title: mRNA-seq of wild-type or p53-deficient B cells expressing MHV68 M2

first: Mark

last: Manzano

address: 4301 W Markham St

institute: University of Arkansas for Medical Sciences

summary: Gammaherpesviruses (GHV) are DNA tumor viruses that establish lifelong latent infections in lymphocytes. For viruses such as Epstein-Barr virus (EBV) and murine gammaherpesvirus 68 (MHV68), this is accomplished through a viral gene-expression program that promotes cellular proliferation and differentiation, especially of germinal center (GC) B cells. Intrinsic host mechanisms to control virus-driven cellular expansion are incompletely defined. Using a small-animal model of GHV pathogenesis, we identify the B cell-specific latency gene M2, an MHV68 mediator of GC B cell differentiation, as a viral gene product that is sufficient to induce p53 in a manner that is dependent on Src kinase activity. To understand the function of M2 in primary B cells, we performed retroviral transduction of M2 or M2.Stop in wild-type or p53-deficient B cells. Our results reveal p53 and cellular proliferation pathways enriched in M2-expressing B cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for retrovirally transduced primary B cells with MHV68 M2, a FSS mutant, M2.Stop, or EBV LMP1

first: J

last: Forrest

first: Shana

last: Owens


title: Mechanisms of multidrug resistance caused by an Ipi1 mutation in the fungal pathogen Candida glabrata

status: Public on Dec 19 2024

city: Miyazaki

first: Taiga

last: Miyazaki

address: 5200 Kihara, Kiyotake

department: Department of Internal Medicine

country: Japan

institute: University of Miyazaki

type: Expression profiling by high throughput sequencing

summary: Multidrug resistance in the pathogenic fungus Candida glabrata is a growing global threat. Here, we study mechanisms of multidrug resistance in this pathogen. Exposure of C. glabrata cells to micafungin (an echinocandin) leads to the isolation of a mutant exhibiting resistance to echinocandin and azole antifungals. The drug-resistant phenotype is due to a non-synonymous mutation (R70H) in gene IPI1, which is known to be involved in pre-rRNA processing in Saccharomyces cerevisiae. Azole resistance in the ipi1-R70H mutant depends on the Pdr1 transcription factor, which regulates the expression of multidrug transporters. We show that the C. glabrata Ipi1 protein physically interacts with the ribosome-related chaperones Ssb and Ssz1, both of which bind to Pdr1. The Ipi1-Ssb/Ssz1 complex inhibits Pdr1-mediated gene expression and multidrug resistance in C. glabrata, in contrast to S. cerevisiae where Ssz1 has been shown to act as a positive regulator of Pdr1. Furthermore, micafungin exposure reduces metabolic activity and cell proliferation in the ipi1-R70H mutant, which may contribute to micafungin tolerance.

overall_design: Gene expression profiling analysis was performed using data obtained from RNA-seq of 2 different C. glabrata strains (wild-type and ipi1-R70H) with or without micafungin exposure. Three biological replicates and two technical replicates were used for RNA-seq analysis.

first: Tatsuro

last: Hirayama

first: Hironobu

last: Nakayama


title: Spatial multi-modal atlas of bone tissue from human femur

status: Public on Dec 18 2024

city: New Orleans

first: Kuan-Jui

last: Su

state: LA

address: 1440 Canal St,suite 1619G

department: Center for Biomedical Informatics and Genomics

country: USA

institute: Tulane University

summary: The skeletal system plays a pivotal role in the human body, and bone-related diseases present an urgent public health challenge. Understanding the bone microenvironment is essential for elucidating the mechanisms underlying bone homeostasis and developing innovative therapeutic strategies for bone diseases such as osteoporosis and osteoarthritis. In this study, we applied spatial and single-cell transcriptomic assays on bone tissue from human femur to comprehensively characterize the multi-dimensional cellular landscape of the human bone marrow microenvironment. We identified one niche related to bone formation and characterized cell-cell communication within bone marrow. Notably, we performed comprehensive dependency analysis, uncovering critical cellular relationships and molecular dependencies within the bone ecosystem. By mapping spatial distributions of gene expression, cellular composition, and pathway activities, we constructed a high-resolution atlas of the human bone microenvironment. This atlas not only delineates the intricate cellular architecture but also illuminates key molecular processes and dependencies governing bone metabolism.

overall_design: Human femoral head bone samples (~1 cm × 1 cm × 0.5 cm) were collected during hip replacement surgeries and immediately fixed in 10% formalin at 4°C for 48 hours. After rinsing with sterile PBS, the samples were decalcified in 14% EDTA for 3 weeks, followed by dehydration in increasing ethanol concentrations, clearing with xylene, and embedding in paraffin.  Spatial transcriptomics was conducted using the Visium CytAssist Spatial Gene Expression for FFPE protocol. Tissue sections were deparaffinized, stained with H&E, and processed with the Visium CytAssist instrument to transfer analytes for downstream library construction and sequencing on an Illumina NovaSeq 6000 system.

first: Weiqiang

last: Lin

first: Yisu

last: Li

first: Chuan

last: Qiu

first: Binghao

last: Zhou

first: Yun

last: Gong

first: Xiao

last: Zhang

first: Di

last: Tian

first: William

last: Sherman

first: Fernando

last: Sanchez

last: Wu

first: Xinyi

last: Xiao

first: Zhe

last: Luo

first: Qing

first: Yiping

last: Chen

first: Hui

last: Shen

first: Hong-Wen

last: Deng


title: Multi-omics analysis in primary T cells elucidates mechanisms behind disease associated genetic loci [RNA-seq]

city: Manchester

first: Jake

last: Butler

address: AV Hill Building, The University of Manchester, Acker Street

country: United Kingdom

institute: University of Manchester

summary: Background: Genome wide association studies (GWAS) have uncovered the genetic basis behind many diseases and conditions. However, most of these genetic loci affect regulatory regions, making the interpretation challenging. Chromatin conformation has a fundamental role in gene regulation and is frequently used to associate potential target genes to regulatory regions. However, previous studies mostly used small sample sizes and immortalized cell lines instead of primary cells. Results: Here we present the most extensive dataset of chromatin conformation with matching gene expression and chromatin accessibility from primary CD4+ and CD8+ T cells to date, isolated from psoriatic arthritis patients and healthy controls. We generated 108 Hi-C libraries (49 billion reads), 128 RNA-seq libraries and 126 ATAC-seq libraries. These data enhance our understanding of the mechanisms by which GWAS variants impact gene regulation, revealing how genetic variation alters chromatin accessibility and structure in primary cells at an unprecedented scale. We refine the mapping of GWAS loci to implicated regulatory elements, such as CTCF binding sites and other enhancer elements, aiding gene assignment. We uncover BCL2L11 as the probable causal gene within the rheumatoid arthritis (RA) locus rs13396472, despite the GWAS variants’ intronic positioning relative to ACOXL, and we identify mechanisms involving SESN3 dysregulation in the RA locus rs4409785. Conclusions: Given these genes’ significant role in T cell development and maturation, our work deepens our comprehension of autoimmune disease pathogenesis, suggesting potential treatment targets. In addition, our dataset provides a valuable resource for the investigation of immune mediated diseases and gene regulatory mechanisms.

overall_design: To understand the regualorty landscape of Psoriatic arthritis, primary cells from Psoriatic arthritis patients and healthy controls have been collected and various omics techniques applied to elucidate the roles of epigenetics and chromatin conformatin in disease.

first: Chenfu

last: Shi

first: Danyun

last: Zhao

first: Antonios

last: Frantzeskos

first: Stefano

last: Rossi

first: James

last: Ding

first: Carlo

last: Ferrazzano

first: Charlotte

last: Wynn

first: Ryan

middle: M

last: Hum

first: Ellie

last: Richards

first: Muskan

last: Gupta

first: Khadijah

last: Patel

middle: F

last: Yap

first: Darren

last: Plant

first: Richard

last: Grencis

first: Paul

last: Martin

first: Antony

last: Adamson

first: Stephen

last: Eyre

first: John

last: Bowes

first: Anne

last: Barton

first: Pauline

last: Ho

first: Magnus

last: Rattray

first: Gisela

last: Orozco


title: The immune profile of circulating autoreactive CD4 T cells is imprinted through tissue activation during autoimmune liver diseases (minibulk)

city: Marseille

first: Pierre

last: Milpied

address: Parc Scientifique de Luminy, case 906

country: France

institute: Centre d'Immunologie de Marseille-Luminy (CIML)

summary: Autoimmune liver diseases (AILD) are immune-mediated disorders in which CD4 T cells play a central role. However, the link between circulating self-antigen-specific CD4 T cells and the targeted tissue has not been extensively studied in AILD. We hypothesized that circulating autoreactive CD4 T cells were clonally and functionally related to dominant intra-hepatic pathogenic CD4 T cell clones. Single cell transcriptomic analysis of circulating self-antigen-specific CD4 T cells revealed a specific B-helper and immuno-exhausted transcriptional profile, which was conserved for different autoantigens, but distinct from several other types of foreign antigen specificities. In the blood, the dominant hepatic CD4 T cell clones had a similar transcriptomic signature and were enriched in the PD-1+ TIGIT+ HLA-DR+ CD4 T cell subset. In a mouse model, antigen-specific CD4 T cells acquired the immuno-exhausted transcriptional profile when they accumulated in the liver after local antigen reactivity. Locally, immune checkpoint molecules controlled the response of antigen-specific CD4 T cells responsible for liver damage. Our study reveals the origin and biology of liver-derived autoreactive CD4 T cells in the blood of AILD patients that are imprinted by the liver environment, and suggest a dysregulation of the immune checkpoint molecules pathways. Our study enables tracking and isolating circulating autoreactive CD4 T cells for future diagnostic and therapeutic purposes.

overall_design: For mini-bulk RNA-seq of in vitro stimulated CD4 T cells, we used a slightly modified version of the Flash-FB5P-seq protocol described above. First, CD4 T cell subsets were sorted on BD FACSAriaII. 500 to 2000 cells per well were stimulated in presence of 2.5µg/ml anti-CD3 and 1µg/ml anti-CD28. After 24h, cells were washed gently in PBS and resuspended in 4µL of specific lysis buffer with the composition described above except for ERCC spike-in mix which we used 10-time more concentrated (0.125 pg/µl). We performed RT-PCR with 16 µl of the RT-PCR mix described above, using 16 cycles of PCR for cDNA amplification (instead of 22 cycles for single-cell assay). Sequencing libraries were prepared and sequenced as described above for Flash-FB5P-seq.

first: Chuang

last: Dong

first: Amedee

last: Renand


title: The immune profile of circulating autoreactive CD4 T cells is imprinted through tissue activation during autoimmune liver diseases (TTm)

overall_design: For tetramer staining, 30 million PBMCs in 200 µL of 5% human serum RPMI medium were stained with 20 µg/mL PE-labeled tetramers at room temperature for 100 minutes. Cells were washed and incubated with anti-PE magnetic beads (Miltenyi Biotec, Germany), and a one-tenth fraction was saved for analysis. The other fraction was passed through a magnetic column (Miltenyi Biotec). After enrichment, cells were stained with appropriate antibodies (Supplementary table 1). Sepsecs187-197 HLA-DRB1 03:01 tetramer was generated by the tetramer core at the Benaroya research institute (Seattle, USA). For scRNA-seq of tetramer-stained CD4 T cells, we used an updated version of FB5P-seq (Flash-FB5P-seq) modified to implement advances developed by Hahaut et al. in the Flash-seq protocol59.


title: Multi-omics analysis in primary T cells elucidates mechanisms behind disease associated genetic loci [Hi-C]

first: Jake

last: Butler

first: Chenfu

last: Shi

first: Danyun

last: Zhao

first: Antonios

last: Frantzeskos

first: Stefano

last: Rossi

first: James

last: Ding

first: Carlo

last: Ferrazzano

first: Charlotte

last: Wynn

first: Ryan

last: Hum

last: Richards

first: Chuan


title: Mitochondria complex III-generated superoxide is essential for IL-10 secretion in macrophages

city: Chicago

first: Rogan

middle: A

last: Grant

state: IL

address: 303 E Superior St, Simpson Querrey Biomedical Research Center 5-522

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

summary: Mitochondrial electron transport chain (ETC) function modulates macrophage biology, however, mechanisms underlying mitochondrial ETC control of macrophage immune responses are not fully understood. Here we report that mutant mice with mitochondrial ETC complex III (CIII)-deficient macrophages exhibit increased susceptibility to influenza A virus and LPS-induced endotoxic shock. Cultured bone marrow-derived macrophages (BMDMs) isolated from these mitochondrial CIII-deficient mice released less IL-10 than controls following TLR3 or TLR4 stimulation. Surprisingly, restoring mitochondrial respiration without generating superoxide using alternative oxidase (AOX) was not sufficient to reverse LPS-induced endotoxic shock susceptibility or restore IL-10 release. However, activation of protein kinase A (PKA) rescued IL-10 release in mitochondrial CIII-deficient BMDMs following LPS stimulation. Additionally, mitochondrial CIII deficiency did not affect BMDM responses to interleukin-4 (IL-4) stimulation. Thus, our results highlight the essential role of mitochondrial CIII generated superoxide in the release of anti-inflammatory IL-10 in response to TLR stimulation

overall_design: Bone-marrow derived macrophages from mice with either intact QPC expression or QPC KO were treated with either LPS, IL-4, or vehicle. BMDMs were stimulated with 0.1µg/mL ultrapure O5:B55 LPS (Invivogen tlrl-pb5lps) or IL-4 10ng/mL for 18h prior to collection.

first: Joshua

middle: S

last: Stoolman

first: Billingham

middle: K

last: Leah

first: Taylor

last: Poor

first: Samuel

middle: E

last: Weinberg

first: Madeline

middle: C

last: Harding

first: Ziyan

last: Lu

first: Jason

last: Miska

first: Marten

last: Szibor

first: GR Scott

last: Budinger

first: Navdeep

last: Chandel


title: Single-cell analysis of circulating autoreactive CD4 T cells of autoimmune hepatitis patients (Figure 3)

city: Nantes

first: Christine

last: Chauveau

address: 30 Boulevard Jean Monnet

institute: CR2TI UMR 1064

summary: The dominant intra-hepatic CD4 T cell clones found in the blood had an autoimmune and immuno-exhausted transcriptional profile transcriptomic signature

overall_design: We performed droplet-based single-cell RNA-seq combined with TCR sequencing of blood PD-1+ CXCR5- mCD4 T cells from four patients to characterize the transcriptional profile of cells with TCR clonotypes detected in the matched liver biopsies. PD-1+CD45RA-CXCR5- CD4 T cells from four distinct AIH patients were sorted on BD FACSAriaII. Cells were run on a Chromium Single Cell Controller using the Chromium Single Cell 5′ V2 Next GEM single cell kit

first: Anaïs

last: Cardon

first: Thomas

last: Guinebretière

first: Chuang

last: Dong

first: Laurine

last: Gil

first: Sakina

last: Ado

first: Pierre-jean

last: Gavlovsky

first: Martin

last: Braud

first: Cynthia

last: Fourgeux

first: Lucas

last: Brusselle

first: Jérôme

last: Gournay

first: Sophie

last: Conchon

first: Pierre

last: Milpied

first: Jeremie

last: Poschmann

first: Amédée

last: Renand


title: Nuclear translocation of TfR1 facilitating tumor progression via p53-mediated gene regulation [Cut&Tag]

status: Public on Dec 27 2024

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

country: China

institute: Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: It is well-known that p53-mediated gene regulation exerts a profound impact on the occurrence, progression, metastasis, and various other facets of tumor. Wherein, activation of p53 downstream DNA damage repair-related genes is able to promote the survival of cancer cells during tumor progression.Notably, it has been substantiated that the transcriptional activity of p53 could be modulated by interactions with other proteins.Therefore, we asked whether the interaction with TfR1 was relevant to the transcriptional regulation of p53 target genes. Our results support the positive regulation of nuclear TfR1 on DNA damage repair-related genes, especially for the NER pathway.

overall_design: To investigate whether TfR1 can bind and compare its binding mode with p53 in the genome, the samples we designed contain groups enriched with TfR1 and rIgG, p53, and mIgG antibodies in HCT-116 cells, with two IgGs being the control group. In addition, there are groups enriched with TfR1 and rIgG antibodies in HCT-116 cells before and after p53 knockdown, respectively

first: Yaxin

last: Hou


title: Co-translational protein aggregation and failed ribosome rescue as a novel broad-spectrum antibacterial mechanism

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Drug-resistant bacteria pose an urgent global health threat, necessitating the development of antibacterial compounds with a novel mode of action. Protein biosynthesis accounts for up to half of the energy expenditure of bacterial cells and consequently inhibiting the efficiency or fidelity of the bacterial ribosome is a major target of existing antibiotics. Here we describe an alternative mode of action to affect the same process; allowing translation to proceed but causing co-translational aggregation of the nascent chain. We found a peptide that acts via this mechanism and is bactericidal against a wide range of pathogenic bacteria, including strains for which novel treatments are most urgently needed such as the ESKAPE pathogens, both in planktonic growth and in biofilms. Proteomics, transcriptomics and biochemical analyses of the inclusion bodies that form in bacteria upon peptide treatment reveal ribosomal proteins, mRNAs and their cognate nascent chains in amyloid-like structures assembled in polar inclusion bodies. The bacterial ssrA ribosome rescue pathway is activated but fails to prevent incorporation of hundreds of proteins into the inclusion bodies. Mechanistically, our results show that disrupting ribosomal quality control via co-translational aggregation constitutes a potent target mechanism for the development of broad-spectrum antibacterials.

overall_design: To investigate the molecular mechanisms underlying inclusion body formation and proteostatic collapse, we began by conducting RNA sequencing (RNA-seq) on bacterial strains treated with P33, a compound known to promote protein aggregation. Additionally, we treated another set of bacteria at 49°C as a positive control for protein aggregation. To minimize variability and ensure robust statistical analysis, five biological replicates were performed for each condition.

first: Ladan

last: Khodaparast

first: Laleh

first: Wu

last: Guiqin

first: Ramon

last: Duran-Romaña

first: Bert

last: Houben

first: Wouter

last: Duverger

first: Matthias

last: De Vleeschouwer

first: Katerina

last: Konstantoulea

first: Fleur

last: Nysen

first: Daniel

middle: J

last: Curwen

first: Lisandra

middle: L

last: Martin

first: Bernard

last: Scorneaux

last: Schalck

first: Jan

last: Michiels

first: Joost

last: Schymkowitz

first: Frederic

last: Rousseau


title: GATA6 is a Novel Regulator of Gene Expression and 3D Genome in Colorectal Cancer (Hi-C DLD-1 cells)

first: Feng

last: Yue

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Northwestern university

summary: Colorectal cancer (CRC) is one of the most lethal and prevalent malignancies with elusive molecular causes. While the abnormal activity of transcription factors has been reported as a vital component of cancer progression, the mechanism through which they function remains unclear. Here, through the analysis of primary human CRC tissue data, we identified GATA6 as a CRC specific regulator, whose expression upregulation is potentially associated with promoter hypomethylation. In the human genome, GATA6 showed preferential binding at tumor specific active enhancers. Through both auxin-inducible degron (AID) and CRISPR knockout, we showed that GATA6 depletion severely impaired clonogenicity and proliferation. GATA6 depletion caused the loss of CRC specific open chromatin, suggesting a specific regulatory role of GATA6 in CRC pathogenesis. Interestingly, we also discovered the co-occupancy of GATA6 with CTCF and its direct involvement in promoter enhancer loops, suggesting the possibility that GATA6 mediate transcriptional regulation through 3D genome. The loss of GATA6 led to alterations in E-P chromatin interactions of a panel of oncogenes, accompanied by the oncogene downregulation. Finally, we showed that GATA6 loss is detrimental to the xenograft tumor growth and thereby rescued mice survival. Taken together, we unrevealed a novel mechanism by which GATA6 contributes to CRC.

overall_design: DLD1-GATA6-AID-IAA7 cell lines were established using the auxin-inducible degron(AID) system, in which target gene GATA6 has been degraded. DLD-1 cells were also engineered to knockout target gene GATA6 using CRISPR/cas9 system.

first: Huijue

last: Lyu

first: Xintong

last: Chen

first: Yang

last: Cheng

first: Te

last: Zhang

first: Ping

last: Wang

first: Josiah

last: Wong

first: Juan

first: Lena

last: Stasiak

first: Leyu

last: Sun

first: Guangyu

last: Yang

first: Lu


title: GATA6 is a Novel Regulator of Gene Expression and 3D Genome in Colorectal Cancer (ATAC-Seq)

overall_design:
DLD1-GATA6-AID-IAA7 cell lines were established using the auxin-inducible degron(AID) system, in which target gene GATA6 has been degraded. DLD-1 cells were also engineered to knockout target gene GATA6 using CRISPR/cas9 system.
ATAC-seq was performed following the exact Omni-ATAC protocol. 50,000 viable cells were used, and the lysis condition was optimized for DLD-1 cells.


title: Spatial transcriptomic sequencing of repaired lung transplanted with human P63+ progenitor [STOmics-seq]

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

summary: KRT5+P63+ progenitor cells located in the basal layer of the airway epithelium have been identified as a promising candidate for lung epithelium repair. Such cells are originated from primitive progenitors in distal airways and could expand/migrate to inflamed damaged lung parenchymal region to form ‘saccule’. To further investigate the characteristics and potential function of the saccule structure, we performed the high-resolution spatial transcriptomic analysis on the 35 dpt lung section.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We isolated the human P63+ progenitors and transplanted the GFP-labelled P63+ progenitors into the bleomycin-injured mouse lung by intratracheal instillation. Mice were sacrificed at 35 days post transplantation and their lung tissue were harvest to detect GFP signal by fluorescence stereomicroscope for Stereo-seq.

first: Yu

last: Zhao

first: Yueqing

last: Zhou

first: Weipan


title: Transcriptomic HIV-1 reservoir profiling reveals a role for mitochondrial functionality in HIV-1 latency

status: Public on Dec 17 2024

city: Amsterdam

first: Neeltje

last: Kootstra

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC, AMC

summary: Identifying cellular mechanisms maintaining HIV-1 latency in the viral reservoir is crucial for devising effective cure strategies. Here we developed a flow cytometry-fluorescent in situ hybridization (flow-FISH) approach using a combination of probes that detects abortive and elongated HIV-1 transcripts for ex vivo isolation and characterization of viral reservoir cells in peripheral blood from people with HIV-1. Following the isolation of three distinct cell populations from CD4+ T cells (i.e. cells harboring transcriptionally latent HIV-1, cells harboring transcriptionally active HIV-1, or uninfected cells), we determined their transcriptomic profile by RNA sequencing (RNAseq). Supervised gene expression analysis identified several differentially expressed mitochondrial genes in infected cell populations compared to uninfected cells, but also in latently infected compared to productively infected CD4+ T cells. Our transcriptomic profiling data shows an association between diminished mitochondrial functioning and the transcriptional activity of the viral reservoir. These findings underline the relevance of metabolic regulation in HIV-1 infection, and support the development of strategies modulating immunometabolism to target viral latency.

overall_design: To investigate the mechanisms underlying HIV-1 latency in the viral reservoir, we designed probes targeting abortive TAR and elongated Gag HIV-1 transcripts for flow-FISH detection and isolation of transcriptionally latent or active HIV-1-infected CD4+ T cells. Using this method, we isolated transcriptionally latent HIV-1-infected cells (TAR+Gag-), transcriptionally active HIV-1-infected cells (TAR+Gag+), and uninfected cells (TAR-Gag-) from the CD4+ T cell population in peripheral blood mononuclear cells (PBMCs) from people with HIV-1 (N=5) by cell sorting. We then performed 3’ RNAseq and gene expression profiling analysis to assess the transcriptomic profiles of the three isolated populations.

first: Shirley

last: Man

first: Jade

last: Jansen

first: Stefanie

last: Kroeze

first: Teunis

middle: B

last: Geijtenbeek


title: Single-cell gene expression profile of primary human peripheral blood natural killer cells grouped into seven phenotypically-defined populations

city: New York

first: M. Kazim

last: Panjwani

state: NY

address: 408 E 69th St

institute: MSKCC

summary: Human peripheral blood natural killer cells are grouped in various ways according to phenotypic and functional characteristics. We sorted peripheral blood natural killer cells from healthy donors into seven surface phenotype-defined populations, hashtagged them, and sequenced them. This analysis permitted simultaneous identification of transcriptional clusters and traceback of the components to their phenotypic groups.

overall_design: Natural killer cells were isolated and sorted into seven populations according to surface expression of CD56, NKG2A, NKG2C, and NKp30 from the PBMCs of two healthy donors. These seven populations were hashtagged and recombined in equal numbers before submission as a single sample for each biological replicate for feature barcode and gene expression sequencing.

first: M

first: Simon

last: Grassmann

first: Joseph

first: Katharine

last: Hsu


title: ZDHHC15 mediates Hippo/YAP pathway palmitoylation and regulates tumor progression

city: Dalian

first: Jianxin

state: Liaoning

address: West Lushun South Road

institute: Dalian Medical University

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

overall_design: Refer to individual Series


title: ZDHHC15 mediates Hippo/YAP pathway palmitoylation and regulates tumor progression [TOV-112D]

summary: The Post-translational modification of Hippo/YAP pathway members plays an important role in regulating the activation of Hippo/YAP pathway and its effects in tumors. S-Palmitoylation, also known as S-acylation,is the most common protein Lipid modification, mainly composed of palmitoyl transferases (PATs) from the DHHC (Asp His His Cys) family Catalysis. The results showed that ZDHHC15 mediated palmitoylation of KIBRA up-regulated the expression of YAP downstream target genes, and regulated the invasion function of breast cancer and ovarian cancer cells. The research results will reveal new regulatory mechanisms of the Hippo pathway

overall_design: Ovarian cancer TOV-112D cells with stable knockdown of ZDHHC15 and shCON as a negative control.  shCON and shZDHHC15 cells were extracted for RNA sequencing

first: Songshu

last: Meng


title: Comparative analysis of transcriptome profiles reveals stage- and TR-dependent gene regulation programs underlying the initiation of tail regeneration in Xenopus tropicalis

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: To investigate what genes/pathways that specific induced by T3/TRs which inhibited tail regeneration. In addition, to detect the gene regulation program that important for regeneration were altered by T3 through TRs during the initiation period of tail regeneration

overall_design: Compare the gene expression of the initiation of tail regeneration at stage56 and stage61 in both wild type and TRdko Xenopus tropicalis

first: Wang

last: Shouhong

first: Zhang

last: Hongen

first: Shi

last: Yun-Bo


title: Multi-omics analysis in primary T cells elucidates mechanisms behind disease associated genetic loci

first: Jake

last: Butler

first: Chenfu

last: Shi

first: Danyun

first: Antonios

last: Frantzeskos

first: Stefano

last: Rossi

first: James

last: Ding

first: Carlo

last: Ferrazzano

first: Charlotte

last: Wynn

last: Hum

first: Ellie

last: Richards

first: Muskan

last: Gupta

first: Khadijah

last: Patel

first: Chuan

last: Yap

first: Darren

last: Plant

first: Richard

last: Grencis

first: Paul

last: Martin

first: Antony

last: Adamson

first: Stephen

last: Eyre

first: John

last: Bowes

first: Anne

last: Barton

first: Pauline

last: Ho

first: Magnus

last: Rattray

first: Gisela

last: Orozco


title: GATA6 is a Novel Regulator of Gene Expression and 3D Genome in Colorectal Cancer (RNA-Seq)

first: Feng

last: Yue

overall_design:
DLD1-GATA6-AID-IAA7 cell lines were established using the auxin-inducible degron(AID) system, in which target gene GATA6 has been degraded. DLD-1 cells were also engineered to knockout target gene GATA6 using CRISPR/cas9 system.
Gene expression profiling analysis using data obtained from RNA-seq.

first: Huijue

last: Lyu

first: Xintong

last: Chen

first: Yang

last: Cheng

first: Te

last: Zhang

first: Ping

last: Wang

first: Josiah

last: Wong

first: Juan

first: Lena

last: Stasiak

first: Leyu

last: Sun

first: Guangyu

last: Yang

first: Lu


title: Cell-type-resolved chromatin accessibility in the human intestine identifies complex regulatory programs and clarifies genetic associations in Crohn's disease

status: Public on Dec 16 2024

first: Yu

last: Zhao

address: 5841 S. Maryland Ave

department: Section of Genetic Medicine, Department of Medicine

institute: The University of Chicago

summary: Crohn's disease (CD) is a complex inflammatory bowel disease resulting from an interplay of genetic, microbial, and environmental factors. Cell-type-specific contributions to CD etiology and genetic risk are incompletely understood. Here we built a comprehensive atlas of cell-type-resolved chromatin accessibility comprising 557,310 candidate cis-regulatory elements (cCREs) in terminal ileum and ascending colon from patients with active and inactive CD and healthy controls.  Using this atlas, we identified cell-type-, anatomic location-, and context-specific cCREs and characterized the regulatory programs underlying inflammatory responses in the intestinal mucosa of CD patients. Genetic variants that disrupt binding motifs of cell-type-specific transcription factors significantly affected chromatin accessibility in specific mucosal cell types. We found that CD heritability is primarily enriched in immune cell types. However, using fine-mapped non-coding CD variants we identified 29 variants located within cCREs several of which were accessible in epithelial and stromal cells implicating cell types from additional lineages in mediating CD risk in some loci. Our atlas provides a comprehensive resource to study gene regulatory effects in CD and health, and highlights the cellular complexity underlying CD risk.

overall_design: We obtained scATAC-seq data from biopsies of the terminal ileum (TI) and ascending colon (AC) from healthy controls and Crohn's disease patients with various inflammation conditions.

first: Ran

last: Zhou

first: Anindita

last: Basu

first: Sebastian

last: Pott


title: Reveal the key mediators of inflammation in Crohn's disease undergoing biological treatments

city: Dallas

first: Bingqing

last: Xie

state: Texas

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

summary: Crohn’s disease (CD) is a major subtype of life-long Inflammatory Bowel Disease (IBD) affecting a growing population in United States. To advance the knowledge in pathology, our study investigates into the common inflammatory feature in CD across different inflammation statuses by single-cell transcriptomics.  First, we provided a detailed mucosal cellular landscape of terminal ileum (TI) and ascending colon (AC), with endoscopic diagnosis (CD inflamed, adjacent-to-inflamed, non-inflamed and non-IBD control), including a cohort of patients undergoing biological treatments. Differences between regions (TI and AC), and features of mucosal inflammation status in cellular composition are captured within the cellular landscapes.  Second, we identified an inflammation cascade that include follicle-associated enterocytes and macrophages via molecules like CCL20 and S100As, as key mediators of CD inflammation. These key mediators serve as hubs in imputed cell-cell interactions under CD inflammation, expanding the interplay network with increasing disease severity.  Finally, we demonstrate a scoring method by surveying the mucosa, using GWAS loci, and transcriptome features including differentially expressed genes (DEGs), and genes from a novel singular value decomposition (SVD)-based co-expression network analysis framework. Applying independently to the epithelial and immune lineage, we identify inflammation signatures that reflect disease severity. Furthermore, we report a short, robust list of epithelial and immune transcript makers whose expressions harmonize with endoscopic diagnosis and histological assessment. These markers are merely within known IBD GWAS loci.  Collectively, this study narrates a shared inflammation pattern involving cells and cytokines for active CD and present a short list of markers for metrical inflammation assessment.

overall_design: scRNA-seq of 79 gut biopsies in terminal ileum and ascending colon from  healthy individuals (n = 17) and Crohn's Disease patients (n = 32) including non-inflamed, adjacent-to-inflamed, and active inflamed region.


title: Targeting breast cancer stem cells by a ROR2 specific antibody

city: Shenzhen

first: Suping

state: Guangdong

address: No. 3688, Nanhai Road, Nanshan District

institute: Shenzhen University

summary: ROR2 is a type I orphan-receptor tyrosine-kinase-like membrane protein. Its expression level is decreased after birth and barely detectable in adulthood. However, it is re-expressed by various cancer cells and is negatively correlated with patients' survival. The role of ROR2 in breast cancer is still unknown.This study demonstrated that ROR2 activates RhoA GTPase, and induces EMT in breast cancer. In addition, ROR2 is enriched in breast CSCs and required for maintaining the stemness features of CSCs. We developed a ROR2 specific antibody that inhibits breast cancer primary tumor growth and metastasis through targeting CSCs.

overall_design: mRNA profile of breast cancer PDXs from  NCG mice treated with ROR2 antibody, B16 or human IgG of irrelevant specificity.

first: Feng

last: Leng

first: Liufeng

last: Wu


title: Dynamic dysregulation of the transcriptome upon deletion of Mecp2 in adult mice [CUT&RUN]

city: Houston

first: Sameer

middle: Subhash

last: Bajikar

state: TX

address: 1250 Moursund St

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Loss of function mutations in methyl Cpg binding protein 2 (MECP2) cause Rett syndrome. Loss of MeCP2 causes global transcriptional dysregulation, but it was unknown whether this transcriptional dysregulation was proximal to Mecp2 function. We deleted Mecp2 from adult mice and performed a time-series CUT&RUN experiment to identify if MeCP2 binding or histone post-translational modficiations are altered immediately upon loss of MeCP2.

overall_design: 16-week old mice harboring a floxed Mecp2 allele and tamoxifen inducible Cre recombinase were treated with tamoxifen or vehicle and whole hippocampal tissue was collected at several time points after tamoxifen treatment. CUT&RUN profiling was performed for MeCP2, several histone post-translational modifications, and IgG.

first: Huda

middle: Y

last: Zoghbi


title: Dynamic dysregulation of the transcriptome upon deletion of Mecp2 in adult mice

summary: Loss of function mutations in methyl Cpg binding protein 2 (MECP2) cause Rett syndrome. Loss of MeCP2 causes global transcriptional dysregulation, but it was unknown whether this transcriptional dysregulation was proximal to Mecp2 function. We deleted Mecp2 from adult mice and performed a time-series RNA-seq experiment to identif what transcripts were altered immediately upon loss of MeCP2.

overall_design: 16-week old mice harboring a floxed Mecp2 allele and tamoxifen inducible Cre recombinase were treated with tamoxifen or vehicle and whole hippocampal tissue was collected at several time points after tamoxifen treatment. PolyA RNA-seq was performed from collected RNA and expression was analyzed for differential expression.


title: Comparison of baseline global gene expression profiles of prostate cancer cell lines LNCaP and DU145

status: Public on Dec 15 2024

city: Astana

first: Syed

middle: Hani

last: Abidi

address: 53, Kabanbay Batyr Ave

country: Kazakhstan

institute: Nazarbayev University

summary: Introduction: DU145 and LNCaP are classic prostate cancer cell lines. Characterizing their baseline transcriptomics profiles (without any intervention) can offer insights into baseline genetic features and oncogenic pathways that should be considered while interpreting findings after various experimental interventions such as exogenous gene transfection or drug treatment.  Methods: LNCaP and DU145 cell lines were cultured under normal conditions, followed by RNA extraction, cDNA conversion, library preparation, and RNA sequencing using the Illumina NovaSeq platform. The sequences were analyzed to identify differentially expressed genes (DEGs) and for gene ontology (GO) and pathway enrichment.  Results: A total of 3916 and 2301 genes were found to be differentially upregulated and downregulated between LNCaP and DU145 cell lines, respectively. The GO and pathway analysis of up-regulated DEGs indicated significant enrichment of genes involved in extracellular matrix organization and cell-substrate adhesion, while down-regulated genes are involved in epithelial cell migration, cell death regulation, and cell proliferation.  Conclusion: The results showed significant differences in baseline gene expression and cellular pathways that may account for the varying metastatic potentials between LNCaP and DU145 cell lines, which should be considered when interpreting findings after experimental interventions.

overall_design: RNAseq based comparison of global gene expression patterns in between LNCaP and DU145 (ATCC: cat# CRL-1740 and HTB-81)

first: Khalid

last: Ahmed

first: Zhannur

last: Omarova

first: Alisalman

last: Sheikh

first: Kulsoom

last: Ghias

first: Syed Hani


title: Single-cell transcriptome of PBMC response to Omicron breakthrough infection

city: Jinan

first: yuwei

last: Zhang

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

institute: SDCDC

summary: To gain a deeper understanding of Omicron waves in the context of vaccination, we performed scRNA-seq together with single-cell V(D)J sequencing using PBMCs from nine Omicron breakthrough infection patients and six vaccinees to identify the possible cellular and molecular response mechanisms after breakthrough infection.

overall_design: We recruited 9 laboratory-confirmed COVID-19 patients and 6 booster vaccinees to form the droplet-based scRNA-seq (10X Genomics). Their ages ranged from 23 to 57 years old, and 7 of them were male. The EDTA anticoagulant peripheral blood from patients and vaccinees was collected in acute phase (within 7 days post symptom onset) and over 1 month after the last vaccination, respectively.

first: Xiaolin

last: Jiang

first: Yuwei

first: Shanshan

last: Han

first: Zengqiang

last: Kou


title: Targeting eEF1A reprograms cellular translation and uncovers alternative broad-spectrum antivirals against cap or m6A protein synthesis routes

city: Badalona

first: Cristina

last: Gálvez

state: Barcelona

address: Ctra. de Canyet s/n

department: Data Management

country: Spain

institute: IrsiCaixa

summary: Plitidepsin is an antitumoral drug safe for treating COVID-19 infection that impairs SARS-CoV-2 replication by targeting the translation elongation factor eEF1A. Here we show that plitidepsin decreased all SARS-CoV-2 transcripts along the early translation of viral R1AB polyproteins and the late synthesis of structural viral proteins. It also reduced de novo cap-dependent translation of viral and non-viral RNAs but affected less than 13% of the host proteome, thus preserving cellular viability. In response to plitidepsin, cells upregulated EIF2AK3 and additional proteins that reduce translation. Other proteins supported proteostasis via ribosome synthesis and cap-independent translation routes, which relied on eIF4G2, PABPC1, and readers such as IGF2BP2. While cap- or internal ribosome entry sites (IRES)-mediated translation pathways were inhibited by plitidepsin, impact on N6-methyladenosine (m6A) translation was limited. The molecular landscape reprogrammed by cells treated with plitidepsin predicted a potential broad-spectrum activity against viruses translated via cap- or IRES-dependent pathways that were suppressed by m6A. In agreement, plitidepsin inhibited the replication of members from the Coronaviridae, Flaviviridae, Pneumoviridae and Herpesviridae families. Yet, it failed to block retroviruses that exploit m6A synthesis routes and are inhibited by drugs against specific m6A readers such as IGF2BP2. By deciphering the molecular fingerprint of cells treated with host-directed therapies targeting protein translation, we identified a rational approach to select for broad-spectrum antivirals with complementary activities and potential to counteract future pandemic viruses.

overall_design: 1x10^6 Vero E6 cells per well seeded in a 24-well plate were infected with D614G at MOI 0.02 in the presence or absence of 50 nM plitidepsin for 4 h, 24 h and 48 h using 3 biological replicates per condition. At the indicated timepoints, cells were lysed with TRIzol™ (Invitrogen, 15596026 and 15596018). RNA was extracted with a Nucleospin RNA Magenerey-Nagel extraction kit and sequenced with Illumina TruSeq RNA w/ Ribo-Zero library, with coverage Novaseq 6000 150bp PE (150x2bp) 60M reads/spl (9Gb/spl) by Macrogen. Paired-end sequencing was performed according to standard TruSeq Stranded Total RNA Reference Guide (1000000040499 v00) protocol using TruSeq Stranded Total RNA Library Prep Gold Kit. All samples passed quality control checks and were aligned using bowtie255 version 2.5.1 to the SARS-CoV-2 variant EPI_ISL_510689 and the reference ASM985889v3. For host alignment, the reference genome GCA_023783515.1 and the human genome (GRCh38, ENSEMBL version 109) were used. RSEM56 v1.3.1 was used to create the indexes of these genomes and calculate the gene expression.

first: Elisa

last: Molina Molina

first: Lluís

last: Revilla

first: Eloi

last: Franco

first: Nuria

last: Izquierdo Useros


title: Organoids as a model system for researching human neuroendocrine tumor of the breast

city: DALIAN

first: Zhao

middle: Dong

last: Yi

address: No. 467, Zhongshan Road, Shahekou District

institute: The Second Hospital of Dalian Medical University

summary: This was the first instance of establishing an organoid model for the neuroendocrine tumor of the breast (NETB). Due to high heterogeneity, this NETB patient-derived organoid provides a robust foundation for clinical research. In the future, it could serve as a reliable tool for disease pathology diagnosis, drug screening, and genetic level studies.

overall_design: The NETB patient-derived organoids of the seventh generation were digested into single cells. Then, the cells in suspension were captured by microfluidic chips (Singleron Biotechnologies, Jiangsu, China).

first: Dongyi

last: Zhao

first: Xue

last: Bai

first: Shida

last: Zhu

first: Zuowei

first: Xuelu

last: Li


title: Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs

status: Public on Dec 14 2024

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

type: Non-coding RNA profiling by high throughput sequencing

summary: Transgenic expression of a double-stranded RNA in plants can induce silencing of homologous mRNAs in fungal pathogens. Although such host-induced gene silencing is well documented, the molecular mechanisms by which RNAs can move from the cytoplasm of plant cells across the plasma membrane of both the host cell and fungal cell are poorly understood. Indirect evidence suggests that this RNA transfer may occur at a very early stage of the infection process, prior to breach of the host cell wall, suggesting that silencing RNAs might be secreted onto leaf surfaces. To assess whether Arabidopsis plants possess a mechanism for secreting RNA onto leaf surfaces, we developed a protocol for isolating leaf surface RNA separately from intercellular (apoplastic) RNA. This protocol yielded abundant leaf surface RNA that displayed an RNA banding pattern distinct from apoplastic RNA, suggesting that it may be secreted directly onto the leaf surface rather than exuded through stomata or hydathodes. Notably, this RNA was not associated with either extracellular vesicles or protein complexes; however, RNA species longer than 100 nucleotides could be pelleted by ultracentrifugation. Furthermore, pelleting was inhibited by the divalent cation chelator EGTA, suggesting that these RNAs may form condensates on the leaf surface. These leaf surface RNAs are derived almost exclusively from Arabidopsis, but come from diverse genomic sources, including rRNA, tRNA, mRNA, intergenic RNA, microRNAs, and small interfering RNAs, with tRNAs especially enriched. We speculate that endogenous leaf surface RNA plays an important role in the assembly of distinct microbial communities on leaf surfaces.

overall_design: smallRNAseq and RNAseq profiling the RNA content of apoplastic washing fluid and leaf surface wash of Arabidopsis plants.

last: Baldrich

first: Lucia M

last: Borniego

first: Meenu

last: Singla-Rastogi

first: Madison

last: McGregor

first: Megha Hastantram

last: Sampangi-Ramaiah

first: Roger

last: Innes

first: Blake

last: Meyers


title: Characterization of Hepatitis B Virus Transcripts in Chronically HBV-infected Chimpanzees and Patients Treated with ARC-520 siRNA Demonstrates Transcriptional Silencing of cccDNA

city: Madison

first: Christine

last: Wooddell

state: WI

address: 502 S Rosa Rd

institute: Arrowhead Pharmaceuticals

summary: Full-length hepatitis B virus (HBV) transcripts of chimpanzees and patients treated with multidose (MD) HBV siRNA ARC-520 and entecavir (ETV) were characterized by single-molecule real-time (SMRT) sequencing, identifying multiple types of transcripts with the potential to encode HBx, HBsAg, HBeAg, core, and polymerase, as well as transcripts likely to be derived from dimers of dslDNA, and these differed between HBeAg-positive (HBeAg+) and HBeAg-negative (HBeAg−) individuals. HBV transcripts from the last follow-up ~30 months post-ARC-520 treatment were categorized from one HBeAg+ (one of two previously highly viremic patients that became HBeAg− upon treatment and had greatly reduced cccDNA products) and four HBeAg− patients. The previously HBeAg+ patient received a biopsy that revealed that he had 3.4 copies/cell cccDNA (two to three orders of magnitude more cccDNA than HBeAg− chimpanzees) but expressed primarily truncated X and HBsAg from iDNA, like two patients that were HBeAg− at the start of the study and had one copy/cell cccDNA. No HBV transcripts were detected in two other HBeAg− patients that had ~0.3 copies/cell cccDNA, one of which had seroconverted for HBsAg. The paucity of cccDNA-derived transcripts in the presence of high cccDNA demonstrates the transcriptional silencing of HBV following MD siRNA treatment with ETV.

overall_design: The initial study with nine chimpanzees aimed to determine the safety, tolerability, and pharmacological effects of ARC-520 siRNA treatment on HBsAg-positive chimpanzees (Pan troglodytes) which are thought to have become infected perinatally [Wooddell et al. Sci Transl Med, 2017]. HBV transcripts were characterized from six of these chimpanzees. The chimpanzees received daily oral entecavir for an 8–20-week lead-in period prior to receiving intravenous ARC-520 (2–4 mg/kg) once every four weeks (Q4W) with continued daily ETV. After 6–10 doses of ARC-520, the siRNA siHBV-75 ± siHBV-74 was tested in the HBeAg− chimpanzees that responded with lower activity to ARC-520. ETV dosing continued 1–2 weeks after the last siRNA dose. Plasma and serum were collected biweekly for the duration of the monitoring period to measure HBsAg, HBeAg, HBV DNA, anti-HBeAg, anti-HBsAg, clinical chemistries and complete blood counts as previously described [Wooddell et al. Sci Transl Med, 2017]. Periodic liver needle biopsies were collected to evaluate HBV DNA and RNA and for histology. All sample collections from the chimpanzees were conducted prior to 14 September 2015, when the U.S. Department of Fish and Wildlife reclassified chimpanzees born in captivity at research centers as endangered. References: 1. Wooddell, C.I., et al., RNAi-based treatment of chronically infected patients and chimpanzees reveals that integrated hepatitis B virus DNA is a source of HBsAg. Sci Transl Med, 2017. 9(409).

middle: I

first: Dean

last: Sanders

last: Xu

first: Lung-Yi

last: Mak

first: Thomas

last: Schluep

first: Wai-Kay

last: Seto

first: Bruce

middle: D

last: Given

first: Man-Fung

last: Yuen


title: Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [3C-seq]

city: Kyoto

first: Naomichi

last: Takemata

address: Kyoto University, Katsura, Nishikyo-ku

department: Synthetic Chemistry and Biological Chemistry

institute: Kyoto University

summary: Structural maintenance of chromosomes (SMC) complexes fold genomes by extruding DNA loops. In eukaryotes, loop-extruding SMC complexes form topologically associating domains (TADs) by being stalled by roadblock proteins. It remains unclear whether a similar mechanism of domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog of the bacterial Smc-ScpAB complex organizes the genome of Thermococcus kodakarensis into TAD-like domains. We also find that TrmBL2, a nucleoid-associated protein that forms a stiff nucleoprotein filament, stalls the T. kodakarensis SMC complex and establishes a boundary at the site-specific recombination site dif. TrmBL2 stalls the SMC complex at tens of additional non-boundary loci with lower efficiency. Intriguingly, the stalling efficiency is correlated with shape properties of underlying DNA sequences. Our study illuminates not only a eukaryotic-like mechanism of domain formation in archaea, but also an unforeseen role of intrinsic DNA shape in large-scale genome organization.

sample_organism:
Thermoplasma acidophilum
Thermococcus kodakarensis

overall_design: To investigate archaeal 3D genomes, 3C-seq was applied to Thermococcus kodakarensis and Thermoplasma acidophilum.

first: Kodai

last: Yamaura

first: Masashi

last: Kariya

first: Ayami

last: Osaka

first: Sonoko

last: Ishino

first: Masataka

last: Yamauchi

first: Tomonori

last: Tamura

first: Itaru

last: Hamachi

first: Shoji

last: Takada

first: Yoshizumi

first: Haruyuki

last: Atomi


title: Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [ChIP-seq]

overall_design: 3C-seq was performed on Thermococcus kodakarensis and Thermoplasma acidophilum. RNA-seq and ChIP-seq were performed on Thermococcus kodakarensis.


title: Pancreatic neuroendocrine tumor: case report of a patient with germline FANCD2 mutation and tumor analysis using single-cell RNA sequencing

city: Moscow

first: Alesya

last: Maluchenko

address: Kulakova str. 20

country: Russia

institute: Moscow Center for Advanced Studies

summary: Neuroendocrine neoplasms are a rare and heterogeneous group of neoplasms. Small sized (≤ 2 cm) pancreatic neuroendocrine tumors (pNETs) are of particular interest, as they are often associated with aggressive behavior, with no specific prognostic or progression markers. This article describes a clinical case characterized by a progressive growth of non-functional pNET requiring surgical treatment, in a patient with a germline FANCD2 mutation, previously not reported in pNETs.

overall_design: Primary pancreatic neuroendocrine tumor sample from one patient was analyzed using single-cell RNA-seq

first: Ekaterina

last: Avsievich

first: Diana

last: Salimgereeva

first: Alesia

first: Zoia

last: Antysheva

first: Ilia

last: Feidorov

first: Mark

last: Voloshin

first: Olga

last: Glazova

first: Denis

last: Maksimov

first: Samira

last: Kaziakhmedova

first: Natalia

last: Bodunova

first: Nikolay

last: Karnaukhov

first: Pavel

last: Volchkov

first: Julia

last: Krupinova


title: Sleeve Gastrectomy Reveals the Plasticity of the Human Gastric Epithelium

city: Jerusalem

first: Danny

last: Ben-Zvi

state: Israel

address: The Institute for Medical Research Israel Canada, The Faculty of Medicine

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: Gastric acidity is essential for the function of the human stomach. pH homeostasis is facilitated by gastrin, a hormone secreted from the gastric antrum in response to a rise in pH, leading to acid secretion from the gastric corpus. Sleeve gastrectomy (SG), a bariatric surgery in which 80% of the gastric corpus is excised, presents a challenge for gastric pH homeostasis. We used histology and single-cell RNA sequencing to study the gastric antrum and corpus epithelium of naïve patients, and of patients who underwent SG years earlier. SG was associated with an increase in a sub-population of acid-secreting parietal cells which overexpress respiratory enzymes and carbonic anhydrase, and an increase in the fraction of histamine-secreting enterochromaffin-like cells (ECLs). Notably, ECLs of SG-operated patients over-expressed genes coding for biosynthesis of neuropeptides and of serotonin. Mathematical modeling of pH homeostasis by gastrin showed that fasting pH is not sensitive to nearly all model parameters. Robustness is a result of the ability of gastrin to induce acid secretion as well as increase the number of ECLs and parietal cells, a feedback analogous to a non-linear proportional and integral feedback control, that drives adaptation of the epithelium to acid-secretion demand. Quantitative predictions of the model on the gastric response to SG were validated in patients: SG induced a 5-fold increase in blood gastrin levels as early as one day post-surgery, and an over 30% increase in the number of parietal cells and ECLs per gland years after surgery. Together, these empirical and modeling data demonstrate how the human gastric epithelium remodels following SG at the molecular and cellular levels, and more generally how trophic hormones such as gastrin enable robust adaptation of tissue function to meet physiological demand.

overall_design: Biopsies from gastric antrum and corpus (including fundus) of 12 female patients were collected. Five patients underwent SG 6.2±2.9 years earlier, and seven did not undergo gastric surgery (naïve). Gastric biopsies were dissociated, enriched for epithelial cells, and underwent scRNAseq

first: Amit

last: Elad

first: Botros

last: Moalem

first: Dana

last: Sender

first: Aya

last: Bardugo

first: Ki-Suk

last: Kim

first: Yhara

last: Arad

first: Haya

last: Benhayon

first: Ayelet

last: Etzyoni

first: Nechemi

last: Greenstein

first: Sarah

last: Knapp

first: Michelle

last: Malis

first: Bailey

last: Peck

first: Itia

last: Samuel

first: Salech

last: Daher

first: Esther

last: Forkosh

first: David

last: Hakhimian

first: Tiberiu

last: Hershcovici

first: Nadav

last: Ilani

first: Lior

last: Katz

first: Moshe

last: Rottenstreich

first: Alez

last: Vainer

first: Yishai

last: Yehuda

first: Eitan

middle: H

last: Zlotnick

first: Abed

last: Nasseradin

first: Idit

last: Shiff

first: Ariel

last: Benson

first: Ronit

last: Grinbaum

first: Siddhartha

last: Mishra

first: Linda

last: Samuelson

first: Darleen

last: Sandoval

first: Rachel

last: Ben-Haroush Schyr


title: ZDHHC15 mediates Hippo/YAP pathway palmitoylation and regulates tumor progression [HCC1954]

first: Jianxin

last: Wang

summary: The Post-translational modification of Hippo/YAP pathway members plays an important role in regulating the activation of Hippo/YAP pathway and its effects in tumors. S-Palmitoylation, also known as S-acylation, is the most common protein Lipid modification, mainly composed of palmitoyl transferases (PATs) from the DHHC (Asp His His Cys) family Catalysis. The results showed that ZDHHC15 mediated palmitoylation of KIBRA up-regulated the expression of YAP downstream target genes, and regulated the invasion function of breast cancer and ovarian cancer cells. The research results will reveal new regulatory mechanisms of the Hippo pathway

overall_design: Breast cancer HCC1954 cells with stable knockdown of ZDHHC15 and shCON as a negative control.  shCON and shZDHHC15 cells were extracted for RNA sequencing

first: Songshu

last: Meng


title: Therapeutic effect of platelet-derived extracellular vesicles on viral myocarditis correlate with biomolecular content

city: Jacksonville

first: DeLisa

last: Fairweather

state: FL

address: 4500 San Pablo Rd S

department: Cardiovascular Medicine

institute: Mayo Clinic

summary: Extracellular vesicles (EVs) can potently inhibit inflammation yet there is a lack of understanding about the impact of donor characteristics on the efficacy of EVs. The goal of this study was to determine whether the sex and age of donor platelet-derived EVs (PEV) affected their ability to inhibit viral myocarditis. PEV, isolated from men and women of all ages, was compared to PEV obtained from women under 50 years of age, which we termed premenopausal PEV (pmPEV). Because of the protective effect of estrogen against myocardial inflammation, we hypothesized that pmPEV would be more effective than PEV at inhibiting myocarditis. We injected PEV, pmPEV, or vehicle control in a mouse model of viral myocarditis and examined histology, gene expression, protein profiles, and performed proteome and microRNA (miR) sequencing of EVs. We found that both PEV and pmPEV significantly inhibited myocarditis; however, PEV was more effective, which was confirmed by a greater reduction of inflammatory cells and proinflammatory and profibrotic markers determined using gene expression and immunohistochemistry. Proteome and miR sequencing of EVs revealed that PEV miRs specifically targeted antiviral, Toll-like receptor (TLR)4, and inflammasome pathways known to contribute to myocarditis while pmPEV contained general immunoregulatory miRs. These differences in EV content corresponded to the differing anti-inflammatory effects of the two types of EVs on viral myocarditis.

overall_design: miRNA (miR) sequencing on PEV and pmPEV products to better understand the effect of miR content on their ability to inhibit myocarditis

first: Beetler

last: Danielle

first: Kocsis

last: Stephen

first: Fairweather

last: DeLisa


title: Psychological stress disturbs bone metabolism via miR-335-3p/Fos signaling in osteoclast

city: Shanghai

first: Jiayao

last: Zhang

address: NO.1239, Republican New Road

institute: Stomatological Hospital and Dental School of Tongji University

summary: Psychological stress interferes with bone metabolism, in which miRNAs may play an important role. To gain an insight into skeletal alterations under psychological stress, sRNA sequencing(sRNA-seq) was performed.

overall_design: Femoral cancellous bone adjacent to the growth plate was dissected and collected separately from the con and cums mice, and analyzed using sRNAseq.

first: Weicai

last: Liu

first: Shuxian

last: Lin

first: Juan

last: Li

first: Yun

last: Zhai


title: Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA shape [RNA-seq]

first: Naomichi

last: Takemata

overall_design: To investigate the role of archaeal Smc-ScpABn in gene regulation, RNA-seq was performed on the Thermococcus kodakarensis strain KU216 and its derivative mutants lacking either Smc, ScpA, or ScpB.

first: Kodai

last: Yamaura

first: Masashi

last: Kariya

first: Ayami

last: Osaka

first: Sonoko

last: Ishino

first: Masataka

last: Yamauchi

first: Tomonori

last: Tamura

first: Itaru

last: Hamachi

first: Shoji

last: Takada

first: Yoshizumi

first: Haruyuki

last: Atomi


title: Epigenome analysis of normal and lung adenocarcinoma (LUAD) samples

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of peripheral blood mononuclear cells(PBMCs) in normal and  LUAD samples. The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 820,000 CpGs in PBMC samples. Samples included 35  LUAD patients and 50 normal controls.

overall_design: Bisulphite converted DNA from the 85 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip.

first: Shibiao

first: Chuanxin

last: Wang


title: Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer [ATAC-seq]

city: Boston

first: Seong Won

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Heterozygous truncating variants in the sarcomere protein titin (TTN) are the most common genetic cause of heart failure. To understand mechanisms that regulate abundant cardiomyocyte TTN expression we characterized highly conserved intron 1 sequences that exhibited dynamic changes in chromatin accessibility during differentiation of human cardiomyocytes from induced pluripotent stem cells (hiPSC-CMs). Homozygous deletion of these sequences in mice caused embryonic lethality, while heterozygous mice demonstrated allele-specific reduction in Ttn expression. A 296 bp fragment of this element, denoted E1, was sufficient to drive the expression of a reporter gene in hiPSC-CMs. Deletion of E1 downregulated TTN expression, impaired sarcomerogenesis, and decreased contractility in hiPSC-CMs. Site-directed mutagenesis of predicted NKX2-5- and MEF2-binding sites within E1 abolished its transcriptional activity. Embryonic mice expressing E1 reporter gene constructs validated in vivo cardiac-specific activity of E1 and the requirement for NKX2-5 and MEF2 binding sequences. Moreover, isogenic hiPSC-CMs containing a rare E1 variant in the predicted MEF2 binding motif that was identified in a patient with unexplained DCM showed reduced TTN expression. Together, these discoveries define an essential, functional enhancer that regulates TTN expression. Manipulation of this element may advance therapeutic strategies to treat DCM caused by TTN haploinsufficiency.

overall_design: We performed ATACseq in WT hiPSCs during differentiation into cardiomyoyctes. hiPSCs were differentiated to cardiomyocytes using the standard protocols. Multiple biological replicates per time point were collected and later merged for peak calling.

first: Lauren

last: Wasson

first: Seongwon

first: Yuri

first: Steven

last: R DePalma

first: Joshua

middle: M

last: Gorham

first: Christine

last: Seidman

first: Jonathan

middle: G


title: Transcriptomic profiling of abiotic stress responses of Elaeis guineensis to drought, salinity, heat, cold and flood stresses

city: Serdang

first: Sime Darby

middle: Plantation

last: Technology Centre

state: Selangor

address: 1st Floor, Block B, UPM-MTDC, Universiti Putra Malaysia

department: Biotechnology & Breeding

country: Malaysia

institute: Sime Darby Plantation Technology Centre Sdn Bhd

summary: Oil palm (Elaeis guineensis) is a highly productive oil crop and the most consumed vegetable oil globally due to its unique oil characteristics. Palm oil production is affected by abiotic stresses, leading to food security issues and huge economic losses. To understand the oil palm responses to different abiotic stresses at the transcriptional level, we performed RNA-Seq analyses of oil palm leaves treated with drought, high salinity, heat, cold and flood stresses compared with controls. A total of 18 libraries (three biological replicates per treatment) were generated with approximately 843 million of total clean reads after data filtering. Clean reads were mapped to the oil palm reference genome at a total mapping rate of more than 70%. The quantification of expression analysis enabled the identification of potential abiotic stress-responsive genes, co-expressed under multiple abiotic stresses and unigenes that were induced by a specific abiotic stress. The availability of these RNA-Seq datasets will provide a better understanding of the abiotic stress response mechanisms to develop climate-resilient oil palm planting materials.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and abiotic stress treated oil palm seedlings.

first: Fong Chin

last: Lee

first: Wan Chin

last: Yeap

first: Shao Yong

last: Kee

first: David

last: Ross Appleton

first: Harikrishna

last: Kulaveerasingam


title: Identification of Selective SWI/SNF Dependencies in Enzalutamide-Resistant Prostate Cancer [CRISPR Screen]

status: Public on Dec 13 2024

city: Vancouver

first: Nathan

middle: A

last: Lack

state: BC

address: 2660 Oak S

country: Canada

institute: Vancouver Prostate Centre

summary: Enzalutamide (ENZA) is a potent second-generation antiandrogen commonly used to treat hormone-sensitive and castration-resistant prostate cancer (CRPC) patients. While initially effective, the response is only temporary and the disease almost always develops resistance. Given that many ENZA-resistant tumors are not driven by specific somatic mutations, there is increasing evidence that epigenetic factors can cause ENZA resistance. To explore how resistance arises we systematically tested all the epigenetic modifiers in castration-resistant and ENZA-resistant prostate cancer models using a custom epigenetic CRISPR library. From this, we identified and validated numerous epigenetic modifiers that were selectivity essential including SMARCC2, a core component of the SWI/SNF complex (or BAF complex) that regulates gene expression by altering DNA accessibility. Additionally, our data demonstrated canonical BAF complex dependency in ENZA-resistance that was also observed following the loss of DPF2, a canonical BAF-specific component. We showed that the chromatin occupancy of SMARCC2 and BRG1 was expanded in acquired ENZA resistance to the regions that overlap with transcriptional activity and CRPC-associated transcription factors that are significantly accessible in CRPC patients. Overall, our study revealed a regulatory role for SMARCC2 in ENZA-resistant prostate cancer and demonstrated the feasibility of targeting the SWI/SNF complex in late-stage PCa.

overall_design: For each cell line, Cas9-expressing cells were generated by lentiviral delivery of lentiCas9-blast (Addgene #52962) virus at multiplicity of infection (MOI) 5. Cells were selected with blasticidin for 5 days and maintained few passages before the CRISPR-Cas9 screen in selective media. For the screen, we used EPIKOL library in lentiGuide-puro (Addgene #52963) backbone that was generated in Koc University laboratories. The sgRNA library was transduced into stable Cas9-expressing PCa cell lines at low multiplicity of infection (MOI=0.3) with a median coverage of 500x cells per sgRNA. 48 hrs after transduction, cells were selected with puromycin for 3 days. At the end of selection, 4e6 cells were collected for sequencing experiments (reference point) and 13.5e6 cells were maintained further up to 15 doubling time to minimize differences in growth rates between cell populations. At 15th doubling time, 4x106 cells were collected for sequencing experiments.

first: Bengul

last: Gokbayrak


title: Identification of Selective SWI/SNF Dependencies in Enzalutamide-Resistant Prostate Cancer

overall_design: Chromatin Immunoprecipitation with sequencing (ChIP-seq) for SWI-SNF complex subunits in ENZA sensitive and resistant cell-ines.

first: Umut

last: Altintas

first: Tunc

last: Morova


title: Downregulation of AATK enhances susceptibility to ferroptosis by promoting endosome recycling in gefitinib-resistant lung cancer cells

city: Kaohsiung City

first: Yu-Peng

last: Liu

state: Not Applicable

address: No.100, Shin-Chuan 1st Road, Sanmin Dist.

country: Taiwan

institute: Kaohsiung Medical University

summary: Ferroptosis has been characterised by disruption of the cell membrane through iron-related lipid peroxidation. However, regulation of iron homeostasis in lung cancer cells which are resistant to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) remains unclear. Transcriptome analysis identified a significant downregulation of apoptosis-associated tyrosine kinase (AATK) mRNA expression in gefitinib-resistant PC9 (PC9-GR) cells, which were found to be more susceptible to ferroptosis inducers. An in-depth analysis of publicly available datasets revealed that downregulation of AATK mRNA was associated with lymph node metastasis and poor prognosis in patients with lung adenocarcinoma. Knockdown of AATK sensitized PC9, HCC827 and H441 cells to the ferroptosis inducer RSL3, whereas ectopic expression of AATK reduced RSL3-induced cell death in PC9-GR and HCC827-GR cells. Compared to PC9 cells, PC9-GR cells exhibited higher transferrin uptake, endosome recycling rate, and increased intracellular iron levels. Blocking iron transport reduced RSL3-induced ferroptosis in PC9-GR cells. Mechanistic studies showed that AATK localized to both early and recycling endosomes. Knockdown of AATK facilitated endosome recycling and elevated intracellular ferrous iron (Fe2+) levels in PC9 cells. Conversely, ectopic expression of AATK delayed endosome recycling and reduced intracellular Fe2+ levels in PC9-GR cells. Inhibition of AATK downregulation-induced iron accumulation decreased RSL3-induced ferroptosis. Taken together, our study indicates that the downregulation of AATK contributes to endosome recycling and iron accumulation, leading to an increased susceptibility to ferroptosis in EGFR-TKI-resistant lung cancer cells.

overall_design: The PC9-GR cell line was established by stepwise escalation of gefitinib from 0.5 μM to 10 μM. The PC9-GR cells were routinely maintained in the complete medium containing 10 μM gefitinib. Prior to the total RNA extraction, PC9-GR cells were cultured in a complete medium without gefitinib for a duration of 7 days. The total RNA samples were obtained from 3 independent biological repeats of PC9 and PC9-GR cell cultures.

first: Wei-Chang


title: High-dimensional analysis reveals increased chromatin heterogeneity and reduced histone acetylation driven by mutant-IDH1 [Cut&Run]

city: Rehovot

first: Efrat

last: Shema

address: 234 Hertzel

department: Department of Immunology & Regenerative Biology

institute: Weizmann Institute of Science

summary: Malignant gliomas are heterogeneous tumors arising in the central nervous system (CNS) driven by epigenetic and metabolic aberrations. Mutations in Isocitrate DeHydrogenase (IDH1/2) enzymes, highly frequent in adult gliomas, confer a gain-of-function activity that favors the conversion of a-ketoglutarate (α-KG) to the oncometabolite 2-hydroxyglutarate (2-HG), a competitive inhibitor of α-KG-dependent enzymes. These include DNA and histone lysine demethylases, resulting in an aberrant hypermethylation phenotype in mutant-IDH-expressing cells. Leveraging epigenetic-focused cytometry by time-of-flight (CyTOF) analysis, we profiled the effect of mutant-IDH1 expression on a broad panel of histone modifications. This analysis revealed extensive remodeling of chromatin patterns by mutant-IDH, with a global reduction in histone acetylation being the most prominent alteration. The loss of histone acetylation occurs rapidly following mutant-IDH1 induction and affects acetylation patterns over enhancers and intergenic regions. Furthermore, cells expressing mutant-IDH1 showed higher epigenetic heterogeneity, which may support the tumorigenic potential of these cells. Our study underscores the tight interaction between chromatin and metabolism dysregulation in glioma, highlighting novel epigenetic pathways affected by mutant-IDH1-driven metabolic rewiring.

overall_design: Cut&Run analysis of immortalized human astrocytes (IHA) induced to express IDH1-R132H for 2d and 7d (control are cells not treated with doxycycline). Primary antibodies used: anti-histone H3K27ac, anti-histone H3K9ac and anti-histone H4K16ac. Secondary antibody anti-rabbit HRP was used as a negative control.

first: Noa

last: Furth

first: Bareket

last: Dassa


title: High-dimensional analysis reveals increased chromatin heterogeneity and reduced histone acetylation driven by mutant-IDH1 [ATAC-seq]

overall_design: ATACseq analysis of immortalized human astrocytes (IHA) induced to express IDH1-R132H for 2d and 7d (control are cells not treated with doxycycline).


title: Single-cell RNA transcriptome reveals embryonic origin of offspring fibrosis due to maternal obesity

status: Public on Dec 12 2024

city: Pullman

first: Min

last: Du

state: WA

address: 1815 Ferdinand's Ln

department: Animal Science

institute: Washington State University

summary: Over 40% of pregnant American women are obese which negatively affects fetal development with long-term consequences for offspring health. Maternal obesity (MO) leads to fibrotic infiltration in skeletal muscle, brown adipose tissue, and other tissues/organs of offspring, but mechanisms remain to be defined. Using a mouse model of diet-induced obesity and unbiased single-cell RNA-sequencing (scRNA-seq), we tested the effeCONs of MO on embryonic fibrogenesis, which serves as the source of fibrogenic and stromal cells in adults. Embryonic somatic tissues were obtained at E9.5, E11.5 and E13.5 of control (CON) and MO mice. Using unsupervised clustering of scRNA-seq data, we identified three major cell clusters with increasing fibrogenic capacity. Compared to CON, the population of fibrogenic cells increased dramatically due to MO, correlated with the elevated expression of transforming growth factor β (Tgfb) and paired related homeobox 1 (Prrx1), as well as fibrogenic genes.

overall_design: Single-cell transcriptomic profiling of mouse embryos on embryonic 9.5, 11.5 and 13.5 day from maternal lean or obese mothers.

first: Md Nazmul

last: Hossain

first: Yao

last: Gao


title: Ethanolamine-induced assembly of microcompartments is required for Fusobacterium nucleatum virulence

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

country: Germany

institute: Bielefeld University

summary: Many bacteria metabolize ethanolamine as a nutrient source through cytoplasmic organelles named bacterial microcompartments (BMCs). Here we investigated the molecular assembly, regulation, and function of BMCs in Fusobacterium nucleatum – a Gram-negative oral pathobiont that is associated with adverse pregnancy outcomes. The F. nucleatum genome harbors a conserved ethanolamine utilization (eut) locus with 21 genes that encode several putative BMC shell proteins and a two-component signal transduction system (TCS), in addition to the enzymes for ethanolamine transport and catabolism. We show that the expression of most of these genes as well as BMC formation is highly increased in wild type fusobacteria when cultured in the presence of ethanolamine as a nutrient source. Deletion of the response regulator EutV eliminated this induction of eut mRNAs and BMCs, thus demonstrating that BMC formation is transcriptionally regulated by the TCS EutV-EutW in response to ethanolamine. Mass spectrometry of isolated BMCs unveiled the identity of the constituent proteins EutL, EutM1, EutM2, and EutN. Consistent with the role of these proteins in BMC assembly and metabolism, deletion of eutN, eutL/eutM1/eutM2, or eutL/eutM1/eutM2/eutN not only affected BMC formation, but also ethanolamine utilization, causing cell growth defects with ethanolamine as nutrient. BMCs also assembled in fusobacteria cultured with placental cells or the culture media, a process that is dependent on the BMC shell proteins. Significantly, we show that the eutN mutant is defective in inducing preterm birth in a mouse model. Together, these results establish that BMC-mediated metabolism of ethanolamine is critical for fusobacterial virulence.

sample_organism: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

overall_design: RNA-seq profiling of F.nucleatum parent and mutant strains

first: Dana

middle: S

last: Franklin

first: Yi-Wei

last: Chen

first: Yimin

first: Angela

last: Agnew

first: Alexis

last: Luu

first: Julian

middle: P

last: Whitelegge

first: Hong

last: Zhou

first: Andreas

last: Tauch

first: Asis

last: Das

first: Hung

last: Ton-That


title: Genome-wide R-loops dynamics and its alteration by Nkapl knockout in mouse testes with ssDRIP-seq

city: Nanjing

first: Chen

last: Xu

address: 101 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: To investigate genome-wide R-loops during meiosis exit and R-loop profiles changes with Nkapl knockout, we employed ssDRIP-seq (single-strand DNA ligation-based library preparation after DNA:RNA hybrid immunoprecipitation by S9.6 and sequencing) in wild-type and Nkapl-KO testes at P21.

overall_design: For ssDRIP-seq, we have biological duplicates. Input was separated, and S9.6 antibody was used for immunoprecipitation of DNA:RNA hybrid in 21d wild-type and Nkapl KO mouse testes.

first: Ruoyu

last: Yan

first: Mingyan

last: Lin

first: Lan

last: Ye


title: High-dimensional analysis reveals increased chromatin heterogeneity and reduced histone acetylation driven by mutant-IDH1 [MARS-seq]

first: Efrat

last: Shema

overall_design: MARS-seq analysis of immortalized human astrocytes (IHA) induced to express IDH1-R132H for 7d (control are cells not treated with doxycycline).

first: Noa

last: Furth

first: Bareket

last: Dassa


title: NKAPL RNA targets in mouse testes with eCLIP-seq

summary: To profile RNA targets of NKAPL on chromatin, we performed eCLIP-seq (enhanced crosslinking immunoprecipitation coupled with sequencing) using 21d wild-type mouse testes.

overall_design: We prepared biological replicate eCLIP-seq libraries of NKAPL. 2% of lysates were used as input and processed in parallel with immunoprecipitated samples.

first: Zhenlong

last: Kang


title: Gene expression alterations with Nkapl knockout or NKAPL frameshift mutation (M349fs)

summary: This study aims to explore the transcriptomic changes in Nkapl-KO, Sox30-KO and Nkapl TGdel/TGdel mouse testes comparing with their wild-type testes. Fresh testes were collected from 21d wild-type, Nkapl-KO, Sox30-KO and Nkapl TGdel/TGdel mice, respectively.

overall_design: For each group, we have biological triplicates. Total RNA was extracted using TRIzol reagent. Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina) according to the manufacturer's instructions.

first: Jie

last: Gong


title: NKAPL binding sites in mouse testis and the genome-wide occupancy of the SOX30/HDAC3 protein complex and RNA Pol II in the absence of NKAPL

summary: To profile genomic binding sites of NKAPL and examine whether its knockout alters the genome-wide occupancy of the SOX30/HDAC3 protein complex and RNA Pol II in mouse testes, wild-type and Nkapl KO testes at postnatal day 21 were harvested for ChIP-seq.

overall_design: Wild-type and Nkapl KO mouse testes were havested at postnatal day 21. ChIP experiments were performed with the indicated antibodies for NKAPL, SOX30, HDAC3, and RNA Pol II. Precipitated DNA was amplified according to ChIP Sequencing Sample Preparation Guide (Illumina).

first: Jinwen

last: Zhang


title: stRNA-seq of brain glioblastoma sample

status: Public on Dec 11 2024

first: Zhennan

last: Tao

address: Nanjing

department: Department of Neurosurgery

institute: Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School

summary: Proneural-mesenchymal transition (PMT) is a phenotypic alteration and contributes to therapeutic resistance and recurrence of glioblastoma (GBM). Macrophages, as a main infiltrating component of tumor immune microenvironment (TIM), can regulate the biological processes of PMT. However, the mechanisms driving this process remain largely unknown. Here, We performed single-cell RNA sequencing (scRNA-seq) (3V3) and Spatial transcriptomics RNA sequencing(stRNA-seq)(1V1) from tumor core and matching tumor periphery samples to discripe the overall landscape of tumor and nontumor cells in gliomas.

overall_design: We profiled freshly isolated cells from tumor core and paired surrounding peripheral tissue in glioma patients. scRNA-seq (3V3) and stRNA-seq(1v1) were used to discripe the overall landscape of tumor and nontumor cells in gliomas.

first: Wanli

last: Yu


title: scRNA-seq of brain glioblastoma sample


title: AKR1C1 Drives Oxaliplatin Chemoresistance by Activation of STAT3 in Colorectal Cancer

city: Wuhan

first: Zhiwen

last: FU

state: Hubei

address: 1277 Jianghan District, Wuhan, China

institute: Wuhan Union Hospital

summary: AKR1C1, a member of the AKR1C family, has been identified as a key player in cancer progression, promoting cancer cell proliferation and inhibiting apoptosis. Here, we identified AKR1C1 as a potential crucial gene significantly associated with oxaliplatin (OXA) sensitivity and unfavorable clinical outcomes through the transcriptome analysis of OXA-sensitive and -resistant colorectal cancer cell lines. Both in vitro and in vivo, AKR1C1 promotes cancer cell proliferation and confers OXA chemoresistance in colorectal cancer cells. Mechanistically, AKR1C1 interacts with and activates STAT3 and increases glutathione (GSH) levels, resulting in chemoresistance in colorectal cancer cells. Moreover, pharmacologic inhibition of AKR1C1 with alantolactone restores the sensitivity of resistant cell lines to OXA and the combined treatment of alantolactone with OXA exhibits superior antitumor effects in mouse xenografts. Collectively, the present study offers compelling evidence that AKR1C1 expression confers resistance to OXA in colorectal cancer, providing a promising strategy to circumvent chemoresistance.

overall_design: To identify the potential key gene(s) that confers the chemoresistance to oxaliplatin treatment in colorectal cancer cell

last: Fu

last: Shi


title: Barcoding Notch signaling in the developing brain

city: Philadelphia

first: Bushra

last: Raj

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania

summary: Developmental signaling inputs are fundamental for shaping cell fates and behavior. However, traditional fluorescent-based signaling reporters have limitations in scalability and molecular resolution of cell types. We present SABER-seq, a CRISPR-Cas molecular recorder that stores transient developmental signaling cues as permanent mutations in cellular genomes for deconstruction at later stages via single-cell transcriptomics. We applied SABER-seq to record Notch signaling in developing zebrafish brains. SABER-seq has two components: a signaling sensor and a barcode recorder. The sensor activates Cas9 in a Notch-dependent manner with inducible control while the recorder obtains mutations in ancestral cells where Notch is active. We combine SABER-seq with an expanded juvenile brain atlas to identify cell types derived from Notch-active founders. Our data reveals rare examples where differential Notch activity in ancestral progenitors is detected in terminally differentiated neuronal subtypes. SABER-seq is a novel platform for rapid, scalable and high-resolution mapping of signaling activity during development.

overall_design: 10x Genomics libraries of single-cell transcriptomes and SABER-seq data, and genomic DNA SABER data

first: Abigail

last: Siniscalco

first: Roshan

last: Perera

first: Jessie

middle: E

last: Greenslade

first: Hemagowri

last: Veeravenkatasubramanian

first: Aiden

last: Masters

first: Hannah

last: Doll


title: Effect of PP2A deficiency on gene expression in CD8+ T cells activation [scRNA-Seq]

city: Hangzhou

first: Kaixiang

last: Zhu

address: 866  Yuhangtang Road

department: school of medicine

institute: Zhejiang university

summary: Protein phosphatase 2A (PP2A) is one of the most abundant serine/threonine phosphatases and plays critical roles in regulating cell fate and function. We previously showed that PP2A regulates the differentiation of CD4+ T cells and the development of thymocytes. Nevertheless, its role in CD8+ T cells remains elusive. By ablating the catalytic subunit α (Cα) of PP2A in CD8+ T cells, we revealed the essential role of PP2A in promoting the effector functions of CD8+ T cells. Notably, PP2A Cα-deficient CD8+ T cells exhibit reduced proliferation and decreased cytokine production upon stimulation in vitro. In vivo, mice lacking PP2A Cα in T cells displayed defective immune responses against lymphocytic choriomeningitis virus infection, associated with reduced CD8+ T cell expansion and decreased cytokine production. Consistently, the ablation of the PP2A Cα subunit in CD8+ T cells results in attenuated antitumor activity in mice. There is a notable decrease in the infiltration of PP2A Cα-deficient CD8+ T cells within the tumor microenvironment, and the cells that do infiltrate exhibit diminished effector functions. Mechanistically, PP2A Cα deficiency impedes CD28-induced AKT Ser473 phosphorylation, thus impairing CD8+ T cell costimulation signal. Collectively, our findings underscore the critical role of phosphatase PP2A as a propeller for CD28-mediated costimulation signaling in CD8+ T cell effector function by fine-tuning T cell activation.

overall_design: To inveatigate the role of PP2A in CD8+ T cell effector function, we isolated CD8+ TILs from  WT and PP2A cKO tumor bearing mice. Then we performed gene expression profiling analysis using data obtained from scRNA-seq of WT and PP2A cKO CD8+ T cells.

first: Yuanling

last: Zhao

first: Lize

last: Wu

first: Linrong

last: Lu


title: Neurodevelopmental and behavioral defects in congenital heart disease [EMX-cre RNAseq]

status: Public on Dec 09 2024

city: Pittsburgh

first: Hisato

last: Yagi

address: 530 45th street, Rangos Res Center 8162

institute: University of Pittsburgh

summary: Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease associated with microcephaly and poor neurodevelopmental outcomes. Here we show that the Ohia HLHS mouse model, with mutations in Sap130, a chromatin modifier, and Pcdha9, a cell adhesion protein, also exhibits microcephaly associated with mitotic block and increased apoptosis leading to impaired cortical neurogenesis. Transcriptome profiling, DNA methylation, and Sap130 ChIPseq analyses all demonstrated dysregulation of genes associated with neurogenesis, cognitive impairment and autism. This involved perturbation of REST transcriptional regulation of neurogenesis, disruption of CREB signaling regulating synaptic plasticity, and defects in neurovascular coupling mediating cerebral blood flow. Adult mice harboring either the Pcdha9 mutation, which showed normal brain anatomy, or forebrain-specific Sap130 deletion via Emx1-Cre, which showed microcephaly, both demonstrated learning and memory deficits and autism-like behavior. These novel findings provide mechanistic insights indicating the adverse neurodevelopment in HLHS may involve cell autonomous/nonautonomous defects and epigenetic dysregulation.

overall_design: Expression profiling using RNA-seq of 6 samples collected from forebrain of Sap130 conditional KO mice (n=3 at E14.5) and their littermate controls (n=3at E14.5).

first: Lo

last: Cecilia

first: Gabriel

last: George

first: Yagi

last: Hisato

first: Bais

last: Abha


title: Single-cell RNA sequencing identifies Endothelial derived HBEGF promoting Pancreatic Beta Cell Proliferation via EGFR-Kmt5a-H4K20me Pathway [bulk RNA-seq]

status: Public on Dec 10 2024

city: Jinan

first: ling

middle: feng

last: lai

address: Number 6699, Qingdao road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary: Pancreatic beta cells mass is dynamically regulated in response to increased physiological demands during pregnancy. We used RNA sequencing (RNA-seq) to analyze the diversity and character of islets cells in pancreas.

overall_design: RNA sequencing (RNA-seq) was applied to analyze isolated islets from mice at virgin and gestational day14.5.

first: Fengling

last: Lai

first: Kaixin

last: Zhou

first: Yingjie

last: Ma

first: Weilin

last: Wang

first: Rundong

first: Rong

last: Huang

first: Tao

last: Xu


title: Effect of PP2A deficiency on gene expression in CD8+ T cells activation [bulkRNA-Seq]

first: Kaixiang

overall_design: To inveatigate the role of PP2A in CD8+ T cell effector function, we isolated naïve CD8+ T cells from 8-week-old  WT and PP2A cKO mice. Then we performed gene expression profiling analysis using data obtained from RNA-seq of WT and PP2A cKO CD8+ T cells stimulated by anti-CD3+CD28 for 1h.


title: USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation

city: Singapore

first: Muhammad

last: Idris

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB / A*STAR

summary: The N6-methyladenosine (m6A) binding protein YTHDF1 emerges as a frequently upregulated oncogene across various cancer types. Its depletion significantly improves the efficacy of cancer immune checkpoint blockade (ICB) treatment. A comprehensive understanding of the molecular mechanisms governing YTHDF1 protein stability is pivotal for enhancing clinical response rates and the effectiveness of ICB in cancer patients. Here, we report that USP5 interacts with YTHDF1, removing K11-linked polyubiquitination on multiple lysine residues to stabilize YTHDF1, thereby conferring its oncogenic properties. In response to insulin, mTORC1 phosphorylates USP5 at S149, promoting its dimerization. Dimerized USP5 then binds to YTHDF1, preventing its degradation. Conversely, the CUL7-FBXW8 E3 ubiquitin ligase promotes K11-linked polyubiquitination and degradation of YTHDF1. USP5 and FBXW8 thus regulate YTHDF1 ubiquitylation at defined residues through mutually exclusive interactions and opposing activities. Furthermore, deficiency in YTHDF1 or USP5 enhances PD-L1 expression and compromises the expression of multiple immune response-related genes, fostering cancer immune evasion. Remarkably, combining USP5 inhibitor treatment with anti-PD-1 immunotherapy reprograms the antitumor T-cell immunity environment, leading to enhanced tumor regression and markedly improved overall survival rates in mouse tumor models. Therefore, in hepatocellular carcinoma and lung cancer patients, USP5 may serve as a promising biomarker for stratifying individuals for anti-PD-1 therapy. Our findings reveal a ubiquitination-dependent regulation of YTHDF1 protein stability influencing immune response gene expression, suggesting USP5 inhibition combined with PD-(L)1 blockade as a novel and promising strategy for cancer treatment.

overall_design:
Since USP5 stabilizes YTHDF1 to regulate immunological response, we wanted to investigate the gene expression profiles of USP5 and YTHDF1 knockout in a liver cancer cell line.
In particular, we compared the changes in immune gene expression patterns to determine the immune reponse genes that were similarly regulated by USP5 and YTHDF1.

first: Shao

first: Xi

last: Lei

first: Lv

last: Yangfan

first: Idris

last: Muhammad

first: Zhang

last: Lin

first: Cao

last: Ya

first: Xiang

last: Jingyi

first: Xu

last: Xi

first: Ong

last: Belinda

last: Qiongyi

first: Peng

first: Yue

last: Xiaoyan

last: Feng

first: Liu

last: Chungang


title: Neurodevelopmental and behavioral defects in congenital heart disease [methylation]

first: Hisato

last: Yagi

overall_design: Methylation profiling using genomic DNA (9 samples collected from brain of Ohia mice (n=3 Severe, n=3 Mild at E15.5) , hetero controls (n=2) and their B6 controls (n=3 at E15.5) on Illumina Infinium MouseMethylation array (MouseMethylation-12v1-0_A1).

first: Lo

last: Cecilia

first: Gabriel

last: George

first: Yagi

last: Hisato

first: Bais

last: Abha


title: Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer.

first: Seong Won

last: Kim

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

overall_design: Refer to individual Series


title: Glycogen Synthase Kinase-3 Inhibition and Insulin Synergistically Enhance Proliferation and Inhibit Maturation of Human iPSC-derived Cardiomyocytes via TCF and FOXO Signaling

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Embryonic signaling pathways exert stage-specific effects during cardiac development, yet the precise cues for proliferation or maturation remain elusive. To address this, we utilized spontaneously beating human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) at day 12 of differentiation and performed a combinatory screen for various dosages of the glycogen synthase kinase-3 (GSK3) inhibitor CHIR99021 and Insulin for the analysis of cell cycle in hiPSC-CMs. Our combinatory screen for proliferation, subsequential downstream sarcomere development and RNA-seq analyses for Insulin/Akt and CHIR99021/Wnt demonstrate synergistic effects on proliferation of immature hiPSC-CMs. Conversely, removal of the Wnt and Insulin stimuli leads to rapid cell cycle exit and facilitates the terminal differentiation of immature hiPSC-CMs. Detailed characterization reveals that Wnt/CHIR99021, but not Insulin, regulates sarcomere homeostasis and architecture of immature hiPSC-CMs. Moreover, we further identify a temporal interplay between CHIR99021/Wnt via TCF and Insulin via FoxO signaling as regulators between proliferation and maturation in immature hiPSC-CMs. This work describes the cues that control proliferation versus terminal differentiation in functional immature hiPSC-CMs, and provides molecular mechanistic understanding between proliferation and maturation development of hiPSC-CMs.

overall_design: D12 hiPSC-CMs from the SCVI 273 line were cultured for 7 days under following conditions with RPMI1640 as base medium: B27 supplement (+insulin) (Sample name = WT), B26 supplement (-insulin) (Sample name = Treat 1), B26 supplement (-insulin) and 3μM CHIR99021 (Sample name = Treat 2), B27 supplement (+insulin) and  3μM CHIR99021 (Sample name = Treat 3). For each sample type, three independent biological replicates are collected.

first: Qianliang

last: Yuan

first: Devin

last: Verbueken

first: Reinier

last: Boon

first: Jan Willem

last: Buikema


title: High-dimensional analysis reveals increased chromatin heterogeneity and reduced histone acetylation driven by mutant-IDH1

first: Efrat

last: Shema


title: Single-cell RNA sequencing identifies Endothelial derived HBEGF promoting Pancreatic Beta Cell Proliferation via EGFR-Kmt5a-H4K20me Pathway [scRNA-seq]

first: ling

last: lai

summary: Pancreatic beta cells mass is dynamically regulated in response to increased physiological demands during pregnancy. We used single-cell RNA sequencing (scRNA-seq) to analyze the diversity and character of islets cells in pancreas.

overall_design: Single-cell RNA sequencing (scRNA-seq) was applied to analyze islets isolated from mice at virgin, different time points of gestation, and day 4 after delivery.

first: Fengling

last: Lai

first: Kaixin

last: Zhou

first: Yingjie

last: Ma

first: Weilin

last: Wang

first: Rundong

first: Rong

last: Huang

first: Tao

last: Xu