potential of plasma cells depends on the unfolded protein response, which is controlled by the transcription factor Xbp1. Here, we analyzed the Xbp1-dependent gene expression program of plasma cells and identified Bhlha15 (Mist1) as the most strongly activated Xbp1 target gene. As Mist1 plays an important role in other secretory cell types, we analyzed in detail the phenotype of Mist1-deficient plasma cells in Cd23-Cre Bhlha15(fl/fl) mice under steady-state condition or upon NP-KLH immunization. Under both conditions, Mist1-deficient plasma cells were 1.4-fold reduced in number and exhibited increased IgM production and antibody secretion compared to control plasma cells. At the molecular level, Mist1 regulated a largely different set of target genes compared to Xbp1. Notably, expression of the Blimp1 protein, which is known to activate immunoglobulin gene expression and to contribute to antibody secretion, was 1.3-fold upregulated in Mist1-deficient plasma cells, which led to a moderate downregulation of most Blimp1-repressed target genes in the absence of Mist1. Importantly, a 2-fold reduction of Blimp1 (Prdm1) expression was sufficient to restore the cell number and antibody expression of plasma cells in Prdm1(Gfp/+) Cd23-Cre Bhlha15(fl/fl) mice to the same level seen in control mice. Together, these data indicate that Mist1 restricts antibody secretion by restraining Blimp1 expression, which likely contributes to the viability of plasma cells.

overall_design: 2 RNA-Seq samples that have not been used for differential analysis (124152-3) and 8 RNA-Seq samples for differential analysis with 4 different conditions and two replicates each: wildtype Plasmacell = 137948 + 137949; Xbp1(fl/fl) Plasmacell = 124150+124151; Cd23-Cre Xbp1(fl/fl)  Plasmabast cell = 124154+124155; Cd23-Cre Bhlha15(fl/fl) Plasmablast cell = 137950+137951. 3 ChIP-Seq samples, 2 different conditions: Bhlha15(fl/fl) R26(BirA/BirA) Plasmablast cell = 124832+124833; Xbp1s(bio/bio) R26(BirA/+) pre-Plasmablast and Plasmablast cell = 29435.

first: Miriam

last: Wöhner

first: Astrid

last: Hagelkruys

first: Peter

last: Bönelt

first: Johannes

last: Stadlmann

first: Daniela

last: Kostanova-Poliakova

first: Theresa

last: Pinter

first: Stephen

last: Konieczny

first: Maria

last: Fischer

first: Markus

last: Jaritz

first: Meinrad

last: Busslinger


title: RNA-seq profiling of forced expression of FoxF2 in Benign Prostate Hyperplasia

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

summary: Since the first forkhead transcription factor was identified, its family members have been implicated in a variety of cellular processes, including embryonic development and disease. The purpose of this experiment was to help understand the role of a transcriptional factor Foxf1 in human benign prostatic hyperplasia.

overall_design: Two groups were profiled by RNA-seq: WPMY1 cells infected with control vector and cells infected with FOXF2.

first: Yiqun

last: Zhang

first: Li

last: Xin


title: The AhR-SRC axis as a therapeutic vulnerability in BRAFi-resistant melanoma

city: RENNES

first: Sebastien

last: CORRE

address: Faculté de médecine, 2 av du Pr Léon Bernard

department: IGDR

institute: CNRS UMR6290

summary: The use of BRAF inhibitors, specific of the BRAFV600E mutation, as a therapeutic strategy for melanoma has significantly improved patient survival. However, resistance mechanisms appear systematically and limit the benefit of treatment. Here we show that AhR transcription factor participates in BRAFi resistance and is associated with the acquisition of an invasive and a dedifferentiated melanoma phenotype by controlling the expression of specific genes. AhR also induces the activation of the c-Src pathway through its phosphorylation, associated with BRAFi resistance. The use of a specific inhibitor of c-Src such as Dasatinib makes it possible to sensitize resistant cells to BRAFi and to prevent the acquisition of an invasive melanoma phenotype by regulating the expression of the AhR-dependent genes.

overall_design: mRNA expression profiles (RNAseq) in BRAFi sensitive and resistant melanoma cell lines invalidated or not for AhR transcription factor (CRISPR-Cas9), or after treatment by ITE, Dasatinib or Bosutinib (Src inhibitors)

first: Anaïs

last: Paris

first: Nina

last: Tardif

first: Francesca

last: Baietti

first: Cyrille

last: Berra

first: Héloïse

last: Leclair

first: Eleonora

last: Leucci

first: Marie-Dominique

last: Galibert

first: Sébastien

last: Corre


title: Hypoxia promotes osteogenesis by facilitating acetyl-CoA-mediated mitochondrial-nuclear communication

first: Peter

last: Tessarz

overall_design: Refer to individual Series


title: Transcriptomic and immunopepdidomic analysis of senescent and non-senescent mouse embryonic fibroblasts (MEF)

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

country: Spain

institute: IRB

summary: We analysed the mRNA expression (by RNA sequencing) of nonsenescent and senescent mouse embryonic fibroblasts (MEF).

overall_design: Non-senescent mouse embryonic fibroblasts (MEF) (3 independent biological replicates) and doxorubicin-treated senescent MEF (3 independent biological replicates) were collected and analysed (6 samples in total).

first: I

last: Marín

first: M

last: Serrano


title: Hypoxia promotes osteonesis via regulation of the mito-nuclear communication [RNA-seq]

first: Andromachi

last: Pouikli

first: Swati

last: Parekh


title: Hypoxia promotes osteonesis via regulation of the mito-nuclear communication [ChIP-seq]


title: GCN2 enhances the growth and progression of prostate cancer by maintaining amino acid homeostasis

city: Indianapolis

first: Kirk

middle: Alan

last: Staschke

state: IN

address: 635 Barnhill Drive, MS4063

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing


title: Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis [ECs_InVivo_D10_RNAseq]

status: Public on Oct 17 2022

city: New

first: Sean

last: Houghton

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Bulk RNA-seq of mouse in vivo liver samples from either control or Erg and Fli1 double knocked out.

overall_design: Mice were intravitally injected with VE-cadherin antibody. Tissues were dissociated by Collagenase Dispase digestion and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cells. Sorted endothelial cells were processed for RNA-seq.

first: Jesus

last: Gomez Salinero

first: Tomer

last: Itkin

first: Shahin

last: Rafii


title: Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis [Liver_InVivo_D7_RNAseq ]


title: Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis [Liver_IL1B_TNFA_RNAseq]

summary: Bulk RNA-seq of mouse in in vitro samples from either control or Erg and Fli1 knock out with or without additional treatment of Il1b + Tnfa

overall_design: Mouse ECs were isolated from the liver of mice with the corresponding genotype. The induction of the deletion of Erg and/or Fli1 in cultured ECs was achieved by the addition of 4-OHT for 48 hours to the culture medium. Cells were cultured for an additional 7 days after the initial addition of tamoxifen before final harvest and analysis. To study the inflammatory response of the ECs, we added both IL1β and TNFα at day 7 after tamoxifen administration and lysed the cells 16 hours afterwards for RNA-seq analysis.


title: A New Approach Methodology (NAM) Based Assessment of Butylated hydroxytoluene (BHT)  for Endocrine Disruption (ED) Potential

city: Cincinnati

first: Nadira

last: De Abrew

state: OH

address: 5299 Spring Grove Ave

department: Global Product Stewardship

institute: The Procter & Gamble Company

summary:
We tested the hypothesis that BHT is an endocrine disruptor by using a Next Generation Risk Assessment (NGRA) method. Four different cell lines: A549, HCC1428, HepG2 and MCF7 were treated with BHT and a series of BHT analogs at 5 different concentrations, RNA was isolated from cell extracts and run on the L1000 gene array platform.  A  toxicogenomics-based assessment was performed by comparing BHT’s unique genomic signature to a large external database containing signatures of other compounds (including many known endocrine disruptors) to identify if any endocrine disruption-related modes of action (MoAs) are prevalent among BHT and other compounds with similar genomic signatures.  In addition, we performed a toxicogenomics-based structure activity relationship (SAR) assessment of BHT and a series of structurally similar analogues to understand if endocrine disruption is a relevant MoA for chemicals that are considered suitable analogs to BHT using the P&G read across framework (Wu et al., 2010).

The platform is GPL20573: Broad Institute Human L1000 epsilon
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20573

overall_design: Four different cell lines: A549, HCC1428, HepG2 and MCF7 were treated with BHT and 15 BHT analogs (16 chemicals/perturbagens) at 5 different concentrations: 50, 100, 250, 500 and 1000 µM for 6 hours in quadruplicate wells per dose. Detailed cell culture, plating, treatment and lysis protocols are described in https://assets.clue.io/resources/sop-cell.pdf. RNA was isolated from cell extracts and run on the L1000 gene array platform.   The data were processed through a computational system, that converts raw fluorescence intensities into differential gene expression signatures. The data at each stage of the pre-processing are available: Level 1 (LXB) - raw, unprocessed flow cytometry data from Luminex scanners. One LXB file is generated for each well of a 384-well plate, and each file contains a fluorescence intensity value for every observed analyte in the well. Level 2 (GEX) - gene expression values per 1,000 genes after deconvolution from Luminex beads. Level 3 (Q2NORM) - gene expression profiles of both directly measured landmark transcripts plus inferred genes. Normalized using invariant set scaling followed by quantile normalization. Level 4 (Z-SCORES) - signatures with differentially expressed genes computed by robust z-scores for each profile relative to control (PC relative to plate population as control; VC relative to vehicle control). Level 5 (SIG) consists of the replicates, usually 3 per treatment, aggregated into a single differential expression vector derived from the weighted averages of the individual replicates.   Raw data files can be analyzed at: https://github.com/cmap/cmapJ where the Broad Institute of MIT and Harvard provided the Connectivity Map software for Java to read and store lxb and GCTX files.

first: K


title: Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis I

summary: Bulk RNA-seq of adult liver endothelial cells after 12 days of Fli1 + Erg knockout and control

overall_design: Mice were intravital injected with VE-cadherin antibody. Tissues were dissociated by Collagenase Dispase digestion and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cels. Sorted endothelial cells were processed for RNA isolation using a Qiagen Mini Kit and RNA was sequenced.

last: Salinero


title: Epigenetic and pharmacological control of pigmentation via the SWI/SNF chromatin remodeling complex

city: TOLEDO

first: Ivana

middle: L.

last: de la Serna

address: 3000 Arlington Ave

department: Cell and Cancer Biology

institute: UNIV OF TOLEDO College of Medicine and Life Sciences

summary: Lineage-specific differentiation programs are activated by epigenetic changes in chromatin structure. Melanin-producing melanocytes maintain a gene expression program ensuring appropriate enzymatic conversion of metabolites into the pigment, melanin, and its transfer to surrounding cells. During neuroectodermal development, SMARCA4, the catalytic subunit of SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complexes, is essential for lineage specification. SMARCA4 is also required for development of multipotent neural crest precursors into melanoblasts, which differentiate into pigment-producing melanocytes. In addition to the catalytic domain, SMARCA4 and several SWI/SNF subunits contain bromodomains which are amenable to pharmacological inhibition. We investigated the effects of pharmacological inhibitors of SWI/SNF bromodomains on melanocyte differentiation. Strikingly, treatment of murine melanoblasts and human neonatal epidermal melanocytes with selected bromodomain inhibitors abrogated melanin synthesis and visible pigmentation. Using functional genomics, iBRD9, a small molecule selective for the bromodomain of BRD9, repressed pigmentation-specific gene expression. Depletion of BRD9 confirmed a requirement for expression of pigmentation genes in the differentiation program from melanoblasts into pigmented melanocytes and in melanoma cells. Chromatin immunoprecipitation assays showed that iBRD9 disrupts the occupancy of bromodomain containing 9 (BRD9) and the catalytic subunit SMARCA4. These data indicate that BRD9 promotes melanocyte differentiation and pigmentation whereas pharmacological inhibition of BRD9 is repressive.

overall_design: Samples include RNA from three independent samples of Melb-a cells that were treated with vehicle control (DMSO) or 10microMolar iBRD9 for 48 hours.


title: RNA-sequencing analysis to investigate genes regulated by CASZ1 in SH-SY5Y (SY5Y) cells.

first: Zhihui

last: Liu

address: 9000 rockville pike

institute: National Cancer Institute

summary: In this study we identified genes regulated by CASZ1b in SY5Y cells.

overall_design: In CASZ1b stably transfected SY5Y cells (SY5YtetCASZ1b), CASZ1b is tetracycline inducible. RNA was isolated from SY5YtetCASZ1b cells that treated with or without tetracycline (Tet) for 48 hr.

first: Carol

middle: J

last: Thiele


title: RNA-sequencing analysis to investigate genes regulated by CASZ1 in SK-N-AS (AS) cells.

summary: In this study we identified genes regulated by CASZ1b in SK-N-AS cells

overall_design: In the CASZ1b stably transfected SK-N-AS cells (AStetCASZ1b), CASZ1b expression is Doxcycline (Dox) inducible . RNA was isolated from AStetCASZ1b cells that treated with or without Dox for 48 hr


title: Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis [Liver_InVivo_ATACseq]

summary: Bulk ATACseq of mouse in vivo liver vascular Endothelial samples either control or Erg and Fli1 knock out.

overall_design: Mice were intravitally injected with VE-cadherin antibody. Tissues were dissociated by Collagenase Dispase digestion and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cells. Sorted endothelial cells were processed for ATAC-seq using the Zymo DNA Clean & Concentrator-5 kit and using NEBNext X2 MasterMix (New England Biolabs).

middle: M


title: Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis [Brain_InVitro_RNAseq]

summary: Bulk RNAseq of mouse in vitro brain samples either control or Erg and Fli1 double knocked out.

overall_design: Cultured brain ECs were labeled with VE-cadherin antibody. Cells were harvested using acutase and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cels. Sorted endothelial cells were processed for RNA isolation using a Qiagen Mini Kit and RNA was sequenced.


title: Pre-T cell receptor Self-MHC Sampling Restricts Thymocyte Dedifferentiation

city: Boston

first: Jonathan

middle: S.

last: Duke-Cohan

state: MA

address: 450 Brookline Avenue JF517

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Programming T lymphocytes to distinguish self from non-self is a vital, multi-step process arising in the thymus. Signalling through the pre-T cell receptor (preTCR), a CD3-associated heterodimer comprising an invariant pTα chain and a clone-specific β chain, constitutes a critical early checkpoint in thymocyte development within the αβ T-cell lineage. Recent work demonstrates that preTCRs arrayed on double negative (DN) thymocytes, like αβ TCRs appearing on double positive (DP) thymocytes, ligate peptides bound to MHC molecules (pMHC) on thymic stroma but via a different molecular docking strategy. Here we show the consequences of those distinctive interactions for thymocyte progression, using synchronized fetal thymic progenitor cultures differing in the presence or absence of pMHC on support stroma, determining single cell transcriptomes at key thymocyte developmental transitions. Although MHC negative stroma fosters αβ T lymphocyte differentiation, the absence of pMHC-preTCR interplay leads to deviant thymocyte transcriptional programming associated with de-differentiation. Highly proliferative DN and DP subsets with antecedent characteristics of T cell lymphoblastic and myeloid malignancies emerge.  Thus, in addition to fostering β chain repertoire broadening for subsequent αβ TCR utilization, preTCR-pMHC interaction limits cellular plasticity to facilitate normal thymocyte differentiation and proliferation that, if absent, introduces significant developmental vulnerabilities.

overall_design: Transcriptional profiling of early thymocytes developing in the presence or absence of peptide-MHC

first: Aoi

last: Akitsu

first: Robert

last: Mallis

first: Cameron

last: Messier

first: Patrick

middle: H

last: Lizotte

first: Wonmuk

last: Hwang

first: Matthew

last: Lang

first: Ellis

last: Reinherz


title: single cell RNA sequencing reveals cellular heterogeneity of DLE and SLE

city: changsha

first: zheng

last: meiling

state: Hunan

address: jiefang middle street

country: China

institute: central south university

summary: Lupus, a server and complex autoimmune disease, is clinically divided into cutaneous lupus erythematosus (CLE) which featured in skin damage, and systemic lupus erythematosus (SLE) which characterized in systemic multi-organ damage. The distinction of these two types of lupus is widely unknown. Here, we collected 23 skin biopsies of healthy control(HC), DLE (discoid lupus erythematosus, a main type of CLE) and SLE, separated epidermis and dermis and performed single cell RNA sequencing through microfluidics based 10x genomics system. Our results demonstrated larger numbers of immune cells infiltrated in skin lesions of DLE than SLE, which may help to distinguish them. Then, non-immune cells such as keratinocytes and fibroblasts were showed functions like immune cells. Moreover, ISGs(interferon stimulated genes), HSP70 coding genes were found to be overexpressed in multi expanded subclusters. Some biological progresses such as autophagy and neutrophil activation were enriched in expanded subclusters.

overall_design:
We collected totally 23 skin biopsies from 5 HC, 8 DLE patients and 10 SLE patients and separated epidermis and dermis. Finally, 14 epidermal single-cell suspensions (4 HC,5 DLE and 5 SLE) and 16 dermal single-cell suspensions (4 HC,5 DLE and 7 SLE) were successfully prepared for scRNA-seq by 10× genomics.
***Please note that raw data is not provided due to patient privacy concerns***

first: Z

last: Meiling

first: M

last: Xiaole

first: O

middle: Y

last: Lianlian

first: S

last: Yang

last: Wenhui

first: H

last: Zhi

last: Yi

first: W

last: Ruifang

first: R

last: Shijia

first: L

last: Hai

last: Wei

first: J

last: Hui

last: Shuang

last: Haijing

last: Sujie

last: Qianjin

last: Ming


title: Beneficial effects of mifepristone treatment in breast cancer patients selected by the progesterone receptor isoform ratio: Results from the MIPRA trial

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: Background: Preclinical data suggest that antiprogestins inhibit the growth of luminal breast carcinomas expressing higher levels of progesterone receptor isoform A (PRA) than isoform B (PRB). Thus, we designed a pre-surgical window of opportunity trial to determine the therapeutic effects of mifepristone in breast cancer patients selected by their high PRA/PRB isoform ratio (MIPRA; NCT02651844). Patients and Methods. Twenty patients bearing luminal breast carcinomas with PRA/PRB>1.5 (determined by Western blots), and PR ≥50%, naive from previous treatment, were included for mifepristone treatment (200 mg/day p.o.; 14 days). Core needle biopsies (CNB) and surgical samples were formalin-fixed for immunohistochemical studies, and others were snap-frozen to perform RNA-Seq, proteomics, and/or Western blots studies. Plasma mifepristone levels were determined by mass spectrometry. The primary endpoint was the comparison of Ki-67 expression pre- and post-treatment. Results: A 49.62% decrease in Ki-67 staining was registered in all surgical specimens compared to baseline (p=0.0003). Using the pre-specified response parameter (30% relative reduction) we identified 14/20 responders. Mifepristone induced gland differentiation, an increase in tumor-infiltrating lymphocytes, a decrease in hormone receptors and pSer118ER expression, and an increase in calregulin, p21, p15, and activated caspase3 expression. RNA-Seq and proteomics studies identified downregulated pathways related to cell proliferation and upregulation of those related to immune bioprocesses and extracellular matrix re-modeling pathways. Conclusion: Our results support the use of mifepristone in luminal breast cancer patients with high PRA/PRB ratios. The combined effects of mifepristone with estrogen receptor modulators deserves clinic evaluation in these patients, to improve endocrine treatment responsiveness.

overall_design: Eight patients bearing luminal breast carcinomas and naive from previous treatment, were treated with  mifepristone (200 mg/day p.o.; 14 days). Core needle biopsies (CNB) and surgical samples were  obtained from pre- and post-treatment respectivelly, and were snap-frozen to perform RNA-Seq.

first: Claudia

last: Lanari

first: Andrés

last: Elía


title: Cdk1-dependent phosphorylation of Clr4Suv39H controls a histone H3 methylation switch that is essential for gametogenesis

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Methylation of histone H3 at lysine 9 (H3K9) is a hallmark of heterochromatin that plays crucial roles in chromatin-dependent gene silencing and maintenance of genome stability by repressing repetitive DNA elements and recruiting downstream factors essential for faithful chromosome segregation. Fundamental principles of these processes have been elucidated in the fission yeast Schizosaccharomyces pombe (S. pombe), in which Clr4, the homologue of mammalian SUV39H, is the sole H3K9 methyltransferase. Although H3K9 methylation has been intensely studied in mitotic cells, occurrence and regulation during sexual differentiation remain largely unknown. Whether distinct H3 methylation states are relevant for gametogenesis is also not known. Here, using diploid S. pombe cells, we map H3K9 methylation genome-wide during the meiotic program and show that constitutive heterochromatin temporarily loses H3K9me2 and becomes H3K9me3 when cells exit mitosis and commit to the meiotic life cycle. Cells lacking the ability to tri-methylate H3K9 exhibit severe meiotic chromosome segregation defects, which does not occur in mitotic cells. Artificially increasing the affinity of the fission yeast heterochromatin protein 1 (HP1) homologue Swi6 towards H3K9me2 rescues chromosome segregation in the absence of H3K9me3. Thus, the H3K9me2 to H3K9me3 switch during early meiosis serves to retain Swi6 at centromeres, which is necessary for cohesin recruitment and kinetochore assembly. Finally, we show that the H3K9 methylation switch is regulated by differential phosphorylation of Clr4 by the cyclin-dependent kinase (CDK) Cdk1. Our results reveal how a highly conserved master regulator of the cell cycle regulates the specificity of the H3K9 methyltransferase and thereby controls the ratio of H3K9me2 to H3K9me3 to prevent unwanted gene silencing and to ensure faithful meiotic chromosome segregation. High degree of conservation of the proteins involved in our study and CDK-dependent phosphorylation of the mammalian SUV39H1 homologue suggest broad conservation of the mechanisms described here.

overall_design: To map H3K9me2 and H3K9me3 during the meiotic programm, fission yeast cells were synchronized for meiotic progression and the repressive histone marks as well as histone H3 was ChIP'ed in 1h intervals. Synchronicity of the meiotic cultures was checked by RNA-sequencing during the meiotic time course and analysis of expression of meiotic genes.  Furthermore, to assess the relationship of Swi6 binding and the degree of H3K9 methylation, Swi6 as well as Swi6Chp1-like-CD was ChIP’ed in the different clr4 backgrounds.

first: Tahsin

last: Kuzdere

first: Valentin

last: Flury

first: Vytautas

last: Iesmantavicius

first: Daniel

last: Hess

first: Marc

last: Bühler


title: Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis II

first: Sean

last: Houghton

summary: Bulk RNAseq of human donor MSCs control and with ERG/FLI1 overexpressed

overall_design: MSCs were introduced with ERG/FLI1 lentivectors or with empty control lentivector. Cells were cultured and passed for 3 weeks as described in the manuscript. Live control MSCs and Live VE-cadherin+ ERG/FLI1 MSCs were sorted for RNAseq analysis.

first: Tomer

last: Itkin

first: Jesus

last: Gomez Salinero

first: Shahin

last: Rafii


title: Estrogen related receptor alpha drives mitochondrial biogenesis and resistance to neoadjuvant chemoradiation in esophageal cancer

city: Amsterdam

first: Mark

last: Dings

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: Following exposure to chemoradiation, EAC cells increase their mitochondrial content and associated metabolic processes, which drives treatment resistance. Inhibition of this response using clinically applicable inhibitors of ESRRA in combination with (chemo)radiation shows promising anti-tumor activities and could be further developed for clinical use.

overall_design: We performed a transcriptomic assessment of pre- and post-treatment patient tissue samples by RNA-Seq, which was validated by immunohistochemistry. Cellular responses to chemoradiation were determined in patient-derived adherent tumor cell cultures exposed to an in vitro approximation of the CROSS regimen. Assessments of metabolic rewiring included bioinformatics, measurement of oxygen consumption and other metrics for mitochondrial fitness, transcriptomic analysis, fluorescence and electron microscopy. The identified metabolic pathway was then targeted by pharmacological and genetic tools in combination with (chemo)radiation in cell viability assays on adherent tumor cell cultures and organoids.

first: Amber

middle: P

last: van der Zalm

first: Maarten

last: Bijlsma


title: Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids

city: Ann Arbor

first: Christiane

last: Wobus

state: MI

address: 1150 West Medical Center Dr

institute: University of Michigan

summary: To investigate the effect of human norovirus infection on the trascriptome of intestinal enteroids in the presence of a Jak kinase inhibitor, Ruxolitinib

overall_design: We infected human intestinal enteroids in 3D upon differentiation and spontaneous polarity inversion in triplicate. Non infected samples were processed in parallel

first: Carmen

last: Mirabelli

first: Roberto

last: Cieza

first: Merritt

last: Gillilland

first: Justin

last: Colacino


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [Histone_modification]

city: Lebanon

first: Xiaofeng

last: Wang

address: 1 Medical Center Dr Rubin Building

institute: Dartmouth College

summary: The mechanism controlling the dynamic targeting of SWI/SNF has long been postulated to be coordinated by transcription factors (TFs), yet identifying and demonstrating the influence of different TFs has proven difficult. In this study we take a multi-omics approach to directly interrogate transient SWI/SNF interactors, chromatin targeting, and the plasticity of the resulting 3D epigenetic landscape. We utilized the novel proximity based labeling technique TurboID to identify the AP1 family as a critical interacting partner for endogenous SWI/SNF complexes. Validation through CUT&RUN profiling demonstrated SWI/SNF targeting enrichment at AP1 bound loci, and SWI/SNF – AP1 cooperation in chromatin targeting. Mapping of 3D chromatin structure via HiChIP revealed AP1-SWI/SNF dependent restructuring of promoter-enhancer architecture and generation of enhancer hubs, ultimately regulating transcription. Through direct interrogation of the SWI/SNF – AP1 interaction, we demonstrate a SWI/SNF functional dependency on AP1 mediated chromatin localization. We propose that pioneer factors such as AP1 bind and target SWI/SNF to inactive chromatin, where it restructures the genomic landscape into an active state through epigenetic rewiring spanning multiple dimensions.

overall_design: Time course CUT&RUN profiling of H3K4me, H3K4me3, H3K27Ac and H3K27me3 in inducible SMARCB1 G401 cell line


title: BCL7A-containing SWI/SNF/BAF complexes modulate mitochondrial bioenergetics during neural progenitor differentiation.

status: Public on Oct 15 2022

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1, Gebaeude 99

institute: DZNE, German Center for Neurodegenerative Diseases

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: CASZ1b regulates regional epigenetic modifications in neuroblastoma

city: Bethesda

first: Zhihui

last: Liu

summary: The restoration of CASZ1b in neuroblastoma cells (SY5Y) results in a re-establishment of enhancers.

overall_design: SY5Y cells stably transfected with tetracycline (Tet) inducible CASZ1b were treated or without Tet, then ChIP experiment was performed using anti-H3K27ac antibody and anti-RNA Pol II antibody.

first: Xiyuan

last: Zhang

first: Carol

last: Thiele


summary: Mammalian SWI/SNF/BAF chromatin remodeling complexes influence cell lineage determination. While the contribution of mammalian SWI/SNF/BAF complexes in neural progenitor cell (NPC) proliferation and differentiation has been reported, little is known about the transcriptional profiles that determine neurogenesis or gliogenesis. Here we report that BCL7A is a modulator of the SWI/SNF/BAF complex and stimulates the genome-wide occupancy of the ATPase BRG1. We demonstrate that BCL7A is dispensable for SWI/SNF/BAF complex integrity, whereas it is essential to regulate Notch/Wnt pathway and mitochondrial bioenergetics in differentiating NPCs. Together, our findings uncover the unique mechanistic contribution of BCL7A-containing SWI/SNF/BAF complex in mitochondria-driven NPC commitment, thereby providing a better understanding of the cell-intrinsic transcriptional processes that connect metabolism, neuronal morphogenesis and cognitive flexibility.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for SMARCA4/BRG1 in mouse and iPSC-derived BCL7A KO NPCs

first: Lena

last: Wischhof

first: Hang-Mao

last: Lee


title: Cooperative ETS Transcription Factors Enforce Adult Endothelial Cell Fate and Cardiovascular Homeostasis

first: Sean

last: Houghton


overall_design: RNA-seq in BCL7A KO versus wt neural progenitor cells


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [SWI_SNF complex]

first: Xiao feng

state: NH

address: 1 Medical Center Dr

overall_design: Time course CUT&RUN profiling of ARID1A, PBRM1 and BRD9 in inducible SMARCB1 G401 cell line


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [ATAC-Seq]

overall_design: Time course ATAC-seq profiling in inducible SMARCB1 G401 cell line


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [RNA-Seq]

overall_design: Time course RNA-seq profiling in inducible SMARCB1 G401 cell line


title: RvD1n-3 DPA downregulates transcription of pro-inflammatory genes in oral epithelial cells and reverses nuclear translocation of transcription factor p65 after TNF-α stimulation

status: Public on Oct 14 2022

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

summary: Specialized pro-resolving mediators (SPMs) are multifunctional lipid mediators that participate in the resolution of inflammation. We have recently described that oral epithelial cells (OECs) express receptors of the SPM resolvin RvD1n-3 DPA and that cultured OECs respond to the RvD1n-3 DPA addition by intracellular calcium release, nuclear receptor translocation and transcription of genes coding for antimicrobial peptides. The aim of the present study was to assess the functional outcome of RvD1n-3 DPA–signaling in OECs. under inflammatory conditions. To this end, we performed transcriptomic analyses of TNF-α-stimulated cells that were subsequently treated with RvD1n-3 DPA and found significant downregulation of pro-inflammatory nuclear factor kappa B (NF-κB) target genes. Further bioinformatics analyses also showed that RvD1n-3 DPA inhibited expression of several genes involved in the NF-κB activation pathway.  Immunofluorescence examination revealed that addition of RvD1n-3 DPA to OECs reversed TNF-α-induced nuclear translocation of NF-κB p65. Co-treatment of the cells with the exportin 1 inhibitor leptomycin B indicated that RvD1n-3 DPA increases nuclear export of p65. Unlike earlier cell cultural studies where SPMs are added before or together with the inflammatory stimulus, the present observations suggest that SPMs also have the potential to be used as a therapeutic aid when inflammation is established.

overall_design: Primary OECs isolated from gingival biopsies and cultured in KSFM were stimulated with TNF-α or vehicle (KSFM, containing <0.1% ethanol) for 30 min (5 % CO2, 37 °C), washed twice with PBS and then incubated with RvD1n-3 DPA (0.1 nM) or vehicle (KSFM, containing <0.1% ethanol) for 5 h (5 % CO2, 37 °C). For each of the four biological conditions (vehicle control, stimulation with TNF-alpha only, incubation with RvD1n-3 DPA only, stimulation with TNF-alpha + incubation with RvD1n-3 DPA) 4 biological replicates were collected.

first: Maria

middle: G

last: Balta

first: Olav

last: Schreurs

first: Rashi

last: Halder

first: Küntziger

last: Thomas

first: Frank

last: Sætre

first: Inger

last: Johanne Blix

first: Espen

middle: S

last: Bækkevold

first: Karl

last: Schenck


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [HiChIP]

first: Xiaofeng

last: Wang

overall_design: Time course HiChIP profiling of K27Ac and ARID1A in inducible SMARCB1 G401 cell line


title: Infection characteristics and transcriptomics of African swine fever virus in Bama mini-pigs

city: wuhan

first: Changjie

last: Lv

state: hubei

address: shizishan street

institute: huazhong agriculture university

summary: To analyse the host responses of Bama mini-pigs to ASFV infection, we chose the spleen and inguinal lymph nodes from Bama mini-pigs infected with ASFV at a dose of 103 HAD50 and the mock group for  transcriptomic analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for spleen and inguinal lymph nodes from Bama mini-pigs infected with ASFV at a dose of 103 HAD50 and the mock group

first: Jingyu

last: Yang

first: Zhong

last: Zou

first: Meilin

last: Jin


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [SWI_SNF_complex]


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes

address: 1 Medical Center Dr, Rubin Building

department: Molecular and Systems Biology

overall_design:
Refer to individual Series

The supplementary file CUT_RUN_peak.bed includes the peaks for all SWI/SNF subunits and AP-1 samples in SubSeries GSE175528 and GSE175532, and SubSeries GSE196955 and GSE196958 of SuperSeries GSE196960.


title: Genome-scale CRISPR screening in a single mouse liver

status: Public on Oct 16 2022

city: Cambridge

first: Kristin

last: Knouse

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

summary: This paper describes the development and implementation of genome-scale CRISPR screening in the mouse liver. As part of this study, RNA sequencing was performed on livers isolated from mice during development, adulthood, and regeneration to identify the entirety of genes expressed in the liver at each time point.

overall_design: Mouse livers were harvested at postnatal day 2, day 15, day 25, week 8, and 6, 12, 24, and 48 hours after partial hepatectomy or carbon tetrachloride injection. Livers from three male C57BL/6J mice were harvested for each time point.

middle: A


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [AP_1_family]

overall_design: Time course CUT&RUN profiling of pJUN, JUND and JUNB in inducible SMARCB1 G401 cell line


title: Qualifying a human Liver-Chip for predictive toxicology: Performance assessment and economic implications

first: Lorna

last: Ewart

address: 27 Drydock Avenue

institute: Emulate Inc.

summary: We assess RNA expression in human primary hepatocytes in Vials Day 0 and Liver-Chips on Day 3 and Day 7 for two different donors. The hepatocytes were co-cultured in Liver-Chip model with Kupffer cells and Liver sinusoidal endothelial cells (LSECs) and stellate cells .

overall_design: Global RNA expression profiles of Vials Day 0 and Liver-Chips Day 3 and Day 7 for two different donors, generated by deep sequencing using Illumina HiSeq 4000.

first: Dimitris

middle: V

last: Manatakis


title: Transcriptional profiling of Candida albicans SC5314, hgc1Δ and cph1Δ/efg1Δ in yeast-and hyphae-inducing conditions at two time points.

city: Jena

first: Enrico

last: Garbe

address: Albert-Einstein-Straße 10

department: (Epi-)Genetics of Fungal Infections

institute: HKI Jena

summary: Goal of this study was to determine metabolic adaptation processes in C. albicans associated to hyphal morphogenesis. Accessory to the metabolic profiling the corresponding transcriptome was investigated. To identify media-specific and general adaptation three different hyphae stimuli were used (M199 pH 7.4, Human serum and N-Aectylglucosamine) were used and compared again two respective yeast conditions (SD and M199 pH 4). Two filamentation-affected mutant strains were included - lacking either two central regulators of filamentation (cph1Δ/efg1Δ) or a downstream effector (hgc1Δ) - for the identification of specfic morphotype-dependent metabolic adaptation in repsonse to hyphae stimuli. Two different time points (90 min and 240 min after transition to test medium) were investigated to define the progression of the examined adaptation processes.

overall_design: C. albicans cells were cultivated in SD medium at 37°C until early log-phase was reached and transferred to the indicated medium, promoting either yeast or hyphae growth and incubated at 37°C for the indicated time.

first: Franziska

last: Gerwien

first: Dominik

last: Driesch

first: Tina

last: Müller

first: Bettina

last: Böttcher

first: Slavena

last: Vylkova


title: Developmental trajectories of thalamic nuclei revealed by single-cell transcriptome profiling and Shh perturbation

city: Philadelphia

first: Pablo

last: Camara

state: PA

address: 3700 Hamilton Walk

institute: University of Pennsylvania

summary: The thalamus is the principal information hub of the vertebrate brain, with essential roles in sensory and motor information processing, attention, and memory. The complex array of thalamic nuclei develops from a restricted pool of neural progenitors. We apply longitudinal single-cell RNA-sequencing and regional abrogation of Sonic hedgehog (Shh) to map the developmental trajectories of thalamic progenitors, intermediate progenitors, and post-mitotic neurons as they coalesce into distinct thalamic nuclei. These data reveal that the complex architecture of the thalamus is established early during embryonic brain development through the coordinated action of four cell differentiation lineages derived from Shh-dependent and independent progenitors. We systematically characterize the gene expression programs that define these thalamic lineages across time and demonstrate how their disruption upon Shh depletion causes pronounced locomotor impairment resembling infantile Parkinson’s disease. These results reveal key principles of thalamic development and provide mechanistic insights into neurodevelopmental disorders resulting from thalamic dysfunction.

overall_design: The thalamic primordia were micro-dissected from three embryos per control and SBE1/5 genotype according to anatomical landmarks at four developmental stages (E12.5, E14.5, E16.5, and E18.5) coinciding with peak periods of thalamic proliferation, neurogenesis, and differentiation (n=24 embryos in total).

first: Kiya

last: Govek

first: Sixing

last: Chen

first: Paraskevi

last: Sgourdou

first: Yao

last: Yao

first: Steven

last: Woodhouse

first: Tingfang

first: Mark

last: Fuccillo

first: Douglas

last: Epstein


title: Next Generation Sequencing  Quantitative Analysis of TEAD Inhibitors in NCI-H226 cells

city: Charlestown

first: Yang

last: Sun

address: 149 13th Street, CBRC 3050E

department: CBRC

institute: Massachusetts General Hospital

summary:
Purpose: The goal of this study is to understand the signaling pathway alteration in NCI-H226 cells treated with TEAD inhibitors.
Methods: Mesothelioma cell line NCI-H226 was chosen to be treated with TEAD inhibitors at 1μM for 24 hours. Total RNA was isolated for the analysis. RNA samples were sent to Novogen for library construction, RNA sequencing and raw data process.  Conclusions: Our study privides gene expression profiling evidence to validate TEAD inhibitors to block TEAD transcriptional activity in mesothelioma cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NCI-H226 cells treated with vehicle control and TEAD inhibitor TM2, K975 and VT103.

first: Xu

last: Wu

first: Lu

last: Hu


title: BCL7A-containing SWI/SNF/BAF complexes modulate mitochondrial bioenergetics during neural progenitor differentiation.

first: Daniele

last: Bano

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27me3 in mouse and iPSC-derived BCL7A KO NPCs

first: Lena

last: Wischhof

first: Hang-Mao

last: Lee


title: Excitatory dysfunction drives network and calcium handling deficits in 16p11.2 duplication schizophrenia iPSC-derived neurons

status: Public on Oct 13 2022

city: Chicago

first: Peter

last: Penzes

state: IL

address: 303 E. Chicago ave

department: Neuroscience

institute: Northwestern University

summary: Background - Schizophrenia (SCZ) is a debilitating psychiatric disorder with a large genetic contribution; however, its neurodevelopmental substrates remain largely unknown. Modeling pathogenic processes in SCZ using human iPSC-derived neurons (iNs) has emerged as a promising strategy. Copy number variations (CNV) confer high genetic risk for SCZ, with duplication of the 16p11.2 locus increasing risk 14.5 fold. Methods - To dissect the contribution of excitatory (iENs) versus GABAergic (iGNs) neurons to SCZ pathophysiology, we induced iNs from CRISPR-Cas9 engineered isogenic and SCZ patient-derived iPSCs, and analyzed SCZ-related phenotypes in iEN monocultures and iEN/iGN cocultures. Results - In iEN/iGN cocultures, we found reduced neuronal network firing rate and synchrony at later, but not earlier, stages of in vitro development. These were fully recapitulated in iEN monocultures, indicating a primary role for excitatory neurons. Transcriptomic analysis of isogenic 16p11.2 duplication (DUP) iENs revealed pathway dysregulation related to neuroarchitecture and calcium ion binding. Consistent with this, isogenic DUP iENs showed reduced dendrite length and calcium imaging revealed deficits in calcium handling. Analysis of iENs from 16p11.2 duplication-carrying SCZ patients (SCZ) revealed overlapping deficits in network synchrony, dendrite arborization and calcium handling. Conclusions - Our results indicate 16p11.2 duplication-dependent alterations to SCZ neurodevelopment. Calcium ion binding was the only altered transcriptomic gene set shared between isogenic and patient-derived iENs, suggesting a central role of calcium signaling in 16p11.2 duplication-mediated pathogenesis. Moreover, excitatory dysfunction during early neurodevelopment is implicated as the basis of SCZ pathogenesis in 16p11.2 duplication carriers and supports network synchrony and calcium handling as outcomes directly linked to this genetic mutation.

overall_design: Isogenic and patient-derived iPSC lines from control/healthy individuals and 16p11.2 duplication carriers were differentiated into iPSC derived neurons. Neurons developed for 7WIV, before mRNA extraction and RNA seqeuncing.

first: Euan

last: Parnell


title: Role of Scx in mouse

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

institute: Zhejiang University

overall_design: Refer to individual Series


title: ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data

first: Yi

last: Xing

address: 3501 Civic Center Blvd

department: Department of Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia

summary: Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read sequencing platforms poses a major challenge. We present ESPRESSO, a computational tool for robust discovery and quantification of transcript isoforms from error-prone long reads. ESPRESSO jointly considers alignments of all long reads aligned to a gene and uses error profiles of individual reads to improve the identification of splice junctions and the discovery of their corresponding transcript isoforms. On both a synthetic spike-in RNA sample and human RNA samples, ESPRESSO outperforms multiple contemporary tools in not only transcript isoform discovery but also transcript isoform quantification. In total, we generated and analyzed ~1.1 billion nanopore RNA-seq reads covering 30 human tissue samples and three human cell lines. ESPRESSO and its companion dataset provide a useful resource for studying the RNA repertoire of eukaryotic transcriptomes.

overall_design: Long-read sequencing (Oxford Nanopore, ONT) was used to profile full-length transcript isoforms in poly(A)-selected RNA extracted from HEK293T cells, PC3E cells, and GS689 cells, each with three replicates. Long-read sequencing was also used to examine full-length transcript isoforms in poly(A)-selected RNA extracted from 30 human tissues.

first: Yuan

last: Gao

first: Feng

last: Wang

first: Robert


title: Morphine Alters Systemic Responses to SIV Infection of Rhesus Monkeys and Changes Brain Macrophage and Microglia Gene Expression Favoring Neuropathogenesis

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

summary: In this study, we investigated longitudinal changes in response to SIV infection of rhesus monkeys in the presence of morphine, compared to animals administered saline, before and after cART treatment. Using single-cell and single-nucleus RNA sequencing (scRNA-seq and snRNA-seq), we examined the effect of morphine on brain-resident macrophages and microglia in these SIV-infected, cART-suppressed animals to better understand the factors responsible for the morphine-induced increased CNS reservoir and the role of opioids in neuropathogenesis.

overall_design: We probed systemic parameters as well as performed single-cell examination of the targets for infection in the brain, microglia and macrophages to investigate the interaction of morphine and SIV to identify novel host specific immune and neurological pathologies. Morphine treatment created an immunosuppressive environment, blunting initial responses to SIV infection which persisted during suppressive antiretroviral drug (ARV) therapy. ARV concentrations and penetration into the cerebrospinal fluid and brain were unchanged by morphine. However, in microglia and brain macrophages, their transcriptional signature was transformed to a neurodegenerative phenotype.

first: Howard

last: Fox

first: Brenda

last: Morsey

first: Shilpa

last: Buch


title: Single cell RNA-seq of limb cells from E12.5 WT and Scx-ko mice

summary: We used single-cell RNA sequencing and a gene knockout mice model to reveal the heterogeneity and differentiation trajectory of embryonic limb cell in both physiological and pathoplogical conditons.

overall_design: Wild type(WT) and Scx-/- limb cells derived from E12.5 mice were captured  on a  high-throughput IFC microfluidic Fluidigm C1 system.

first: Hongwei

last: Ouyang

first: Junxin

last: Lin


title: Differences in whole kidneys and renal F4/80+ macrophages in mice with the major and minor allele of the rs3184504 polymorphism after hypertension induction

city: Nashville

first: Matthew

last: Alexander

state: TN

address: 1211 Medical Center Drive

institute: Vanderbilt University Medical Center

summary: To determine differences in kidney and renal F4/80+ macrophage gene expression between mice homozygous for the Arg-encoding versus the Trp-encoding rs3184504 polymorphism after 4 weeks of angiotensin II infusion.

overall_design: Crispr-Cas9 was used to create mice homozygous for the Arg-encoding major allele and the Trp-encoding minor allele of the rs3184504 polymorphism. Kidneys and renal F4/80+ macrophages were isolated from these mice after 4 weeks of angiotensin II infusion to induce hypertension.

first: Meena

last: Madhur


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [AP_1 family]

first: Xiao feng

first: Xiaofeng


overall_design:
Refer to individual Series

The supplementary file CUT_RUN_peak.bed includes the peaks for all SWI/SNF subunits and AP-1 samples in SubSeries GSE196955 and GSE196958, and SubSeries GSE175528 and GSE175532 of SuperSeries GSE175534.


title: ID1 and CEBPA coordinate epidermal progenitor cell

city: Stockholm

first: Maria

last: Genander

address: Tomtebodavägen 16

department: Department of Cell and Molecular Biology

institute: Karolinska Institutet

summary: The regulatory circuits that coordinate epidermal differentiation during development are still not fully understood. Here we report that the transcriptional regulator ID1 is enriched in basal epidermal progenitor cells and find ID1 expression to be diminished upon differentiation. In utero silencing of Id1 impairs progenitor cell proliferation, leads to precocious delamination of targeted progenitor cells and enables differentiated keratinocytes to retain progenitor markers and characteristics. Transcriptional profiling suggests ID1 acts by mediating adhesion to the basement membrane while inhibiting spinous layer differentiation. Co-immunoprecipitation reveals ID1 binding to transcriptional regulators of the class I bHLH family. We localize bHLH Tcf3, Tcf4 and Tcf12 to epidermal progenitor cells during epidermal stratification and established TCF3 as a downstream effector of ID1-mediated epidermal proliferation. Finally, we identify crosstalk between CEBPA, a known mediator of epidermal differentiation, and Id1 and demonstrate that CEBPA antagonizes BMP-induced activation of Id1. Our work establishes ID1 as a key coordinator of epidermal development, acting to balance progenitor proliferation with differentiation and unveils how functional crosstalk between CEBPA and Id1 orchestrates epidermal lineage progression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary epidermal  cells comparing control (shScr) with Id1 silenced (shId1) with ID1 overexpression (ID1 dox) as progenitors or upon differentiation.

first: Wei

last: Yang

first: Christina

last: Kantzer


title: Peptide ligand-mediated trade-off between plant growth and stress response

city: Nagoya

first: Yoshikatsu

last: Matsubayashi

state: Aichi

address: Chikusa

department: Graduate School of Science

institute: Nagoya University

summary: The decision of whether to grow or to divert energy to stress response is a key physiological trade-off for plants seeking to survive under fluctuating environments. However, the cell-to-cell communication underlying this decision is largely unknown. Here we show that three orphan leucine-rich repeat receptor kinases (LRR-RKs) act as direct ligand-perceiving receptors for PSY-family peptides and play a key role in local switching between two opposing pathways. In contrast to the known LRR-RKs which activate signaling upon ligand binding, PSY receptor (PSYR) signaling, which intrinsically induces a stress response, usually is repressed by ligands to permit growth. Conversely, PSYRs activate the expression of various genes encoding stress response transcription factors upon depletion of the ligands. Loss of PSYRs resulted in defects in the plant’s tolerance to both biotic and abiotic stresses. This ligand-deprivation-dependent activation system enables plants to exert exquisitely tuned regulation of stress responses in the tissues proximal to metabolically dysfunctional damaged sites where ligand production is impaired.

overall_design: Genome-wide transcriptome analysis in roots of tpst-1 mutant, tpst/psyr1,2,3 quadruple mutant and PSY5 treated tpst-1 mutant. Transcriptome analysis in shoots of WT, tpst-1 mutant, psyr1,2,3 triple mutant, tpst/psyr1,2,3 quadruple mutant and PSY5 treated tpst-1 mutant.

first: Mari

last: Ogawa-Ohnishi

first: Tomohide

last: Yamashita

first: Mitsuru

last: Kakita

first: Takuya

last: Nakayama

first: Yuri

last: Ohkubo

first: Yoko

last: Hayashi

first: Yasuko

first: Taizo

last: Nomura

first: Saki

last: Noda

first: Hidefumi

last: Shinohara


title: Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP1 shapes 3D enhancer landscapes [SWI_SNF complex AP1 KD]

last: Wang

summary: The mechanism controlling the dynamic targeting of SWI/SNF has long been postulated to be coordinated by transcription factors (TFs), yet identifying and demonstrating the influence of different TFs has proven difficult. In this study we take a multi-omics approach to directly interrogate transient SWI/SNF interactors, chromatin targeting, and the plasticity of the resulting 3D epigenetic landscape. We utilized the novel proximity based labeling technique TurboID to identify the AP1 family as a critical interacting partner for endogenous SWI/SNF complexes. Validation through CUT&RUN profiling demonstrated SWI/SNF targeting enrichment at AP1 bound loci, and SWI/SNF – AP1 cooperation in chromatin targeting. Mapping of 3D chromatin structure via HiChIP revealed AP1-SWI/SNF dependent restructuring of promoter-enhancer architecture and generation of enhancer hubs, ultimately regulating transcription. Through direct interrogation of the SWI/SNF – AP1 interaction, we demonstrate a SWI/SNF functional dependency on AP1 mediated chromatin localization. We propose that pioneer factors such as AP1 bind and target SWI/SNF to inactive chromatin, where it restructures the genomic landscape into an active state through epigenetic rewiring spanning multiple dimensions.

overall_design: Time course CUT&RUN profiling of ARID1A, PBRM1 and BRD9 in inducible SMARCB1 G401 cell line under the condition of AP-1 KD


title: Self-organizing in vitro mouse neural tube organoids mimic embryonic development

status: Public on Oct 12 2022

city: Lausanne

first: Matthias

last: Lütolf

address: AI 1208 Station 15

department: Sciences de la vie

institute: EPFL

summary: Self-elongating neural tube organoids recapitulate key aspects of the morphology, anterior-posterior patterning, neural crest emergence and neural differentiation of mouse embryo in vivo by self-organization. We used single-cell RNA sequencing (scRNA-seq) to analyse the cell types and to reveal the sequence of transcriptional events in the emergence of neural crest cells and neural differentiation.

overall_design: 10x single-cell RNA-seq of mouse neural tube organoids at day 6 (in duplicates), 7, 8, and 10.

first: JiSoo

last: Park

first: Hao-An

last: Hsiung

last: Lutolf


title: Mesenchymal stem cell-laden matrigel microspheres printing enables large skin wound regeneration

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Province

address: nanshan street

institute: Tsinghua University

summary: High cell density Matrigel beads (HDB)  were printinto onto large skin wounds (10 mm and 15 mm). Compared with acellular beads printing, HDB group could achieve more efficient injury regeneration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse skin cells under different treatment.

first: Yuanxiong

last: Cao


title: Transcriptomic profiling of peripheral blood mononuclear cells in sarcoidosis and matched controls in A Case Controlled Etiologic Study of Sarcoidosis (ACCESS)

first: Christian

last: Ascoli

address: 840 S Wood Street, Room 920-N CSB

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

institute: University of Illinois at Chicago

summary:
Introduction:
In sarcoidosis, peripheral lymphopenia and anergy have been associated with increased inflammation and maladaptive immune activity, likely promoting development of chronic and progressive disease. However, the molecular mechanisms that lead to reduced lymphocyte proportions, particularly CD4+ T-cells, have not been fully elucidated. We posit that paradoxical peripheral lymphopenia is characterized by a dysregulated transcriptomic network associated with cell function and fate that results from altered transcription factor targeting activity.

Methods:
Messenger RNA-sequencing (mRNA-seq) was performed on peripheral blood mononuclear cells (PBMCs) from ACCESS study subjects with sarcoidosis and matched controls and findings validated on a sarcoidosis case-control cohort and a sarcoidosis case series. Preserved PBMC transcriptomic networks between case-control cohorts were assessed to establish cellular associations with gene modules and define regulatory targeting involved in sarcoidosis immune dysregulation utilizing weighted gene co-expression network analysis and differential transcription factor involvement analysis. Network centrality measures identified master transcriptional regulators of subnetworks related to cell proliferation and death. Predictive models of differential PBMC proportions constructed from ACCESS target gene expression corroborated the relationship between aberrant transcription factor regulatory activity and imputed and clinical PBMC populations in the validation cohorts.

Results:
We identified two unique and preserved gene modules significantly associated with sarcoidosis immune dysregulation. Strikingly, increased expression of a monocyte-driven, and not a lymphocyte-driven, gene module related to innate immunity and cell death was the best predictor of peripheral CD4+ T-cell proportions. Within the gene network of this monocyte-driven module, TLE3 and CBX8 were determined to be master regulators of the cell death subnetwork. A core gene signature of differentially over-expressed target genes of TLE3 and CBX8 involved in cellular communication and immune response regulation accurately predicted imputed and clinical monocyte expansion and CD4+ T-cell depletion.

Conclusions:
Altered transcriptional regulation associated with aberrant gene expression of a monocyte-driven transcriptional network likely influences lymphocyte function and survival. Although further investigation is warranted, this indicates that crosstalk between hyperactive monocytes and lymphocytes may instigate peripheral lymphopenia and underlie sarcoidosis immune dysregulation and pathogenesis. Future therapies selectively targeting master regulators, or their targets, may mitigate dysregulated immune processes in sarcoidosis and disease progression.

overall_design: Examination of PBMC gene expression comparing treatment naive cases of sarcoidosis to matched controls from the ACCESS study.

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