title: Characterize compounds that affect V(D)J recombination and chromsomal translocation using MP-HTGTS

city: Stanford

first: Jinglong

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

summary: V(D)J recombination represents a vital mechanism responsible for generating antibodies and T-cell receptors (TCR). This intricate process encompasses various stages, such as chromatin looping, RAG1/2 incision, end processing, and ligation. In our study, we conducted extensive screening using a diverse array of drugs from the FDA-approved list. Our primary objective was to gain insights into the impact of these drugs on V(D)J recombination and to elucidate potential side effects associated with their use. Notably, among the drugs examined, HDAC inhibitors stood out as they appeared to modulate V(D)J recombination initiation by potentially regulating upstream events. This investigation contributes valuable information to our understanding of how pharmaceutical agents may influence the intricate process of V(D)J recombination and highlights the distinctive role played by HDAC inhibitors in this context.

overall_design: Various murine proB cells including WT and Ku70-/-  were arrested by STI-571 to induce V(D)J recombination, the V-J recombination in IgK locus were systematically captured using all four JK1 coding end as bait by HTGTS.

middle: L

last: Frock


title: Synthetic reversed sequence reveals default chromatin states [mESC_Chip-seq]

status: Public on Dec 30 2023

city: New York

first: Brendan

middle: R.

last: Camellato

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

country: USA

institute: NYU Langone Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Most of human genome may show evidence of transcription, yet annotated transcripts account for less than 5%. The basis for this major discrepancy is not clear, and it remains uncertain whether excess transcription is functional, or simply a byproduct of pervasive, non-specific RNA polymerase binding and transcription initiation. Understanding the default state of the genome would be informative in determining whether the observed pervasive activity is functional. The genome of any extant organism has undergone billions of years of evolution, making it unclear whether any observed genomic activity, or lack thereof, has been selected for. We sought to address this question by introducing a completely novel 101 kb locus into the genomes of two eukaryotic organisms, S. cerevisiae and M. musculus, and characterizing its genomic activity based on chromatin accessibility, chromatin states, and transcription. The locus was designed by reversing, but not complementing, the sequence of the human HPRT1 locus, including ~30 kb of both upstream and downstream regulatory regions, allowing retention of sequence features like repeat frequency and GC content but ablating coding information and transcription factor binding sites. We also compared this reversed locus with a synthetic version of the normal human HPRT1 locus in both organismal contexts. Neither the synthetic HPRT1 locus nor its reversed version evolved to harbor yeast promoters. Nevertheless, we observed widespread transcriptional activity of both loci in yeast, and this pervasive activity was observed both when the loci were present as episomes and when chromosomally integrated. In the latter case, it was obvious that the accessibility and level of transcription initiation substantially exceeded that of the flanking native yeast genome sequences. In contrast, when integrated in the mouse genome, the synthetic HPRT1 locus showed transcriptional activity corresponding precisely to the HPRT1 coding sequence, whereas the reverse locus displayed no activity at all, but was instead actively repressed by Polycomb machinery. Together, these results show that novel genomic sequences lacking coding information are active in yeast, but repressed in mouse stem cells, indicating a major difference in default genomic states between these two divergent eukaryotes, with implications for understanding pervasive transcription and the birth of new genes.

overall_design: Exploratory RNA-seq was performed to investigate whether synthetic HPRT1 and HPRT1R sequences are transcribed in mouse embryonic stem cells, and to compare to the rest of the respective genome.

middle: R

first: Ran

last: Brosh

first: Hannah

middle: J

last: Ashe

first: Matthew

middle: T

last: Maurano

first: Jef

middle: D

last: Boeke


title: Synthetic reversed sequence reveals default chromatin states [mESC_ATAC-seq]

overall_design: Exploratory ATAC-seq was performed to investigate whether synthetic HPRT1 and HPRT1R sequences are accessible in mouse embryonic stem cells, and to compare to the rest of the respective genome.


title: Mapping the human diabetic methylome

status: Public on Dec 31 2023

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

type: Methylation profiling by high throughput sequencing

summary: Using methyl CpG binding domain capture and deep sequencing (MBD-seq) we examined white blood cells isolated from individuals with or without diabetic complications and non-diabetic controls. Sample where obatined from the Finnish Diabetic Nephropathy Study (FinnDiane)

overall_design: Profling differences in genome-wide DNA methylation between diabetics/non-diabetics and diabetics with or without complications

first: Ishant

last: Khurana

first: Mark

last: Ziemann

first: Anna

last: Syreeni

first: Antony

last: Kaspi

first: Carol

last: Forsblom

first: Per-Henrick

last: Groop


title: Synthetic reversed sequence reveals default chromatin states [Yeast_ATAC-seq]

overall_design: Exploratory ATAC-seq was performed to investigate whether synthetic HPRT1 and HPRT1R sequences are accessible in yeast, and to compare to the rest of the respective genome.


title: Synthetic reversed sequence reveals default chromatin states [mESC_RNA-seq]

type: Expression profiling by high throughput sequencing


title: Impact of Tet inhibition by Bobcat339 on gene expression of porcine parthenogenetic embryos

city: Wuhan

first: fan

last: chen

state: Hubei

address: Nanhu Av. 4

country: China

institute: Hubei Academy of Agricultural Sciences

summary: To explore the effects of Tet on porcine  pre-implantation embryogenesis, we utilized  Bobcat339, a specific small-molecule inhibitor of the Tet protein, to treat parthenogenetic 4-cell stage embryos.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and 50 µM Bobcat339 4-cell embryos.

first: Fan

last: Chen

first: Yan

middle: Z

last: Bi


last: Wang

state: California

address: 269 Campus Drive

institute: Stanford Medicine

summary: Chromosome translocation plays a crucial role in the development of tumors, but its underlying biological mechanisms, especially in human cells, remain poorly understood. In this study, we aimed to shed light on the mechanisms governing chromosome translocation in K562 cells. To investigate this, we initiated the process by inducing two double-strand breaks (DSBs) using Cas9 sgRNA and subsequently quantified the frequency of chromosome translocation events. Furthermore, we explored the influence of several compounds by introducing them alongside the DSBs, allowing us to assess their impact on chromosome translocation. Our research unveiled the identification of two noteworthy compounds, HDAC inhibitors and HSP90 inhibitors, which were found to significantly enhance the occurrence of chromosome translocation. These findings contribute to a deeper understanding of the molecular processes involved in tumorigenesis and provide potential targets for future therapeutic interventions.

overall_design: We induced DNA double-strand breaks (DSBs) using CRISPR-Cas9 technology in  K562-derived cell line K562-Bcl2. These cell lines were subjected to different treatment conditions. To capture translocation events, we utilized one of the DSB site RAG1L as a bait, which allowed us to detect its ligation with the remaining DSB site(s) using high-throughput genome translocation sequencing (HTGTS) in microplate.

first: Richard


title: Synthetic reversed sequence reveals default chromatin states [Yeast_RNA-seq]

overall_design: Exploratory RNA-seq was performed to investigate whether synthetic HPRT1 and HPRT1R sequences are transcribed in yeast, and to compare to the rest of the respective genome.


title: Synthetic reversed sequence reveals default chromatin states

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

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: Refer to individual Series


title: Single-cell transcriptome depicts the molecular dynamics of synapse formation in mouse hippocampus

city: Beijing

last: Wei

address: Haidian District, Beijing Summer Palace Road No. 5

institute: Peking University

summary: Synapses are asymmetric junctions between presynaptic and postsynaptic neurons that mediate information transfer in the brain. The proper formation of functional synapses is crucial for synaptic transmission and brain function. However, how neurons initially recognize each other to form synapses remain to be elucidated. Here, we performed single-cell RNA sequencing of the cultured hippocampal  cells on the critical time points during synapse development. . We first built comprehensive single-cell transcriptomic atlas of hippocampus undergoing synapse formation. Furthermore, we focused on neurons, and systematically analyzed temporal dynamic functional transcription factors hubs.. We identified that transcription factors, such as EGR family genes, AP-1 family genes, NeuroD family genes, NF1 family genes, may act as key regulators of synapse formation. Besides, we provided the resources of increased membrane and secretory proteins associated with synapse formation, which including previously reported synapse formation genes, Nlgn3, Nectin1, Dag1, Snap25, and the newly identified potential genes, Tmem65, Grm5, Olfm1, Timp3. Finally, we analyzed the changes of cell communication signaling pathways in neurons before and after synapse formation, and identified several important signaling pathways, including NRXN, NCAM, BMP, NEGR, and so on. Collectively, our work provided a holistic view of the molecular dynamics of the hippocampal synapse formation.

overall_design: Single cells were sorted and used for 10x Genomics scRNA seq analyses across four key development time points days in vitro (DIV) 1,3,5,7.

first: Mengping

first: Chao

last: Zhang

first: Wei

last: Tao

first: Chen


title: YTHDF2 promotes DNA damage repair by positively regulating the histone methyltransferase SETDB1 in spermatogonia

city: yangling

first: guo

last: ming

state: shanxi province

address: 22 Xinong Road, Yangling Demonstration Zone, Yangling District, Xianyang City

department: College of Animal Science and Technology

institute: Northwest Agriculture & Forestry University

summary:
we reported that in the absence of YTHDF2, spermatogonia showed significantly enhanced sensitivity to etoposide and promoted apoptosis, demonstrating that the importance of YTHDF2 in the etoposide-responsive DNA damage response (DDR). Multiple modifications involved in the DDR, some of which recruit repair factors to the sites of DNA damage.
N6-methyladenosine (m6A) as a crucial component of the DNA damage repair system responding to DNA lesions. Meanwhile, H3K9me3 has been implicated in DDR, which provides site for DDR factors binding to DNA lesion. Importantly, ablation of Ythdf2 reduced SETDB1 and H3K9me3 levels, and SETDB1 overexpression qualitatively suppressed the DNA damage associated with YTHDF2 loss.

overall_design: transcriptome analysis of GC1 spermatagonia cells; 3 replicates each: WT, Ythdf2-ko, Ythdf2-ko-OE-CTR, Ythdf2-koOE-setdb1

first: Ming

last: Guo

first: Xueliang

last: li


title: Amyloid driven clonally expanded CD8+ effector memory T cells infiltrate Alzheimer’s disease bigenic mouse models

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: Gross Hall, 845 Health Sciences Rd

institute: University of California, Irvine

summary: Alzheimer’s Disease (AD) is the most common cause of age-related dementia and the sixth leading cause of death in the United States. AD neuropathology is primarily characterized by the accumulation of extracellular beta-amyloid (Aβ) plaques and intraneuronal neurofibrillary tau tangles. In addition to these hallmark AD pathologies, many other important pathological changes occur in the brains of AD patients, including synaptic and neuronal loss and neuroinflammation. Most recently, genome-wide association studies (GWAS) have provided substantial new evidence that immune dysfunction may contribute to the development and progression of AD. To date over 60 GWAS loci have been identified and almost two thirds of these genes are highly expressed in microglia, the resident innate immune cell of the brain. These genetic discoveries have in turn inspired many new studies of microglial biology and the role of these cells in AD. In contrast, the role of the adaptive immunity in AD remains understudied, despite evidence that many of AD risk genes are also highly expressed in T and B cells. To investigate the role of T cell infiltration in AD, we examined T cells from immune-deficient AD mice via bone marrow transplantation studies using flow cytometry and immunohistochemistry; and from immune-intact transgenic AD model mice using flow cytometry, immunohistochemistry, and single-cell RNA sequencing. Our experiments demonstrate that multiple T cell subtypes infiltrate the AD brain, and that effector memory CD8 T cells are specifically enriched in response to Aβ pathology or a combination of Aβ and tau pathologies. Single-cell sequencing analysis revealed high expression of over 40 AD risk genes between several T cell sub-populations, implying a need for more research of these T cell phenotypes in AD development. Additionally, T-cell receptor (TCR) sequencing revealed increased clonal expansion of T cells from mice that developed Aβ pathology or Aβ and tau pathology, suggesting amyloid-driven recruitment and clonal expansion of T cells in these mice. Ultimately, this study demonstrates the crucial importance of investigating the role of T cells in AD and provides a guide for future experiments to continue to enhance our understanding of AD immunology.

overall_design: Single cell RNA and TCR sequencing of T cells from the brains of 9-month-old female WT, 5XFAD, PS19, and PS-5X mice. Each sample contains a pool of T cells from multiple mice of the same sex and genotype. The WT and 5XFAD genotypes have 2 samples (2 separate pools) and the PS19 and PS-5X genotypes have 1 sample (1 pool).

first: Jessica

last: Sanchez

first: Jaclyn

last: Beck

first: Sepideh

last: Kiani Shabestari

first: Samuel

middle: E

last: Marsh

first: Laura

last: McIntyre

first: Vanessa

middle: M

last: Scarfone

first: Pauline

middle: U

last: Nguyen

first: Erika

middle: S

last: Varady

first: Jorge

last: Silva

first: Christel

last: Claes

first: Joia

last: Capocchi

first: Jean

last: Chadarevian

first: Alina

last: Lahian

first: Matthew

last: Inlay

first: Craig

last: Walsh

first: Hayk

last: Davtyan


city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

summary: Integrated multiomics (scATACseq and scRNAseq) of 2D10 cells treated with small molecules for 24hrs.

overall_design: 2D10 latent HIV clone of Jurkat cells were treated with the indicated inhibitors for 24 hours and processed for simultaneous scRNA seq and ATACseq using the 10x genomics multiomic approach; 10x genomics product#1000285. Alignment was performed with cellranger-arc v2.0.1

first: Ashokkumar

last: Manickam

first: Jackson

last: Peterson

first: David

last: Margolis

first: Yuchao

last: Jiang


title: Intermediate filaments are regulators organismal lifespan in C. elegans

city: Chongqing

first: Yuxi

last: Dai

address: Daxuecheng west street, Huxi town, Shapingba

institute: Chongqing university

summary:
Purpose: Try to find out whether germline loss retards the normal somatic aging
Methods: Employed transcriptome analysis in both young and aged germline-deficient animals and identified genes that are normally decreased during aging in wild-type (WT) worms but are well maintained in aged germline-deficient animals
Results: Compared with D1, there were 1834 genes downregulated at D6, while only 441 genes showed increased expression

overall_design: Wild type Caenorhabditis elegans and glp-1 mutants are 25°C-cultivated  to the D1 adult , and keep at 20°C  to D6. Then  total mRNA profiles were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000

first: Haiqing

last: Tang


title: YTHDF1 facilitates PRC1 mediated H2AK119ub   in Human ES Cells

city: Guangzhou

first: Jingyuan

last: Zhang

address: 190 Kaiyuan Avenue,Science Park

institute: Guangzhou National Labratory

summary: Polycomb repressive complexes( PRCs) play critical role in cell fate decisions during normal development as well as disease progression through mediate histone modifications such as H3K27me3 and H2AK119ub. How exactly PRCs recruited to chromatin remains to be fully illuminated. Here, we report that YTHDF1, a N6-methyladenine (m6A) RNA reader previously known being mainly cytoplasmic, associates with RNF2, a PRC1 protein that mediates H2AK119ub in human embryonic stem cells (hESCs).  Specifically, a portion of YTHDF1 localizes in the nuclei and associates with RNF2/ H2AK119ub on a subset of gene loci related to neural development functions. Knock-down YTHDF1 attenuates H2AK119ub modification on these genes and promotes neural differentiation in hESCs. Our findings provide another non-canonical mechanism of YTHDF1 to participate in PRC1 mediated chromatin modification in hESCs.

overall_design: We compared  H2AK119ub ChIP-seq signal intensities in YTHDF1 KD and WT human ESCs.

first: Tianyu

last: Wang

first: Guangjin

last: Pan


title: YTHDF1 facilitates PRC1 mediated H2AK119ub in Human ES Cells

summary: Polycomb repressive complexes( PRCs) play critical role in cell fate decisions during normal development as well as disease progression through mediate histone modifications such as H3K27me3 and H2AK119ub. How exactly PRCs recruited to chromatin remains to be fully illuminated. Here, we report that YTHDF1, a N6-methyladenine (m6A) RNA reader previously known being mainly cytoplasmic, associates with RNF2, a PRC1 protein that mediates H2AK119ub in human embryonic stem cells (hESCs). Specifically, a portion of YTHDF1 localizes in the nuclei and associates with RNF2/ H2AK119ub on a subset of gene loci related to neural development functions. Knock-down YTHDF1 attenuates H2AK119ub modification on these genes and promotes neural differentiation in hESCs. Our findings provide another non-canonical mechanism of YTHDF1 to participate in PRC1 mediated chromatin modification in hESCs.

overall_design: We compared the YTHDF1, RNF2 binding sites and H2AK119ub modified sites in WT human ESCs by CHIP-seq. Meanwhile we also compared  YTHDF1 signal in YTHDF1 KD and WT human ESCs by ChIP-seq. ChIP-seq experiments were performed in two biological replicates, and ChIP-seq Replicates were merged into one BED file.


title: miRNA-Seq of MEF cells with or without Fbxw7 knock out

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

type: Non-coding RNA profiling by high throughput sequencing

summary: This study describes the transcriptome profiling of MEF cells with or without Fbxw7 knock out

overall_design: miRNA-Seq profiling on of MEF cells with or without Fbxw7 knock out. WT profiling compare with knock out can get specific gene expression profiling related to Fbxw7 in MEF cells.

first: Yi

last: Sun


title: Genome-wide distribution of MLL4, H3K4me1 and H3K4me3 in MEF cells

summary: The MLL4,H3K4me1 and H3K4me3 levels are compared with or without the fbxw7 KO in MEF cells

overall_design: Cut & Run profiling of MLL4, H3K4me1 and H3K4me3 with or without the fbxw7 KO in MEF cells


title: An integrative mRNA and ncRNA analysis of human carotid atherosclerosis

first: chuanjue

last: cui

address: No.167th Beilishi Road, Xicheng District

department: Division of Dyslipidemia, State Key Laboratory of Cardiovascular Disease,

institute: Fu Wai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Atherosclerosis (AS) is the underlying pathological process of severe cardiovascular or cerebrovascular diseases, whereas the molecular and cellular complexity of AS remains poorly elucidated. We here compared the expression of mRNA, lncRNA, circRNA in peripheral white blood cells (PWBCs) from carotid atherosclerotic plaque (CAP)-positive patients and CAP-negative controls through mRNA, lncRNA, and circRNA microarrays. A total of 552 mRNAs, 1,296 lncRNAs and 667 circRNAs were altered in the pathogenesis of AS.

overall_design:
mRNA, lncRNA, circRNA expression in peripheral white blood cells (PWBCs) from carotid atherosclerotic plaque (CAP)-positive patients and CAP-negative controls

**Submitter states that raw data cannot be uploaded until approved by the Human Genetic Resources Center of China**

first: Chuanjue

last: Cui

first: Jian

middle: j

last: Li


title: Transcriptional regulation of hematopoietic stem cell progenitors and acute myeloid leukemia by the IRE1a-XBP1 pathway

first: Akanksha

last: Verma

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptional regulation of hematopoietic stem cell progenitors and acute myeloid leukemia by the IRE1a-XBP1 pathway [KO]

summary: The inositol-requiring enzyme-1a (IRE1a), through its key effector transcription factor X-box binding protein-1 (XBP1), regulates cell fate and malignancy in a tissue and cell-specific manner. Here, we define the transcriptional perturbations associated with IRE1a deficiency in normal murine hematopoieitic stem cell (HSC) progenitors and HSC progenitors expressing Flt3 internal tandem duplication (FLT3-ITD) allele, a myeloid leukemia oncogne. Beyond its classical role in activating genes involved in restoring cellular proteostasis during the unfolded protein response (UPR), our transcriptome analysis reveal XBP1-dependent regulation of genes involved in diverse biological processes required for HSC homeostasis and acute myeloid leukemia (AML) development.

overall_design: Transcriptome of normal and Flt3-ITD expressing hematopoietic cells from murine bone marrow (BM) were determined using TruSeq Stranded mRNA Libraries. The complete data set contains a total of 24 samples comprising triplicates of Lin-Sca1+cKit+ (LSK) and granulocyte-macrophage progenitors (GMP) from the following mouse genotypes: wildtype (WT), Flt3-ITD (ITD), Ern1(fl/fl)-VavCre (IRE1_KO) and Ern1(fl/fl)-VavCre-Flt3-ITD (IRE1_KO_ITD).

first: Olivier

last: Elemento

first: Laurie

last: Glimcher

first: Stanley

last: Adoro


title: Transcriptional regulation of hematopoietic stem cell progenitors and acute myeloid leukemia by the IRE1a-XBP1 pathway [overexpression]

summary: The inositol-requiring enzyme-1a (IRE1a), through its key effector transcription factor X-box binding protein-1 (XBP1), regulates cell fate and malignancy in a tissue and cell-specific manner. Here, we define the transcriptional perturbations associated with induction of XBP1 (encoded by the XBP1S gene generated by IRE1a) eficiency in patient derived human AML cells. Beyond its classical role in activating genes involved in restoring cellular proteostasis during the unfolded protein response (UPR), our transcriptome analysis reveal XBP1-dependent regulation of genes involved in diverse biological processes required for HSC homeostasis and acute myeloid leukemia (AML) development.

overall_design: Transcriptome of two patient-derived human AML cells (#41 and #88) transduced with control lentivirus (in triplicates, C1, C2 and C3) or XBP1 (X1, X2 and X3) were determined using TruSeq Stranded mRNA Libraries. The complete data set contains a total of 12 samples


title: RNA-Seq analysis of the TB-019 GSK M72/AS01E trial

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

summary: This project involves RNA-Seq analysis of samples obtained from the Phase IIA clinical trial TB-019 (NCT01669096) which evaluated kinetics of response, safety, and immunogenicity of the GSK Mycobacterium tuberculosis (MTB) vaccine M72/AS01E (“GSK M72”).  GSK M72 consists of the M72 recombinant fusion of Mycobacterium tuberculosis (MTB) proteins Rv0125 and Rv1196 in combination with the liposome, TLR4 ligand (MPL), and QS21 saponin adjuvant AS01E (Leroux-Roels et al., 2013).

overall_design: This project  involved sample collection from 18 according-to-protocol subjects that were vaccinated twice with 10μg M72/AS01E.  Responses were measured at three time points in PBMC , with the majority of measurements being made early after the 2nd dose of the vaccine.   The  analyses will be performed on  RNA samples collected from all eighteen subjects at the D0, D31, and D37 time points.  Altogether, 54 samples were analyzed.

first: Smitha

last: Shankar


title: Transcriptome of MEF cells with or without Fbxw7 knock out

overall_design: RNA-Seq profiling on of MEF cells with or without Fbxw7 knock out. WT profiling compare with knock out can get specific gene expression profiling related to Fbxw7 in MEF cells.


title: Induction of lung progenitor cell-like organoids by porcine pluripotent stem cells

status: Public on Dec 29 2023

city: Yangling

first: Xinchun

last: Yang

state: shannxi

address: No. 3, Taicheng Road

institute: Northwest A&F University

summary: Organoids are in vitro 3D models that are generated using stem cells to study organ development and regeneration. Despite the extensive research on lung organoids, there is limited information on pig lung cell generation or development. Here, we identified five epithelial cell types along with their characteristic markers using scRNA-seq. Additionally, we found that NKX2.1 and FOXA2 acted as the crucial core transcription factors in porcine lung development. The presence of SOX9/SOX2 double positive cells was identified as a key marker for lung progenitor cells. The Monocle algorithm was used to create a pseudo-temporal differentiation trajectory of epithelial cells, leading to the identification of signaling pathways related to porcine lung development. Moreover, we established the differentiation method from porcine pluripotent stem cells (pPSCs) to SOX17+FOXA2+ definitive endoderm and NKX2.1+FOXA2+CDX2- anterior foregut endoderm (AFE). The AFE are further differentiated into lung organoids while closely monitoring the differentiation process. We showed that NKX2.1 overexpression facilitated the induction of lung organoids and supported subsequent lung differentiation and maturation. This model offers valuable insights into studying the interaction patterns between cells and the signaling pathways during the development of the porcine lung.

overall_design: In order to study the process of porcine pluripotent stem cells inducing lung progenitor organoids, we selected four differentiation stages: pluripotent stem cells,  definitive endoderm, anterior foregut endoderm and lung progenitor organoids for RNA-SEQ

first: Xiaolong

last: Wu

first: Yuqi

first: Wenhao

first: Xiaojie

first: Liming

last: Yuan

first: Taiyong

last: Yu

first: Shiqiang

first: Jinlian

last: Hua


title: Effect of SIgA amplification on epithelial cells of small intestine during anti-PD-L1 immunotherapy treatment [Epithelial_cells_RNAseq]

city: Bellinzona

first: Fabio

last: Grassi

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine

summary: The gut microbiota is essential for many aspects of host physiology, and locally generated secretory IgA (SIgA) modulates its function. Microbiota community determines the efficacy of immune checkpoint blockade (ICB) in cancer immunotherapy. Extracellular ATP (eATP) released by the microbiota restricts the SIgA repertoire by limiting T follicular helper (Tfh) cells activity in the Peyer’s Patches (PPs) via stimulation of ionotropic P2X7 receptor. Here we show that SIgA amplification by oral administration of the ATP hydrolysing enzyme apyrase corrects enteropathic features of ICB and improves the therapeutic outcome.

overall_design: Epithelial cells were sorted as Zombie- EPCAM+CD45- from the ileum of MC38 tumor-bearing mice treated with anti-PD-L1 or in combination with apyrase at day 12 after tumor injection


title: MLL4, H3K4me1 and H3K4me3 Cut&Run in MEF cells; transcriptome of MEF cells with or without Fbxw7 knock out

first: Fengbiao

last: Mao

overall_design: Refer to individual Series


title: RNA chip expression profiling analysis of HGC-27 cells after oxymatrine intervention, Agilent Human ceRNA Microarray 2019 (4*180k, Design ID: 086188) chip

first: Zhengsen

last: Jin

address: Chaoyang District North Third Ring Road East No.11

institute: Beijing University of Chinese Medicine

summary:
In this study, we intervened HGC-27 cells with oxidized sophoridine alkaloid (OMT) at a concentration of 2.64 mg/mL for a duration of 48 hours. Subsequently, we conducted comprehensive chip expression profiling analysis on these intervened HGC-27 cells as well as normal HGC-27 cells, encompassing mRNA, lncRNA, and circRNA. We employed the Agilent Human ceRNA Microarray 2019 (4*180k, Design ID: 086188) chip for the expression profiling.
To ensure analysis reliability, we quantified the total RNA of samples initially and then assessed the integrity of RNA using Agilent Bioanalyzer 2100 (Agilent Technologies). Following RNA quality inspection, we followed a standardized procedure to label the samples and hybridize them with the chips, followed by elution. The labeling process involved reverse transcription of total RNA into double-stranded cDNA, followed by synthesis of cRNA labeled with Cyanine-3-CTP (Cy3). After hybridization of labeled cRNA with the chips, we used the Agilent Scanner G2505C (Agilent Technologies) for scanning to obtain raw images.
In the data processing phase, we employed the Feature Extraction software (version 10.7.1.1, Agilent Technologies) to process the raw images and extract data. Subsequently, we performed quantile normalization on the raw data to ensure data consistency. Following normalization, we filtered the data, ensuring that at least 75% of probes from each group of samples were detected, and these retained probes were used for subsequent comparison and analysis.
In essence, our study culminated in a comprehensive exploration of gene expression dynamics, regulatory RNA elements, and their potential roles in the context of HGC-27 cells under the influence of OMT intervention.

overall_design:
This was an in vitro study with two experimental groups:
HGC-27 cells treated with 2.64 mg/mL oxidized sophoridine alkaloid (OMT) for 48 hours (intervention group)
Untreated HGC-27 cells (control group)
Each group had 3 biological replicates for a total of 6 samples.
Comprehensive RNA expression profiling was performed on all samples using the Agilent Human ceRNA Microarray 2019 (4*180k, Design ID: 086188). Total RNA quality and integrity were assessed before labeling and hybridization to the microarray chips. Raw image data was processed and normalized before statistical comparisons between the intervention and control groups were made to identify differentially expressed mRNAs, lncRNAs, and circRNAs.


title: Rigor and Reproducibility of Acoustofluidics of saliva from healthy donors

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

summary: This is for Rigor and Reproducibility study to demonstrate the reproducibility of AFS SOP for EV separation, RNA isolation, and RNA analysis by using saliva samples from healthy individuals. Blinded saliva samples have been processed by two independent AFS operators for EV separation and subjected to miRNA-seq analysis. EV-associated miRNA seqeunces were used as a monitoring tool for Rigor and Reproducibility of AFS process between operators.

overall_design: Saliva samples from healthy volunteers (5 female and 5 male) were collected based on our research SOP and split into two fractions for AFS analysis by two independent operators. Resulting two AFS fractions (waste and collected) per sample per operator were blinded and sent to UCSD for miRNA-seq analysis. Resulting sequencing data have been analyzed for the statistical evaluation of Rigor and Reproducibility in AFS separation of EV’s. This has been determined by evaluating the statistical difference in miRNA’s existing in EV’s separated from each sample by two independent operators.

first: David

last: Wong

first: Tony

last: Huang

first: Yong

last: Kim

first: Louise

last: Laurent

first: Jianping

last: Xia

first: Abbas

last: Hakim


title: Next Generation Sequencing of transcriptomes in GFP+-HSCs sorted from bone marrow of mice receiving HSCs subjected to control RNA or miR-31-5p inhibitor treatment.

first: Wenbin

last: Zhong

address: No.601, West Huangpu Avenue

institute: Jinan University

summary:
Purpose: The goals of this study is to uncover the difference of transcriptomes that are essential for HSCs malignant transformation driven by miR-31-5p inhibition.
Methods: GFP+-HSCs sorted from bone marrow mRNA profiles of mice receiving HSCs subjected to control RNA or miR-31-5p inhibitor treatment were generated by deep sequencing, using Illumina NovaSeq 6000 sequencer for 318 cycles.Reads that passed the Illumina quality filters were kept for the subsequent analyses. Adapters were trimmed from the reads, and reads shorter than 17 nt were discarded. The reads were mapped to the Mouse mRNA reference database using FANSe3 algorithm on Chi-Cloud NGS Analysis Platform (Chi-Biotech Co. Ltd., Shenzhen, China).
Results: We use edgeR to analysis with a |log2 (FoldChange)| > 1 and p value <0.01. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to promote HSCs malignant driven by miR-31-5p inhibition.
Conclusions: Our study represents the first detailed analysis of transcriptomes that promote T-cell malignant transformation driven by HTVL-1 oncogene Tax.

overall_design: Examination of transcriptomes in GFP+-HSCs sorted from bone marrow of mice receiving HSCs subjected to control RNA or miR-31-5p inhibitor treatment.


title: Single-Cell RNA-Seq Analysis of Patient Myeloid-Derived Suppressor Cells and the Response to Inhibition of Bruton’s Tyrosine Kinase

city: Columbus

first: William

last: Carson III

state: OH

address: 420 W 12th ave

institute: The Ohio State University

summary: Myeloid-derived suppressor cell (MDSC) levels are elevated in cancer patients and contribute to reduced efficacy of immune checkpoint therapy. MDSC express Bruton’s Tyrosine Kinase (BTK) and BTK inhibition with ibrutinib, an FDA-approved irreversible inhibitor of BTK, leads to reduced MDSC expansion/function in mice and significantly improves the anti-tumor activity of anti-PD-1 antibody treatments. Single-cell RNA sequencing (scRNA-seq) was used to characterize the effect of ibrutinib on gene expression of FACS-enriched MDSC from patients with different cancer types (breast, melanoma, head and neck squamous cell cancer - HNSCC). Melanoma patient MDSC were treated in vitro for 4h with 5 µM ibrutinib or DMSO, processed for scRNA-seq using the Chromium 10x Genomics platform, and analyzed via the Seurat v4 standard integrative workflow. Baseline gene expression of MDSC from breast and HNSCC cancer patients revealed similarities among the top expressed genes.  In vitro ibrutinib treatment of MDSC from melanoma patients resulted in significant changes in gene expression. GBP1, IL 1β and CXCL8 were among the top downregulated genes while RGS2 and ABHD5 were among the top upregulated genes (p<0.001). double positive CD14+CD15+ MDSC and PMN-MDSC responded similarly to BTK inhibition and exhibited more pronounced gene changes when compared to early MDSC and M-MDSC.  Pathway analysis revealed significantly downregulated pathways including TREM1, nitric oxide signaling, and IL 6 signaling (p<0.004). ScRNA-seq revealed characteristic gene expression patterns for MDSC from different cancer patients.  BTK inhibition led to the downregulation of multiple genes and pathways important to MDSC function and migration.  Myeloid-derived suppressor cell (MDSC) levels are elevated in cancer patients and contribute to reduced efficacy of immune checkpoint therapy. MDSC express Bruton’s Tyrosine Kinase (BTK) and BTK inhibition with ibrutinib, an FDA-approved irreversible inhibitor of BTK, leads to reduced MDSC expansion/function in mice and significantly improves the anti-tumor activity of anti-PD-1 antibody treatments. Single-cell RNA sequencing (scRNA-seq) was used to characterize the effect of ibrutinib on gene expression of FACS-enriched MDSC from patients with different cancer types (breast, melanoma, head and neck squamous cell cancer - HNSCC). Melanoma patient MDSC were treated in vitro for 4h with 5 µM ibrutinib or DMSO, processed for scRNA-seq using the Chromium 10x Genomics platform, and analyzed via the Seurat v4 standard integrative workflow. Baseline gene expression of MDSC from breast and HNSCC cancer patients revealed similarities among the top expressed genes.  In vitro ibrutinib treatment of MDSC from melanoma patients resulted in significant changes in gene expression. GBP1, IL 1β and CXCL8 were among the top downregulated genes while RGS2 and ABHD5 were among the top upregulated genes (p<0.001). double positive CD14+CD15+ MDSC and PMN-MDSC responded similarly to BTK inhibition and exhibited more pronounced gene changes when compared to early MDSC and M-MDSC.  Pathway analysis revealed significantly downregulated pathways including TREM1, nitric oxide signaling, and IL 6 signaling (p<0.004). ScRNA-seq revealed characteristic gene expression patterns for MDSC from different cancer patients.  BTK inhibition led to the downregulation of multiple genes and pathways important to MDSC function and migration.

overall_design: Whole blood was collected from one patient with stage IV head & neck squamous cell carcinoma, one patient with breast cancer, and two patients with advanced melanoma (one with stage IIID and one stage IIIA disease).

first: Himanshu

last: Savardekar


title: Gene expression profile at single cell level of tumor-infiltrating immune cells from mice treated with anti-PD-L1+E.colipBAD28 vs anti-PD-L1+E.colipApyr [CD45positive_TILs_scRNAseq]

overall_design: CD45+ cells were immediately sorted from MC38 tumor-bearing mice treated with anti-PD-L1+E.colipBAD28  or anti-PD-L1+E.colipApyr at day 18 from tumor injection and analyzed using scRNA-seq


title: Integrated single-cell multiomic analysis of HIV latency reversal reveals novel regulators of viral reactivation

status: Public on Dec 28 2023

first: Yuchao

last: Jiang

address: 3101 McGavran-Greenberg Hall

institute: University of North Carolina at Chapel Hill

summary: Despite the success of antiretroviral therapy, HIV cannot be cured because of a reservoir of latently infected cells that evades therapy. To understand the mechanisms of HIV latency, we employed an integrated single-cell RNA-seq/ATAC-seq approach to simultaneously profile the transcriptomic and epigenomic characteristics of ~125,000 latently infected primary CD4 cells after reactivation using three different latency-reversing agents.

overall_design: Latent CD4D6 cells were treated with HIV latency reversal agents (SAHA/VOR, prostratin, and iBET151) and control (DMSO) for 24 hours and processed for scRNA-seq and scATAC-seq by the 10X Genomics Multiome ATAC + Gene Expression protocol.

first: Manickam

last: Ashokkumar

first: Wenwen

last: Mei

first: Jackson

last: peterson

last: Margolis

first: Edward

last: Browne


title: RAGE/SNAIL signaling drives Epithelial-Mesenchymal plasticity in metastatic Triple-Negative Breast Cancer

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

summary:
Epithelial-Mesenchymal plasticity plays a fundamental role both in embryogenesis and in tumor cell dissemination during tumor progression. The receptor for advanced glycation end products (RAGE) is a driver of cell plasticity in fibrotic diseases; however, its role and molecular mechanism in triple-negative breast cancer (TNBC) remains unclear. Here, we demonstrate that RAGE signaling maintains the mesenchymal phenotype of aggressive TNBC cells by enforcing the expression of SNAIL. We uncover a crosstalk mechanism between the TGF-β and RAGE pathways that is required for the acquisition of mesenchymal traits in TNBC cells. Consistently, RAGE inhibition elicits epithelial features that block migration and invasion capacities.
Since RAGE is a sensor of the tumor microenvironment (TME) and the highly glycolytic rate of tumors induces an acidic TME, we modeled acute acidosis in TNBC cells and showed it promotes enhanced production of RAGE ligands and the activation of RAGE-dependent invasive properties. Furthermore, acute acidosis increases SNAIL levels and tumor cell invasion in a RAGE-dependent manner. Finally, we demonstrate that in vivo inhibition of RAGE reduces metastasis incidence and expands survival, consistent with molecular effects that support the relevance of RAGE signaling in EMT plasticity. These results uncover new molecular insights on the regulation of EMT phenotypes in cancer metastasis and provide rationale for pharmacological intervention of this signaling axis.

overall_design: Gene expression profiling analysis of RNA-seq data to identify genes over and under-expressed in MDA-MB-231 cells treated with/or without DMSO or Azeliragon (AZ). Three replicates of each condition were performed.

first: Josep

last: Villanueva

first: Mireia

last: Pujals


title: CSGALNACT2 Restricts Ovarian Cancer Migration and Invasion by Modulating MAPK/ERK Pathway through DUSP1

city: shanghai

first: Ma

last: mingjun

address: Shanghai First Maternity and Infant Hospital一妇婴保健院

institute: Tongji University

summary: Abstract Purpose Ovarian cancer is one of the leading causes of cancer-related death among women. CSGALNACT2 is a vital Golgi transferase and is related to a variety of human diseases. However, its expression pattern and function in ovarian cancer remain uncertain.   Methods The Cancer Genome Atlas and GEPIA databases were used to assess the expression of CSGALNACT2 in ovarian cancer patients. RNA-seq, qRT-PCR, and IHC were used to verify the expression of CSGALNACT2 in ovarian cancer tissues. Then, in vivo and in vitro experiments were conducted to evaluate the role of CSGALNACT2 in the progression of ovarian cancer. RNA-seq and GSEA were used to reveal the potential biological function and oncogenic pathways of CSGALNACT2.  Results We demonstrated that the mRNA expression and protein level of CSGALNACT2 were significantly downregulated in ovarian cancer and ovarian cancer metastatic tissues. CSGALNACT2 can significantly inhibit the migration, invasion, and clonogenic growth of ovarian cancer in vitro and is progressively lost during ovarian cancer progression in vivo. CSGALNACT2 suppresses ovarian cancer migration and invasion via DUSP1 modulation of the MAPK/ERK pathway through RNA-seq, KEGG analysis, and Western blotting. Moreover, CSGALNACT2 expression was correlated with immune cell infiltration and had prognostic value in different immune cell-enriched or decreased ovarian cancer. In addition, patients with CSGALNACT2 downregulation are less likely to benefit from immunotherapy.  Conclusion As an ovarian cancer suppressor gene, CSGALNACT2 inhibits the development of ovarian cancer, and it might be used as a prognostic biomarker in patients with ovarian cancer.

first: Mingjun

last: Ma

first: Chao

last: Wang

first: Meixuan

last: Wu

first: Sijia

last: Gu

first: Jiani

last: Yang

first: Yue

last: Zhang

first: Shanshan

last: Cheng

first: Shilin

last: Xu

first: Minghai

first: Yongsong

first: Yaqian

last: Zhao

first: Xiu

last: Tian

first: Dominic

middle: C

last: VOON

first: Jindan

last: Sheng

first: Yu


title: Muscle transcriptome analysis of Duroc x Luchuan crossed pigs with extreme phenotypes of intramuscular fat content using RNA sequencing

first: xuewen

last: xu

address: Shizishan street, No.1

institute: Huazhong Agricultural University

summary: Intramuscular fat (IMF) content is the determining factor for meat taste. To reveal the genetic basis of IMF content, genetic studies have made some progress in lean-type pig breeds, but fewer studies have been conducted in Chinese fat-type pigs. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality. In the present study, we measured the IMF content for 265 crossed pigs of Duroc x Luchuan pigs, from which individuals with extremely high (6.03% ± 0.58%, n = 12) and low (1.67% ± 0.42%, n = 12) IMF contents were selected to identify differentially expressed genes (DEGs) related to IMF content in the longissimus dorsi. RNA sequencing for 24 samples in total identified 312 differentially expressed transcripts that were significantly enriched in triglyceride biosynthesis- and metabolism-related processes (p-value ≤ 0.05 and fold change ≥ 1.5). Functional enrichment analysis revealed that the PPAR signaling pathway was the most significantly enriched pathway (p-value = 0.024, represented by ADIPOQ, FABP3, FABP4, LPL, PLIN4 and SCD). When a more stringent condition was applied (gene-based q-value ≤ 0.2 and fold change ≥ 1.5), only 17 transcripts remained to be differentially expressed, including LEP, ATP6V1F, SDR16C5, TUSC5, MPZ, PRX, PTPN4, BEX1, MVB12B, ZFP62, P4HA2, IDH2, THOC7, KRT14, FCGRT, MYPN and LPL. Among these DEGs, TUSC5 was significantly upregulated in the group of high IMF contents (log2FC = 1.114, p-value = 3.02E-5) and was suspected as a strong new candidate gene affecting porcine IMF content since it was the target gene of PPAR-gamma. The present study provided new data and candidate genes for the genetic study of porcine IMF content.

overall_design: Transcriptome sequencing in longissimus dorsi muscle of 24 pigs from the crossing of 8 Duroc boars and 112 Luchuan sows

first: Huan

last: Long

first: Tingting


title: MicroRNA profiling of royal jelly extracellular vesicles and their potential role in cell viability and reversing cell apoptosis

city: Daejeon

first: Islam

last: Saadeldin

address: Dehak ru

country: South Korea

institute: Chungnam National University

summary: We provide a detailed analysis of miRNA in the royal jelly nanovesicles.

overall_design: Royal jelly were collected three times (n=3) and diluted 10 times with phosphate-buffered saline (PBS). Royal jelly exosomes were isolated through commercial kits and used for RNA extraction and sequencing.

first: Jongki

last: Cho

first: Sanghoon

last: Lee

first: Seonggyu

last: Bang


title: TRAIP suppresses bladder cancer progression by catalyzing K48-linked polyubiquitination of MYC

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary: Tumor necrosis factor (TNF) receptor-associated factor (TRAF)-interacting protein (TRAIP), a RING domain-containing E3 ligase, has emerged as a key player in safeguarding genome integrity and is closely linked to cancer. Here, we discovered that TRAIP exhibits low expression in bladder cancer (BLCA), which correlates with poor prognosis. TRAIP exerts inhibitory effects on bladder cancer cell proliferation and migration both in vitro and in vivo. MYC serves as a newly identified target for TRAIP, with direct interaction leading to the promotion of K48 polyubiquitination at K428/430 lysine residues, subsequently resulting in proteasome-dependent degradation and downregulation of MYC's transcriptional activity. This process effectively hinders the progression of bladder cancer. Restoration of MYC expression rescues the suppressed proliferation and migration of bladder cancer cells induced by TRAIP. Furthermore, our investigation also demonstrates that MYC binds to the transcriptional start region of TRAIP, exerting regulatory control over TRAIP transcription. Consequently, this interaction establishes a negative feedback loop that prevents excessive expression of MYC. In summary, our study uncovers a novel mechanism by which TRAIP inhibits the progression of bladder cancer through the ubiquitinated degradation of MYC.

overall_design: To investigate the downstream mechanism of TRAIP regulation of bladder cancer, we performed RNA sequencing on three repeated siNC and siTRAIP-treated T24 cells.

first: Jingtian

last: Yu

first: Xinghuan

last: Wang


title: 16S V3-V4 -based microbial profiling of stool, skin and saliva  samples of patients affected by systemic sclerosis (SSc)

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Systemic sclerosis (SSc) is a complex and still unclear rare disease associated with fibrosis in multiple organs. Microbiota has recently emerged as an important environmental factor in SSc pathogenesis, either at gut, oral and skin level.

sample_organism:
human skin metagenome
human saliva metagenome
human feces metagenome

overall_design: DNA extraction from stool, skin and saliva samples collected from 26 patients affected by SSc, generatoin of amplicons of the variable V3–V4 region of the bacterial 16S rRNA gene and  paired-end  sequencing (2 × 300 cycles) on the Illumina MiSeq platform.


title: Concerted epithelial and stromal changes during progression of Barret’s Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis

status: Public on Dec 27 2023

city: Montreal

first: Lorenzo

last: Ferri

state: Quebec

address: 1650 Cedar Avenue

department: Surgery & Oncology

country: Canada

institute: McGill University

summary: Esophageal adenocarcinoma arises from Barrett’s esophagus, a precancerous metaplastic replacement of squamous by columnar epithelium in response to chronic inflammation. Multi-omics profiling, integrating single-cell transcriptomics, extracellular matrix proteomics, tissue-mechanics and spatial proteomics of 64 samples from 12 patients’ paths of progression from squamous epithelium through metaplasia, dysplasia to adenocarcinoma, revealed shared and patient-specific progression characteristics. The classic metaplastic replacement of epithelial cells was paralleled by metaplastic changes in stromal cells, ECM and tissue stiffness. Strikingly, this change in tissue state at metaplasia was already accompanied by appearance of fibroblasts with characteristics of carcinoma-associated fibroblasts and of an NK cell-associated immunosuppressive microenvironment. Thus, Barrett’s esophagus progresses as a coordinated multi-component system, supporting treatment paradigms that go beyond targeting cancerous cells to incorporating stromal reprogramming.

overall_design: We performed single cell RNA sequencing (scRNA-seq) on adjacent normal (gastritis), metaplastic, dysplastic, or cancerous stomach tissues from 5 patients with gastric cancer.

first: Michael

middle: K

last: Strasser

first: David

last: Gibbs

first: Haig

last: Djambazian


title: Coagulation Factor XIII-Binding Aptamers as Bivalent Ligands Targeting Fibrin and Activated Platelets in the Thrombus

city: Taoyuan

first: Kai Wen

last: Cheng

address: 259 Wen-Hwa 1st Road, Kwei-Shan

department: Physiology and Pharmacology

country: Taiwan

institute: Chang Gung University

summary: Thromboembolic diseases are commonly associated with thrombus-induced ischemia and tissue damage; identification of the location of the thrombus, or thrombus-targeting, may facilitate diagnosis and target therapy. We hypothesized that aptamers with high affinity and specificity for coagulation factor XIII (FXIII) can serve as thrombus-targeting probes. With systematic evolution of ligands by exponential enrichment technology and semi-activated FXIII (FXIII’) as the target, guanine-rich FXIII’-binding aptamers (FAs; 76 nt) were selected from a library of single-stranded DNA. Next generation sequencing identified FAs with the highest frequency; bio-layer interferometry revealed a dissociation constant (Kd) from 0.7 to 2.5 nM. Truncation with preservation of a conserved region based on entropy analysis resulted in three truncated FAs (FATs; 41-47 nt) that exhibited 4-fold signal in binding to activated vs. resting platelets, as determined by flowcytometry. In addition, FAT2  exhibited up to 4.2-fold binding of that from scrambled ssDNA to platelet/fibrin clot or whole blood clot in vitro, suggesting binding to both activated plateltes and fibrin. FAT2 also exhibited targeting effects in a microcirculatory thrombosis model in mice. Nevertheless, FATs induced no effect on blood coagulation, as determined by thromboelastometry. In conclusion, FXIII-binding aptamers are potentially amenable to thrombus targeting in theranostic application of thromboembolic diseases.

overall_design: To development FXIII-targeting aptamer for thrombus imaging

first: Kai-Wen

first: Ching-Ping

last: Tseng

first: Yu-Shiuan

last: Tzeng

first: Wei-Shan

last: Fu

first: Hsuan

last: Liu

first: Guang-Wu

last: Chen

first: Hsiang-Ruei

last: Liao

first: Yunn-Hwa

last: Ma


title: Microarray analysis of LncRNAs expression in metastatic Head and Neck Squamous Cell Carcinoma (HNSCC) and non-metastatic HNSCC tissues

city: Beijing

first: Yujia

address: 22 Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

summary: Analysis of different LncRNA expression in 4 paired metastatic HNSCC and non-metastatic HNSCC samples

overall_design: Metastatic HNSCC vs non-metastatic HNSCC

first: Lingfei

last: Jia


title: Gene expression profiles of MLL-AF9 leukemia cells in C57BL/6 mice and Rag2-/- mice

city: Tokyo

first: Susumu

last: Goyama

address: 4-6-1 Shirokanedai, Minato-ku

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

summary: The relative importance of T/B lymphocytes and NK cells during acute myeloid leukemia (AML) progression has been unclear. In this study, we compared gene expression profiles of mouse AML cells expressing MLL-AF9 collected from  immunologically normal wild-type (WT) C57BL/6 mice, Rag2-/- mice lacking mature T and B cells, and NSG mice lacking T, B and NK cells.

overall_design: MLL-AF9 leukemia cells coexpressing GFP were transplanted into immunologically normal C57BL/6 mice, Rag2-/- mice lacking mature T and B cells, and NSG mice lacking T, B and NK cells. GFP+ leukemia cells were collected from bone marrow and isolated using cell sorter before RNA extraction.

first: Emi

last: Sugimoto


title: Insights into molecular mechanisms of skin color variation in hybrid F1 of wild-type rainbow trout ♂ × yellow mutant rainbow trout ♀ through whole transcriptome and ceRNA network analysis

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

summary: Rainbow trout (Oncorhynchus mykiss) is a well-known economical fish globally, and its market value and acceptance are greatly influenced by skin color. However, the molecular mechanisms underlying skin color variation in rainbow trout remains largely unknown. In this study, we compared the expression profiles of whole transcriptome in dorsal skin from wild-type (WTrt) and yellow mutant rainbow trout (YMrt) that are F1 generation of WTrt ♂ × YMrt ♀. A total of 115 differentially expressed (DE) mRNAs, 126 lncRNAs, 18 circRNAs and 56 miRNAs were identified, and several core genes (gch1, pts, slc2all, pax7a/pax7b, dgat2, plin6 and pnpla2)   involved in pteridine and carotenoid synthesis were significantly upregulated in YMrt. Interestingly, we found that melanogenesis-related genes tyr, dct, mitfa and pmel were also notably elevated in YMrt. Functional enrichment analysis revealed some pigmentation-related GO terms and KEGG pathways, including pteridine-containing compound biosynthetic process, pigment metabolic process, melanosome, melanosome transport, tyrosine metabolism and melanogenesis. Based on competing endogenous RNA analysis, there were 25 and 21 lncRNA-miRNA-mRNA networks targeted to gch1 and mitfa, such as LOC110496571-miR-96-x-gch1, LOC110508587- miR-182-x-gch1, LOC110494316-miR-21-y-mitfa and LOC110526055- miR-182-x-mitfa. Additionally, one (novel_circ_000056), eight (including novel_circ_005436 and novel_circ_005586) and three circRNAs (novel_circ_000382, novel_circ_002592 and novel_circ_005868) were found to regulate dgat2, gch1 and mitfa by targeting 21 miRNAs. This study provides a systematic perspective on the potential functions of these DEmRNAs and ncRNAs, and lays a foundation for further study on the molecular mechanisms governing rainbow trout skin color variation.

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: Gene expression profiles of newly generated MLL-AF9 leukemia cells and aggressive MLL-AF9 leukemia cells generated through serial transplantations.

summary: Immunogenicity of acute myeloid leukemia (AML) keeps changing during tumor evolution, showing a trend that the aggressive AMLs generate through serial transplantations are susceptible to NK cell-mediated tumor suppression. To access molecular differences between the newly developed AML cells  and aggressive AML cells generated through serial transplantations, we performed RNA-seq using newly generated mouse AML cells trasduced with MLL-AF9, and the aggressive MLL-AF9 cells obtained after 5 times serial transplantations in the non-irradiated recipient mice.

overall_design: Newly generated or aggressive MLL-AF9 leukemia cells coexpressing GFP were transplanted into C57BL/6 mice. GFP+ leukemia cells were collected from bone marrow and isolated using cell sorter before RNA extraction.

first: Jingmei

last: Li

first: Wenyu

last: Zhang


title: Lymph Node Stromal Cell Responses to Perinatal T Cell Waves, A Temporal Atlas

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

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

overall_design: Refer to individual Series


title: Small RNA-seq Reveals Key microRNAs Involved in Cell Differentiation Arrest in Acute Myeloid Leukemia

city: Weifang

first: Wenxia

last: Su

address: No 7166, Baotong West Street

institute: Weifang Medical University

summary: MicroRNAs(miRNAs) are a class of small non-coding RNAs that have been shown to play a crucial role in normal hematopoiesis and leukemogenesis. In this study, we aimed to identify key miRNAs relevant to differentiation arrest in acute myeloid leukemia (AML). Next-generation small RNA sequencing (RNA-seq) was performed on paired bone marrow samples from 5 AML patients at initial diagnosis and first complete remission (CR). Differentially expressed miRNAs (DEMs) at initial diagnosis as compared to CR were analyzed for each case.

overall_design: Bone marrow samples were obtained from 5 AML patients at initial diagnosis and complete remission, and total RNA was extracted from the mononuclear cells of bone marrow, and  small RNA sequencing was performed

first: Cunru

last: Zou

first: Xuehong

last: Ran

first: Liping


title: Lymph Node Stromal Cell Responses to Perinatal T Cell Waves, A Temporal Atlas [scRNA-Seq]

summary: The perinatal period is a critical time-window in establishing T-cell tolerance. Regulatory T cells (Tregs) made during the first two weeks of life are key drivers of perinatal tolerance induction, but how these cells are generated and operate has not been established. To elucidate the unique environment murine perinatal Tregs encounter within the lymph nodes (LNs) as they first emerge from the thymus, and how it evolves over the succeeding days, we employed single-cell RNA sequencing to generate an atlas of the early LN niche. A highly dynamic picture emerged, the stromal-cell compartment showing the most striking changes and putative interactions with other LN cell compartments. In particular, LN stromal cells showed increasing potential for lymphocyte interactions with age. Analogous studies on mice lacking α:β T cells or enriched for autoreactive α:β T cells revealed an acute stromal-cell response to α:β T cell dysfunction, largely reflecting dysregulation of Tregs. Punctual ablation of perinatal Tregs induced stromal-cell activation that was dependent on both interferon-gamma signaling and activation of conventional CD4+ T cells. These findings elucidate some of the earliest cellular and molecular events in perinatal induction of T-cell tolerance, providing a framework for future explorations.

overall_design: Pooled inguinal, axillary and brachial LNs were isolated from female WT and KO littermates aged D4-6, D12-15 and D30-45. Each replicate was processed, encapsulated, and sequenced independently. Samples were gently digested and cytofluorometrically sorted according to CD45.2 expression and encapsulated using the Chromium Single cell 3’ v3 (10x Genomics).

first: Jayewickreme

last: Teshika

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Lymph Node Stromal Cell Responses to Perinatal T Cell Waves, A Temporal Atlas [bulkRNA-Seq]

overall_design: Pooled inguinal, axillary, and brachial lymph nodes from day 5 and week 2 B6 mice were gently digested and flow-cytometrically purified. 500-1000 fibroblastic reticular cells, Ly6CHi monocyte-macrophages, or Ly6CLo monocyte-macrophages were doubles sorted according to the following gating strategies. FRC: CD45-,CD31-,Pdpn+Pdgfra+; monocyte-macrophages were gated as Lin(Thy1, CD3e,CD19,NK1.1,Ly6G,BST2)-, CD11b+, CD64+ cells and gated depending on Ly6CHi vs Lo expression.

first: Teshika

last: Jayewickreme


title: Transcriptional Profiles of Pulmonary Artery Endothelial Cells in Pulmonary Hypertension

city: Providence

first: Navneet

last: Singh

state: Rhode Island

address: 593 Eddy Street, POB Suite 334

department: Medicine

institute: Brown University

summary: Pulmonary arterial hypertension (PAH) is characterized by endothelial cell (EC) dysfunction. There are no data from living patients to inform whether differential gene expression of pulmonary artery ECs (PAECs) can discern disease subtypes, progression and pathogenesis. We aimed to further validate our previously described method to propagate ECs from right heart catheter (RHC) balloon tips and to perform additional PAEC phenotyping. We performed bulk RNA sequencing of PAECs from RHC balloons. Using unsupervised dimensionality reduction and clustering we compared transcriptional signatures from PAH to controls and other forms of pulmonary hypertension. Select PAEC samples underwent single cell and population growth characterization and anoikis quantification.  Fifty-four specimens were analyzed from 49 subjects. The transcriptome appeared stable over limited passages. Six genes involved in sex steroid signaling, metabolism, and oncogenesis were significantly upregulated in PAH subjects as compared to controls. Genes regulating BMP and Wnt signaling, oxidative stress and cellular metabolism were differentially expressed in PAH subjects. Changes in gene expression tracked with clinical events in PAH subjects with serial samples over time. Functional assays demonstrated enhanced replication competency and anoikis resistance. Our findings recapitulate fundamental biological processes of PAH and provide new evidence of a cancer-like phenotype in ECs from the central vasculature of PAH patients. This “cell biopsy” approach may provide insight into EC heterogeneity within the lung and a therapeutic screening approach in PAH.

overall_design: To profile bulk gene expression of human pulmonary artery endothelial cells (PAECs) harvested from the tips of right heart catheter balloon tips, we submited PAECs for bulk RNA sequencing and performed comparitive analysis.

first: Carsten

last: Eickhoff

first: Augosto

last: Garcia-Agundez

first: Paul

last: Bertone

first: Sunita

last: Paudel

first: Dhananjay

last: Tambe

first: Leslie

middle: A

last: Litzky

first: Katherine

last: Cox-Flaherty

first: James

last: Klinger

first: Sean

middle: F

last: Monagahn

first: Christopher

last: Mullin

first: Mandy

last: Pereira

first: Thomas

last: Walsh

first: Mary

last: Whittenhall

first: Troy

last: Stevens

first: Elizabeth

middle: O

last: Harrington

first: Corey

last: Ventetuolo


title: Concurrent gliomas in patients with multiple sclerosis

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

type: Methylation profiling by genome tiling array

summary:
Background: Concurrent malignant brain tumors in patients with multiple sclerosis (MS) constitute a rare but paradigmatic phenomenon for studying neuroimmunological mechanisms from both molecular and clinical perspectives.
Methods: A multicenter cohort of 26 patients diagnosed with both primary brain tumors and multiple sclerosis was studied for disease localization, tumor treatment-related MS activity, and molecular characteristics specific for diffuse glioma in MS patients.
Results: MS neither predisposes nor protects from the development of gliomas. Patients with glioblastoma WHO grade 4 without isocitratdehydrogenase (IDH) mutations have a longstanding history of MS, whereas patients diagnosed with IDH-mutant astrocytoma WHO grade 2 receive multiple sclerosis diagnosis mostly at the same time or later. Concurrent MS is associated with a lesser extent of tumor resection and a worse prognosis in IDH-mutant glioma patients (PFS 32 vs. 64 months, p=0.0206). When assessing tumor-intrinsic differences no distinct subgroup-defining methylation pattern is identified in gliomas of MS patients compared to other glioma samples. However, differential methylation of immune-related genetic loci including human leukocyte antigen locus on 6p21 and interleukin locus on 5q31 is found in MS patients vs. matched non-MS patients. In line, inflammatory disease activity increases in 42% of multiple sclerosis patients after brain tumor radiotherapy suggesting a susceptibility of multiple sclerosis brain tissue to pro-inflammatory stimuli such as ionizing radiation.
Conclusions: Concurrent low-grade gliomas should be considered in multiple sclerosis patients with slowly progressive, expansive T2/FLAIR lesions. Our findings of typically reduced extent of resection in MS patients and increased MS activity after radiation may inform future treatment decisions.

overall_design: Array-based methylation profiling of a cohort of 26 patients diagnosed with both primary brain tumors and multiple sclerosis.

first: Katharina

last: Sahm


title: β-adrenergic signaling promotes morphological maturation of astrocytes in female mice

city: San Francisco

first: Marci

last: Rosenberg

address: 1651 4th Street

department: Psychiatry

institute: UCSF

summary: Astrocytes play essential roles in the developing nervous system, including supporting synapse function. These astrocyte support functions emerge coincident with brain maturation and may be tailored in a region-specific manner. For example, gray matter astrocytes have elaborate synapse-associated processes and are morphologically and molecularly distinct from white-matter astrocytes. This raises the question of whether there are unique environmental cues that promote gray matter astrocyte identity and synaptogenic function. We previously identified adrenergic receptors as preferentially enriched in developing gray versus white matter astrocytes, suggesting that noradrenergic signaling could be a cue that promotes the functional maturation of gray matter astrocytes. We first characterized noradrenergic projections during postnatal brain development in mouse and human, finding that process density was higher in the gray matter and increased concurrently with astrocyte maturation. RNA-sequencing revealed that astrocytes in both species expressed ɑ and β adrenergic receptors. We found that stimulation of β adrenergic receptors increased primary branching of rodent astrocytes in vitro. Conversely, astrocyte-conditional knockout of the β1 adrenergic receptor reduced the size of gray matter astrocytes, and led to dysregulated sensorimotor integration in female mice. These studies suggest that adrenergic signaling to developing astrocytes impacts their morphology and has implications for adult behavior, particularly in female animals. More broadly, they demonstrate a mechanism through which environmental cues impact astrocyte development. Given the key roles of norepinephrine in brain states such as arousal, stress, and learning, these findings could prompt further inquiry into how developmental stressors impact astrocyte development and adult brain function.

overall_design: 8 samples total consisting of 4 biological replicates per group of flow sorted astrocytes from cortical or subcortical tissue at P29

first: Marlesa

middle: I

last: Godoy

first: Sarah

last: Wade

first: Mercedes

last: Paredes

first: Ye

last: Zhang

first: Anna

middle: V

last: Molofsky


title: NET formation is a default epigenetic program controlled by PAD4 in apoptotic neutrophils

city: La Jolla

first: Ben

last: Croker

address: 9500 Gilman Drive

department: Department of Pediatrics

institute: University of California San Diego

summary: Neutrophil extracellular traps (NETs) counteract bacterial and fungal pathogens but can also promote thrombosis, autoimmunity, and sterile inflammation. The presence of citrullinated histones, generated by the peptidylarginine deiminase 4 (PAD4), is synonymous with NETosis and is considered independent of apoptosis. Mitochondrial- and death receptormediated apoptosis promote GSDME-dependent calcium mobilization and membrane permeabilization leading to histone H3 citrullination (H3Cit), nuclear DNA extrusion, and cytoplast formation. H3Cit is concentrated at the promoter in bone marrow neutrophils, and redistributes in a coordinated process from promoter to intergenic and intronic regions during apoptosis. Loss of GSDME prevents nuclear and plasma membrane disruption of apoptotic neutrophils, but prolongs early apoptosis-induced cellular changes to the chromatin and cytoplasmic granules. Apoptotic signaling engages PAD4 in neutrophils, establishing a cellular state that is primed for NETosis, but that occurs only upon membrane disruption by GSDME, thereby redefining the end-of-life for neutrophils.

overall_design: Cut&Tag for citrullinated histones (H3Cit) in BM neutrophils treated with or without death stimuli

first: Yanfang

middle: P

last: Zhu

first: Lai

last: Wong

first: Ruslan

last: Sadreyev

first: Kate

middle: L

last: Jeffrey


title: Single Cell RNA Sequencing of Adult Mouse Intervertebral Disc Cells

city: Philadelphia

first: Lachlan

middle: James

last: Smith

state: Pennsylvania

address: 371 Stemmler Hall, 3450 Hamilton Walk

department: Department of Orthopaedic Surgery

institute: University of Pennsylvania

summary: Intervertebral disc degeneration is a leading cause of chronic low back pain. Cell-based strategies that seek to treat disc degeneration by regenerating the central nucleus pulposus hold significant promise, but key challenges remain. One of these is the inability of therapeutic cells to effectively mimic the performance of native nucleus pulposus cells, which are unique amongst skeletal cell types in that they arise from the embryonic notochord. In this study we use single cell RNA sequencing to demonstrate emergent heterogeneity amongst notochord-derived nucleus pulposus cells in the postnatal mouse disc. Specifically, we established the existence of early and late stage nucleus pulposus cells, corresponding to notochordal progenitor and mature cells, respectively. Late stage cells exhibited significantly higher expression levels of extracellular matrix genes including aggrecan, and collagens II and VI, along with elevated TGF-β and PI3K-Akt signaling. Additionally, we identified Cd9 as a novel surface marker of late stage nucleus pulposus cells, and demonstrated that these cells were localized to the nucleus pulposus periphery, increased in numbers with increasing postnatal age, and co-localized with emerging glycosaminoglycan-rich extracellular matrix.

overall_design: Cells were isolated from intervertebral discs of P30 shh-cre:R26R-tdTomato mice. TdTomato+ cells were enriched using fluorescence activated cell sorting and analyzed using single cell RNA-sequencing. Three replicate sequencing batches were performed, each comprising pooled cells from litter matched animals. Libraries were generated using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium dual Index Kit, and paired-end sequencing was performed at a targeted depth for each library of 20,000 mean reads per cell (NovaSeq 6000; Illumina, San Diego, USA). Nucleus pulposus cells were identified within the total sequenced cell population by expression of established markers Krt8, Krt18, Krt19 and T.

first: Chenghao


title: Endoplasmic reticulum protein TXNDC5 interacts with PRDX6 and HSPA9 to regulate glutathione metabolism and lipid peroxidation in hepatic AML12 cell line

city: Zaragoza

first: Jesus

last: Osada

state: Spain

address: C/ Miguel Servet 177

department: Biochemistry and Molecular Biology

institute: Universidad de Zaragoza

summary: The goal of this study was to determine TXNDC5 hepatic transcriptome interaction by comparing high-throughput data for KO vs. WT AML12 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AML12 cells and its KO and KI derivatives. TXNDC5 was overexpress using the safe-harbour ROSA26 in which the construc

first: Seyed

last: Hesamoddin Bidooki

first: Javier

last: Sanchez Marco


title: Decoding target genes of ESRP1 by crosslinking-immunoprecipitation and high-throughput sequencing (CLIP seq)

city: Wuhan

first: Chengguo

last: Li

address: Union Hospital, No. 1277 Jiefang Avenue

institute: Wuhan Union Hospital

summary: RNA-binding proteins and their mediated alternative splicing play important roles in tumor cell invasion and migration. Here, we report that ESRP1 is a key regulator of gastric cancer cell metastasis. Overexpression of ESRP1 inhibits the invasion and migration of gastric cancer cells, in vivo and in vitro. Through crosslinking-immunoprecipitation and high-throughput sequencing (CLIP seq), we revealed that ESRP1 binding to the CLSTN1 mRNA and mediated its exon skipping, which may be a key mechanism for its inhibition of gastric cancer cell invasion and metastasis. Taken together, our data provide a molecular framework for the role of ESRP1 in gastric cancer development.

overall_design: SGC7901 gastric cancer cell line with stable overexpression of ESRP1 was established, And then CLIP seq for ESRP1 was conducted.

first: Yuping

last: Yin

first: Ruikng

last: Tao

first: Yao

last: lin

first: Tao

last: Wang

first: Qian

last: Shen

first: Runze

first: Kaixiong

first: Weizhen

last: Liu


title: Dose dependent reprogramming of neutrophils by LPS

city: Blacksburg

first: Liwu

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

summary: We have performed analyses of murine primary bone marrow derived neutrophils challenged with either ultra-low dose or high dose of LPS.  Neutrophils can be differentially programmed to distinct states by varying dosages of LPS. Purified bone marrow neutrophils were treated with PBS, 100 pg/ml LPS or 100 ng/ml LPS overnight, and harvested for scRNAseq analysis to examine their profiles of gene expression.

overall_design: WT murine neutrophils were treated with either PBS, 100pg/ml LPS or 100 ng/ml LPS overnight

first: RuiCi

last: Lin

first: Ziyue

last: Yi


title: Transcriptomic Profiling of Polycystic Kidney Disease Identifies Paracrine Factors in the Early Cyst Microenvironment

city: Leiden

first: Sevtap

middle: Aysu

last: Yasinoglu

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

summary: Initial cysts that are formed upon Pkd1 loss in mice impose persistent stress on surrounding tissue and trigger a cystic snowball effect, in which local aberrant PKD-related signaling increases the likelihood of new cyst formation, ultimately leading to accelerated disease progression. Although many pathways have been associated with PKD progression, the knowledge of early changes near initial cysts is limited. To perform an unbiased analysis of transcriptomic alterations in the cyst microenvironment, microdomains were collected from kidney sections of iKsp-Pkd1del mice with scattered Pkd1-deletion using Laser Capture Microdissection. These microdomains were defined as F4/80-low cystic, representing early alterations in the cyst microenvironment, F4/80-high cystic, with more advanced alterations, or non-cystic. RNA sequencing and differential gene expression analysis revealed 953 and 8088 dysregulated genes in the F4/80-low and F4/80-high cyst microenvironment, respectively, when compared to non-cystic microdomains. In the early cyst microenvironment, several injury-repair, growth, and tissue remodeling-related pathways were activated, accompanied by mild metabolic changes. In the more advanced F4/80-high microdomains, these pathways were potentiated and the metabolism was highly dysregulated. Upstream regulator analysis revealed a series of paracrine factors with increased activity in the early cyst microenvironment, including TNFSF12 and OSM. In line with the upstream regulator analysis, TWEAK and Oncostatin-M promoted cell proliferation and inflammatory gene expression in renal epithelial cells and fibroblasts in vitro. Collectively, our data provide an overview of molecular alterations that specifically occur in the cyst microenvironment and identify paracrine factors that may mediate early and advanced alterations in the cyst microenvironment.

overall_design: RNA sequencing analysis of microdissected tissue collected from frozen kidney sections of male iKspCre-Pkd1del mice, either from non-cystic microdomains, F4/80-low cyst microenvironment, or F4/80-high cyst microenvironment

first: Thomas

middle: B

last: Kuipers

first: Hailiang

last: Mei

first: Hans

middle: J

last: Baelde

first: Dorien

last: Peters

first: Louise

last: Van der Weerd

first: Ernst

last: Suidgeest


title: Effect of the LSD-1 Inhibitor RN-1 on g-globin and Global gene expression during Erythroid Differentiation in Baboons

city: Chicago

first: Donald

last: Lavelle

state: IL

address: 2030 W. Taylor St., Room 6215

institute: University of Illinois at Chicago

summary: Increased levels of Fetal Hemoglobin reduce the severity of symptoms of patients with sickle cell disease and decrease the risk of death.  An affordable, small molecule drug that stimulates HbF expression in vivo would be ideally suited to treat the large numbers of SCD patients that exist worldwide.  Our previous work showed that administration of the LSD1 (KDM1A) inhibitor RN-1 to normal baboons increased Fetal Hemoglobin (HbF) and was tolerated over a prolonged treatment period.  HbF elevations were associated with changes in epigenetic modifications that included increased levels of H3K4 di-and tri-methyl lysine at the g-globin promoter.  While dramatic effects of the loss of LSD1 on hematopoietic differentiation have been observed in murine LSD1 gene deletion and silencing models, the effect of pharmacological inhibition of LSD1 in vivo on hematopoietic differentiation is unknown. The goal of these experiments was to investigate the in vivo mechanism of action of the LSD1 inhibitor RN-1 by 1) determining its effect on g-globin expression in highly purified subpopulations of bone marrow erythroid cells enriched for varying stages of erythroid differentiation isolated directly from baboons treated with RN-1 and also by 2) investigating the effect of RN1 on the global transcriptome in a highly purified population of proerythroblasts.   Our results show that RN-1 administered to baboons targets an early event during erythroid differentiation responsible for γ-globin repression and increases the expression of a limited number of genes including genes involved in erythroid differentiation such as GATA2, GFi-1B, and LYN.

overall_design: The effect of RN-1 on global gene expression was investigated by RNAseq analysis of CD105+CD34-CD117+bRBC+ FACS-purified BM cells (proerythroblasts) of untreated control baboons (n=2) and baboons treated with both short-term (0.25mg/kg/d; 3d; n=2) and long-term schedules (0.25mg/kg/d; 5d/wk; >265d; n=2).   The untreated control and short-term treatment samples were obtained from the same two individual baboons, PA897 and PA8548. The long-term treatment samples were obtained from two different baboons (PA8695, LTT1, PA8698 LTT2). ).  Gene expression differences between these long-term treatment samples were compared directly with the two control samples from PA8697 (CTRL 1) and PA8548 (CTRL 2).

first: Vinzon

last: Ibanez

first: Kestis

last: Vaitkus

first: Maria

last: Ruiz

first: Zhengdeng

last: Lei

first: Mark

last: Maienschein-Cline

first: Zareema

last: Arbieva


title: A Short Peptide Protects from Age-Onset Proteotoxicity

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: Aberrant protein aggregation jeopardize cellular functionality and underlies the development of a myriad of late-onset maladies including Alzheimer’s disease (AD) and Huntington’s disease (HD). Accordingly, molecules that mitigate the toxicity of hazardous protein aggregates are of great interest as potential future therapeutics. Here we asked whether a small peptide, composed of five amino acids (5MER peptide) that was derived from the human pro-inflammatory CD44, could protect model nematodes from the toxicity of aggregative proteins that underlie the development of neurodegenerative disorders in humans. We found that the 5MER peptide mitigates the toxicity that stems from both, the AD-causing Aβ peptide and a stretch of poly-glutamine that is accountable to the development of several disorders including HD, without affecting lifespan. This protection was dependent on the activity of the aging-regulating transcription factors and associated with enhanced Aβ and polyQ35-YFP aggregation. A transcriptomic analysis unveiled that the peptide modulates the expression of various genes including these which are known as protein homeostasis (proteostasis) regulators such as txt-13, and modifiers of proteasome activity. The knockdown of txt-13 protects worms from proteotoxicity to the same extent as the 5MER peptide, suggesting that the peptide activates the transcellular chaperone signaling to promote proteostasis. Together, our results propose that the 5MER peptide should be considered as a component of future therapeutic cocktails for the treatment of neurodegenerative maladies.

overall_design: Four synchronized groups of CL2006 worms (expressing Aβ) were included in the experiment: (i) animals that were grown on EV bacteria and were either exposed to the buffer (EV0, control) or (ii) treated with the 5MER peptide (EVP). These worms express Aβ uninterruptedly and thus, were challenged by high levels of proteotoxicity. (iii) Aβ RNAi-treated CL2006 worms that were either exposed to the buffer (AB0), or (iv) treated with the 5MER peptide (ABP). In the two latter groups (iii and iv) the expression of Aβ is largely suppressed and the animals are not challenged by a severe proteotoxic stress.

first: Ehud

last: Cohen

first: Hassan

last: Elsana

first: Reut

last: Bruck-Haimson

first: Huadong

last: Zhu

first: Irit

first: Adam

last: Zaretsky

first: Hana

last: Boocholez

first: Noa

last: Roitenberg

first: Lorna

last: Moll

first: Atif

last: Ahmed Siddiqui

first: David

last: Naor


title: ORAI1 channel function is a driver in oral cancer progression and pain

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

summary: Oral cancer causes pain associated with cancer progression. The mechanism(s) underlying the pain is not fully understood. We report here that the function of the Ca2+ channel ORAI1 is an important regulator of oral cancer pain. ORAI1 was highly expressed in tumor samples from oral cancer patients and ORAI1 activation caused sustained Ca2+ influx in human oral cancer cells. RNA-seq analysis showed broad modulation of oral cancer markers such MMPs and pain modulators by ORAI1. Inoculation of oral cancer cells lacking ORAI1 into mouse paws reduced ectopic tumor growth and allodynia, reducing secreted MMP1 levels and the excitation of trigeminal ganglia (TG) neurons. The stimulation of TG neurons with MMP1 evoked an increase in action potentials. These data demonstrate an important role of ORAI1 in oral cancer progression likely by controlling the expression of MMP1 resulting in increased cancer progression and pain

overall_design: Human oral cancer cell lines (HSC-3) were cultured in Dulbecco’s modified eagle medium (DMEM, Gibco, #11885-084) supplemented with 10% fetal bovine serum (FBS, Gibco, #26140-079) and 1% penicillin-streptomycin (PS, Gibco, #15140-122). Cells were harvested by treating 0.25 % Trypsin/EDTA (Gibco, #25200-072) and subcultured (2-3x105 cells) in 100 mm dishes at 37oC in a humidified 20 % O2/ 5 % CO2 incubator for 3-4 days. Cells were stimulated with 25 µM cyclopiazonic acid (CPA, Sigma, #1530) in the presence/absence of the ORAI inhibitor synta-66 for 3 hours before washing the cells and isolating the mRNA. The Illumina sequencing run produced 774,131,516 raw paired-end reads from 12 samples (54,874,503-71,100,845 reads). Quality control of raw sequencing reads was performed using FastQC (v0.11.5).Low-quality reads, sequencing adapters and overrepresented K-mers were removed using Trimmomatic (v0.32) resulting a total of 708,579,673 trimmed reads (46,791,160-66,701,914). The reads were aligned to the Human reference genome (Ensembl release 84-GRCh38) using the STAR aligner (v2.5.2a) and default alignment parameters to produce BAM files. HTSeq-Count (v0.6.1p1) was then used to generate read counts per gene based on the 84-GRCh38 GTF considering that the RNASeq library is stranded. The counts generated were then filtered to remove unexpressed or very lowly expressed genes to retain only genes with a minimum of 5 reads in 50% of samples in at least one of the three conditions investigated. Differential gene expression analysis was then performed using the filtered count data and the DESeq2 (1.28.1) program. Both unsupervised (PCA and correlation analysis) and supervised analyses were done using DESeq2. Statistical significance was analyzed using the Benjamini-Hochberg FDR (5%) and fold change of 1.5. Both FDR values and fold change were generatedusing DESeq2.Data transformation was performed using variance stabilizing transformation (VST). Heatmaps of levels of gene expression and fold change were constructed using the Ward method implemented in JMP Genomics (SAS Institute).

first: Ga-Yeon

last: Son

first: Nguyen

middle: H

last: Tu

middle: D

last: Santi

first: Santiago

last: Loya Lopez

first: Guilherme

last: Souza Bomfim

first: Manikandan

last: Vinu

first: Fang

last: Zhou

first: Ariya

last: Chaloemtoem

first: Rama

last: Alhariri

first: Rajesh

last: Khanna

first: Yi

last: Ye

first: Rodrigo

last: Lacruz


title: Further inhibition of Histone H2A ubiquitination protects myocardium against ischemia/reperfusion injury through enhancing glycolysis and improving mitochondrial function via promoting Hsp27 expression [III]

city: Daqing

first: Long

middle: Pi

last: Shi

state: Heilongjiang

address: No.39, Xinyang Road, Longfeng District, Daqing City

department: Department of Pharmacology

institute: Harbin Medical University

summary: H2Aub Chip-seq was undertaken in rats with myocardial ischemia injury to derive a list of signaling pathways and  genes

overall_design: Ischemia was observed when the left anterior descending (LAD) coronary artery was ligated around the PE-10 tube with moving nodule with 6-0 sutures, and occlusion of the left anterior descending coronary artery was confirmed by elevation of the ST segment of the electrocardiogram.

first: Pilong

first: Minghui

last: Li

first: Jiabi

last: Wu

first: Hongli

last: Sun


title: Further inhibition of Histone H2A ubiquitination protects myocardium against ischemia/reperfusion injury through enhancing glycolysis and improving mitochondrial function via promoting Hsp27 expression [II]

summary: RNA-seq was undertaken in rats with or without myocardial ischemia injury to derive a list of signaling pathways and differentially expressed genes


title: Effect of different hydrostatic pressures on mouse metatarsal and hip cartilage tissues

city: Brighton

first: Katherine

middle: Ann

last: Staines

address: Lewes Road

country: United Kingdom

institute: University of Brighton

summary: Chondrocytes are subject to continuous loads placed upon them throughout development and physical activity. Normal physiological loads enable the maintenance of the articular cartilage health, however abnormal loads contribute to pathological joint ageing. Similarly, the growth plate cartilage is exposed to a number of loads during growth and development. Due to the high-water content of cartilage, hydrostatic pressure is considered one of the main biomechanical influences on chondrocytes and it plays an important role in the mechanoregulation of cartilage. Therefore in this study we conducted RNA-seq analysis of ex vivo hip cap (articular) and metatarsal (growth) cartilage cultures after physiological and injurious hydrostatic pressure. Gene expression in response to 5mPa (physiological) or 50mPa (injurious) hydrostatic pressure was quantified by transcriptome analysis using the Illumina platform

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hip and metatarsal cartilage tissues exposed to 5mPa (physiological) or 50mPa (injurious) or 0mPa (control) hydrostatic pressure.

first: Lucie

middle: E

last: Bourne

first: Andrew

middle: R

last: Hesketh

first: Aikta

last: Sharma

first: Giselda

last: Bucca

first: Peter

middle: G

last: Bush


title: Effect of overexpression of ESRP1 on gene expression of SGC7901 gastric cancer cells

first: Chengguo

state: Hubei

summary: RNA-binding proteins and their mediated alternative splicing play important roles in tumor cell invasion and migration. Here, we report that ESRP1 is a key regulator of gastric cancer cell metastasis. Overexpression of ESRP1 inhibits the invasion and migration of gastric cancer cells, in vivo and in vitro. Furthermore, we found that ESRP1 causes a wide range of alternative splicing events, and ESRP1-mediated CLSTN1 exon skipping may be a key mechanism for its inhibition of gastric cancer cell invasion and metastasis. Taken together, our data provide a molecular framework for the role of ESRP1 in gastric cancer development.

overall_design: In order to study the role and mechanism of ESRP1 in the invasion and migration of gastric cancer cells, we established the SGC7901 gastric cancer cell line with stable overexpression of ESRP1. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

first: Yuping

last: Yin

first: Ruikng

last: Tao

first: Yao

last: lin

first: Tao

last: Wang

first: Qian

last: Shen

first: Runze

first: Kaixiong

first: Weizhen

last: Liu


title: Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency

city: Munich

first: Stephan

last: Hamperl

state: Bayern

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz-Zentrum Munich

summary: Stochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of specific genomic loci after targeted purification in their native chromatin context. Applying MATAC-Seq to selected early-efficient (EE) and late-inefficient (LI) budding yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an optimal 100-115bp nucleosome-free region in combination with surrounding well-positioned nucleosomes and open +2 linker region is a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during DNA replication of eukaryotic cells. Consequently, our single-molecule assay for chromatin accessibility will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.

overall_design: Nanopore sequencing analysis of chromatin accessibility using DNA methylation footprinting of specific chromosomal domains containing selected replication origins that were purified by a site-specific recombination and affinity purification system

first: Anna

last: Chanou

first: Karoline

last: Holler

first: Tobias

last: Straub


title: Chromosome 8p-engineering and CRISPR-Cas9 viability screening reveal increased  metastatic capacity of liver cancer cells targetable by patient-specific synthetic lethality

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

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

overall_design: Refer to individual Series


title: Chromosome 8p-engineering and CRISPR-Cas9 viability screening reveal increased  metastatic capacity of liver cancer cells targetable by patient-specific synthetic lethality [Th]

summary: Large-scale chromosomal aberrations are prevalent in human cancer but their functional effects remain poorly understood. We describe the establishment of chromosome-engineered hepatocellular carcinoma cell lines using a dual guided CRISPR-Cas9 genome editing strategy. A mega base-sized region on chromosome 8p (chr8p) was heterozygously deleted mimicking a frequently observed copy number alteration (CNA) of solid tumors. Using this unique model system, we delineated the functional consequences of chr8p loss and its impact on metastatic behavior and patient survival. We found that metastasis associated genes on chr8p act in concert to induce an aggressive and invasive phenotype characteristic for chr8p deleted tumors. The conjunction of engineered  chromosome-scale CNAs and genome-wide CRISPR-Cas9 viability screenings served as a powerful tool for the discovery of novel synthetic lethal targets and vulnerabilities accompanying patient-specific copy number changes. Using this target identification strategy, we showed that chr8p deletion sensitizes tumor cells to targeting of the reactive oxygen sanitizing enzyme Nudix hydrolase 17 (NUDT17).

overall_design: The chromosome 8p arm was heterozygously deleted in the human HCC cell lines HLF, HLE and HCC68 using CRISPR-Cas9 technology. 2 unaltered HLF, 1 unaltered HLE, 1 unaltered HCC68 clone,  2 HLF clones with chr8p loss, 1 HLE clone with chr8p loss and 1 HCC68 clone with chr8p loss were sequenced in triplictaes.

first: Thorben

last: Huth

first: Eva

last: Eiteneuer


title: Eribulin is an immune potentiator in breast cancer by up-regulating human leukocyte antigen class I expression via the induction of NLRC5

city: Sapporo

first: Yoshihiko

last: Hirohashi

address: South-1 West-17, Chuo-Ku

department: Pathology

institute: Sapporo Medical University

summary: The effect of Eribulin in RNA expression was addressed by RNA-sequence using Eribulin treated MCF7 breast cancer cell line.

overall_design: MCF7 cells were treated by Eribulin (10nM) for 2day, then total RNA was isolated and analyzed by RNA-sequence.

first: Asaka

last: Wada

first: Sadahiro

last: Iwabuchi


title: Further inhibition of Histone H2A ubiquitination protects myocardium against ischemia/reperfusion injury through enhancing glycolysis and improving mitochondrial function via promoting Hsp27 expression [I]

first: Long

last: Shi

summary: RNA-seq was undertaken in rats with or without myocardial ischemia-reperfusion injury to derive a list of signaling pathways and differentially expressed genes

overall_design: Ischemia was observed when the left anterior descending (LAD) coronary artery was ligated around the PE-10 tube with moving nodule with 6-0 sutures, and occlusion of the left anterior descending coronary artery was confirmed by elevation of the ST segment of the electrocardiogram. Ischemia is released after 30 min for reperfusion. 6 h after reperfusion, the heart was harvested for the following experiment.

first: Pilong

first: Minghui

last: Li

first: Jiabi

last: Wu

first: Hongli

last: Sun


title: Further inhibition of Histone H2A ubiquitination protects myocardium against ischemia/reperfusion injury through enhancing glycolysis and improving mitochondrial function via promoting Hsp27 expression