title: Incorporation of human iPS cell-derived stroma creates a pancreatic cancer organoid with heterogeneous cancer-associated fibroblasts [scRNA-Seq]

first: kenta

last: takeuchi

overall_design: Two types of fused pancreatic cancer organoid(FPCO) generated by patiend-derived pancreatic cancer organoids(PCOs), hiPSC-derived mesenchymal cells(hiPSC-MC) and vascular endothelial cells(hiPSC-EC).

first: Kenta

last: Takeuchi

first: Shunsuke

last: Tabe

last: Takahashi

first: Megumi

last: Matsuo

first: Yasuharu

last: Ueno

first: Yoichi

last: Furukawa

first: Kiyoshi

last: Yamaguchi

first: Masayuki

last: Ohtsuka

first: Soichiro

last: Morinaga

first: Yohei

last: Miyagi

first: Tomoyuki

first: Naok

last: i Tanimizu

first: Hideki

last: Taniguchi


title: The function of 3-Indolepropionic acid(IPA) in intestinal homeostasis

status: Public on Nov 13 2023

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: Intraepithelial immune cells and intestinal epithelial cells from the small intestine of mice were analyzed for the investigation of the impact of IPA.

overall_design: C57BL/6J male mice (8 weeks) were fed on high-fat diet (HFD) + l-NAME containing either control (CON) or high IPA (562.5 mg IPA/kg diet) for 7 weeks before dissection and small intestines were isolated. Cells from small intestine epithelium layer were sorted for DAPI- live cells and analyzed using 10x Genomics Chromium droplet single cell RNA sequencing (scRNA-seq).  Each sample is pooled from two individual mice.

first: Aldons

last: Lusis

first: Yuchen

last: Wang


title: Mutations in CHEK2 affect the tumor immune microenvironment and increase the response to PD-1 inhibitor therapy

city: Shanghai

first: Pingping

last: Xu

address: 145 Middle Shandong Road

country: China

institute: Shanghai Institute of Digestive Diseases, Renji Hospital, Shanghai Jiao-Tong University School of Medicine

summary: To elucidate whether CHEK2 mutations has effects on tumor microenvironment after immune checkpoint blockade therapy, we performed RNA-seq analysis of tumor tissues of mice receiving PBS or anti-PD-1 therapy to compare the gene expression profiles.

overall_design: RNA-seq was performed on MC38 and B16 tumors tissues of mice in CHEK2-knock out and CHEK2-WT cells which received PBS(N=3) or anti-PD-1(N=3).

first: Xu

last: Pingping


summary: To elucidate whether CHEK2 mutations has a similar effect on the tumor microenvironment and response to immune checkpoint blockade therapy as mutations in POLE, we performed RNA-seq analysis of tumor tissues of mice receiving PBS or anti-PD-1 therapy to compare the gene expression profiles.

overall_design: RNA-seq was performed on CT26 tumors tissues of mice in POLE-mutant and vector cells which received PBS(N=5) or anti-PD-1(N=5).


title: Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA

city: Boston

first: Richard

middle: Stefan

last: Isaac

state: MA

address: 77 Avenue Louis Pasteur, NRB 356

department: Genetics

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other machinery important for nuclear genome compaction, it remains unresolved how mtDNA is packaged into individual nucleoids. In this study, we used long-read single-molecule accessibility mapping to measure the compaction of individual full-length mtDNA molecules at near single-nucleotide resolution. We found that, unlike the nuclear genome, human mtDNA largely undergoes all-or-none global compaction, with most nucleoids existing in an inaccessible, inactive state. Highly accessible mitochondrial nucleoids are co-occupied by transcription and replication components and selectively form a triple-stranded displacement loop structure. In addition, we showed that the primary nucleoid-associated protein TFAM directly modulates the fraction of inaccessible nucleoids both in vivo and in vitro, acting consistently with a nucleation-and-spreading mechanism to coat and compact mitochondrial nucleoids. Together, these findings reveal the primary architecture of mtDNA packaging and regulation in human cells.

overall_design: Refer to individual Series for more information. ATAC-seq to assess bulk averaged DNA accessibility in HeLa S3 mitochondrial DNA. mtFiber-seq to measure per-nucleoid mitochondrial DNA accessibility. RNA-seq to measure changes in transcript levels during human skeletal myoblast differentiation


title: Gene expression profile at single cell level of plasma cells (PCs) from human bone marrow

status: Public on Nov 12 2023

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Antibody-secreting plasma cells (PCs) are generated in secondary lymphoid organs, but are reported to reside in an emerging range of anatomical sites. Analysis of the transcriptome of different tissue-resident (Tr)PC populations revealed that they each have their own transcriptional signature indicative of functional adaptation to the host tissue environment. In contrast to expectation, all TrPCs were extremely long-lived, regardless of their organ of residence, with the longevity influenced by intrinsic factors like the immunoglobulin isotype. Analysis at single-cell resolution revealed that the bone marrow is unique in housing a compendium of PCs generated all over the body that retain aspects of the transcriptional program indicative of their tissue of origin.

overall_design: Plasma cells were isolated from the bone marrow of a healthy adult human donor and analyzed using scRNAseq.

first: Ilariya

last: Tarasova

first: Junli

last: Nie


title: Deletion of the mitochondrial calcium uniporter in adipose tissue promotes energy expenditure and alleviates diet-induced obesity

city: Nanning

first: Lei

last: Zhou

state: Guangxi

address: Daxuedong Road, Xixiangtang District

department: College of Animal Science and Technology

institute: Guangxi University

summary: Objectives: Studies have shown a correlation between obesity and mitochondrial calcium homeostasis, yet it is unclear whether and how Mcu regulates adipocyte lipid deposition. This study aims to provide new potential target for the treatment of obesity and related metabolic diseases, and to explore the function of Mcu in adipose tissue. Methods: We firstly investigated the role of mitoxantrone, an Mcu inhibitor, in the regulation of glucose and lipid metabolism in mouse adipocytes (3T3-L1 cells). Secondly, C57BL/6J mice were used as a research model to investigate the effects of Mcu inhibitors on fat accumulation and glucose metabolism in mice on a high-fat diet (HFD), and by using CRISPR/Cas9 technology, adipose tissue-specific Mcu knockdown mice (Mcu fl/+ AKO) and Mcu knockout of mice (Mcu fl/fl AKO) were obtained, to further investigate the direct effects of Mcu on fat deposition, glucose tolerance and insulin sensitivity in mice on a high-fat diet. Results: we found the Mcu inhibitor reduced adipocytes lipid accumulation and adipose tissues mass in mice fed an HFD. Both Mcu fl/+ AKO mice and Mcu fl/fl AKO mice were resistant to HFD-induced obesity, compared to control mice. Mice with Mcu fl/fl AKO showed improved glucose tolerance and insulin sensitivity as well as reduced hepatic lipid accumulation. Mechanistically, inhibition of Mcu promoted mitochondrial biogenesis and adipocyte browning, increase energy expenditure and alleviates diet-induced obesity. Conclusion: Our study demonstrates a link between adipocyte lipid accumulation and mCa2+ levels, suggesting that adipose-specific Mcu deficiency alleviates HFD-induced obesity and ameliorates metabolic disorders such as insulin resistance and hepatic steatosis. These effects may be achieved by increasing mitochondrial biosynthesis, promoting white fat browning and enhancing energy metabolism.

overall_design: To investigate the function of Mcu in the regulation of glucose and lipid metabolism in vitro and in vivo, 3T3-L1 cells and C57BL/6J mice were treated with an Mcu inhibitor, and by using CRISPR/Cas9 technology, adipose tissue-specific Mcu knockdown mice (Mcu fl/+ AKO) and Mcu knockout of mice (Mcu fl/fl AKO) were obtained. Then to explore the difference of gene expression profiles between Mcu fl/fl AKO mice and the controls in the condition of high-fat diet, RNA-seq was performed on both white adipose tissue and brown adipose tissue.


title: Notch signaling and Bsh homeodomain activity are integrated to diversify Drosophila lamina neuron types

city: Eugene

first: Chris

last: Doe

address: 1440 Franklin Blvd

institute: University of Oregon

summary: Notch signaling is an evolutionarily conserved pathway for specifying binary neuronal fates, yet how it specifies different fates in different contexts remains elusive. In our accompanying paper, using the Drosophila lamina neuron types (L1-L5) as a model, we show that the primary homeodomain transcription factor (HDTF) Bsh activates secondary HDTFs Ap (L4) and Pdm3 (L5) and specifies L4/L5 neuronal fates. Here we test the hypothesis that Notch signaling enables Bsh to differentially specify L4 and L5 fates. We show asymmetric Notch signaling between newborn L4 and L5 neurons, but they are not siblings; rather, Notch signaling in L4 is due to Delta expression in adjacent L1 neurons. While Notch signaling and Bsh expression are mutually independent, Notch is necessary and sufficient for Bsh to specify L4 fate over L5. The NotchON L4, compared to NotchOFF L5, has a distinct open chromatin landscape which allows Bsh to bind distinct genomic loci, leading to L4-specific identity gene transcription. We propose a novel model in which Notch signaling is integrated with the primary HDTF activity to diversify neuron types by directly or indirectly generating a distinct open chromatin landscape that constrains the pool of genes that a primary HDTF can activate.

overall_design: To determine if L4 and L5 have differing open chromatin regions and Bsh genome-binding sites, we used Targeted DamID (TaDa) to profile both open chromatin (Dam-alone binding) and Bsh genome-binding loci (Dam:Bsh binding)

first: Chundi

first: Tyler

middle: B

last: Ramos

first: Owen

last: Marshall

middle: Q


title: Bone Stromal Glutamine Renders Tumor cell PARP Inhibitor Resistance

city: Beijing

first: Hanqiu

last: Zheng

address: Qinghuayuan Sub-District, Haidian District

department: School of Medicine

institute: Tsinghua University

summary: The majority of patients with late-stage breast cancer develop distal bone metastases. The bone microenvironment can affect response to therapy, and uncovering the underlying mechanisms could help identify improved strategies for treating bone metastatic breast cancer. Here, we observed that osteoclasts reduced the sensitivity of breast cancer cells to DNA damaging agents, including cisplatin and the PARP inhibitor (PARPi) olaparib. Metabolic profiling identified elevated glutamine production by osteoclasts. Glutamine supplementation enhanced the survival of breast cancer cells treated with DNA damaging agents, while blocking glutamine uptake increased sensitivity and suppressed bone metastasis. GPX4, the critical enzyme responsible for glutathione oxidation, was upregulated in cancer cells following PARPi treatment through stress-induced ATF4-dependent transcriptional programming. Increased glutamine uptake and GPX4 upregulation concertedly enhanced glutathione metabolism in cancer cells to help neutralize oxidative stress and generate PARPi resistance. Analysis of paired patient samples of primary breast tumors and bone metastases revealed significant induction of GPX4 in bone metastases. Combination therapy utilizing PARPi and zoledronate, which blocks osteoclast activity and thereby reduces the microenvironmental glutamine supply, generated a synergistic effect in reducing bone metastasis. These results identify a role for glutamine production by bone-resident cells in supporting metastatic cancer cells to overcome oxidative stress and develop resistance to DNA-damaging therapies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 5×10^5 MDA-MB-231 cells were plated on 10 cm dishes and cultured for 24 hours. Cells were then treated with either DMSO or 40 μM Olaparib for 3 days. Cells were lysed for RNA extraction and cDNA library construction and RNA-seq analysis; Macrophages were isolated from bone marrow cells flushed from the tibia of 6-week-old C57/BL6 mice and filtered through a 70 μm cell-strainer before over-night culture in α-MEM with 10% FBS. The following day non-adherent cells were plated and supplemented with 50 ng/ml M-CSF for 2 days. 2×106 Cells were then re-plated in 12 well plates at the presence of 100 ng/ml RANKL in DMEM plus 10% FBS, with media changed every 2 days (media was changed twice a day from Day 5 and on). Matured osteoclasts and macrophages were lysed for RNA extraction and cDNA library construction and RNA-seq analysis.

first: Huijuan

last: Fan

first: Zhanao


title: Comparative transcriptomics of the garden dormouse hypothalamus during early torpor, late torpor and interbout arousal of hibernation

city: Ulm

first: Annika

last: Herwig

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

country: Germany

institute: Ulm University

overall_design: Garden dormice (Eliomys quercinus, Gliridae) hibernated under constant darkness without food and water at 5 °C. Hypothalamic samples were dissected during early torpor (ET, one or two days torpid, n = 4, Tb = 5 °C), late torpor (LT, nine or ten days torpid, n = 3, Tb = 5 °C), or interbout arousal (IBA, normal metabolism for two of about four hours, n = 4, Tb = 37 °C).

first: Elena

last: Haugg

first: Sylvain

last: Giroud


title: MeCP2 Represses the Activity of Topoisomerase IIb in Long Neuronal Genes [ChIP-Seq]

status: Public on Nov 11 2023

city: St. Louis

first: Harrison

last: Gabel

state: MO

address: 4523 Clayton Ave

department: Neuroscience

institute: Washington University in St. Louis

summary: A unique signature of neuronal transcriptomes is the high expression of the longest genes in the genome (e.g. >100 kilobases). These genes encode proteins with essential functions in neuronal physiology, and disruption of long gene expression has been implicated in neurological disorders. DNA topoisomerases resolve topological constraints that arise on DNA and facilitate the expression of long genes in neurons. Conversely, methyl-CpG binding protein 2 (MeCP2), which is disrupted in Rett syndrome, can act as a transcriptional repressor to downregulate the expression of long genes. The molecular mechanisms underlying the regulation of long genes by these factors are not fully understood, however, and whether or not they directly influence each other is not known. Here, we identify a functional interaction between MeCP2 and Topoisomerase II-beta (TOP2b) in neurons. We show that MeCP2 and TOP2b physically interact in vivo and map protein sequences sufficient for their physical interaction in vitro. We profile TOP2b activity genome-wide in neurons and detect enrichment at regulatory regions and gene bodies of long neuronal genes, including long genes regulated by MeCP2. Further, we find that knockdown and overexpression of MeCP2 leads to altered TOP2b activity at MeCP2-regulated genes. Our findings uncover a mechanism by which MeCP2 inhibits the activity of TOP2b at long genes in neurons and suggest that this mechanism is disrupted in neurodevelopment disorders caused by mutation of MeCP2.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for TOP2b and the histone modification H3K27ac in primary neuron cultures.

first: Sabin

middle: A

last: Nettles

first: Yoshiho

last: Ikeuchi

first: Katheryn

last: Lefton

first: Ladan

last: Abbasi

first: Alyssa

last: Erickson

first: Chibueze

last: Agwu

first: Thomas

last: Papouin

first: Azad

last: Bonni

middle: W


title: MeCP2 Represses the Activity of Topoisomerase IIb in Long Neuronal Genes

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

overall_design: Refer to individual Series


title: MeCP2 Represses the Activity of Topoisomerase IIb in Long Neuronal Genes [RNA-Seq]

overall_design: Profiling gene expression analysis of RNA-seq data in primary neuron cultures in which MeCP2 protein expression was manipulated (e.g. MeCP2 overexpression, MeCP2 knockdown, control).


title: Incorporation of human iPS cell-derived stroma creates a pancreatic cancer organoid with heterogeneous cancer-associated fibroblasts

city: Minato Ku

first: kenta

last: takeuchi

state: Tokyo To

address: 4-6-1, Shirokanedai

country: Japan

institute: The Institute of Medical Science, The University of Tokyo


title: The alternative Nucleosome Remodeling Factor complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions (ATAC-seq)

city: London

first: Aliaksandra

last: Radzisheuskaya

address: 237 Fulham road

department: Cancer Biology

country: United Kingdom

institute: The Institute of Cancer Research

summary: Efficient treatment of Acute Myeloid Leukemia (AML) patients remains a challenge despite recent advances. Here using a CRISPRi screen targeting chromatin factors, we identified BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader modules of BPTF are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.

overall_design: 2 ATAC-sequencing experiments; the negative controls for each set are clearly specified in the title. Experiment 1: assessing the effect of BPTF KO on chromatin accessibility. Experiment 2: assessing the effect of SMARCA5 KO on chromatin accessibility. 2 biological replicates per sample were used. Experiment 3: ATAC-sequencing experiment assessing the effect of rapid SMARCA5 degradation on chromatin accessibility. 2 biological replicates per sample were used. The cells were treated with DMSO or dTAG-V1, as indicated in the sample name.

first: Kristian

last: Helin


title: Characterisation of the molecular signature of an 8 week-old human embryonic notochord

city: Hong Kong

first: Xinyi

last: Lin

state: NY

address: 562-570, Queen's Road West， Hong Kong Island

institute: The University of Hong Kong

summary: During embryonic development, the notochord is the precursor to the nucleus pulposus (NP) in the intervertebral disc (IVD), where the notochord cells differentiate to become notochordal-like cells in the NP, and are considered as potential progenitor cells to support the function of the NP. With aging and degeneration, there is a loss of these cells from the NP which ultimately affects IVD function. The characterisation of the molecular signature of the 8 week-old (gestational age) human embryonic notochord is a valuable resource to better understand the development from the notochord to the NP progenitors and as a benchmark for comparison to other datasets.

overall_design: Embyronic notochord was isolated from an 8 week old gestational age human fetus and enzymatically digested to single cells. Cells were prepared for single cell RNA-seq (10X genomics) as per manufacturer’s protocol.

first: Danny

last: Chan

first: Vivian

last: Tam


title: In vitro differentiation of pluripotent stem cells towards notochordal-like cells

summary: Description: The intervertebral disc (IVD) is a joint in the spine that is comprised of three major structures, the nucleus pulposus (NP), annulus fibrosus (AF) and cartilaginous endplate (EP). The NP is a proteoglycan-rich structure which contains a heterogenous population including the presence of progenitors such as the notochordal-like cells (NLCs) and NP cells, which are responsible for the synthesis and turnover of extracellular matrix in the NP. During aging and degeneration, there is a loss of cells, hydration, and changes in the ECM, that leads to the alterations in the biomechanical function of the IVD. The replenishment of cells, in particular, the progenitors are a potential therapy for IVD degeneration. However, a major challenge lies in obtaining sufficient numbers of healthy cells for treatment. This study used a 3 part protocol to differentiate pluripotent stem cells into NLCs in vitro.

overall_design: H1-derived ESCs were differentiated towards notochordal-like cells using a 3 step differentiation protocol. Cells were processed for single cell RNAseq using the 10X genomics platform


title: Gene expression profile at single cell level of notochordal-like cells (NLC) derived from human induced pluripotent stem cells (hiPSC) differentiation

summary: Notochordal cells are considered as a rare cell type ensuring signaling function required for proper development and homeostasis in various tissues. We used single cell RNA sequencing (scRNA-seq) to characterize gene signature of notochordal-like cells and understand heterogeneity of co-emerging cell types during in vitro differentiation.

overall_design: hiPS-NLC differentiating cells were dissociated and labelled with cell-multiplexing oligos (CMO) according to hiPSC line origin and treatment and analyzed using scRNAseq.

first: Julie

last: Warin

first: Anne

last: Camus

first: Frank

last: Riemers

first: Marianna

last: Tryfonidou


title: The alternative Nucleosome Remodeling Factor complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions (RNA-seq)

overall_design: Cells transduced with either a non-targeting sgRNA (sgNegCtrl, 3 biological replicates) or 2 sgRNAs inducing knockout of BPTF (3 biological replicates for each)


title: The alternative Nucleosome Remodeling Factor complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions


title: Young and undamaged recombinant albumin alleviates T2DM by improving hepatic glycolysis through EGFR and protecting islet β cells in mice

city: beijing

first: Anji

last: Ju

state: beijing

address: Tsinghua University,Beijing,China

summary: Type 2 Diabetes Mellitus (T2DM) is a severe disease that has reached epidemic proportions. In this study, treatment of T2DM mice with young, undamaged, and ultrapure recombinant mouse serum albumin (rMSA) increased their serum albumin levels, which resulted in a reversal of the disease including reduced fasting blood glucose levels, improved glucose tolerance, increased glucose-stimulated insulin secretion, and alleviated islet atrophy. At the cellular level, rMSA improved glucose uptake and glycolysis in hepatocytes. Mechanistically, rMSA reduced the binding between CAV1 and EGFR to increase EGFR activation leading to PI3K-AKT activation. Furthermore, rMSA extracellularly reduced the rate of fatty acid uptake by islet β-cells, which relieved the accumulation of intracellular ceramide, endoplasmic reticulum stress, and apoptosis. This study provided the first clear demonstration that injections of young, undamaged, and ultrapure recombinant serum albumin can alleviate T2DM in mice.

overall_design: A total of 6 liver samples from mice i.v. injected with isometric saline (n=3) or rMSA (n=3; 1.5g/kg b.w.) for 9 weeks were randomly selected to explore the chronic effects of rMSA on the hepatic gene expression profile. The AML12 hepatocytes were respectively treated with vehicle, insulin (10 nM), rMSA (600 μM), or insulin+rMSA for 24h and subjected to RNA-seq.

first: Hongyi

last: Liu

first: Xuan

last: Dong

first: Zongrui

last: Luo

first: Jiaze

last: Tang

first: Boyuan

last: Ma

first: Yan

last: Fu

first: Yongzhang


title: The alternative Nucleosome Remodeling Factor complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions (Cut&Run)

first: Aliaksandra

overall_design: 3 Cut&Run experiments. Experiment 1: BPTF genomic localization in wild type and BPTF KO cells. Experiment 2: HA-tagged SMARCA5 genomic localization in HA-SMARCA5-dTAG KI cell line treated with DMSO or with dTAG-V1. Experiment 3: BPTF genomic localization in wild type cells or in cells with BPTF truncations. 2 biological replicates were used for all the experiments. Experiment 4: CTCF Cut&Run in wild-type, BPTF KO and SMARCA5 KO THP-1 cells. The data for two indepdendent experiments is provided, the second experiment in 2 biological replicates. Experiment 5: CTCF, BPTF and SMARCA5 genomic profiling by Cut&Run in U937 and OCI-AML2 cells.


title: Modeling Post-Implantation Human Development to Yolk Sac Blood Emergence

status: Public on Nov 10 2023

city: Pittsburgh

first: Mo

middle: Reza

last: Ebrahimkhani

state: PA

address: 3550 Terrace Street, Scaife Hall A804

department: Department of Pathology

institute: University of Pittsburgh

summary: Implantation of the human embryo commences a critical developmental stage that comprises profound events including axis formation, gastrulation, and the emergence of yolk sac hematopoietic system. Our mechanistic knowledge of this window of human life remains limited due to restricted access to in vivo samples for both technical and ethical reasons. Stem cell models of human embryo have emerged to help unlock the mysteries of this stage. Here, we present a model of early post-implantation human embryogenesis (embryoid) with an extra-embryonic endoderm and mesoderm niche to support early hematopoiesis. This human embryo model is genetically inducible, and its unanticipated self-organization results in the development of the amniotic cavity, formation of bilaminar disc embryonic morphology, an anterior hypoblast pole and posterior domain. The extra-embryonic layer of iDiscoid presents multilineage yolk sac tissue morphogenesis with extra-embryonic mesoderm and lacks trophoblast. Its development captures distinct waves of yolk sac hematopoiesis including the emergence of erythroid, myeloid and lymphoid cells . iDiscoid offers an easy-to-use, high-throughput, reproducible, and scalable platform to probe multifaceted aspects of human development and blood formation at early post-implantation stage. It will provide a tractable human-based model for drug testing, disease modeling, and a unique cell source for regenerative medicine.

overall_design: To investigate the cell types that develop from this model system over time, we conducted scRNAseq on this model at a number of different ages for the purposes of identifying cell development and comparing the transcriptomes to existing human embryo data.

first: Joshua

last: Hislop

first: Qi

last: Song

first: Kamyar

last: Keshavarz F.

first: Amir

last: Alavi

first: Rayna

last: Schoenberger

first: Ryan

last: LeGraw

first: Jeremy

last: Velazquez

first: Tahere

last: Mokhtari

first: Mohammad

last: Naser Taheri

first: Matthew

last: Rytel

first: Susana

middle: M

last: Chuva de Sousa Lopes

first: Simon

last: Watkins

first: Donna

last: Stolz

first: Samira

last: Kiani

first: Berna

last: Sozen

first: Ziv

last: Bar-Joseph

middle: R


title: Effect of Aurora-A knockdown on gene expression in murine CRC cell lines.

city: Tainan

first: Shiang-Jie

last: Yang

address: No.1, University Road, Tainan City 701, Taiwan (R.O.C)

department: Institute of Basic Medical Sciences

country: Taiwan

institute: National Cheng Kung University

summary: We aim to investigate the gene expression profile regulated by Aurora-A in murine CRC cell lines to identify genes that are either positively or negatively modulated by Aurora-A.

overall_design: Aurora-A was knocked down in CT26 and MC38 cells using lentiviral-mediated short hairpin RNA (lenti-shmaurka-1). Cells transduced with lenti-shGFP served as the control group.  At 48 hours post-seeding, the Aurora-A knockdown cells were harvested, and the RNA was extracted for comparative gene expression profiling using RNA-seq.

first: Liang-Yi

last: Hung

first: Ming-Derg

last: Lai


title: RNA m6A methylation suppresses insect juvenile hormone degradation to minimize fitness costs in response to a pathogenic attack

first: Zhaojiang

last: Guo

address: No. 12, Zhongguancun South Street, Haidian District, Beijing 100081; China

department: Department of Plant Protection

institute: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences

summary: Bioinsecticides and transgenic crops based on the bacterial pathogen Bacillus thuringiensis (Bt) can effectively control diverse agricultural insect pests, nevertheless, insect resistance evolution without causing obvious fitness costs has seriously eroded the sustainable use of these Bt products. Recently, we have discovered that an increased titer of juvenile hormone (JH) favors an insect host (Plutella xylostella) to enhance fitness whilst resisting the Bt pathogen, however, the underlying regulatory mechanisms of the increased JH titer is obscure. Here, we define the involvement of N6-methyladenosine (m6A) RNA modification in modulating the availability of JH in this process. Specifically, we found that two m6A methyltransferase subunit genes, PxMettl3 and PxMettl14, repressed the expression of a key JH-degrading enzyme JH esterase (JHE) to induce an increased JH titer, mitigating the fitness costs associated with a robust defense against the Bt pathogen. This study identifies an as-yet uncharacterized m6A-mediated epigenetic regulator of insect hormones for maintaining fitness during pathogen defense and unveils an emerging Bt resistance-related m6A methylation atlas in insects, which further expands the functional landscape of m6A modification and showcases the pivotal role of epigenetic regulation in host-pathogen interactions.

overall_design: To explore the role of m6A modification in the resistance of Plutella xylostella to Bt Cry1Ac, we performed m6A-seq analysis on midgut tissues of Bt Cry1Ac susceptible and resistant strains


title: Efficient and Safe Therapeutic Use of Paired Cas9-Nickases for Primary Hyperoxaluria Type 1

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: The therapeutic use of adeno-associated viral vector (AAV)-mediated gene disruption using CRISPR-Cas9 is limited by potential off-target modifications and the risk of uncontrolled integration of vector genomes into CRISPR-mediated double-strand breaks. To address these concerns, we explored the use of AAV-delivered paired Staphylococcus aureus nickases (D10ASaCas9) to target the Hao1 gene for the treatment of primary hyperoxaluria type 1 (PH1). Our study demonstrated effective Hao1 gene disruption, a significant decrease in glycolate oxidase expression, and a therapeutic effect in PH1 mice. The assessment of undesired genetic modifications through CIRCLE-seq and CAST-Seq analyses revealed neither off-target activity nor chromosomal translocations. Importantly, the use of paired-D10ASaCas9 resulted in a significant reduction in AAV integration at the target site compared to SaCas9 nuclease. Additionally, our study highlights the limitations of current analytical tools in characterizing modifications introduced by paired D10ASaCas9, necessitating the development of a custom pipeline for more accurate characterization. These results describe a positive advance towards a safe and effective potential long-term treatment for PH1 patients.

overall_design: Mouse embryonic fibroblasts (MEFs) were treated with single and paired SaCas9 nucleases targeting Hao1. Genotoxicity was assesed via CAST-Seq.

first: Laura

last: Torella

first: Gloria

last: Gonzalez-Aseguinolaza

first: Julia

last: Klermund

first: Toni

last: Cathomen


title: The alternative Nucleosome Remodeling Factor complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions (Hi-C)

first: Aliaksandra

last: Radzisheuskaya

overall_design: Cells transduced with either a non-targeting sgRNA (sgNegCtrl, 2 biological replicates) or sgRNAs inducing knockout of BPTF (2 biological replicates) or SMARCA5 (2 biological replicates)

first: Kristian

last: Helin


title: Defining the mechanisms of action to the anti-PD-1+LAG-3 and anti-PD-1+CTLA-4 combinations in melanoma flank models

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

summary: We used single cell (sc) RNA-seq to analyze responding SM1 melanoma flank tumors and SM1 brain metastases to explore the mechanism of action of the anti-PD-1+LAG-3 and the anti-PD-1+CTLA-4 combination.

overall_design: Tumors were harvested at the endpoint under sterile conditions and weighed. Single-cell suspensions were prepared by enzymatic digestion, using a MACS tumor dissociation kit. The cell count and viability were analyzed by staining the cells with AO/PI stain on the Nexcelom Cellometer K2. Analysis was done using sc-RNAseq.

first: Manali

last: Phadke

first: Zhihua

last: Chen

first: Chaomei

last: Zhang


title: A study on the impact of the absence of the NIP or NrpR gene on gene expression of Streptococcus salivarius K12 (SAL)

status: Public on Nov 18 2023

city: Houston

first: Muthiah

last: Kumaraswami

state: Texas

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

summary: NIP and NrpR forms a pair for the transcriptional regulator in Streptococcus salivarius K12 (SAL). To explore the target genes regulated by the NIP-NrpR pair in Streptococcus salivarius K12 (SAL), we generated mutants in which the NIP or NrpR gene has been knocked down through complement recombination. Comparative  transcriptome profiling of WT, ▲nrpR, and nip* mutant strains revealed that the sar BGC is the major regulatory target controlled by the NIP signaling pathway in SAL.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different samples at the exponential growth phase of SAL. Comparative gene expression profiling analysis of RNA-seq data between wild type and mutant, total RNA was isolated from 3 independent growths (3 biological replicates)

first: Hackwon

last: Do

first: Nishanth

last: Makthal


title: MeCP2 Represses the Activity of Topoisomerase IIb in Long Neuronal Genes [eTIP-Seq]

first: Harrison

last: Gabel

overall_design:
Etoposide-mediated topoisomerase immunoprecipitation DNA-sequencing (eTIP-seq) for TOP2b.
eTIP-seq performed on 12 days in vitro (DIV12) cultured cortical neurons that were dissected from embryonic day 14.5 (E14.5) mouse pups that were untreated or transduced with lentivirus.

first: Sabin

last: Nettles

first: Yoshiho

last: Ikeuchi

first: Katheryn

last: Lefton

first: Ladan

last: Abbasi

first: Alyssa

last: Erickson

first: Chibueze

last: Agwu

first: Thomas

last: Papouin

first: Azad

last: Bonni


title: Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls (RNA-Seq)

city: Grand Rapids

first: Lena

last: Brundin

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: To investige gene expression and methylation changes in the suicide decedents group from postmortem brain tissues

overall_design:
We compared genome wide gene expression and methylation differences between the suicide decedents group (n=29) and mental healthy group who died by natural causes (n =31).
This submission represents the transcriptome component of study.

first: Qiong

last: Sha


title: Molecular basis of retinal remodeling in a Zebrafish model of Retinitis Pigmentosa

first: John

last: O'Brien

address: 4401 Martin Luther King Blvd

department: Vision Science

institute: University of Houston College of Optometry

summary: A hallmark of inherited retinal degenerative diseases such as Retinitis Pigmentosa (RP) is progressive structural and functional remodeling of the remaining retinal cells as photoreceptors degenerate. Extensive remodeling of the retina stands as a barrier for the successful implementation of strategies to restore vision. To understand the molecular basis of remodeling, we performed analyses of single-cell transcriptome data from adult Zebrafish retina of wild-type and a P23H mutant rhodopsin transgenic model of RP with continuous degeneration and regeneration. We provide a benchmark atlas of retinal cell type transcriptomes in Zebrafish and find changes in all retinal cell types in the P23H model. These include widespread oxidative stress, changes in reliance on oxidative metabolism and glycolysis, widespread synaptic remodeling, and changes in circadian rhythm regulation. This comprehensive transcriptomic analysis provides a molecular road map to understand how the retina remodels in the context of chronic retinal degeneration with ongoing regeneration.

overall_design: We have performed single-cell RNA Sequencing (sc-RNA Seq) of adult retina to assess the transcriptomic remodeling that takes place in the P23H Zebrafish model. In addition to providing a benchmark atlas of retinal cell type transcriptomes in the wild-type adult Zebrafish retina, we find transcriptional changes in essentially all cell types, reflective of the remodeling that has gone on in the chronic disease.

first: Abirami

last: Santhanam

first: Eyad

last: Shihabeddin

first: Haichao

last: Wei

first: Jiaqian

last: Wu


title: N-acetyltransferase NAT10 Controls Cell Fates via RNA Cytidine Acetylation

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

summary:
We show that NAT10-ac4C axis significantly regulates cell fates. To identify the molecular mechanisms of NAT10-ac4C-ANP32B axis in cell-fate transitions, we construct shNAT10 and shANP32B hESCs.
acRIP-seq of shCTR and shNAT10 hESCs.
We profiled ATAC-seq in shCTR, shNAT10, and shANP32B hESCs.
We profiled H3K4me3 and H3K27me3 modifications and the binding of ANP32B by CUT&Tag in shCTR and shNAT10 hESCs.

overall_design:
RNA-seq to find transcriptional differences between shCTR and shNAT10 hESCs and also as the input of acRIP-seq.acRIP-seq to identify acetylation targets.

ATAC-seq to observe the changes in chromatin accessibility with NAT10 or ANP32B suppression.

H3K4me3 and H3K27me3 CUT&Tag to examine their changes after NAT10 suppression. ANP32B CUT&Tag to profile the genome-wide chromatin binding of ANP32B.

RNA-seq to find transcriptional differences between shCTR and shANP32B cells.

We performed ATAC-seq to explore the regulation of ANP32B on chromatin accessibility in cell-fate transitions.

first: Zhensheng

last: Hu

first: Jie

last: Cao

first: Lianyu

last: lin

first: Jianzhao

last: Liu

first: Saiyong

last: Zhu


title: Cancer immunotherapy via synergistic co-activation of myeloid cells [RNA-seq]

city: Philadelphia

first: Max

last: Wattenberg

state: PENNSYLVANIA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Myeloid cells coordinate T cell immune evasion in cancer yet are pliable and possess anti-tumor potential. Here, by co-targeting activation molecules we leverage the myeloid compartment as a therapeutic vulnerability in cancer. Myeloid cells in solid tumors expressed activation receptors including the pattern recognition receptor CLEC7A and the TNF receptor superfamily member CD40. In mouse models of checkpoint inhibitor-resistant pancreatic cancer, co-activation of CLEC7A, via systemic β-glucan therapy, and CD40, with agonist antibody treatment, eradicated established tumors and induced immunological memory. Anti-tumor activity was dependent on a cDC1 – T cell axis but did not require classical T cell cytotoxicity or blockade of checkpoint molecules. Rather, targeting CD40 drove T cell-derived IFNγ signaling which converged with CLEC7A activation to program distinct macrophage subsets to facilitate tumor responses. Thus, productive cancer immune surveillance can be invoked by co-activation of complementary myeloid signaling pathways.

overall_design: Comparative gene expression from RNAseq conducted on bulk orthotopic tumors (PDA.7940B mouse tumor cells) untreated or 10 days post-treatment with beta-glucan, anti-CD40 or beta-glucan and anti-CD40

first: Heather

last: Coho

first: Veronica

last: Herrara

first: Kathleen

last: Graham

first: Meredith

middle: L

last: Stone

first: Yuqing

last: Xue

first: Renee

last: Chang

first: Christopher

last: Cassella

first: Mingen

first: Shaanti

last: Choi-Bose

first: Stacy

last: Thomas

first: Hana

last: Choi

first: Yan

last: Li

first: Lauren

last: Melendez

first: Kelly

last: Markowitz

first: Michael

last: Giannone

first: Nandita

last: Bose

first: Gregory

last: Beatty


title: Cancer immunotherapy via synergistic co-activation of myeloid cells [scRNA-seq]

first: Max

last: Wattenberg

summary: The goal of this study was to define the impact of beta-glucan (CLEC7A agonist), anti-CD40 (agonist) and the combination of beta-glucan and anti-CD40 on the intra-tumoral immune landscape of mouse orthotopic pancreatic tumors using single-cell RNA sequencing.

overall_design: This repository contains single-cell RNA sequencing of mouse  (PDA.7940B mouse tumor cells) (n=2 samples/condition) untreated or 8 days post-treatment with beta-glucan, anti-CD40 or beta-glucan and anti-CD40. Two samples (consisting of 2-3 pooled tumors) per treatment condition were processed. Tissues were mechanically minced and digested with collagenase/DNase and filtered. Dead cells were removed using a Dead cell removal kit (Miltenyi) and single-cell cDNA libraries were prepared at the CHOP Single Cell Genomics Core at the University of Pennsylvania.

first: Heather

last: Liu


title: CRISPR screening in human trophoblast stem cells reveals both shared and distinct aspects of human and mouse placental development

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

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

overall_design: Refer to individual Series


title: ChIP-seq analysis of primary human dermal fibroblasts overexpressing ANKRD1 in human dermal fibroblasts (HDFs)

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Stromal cell senescence plays a crucial role in activating cancer-associated fibroblasts (CAFs). The Androgen receptor (AR) function oversees cellular senescence and CAF activation. Here, we identify the mesenchymal-specific transcriptional coregulator ANKRD1 as a key driver of CAF conversion. ANKRD1 is strongly upregulated in CAFs and under direct negative control of AR, and its loss impairs the pro-tumorigenic potential of CAFs. ANKRD1 controls a CAF-specific gene expression program and is associated with poorer survival of HNSCC, lung, and cervical SCC patients. Mechanistically, ANKRD1 binds to the chromatin on CAF gene regulatory regions in a complex with the AP1 transcription factor family. We show that ANKRD1 enhances the AP1 DNA binding activity to CAF gene promoters. Targeting ANKRD1 with the FANA antisense oligonucleotides reverts CAFs into a normal fibroblast, disrupts AP1 complex formation, and blocks CAF’s pro-tumorigenic potential in an orthotopic model of SCC, thus representing an exciting target for stroma-oriented cancer therapy.

overall_design: ChIP-Seq was run with antibody the V5 tag in ANKRD1 over-expressing fibroblasts and compared with Input control.

first: Mazzeo

last: Luigi

first: Dotto

middle: G

last: Paolo


title: Transcriptomic analysis of human dermal fibroblasts overexpressing ANKRD1.

overall_design: Human dermal fibrloblasts with ANKRD1 overexpression versus control were run in triplicates.

first: Gian

middle: P

last: Dotto


title: Transcriptomic analysis of CAFs with silencing of ANKRD1.

overall_design: Gene expression of CAFs with ANKRD1 silencing were analyzed and compared to correspondent controls. Experiments were run in quadruplicate.


title: Mitral valve transcriptome analysis in thirty-four age-matched Cavalier King Charles Spaniels with or without congestive heart failure caused by myxomatous mitral valve disease

city: Frederiksberg

first: Peter

last: Karlskov-Mortensen

state: Select One...

address: Grønnegårdsvej 3

department: IVH

country: Denmark

institute: University of Copenhagen

summary: We here report the results of a mitral valve transcriptome study designed to identify genes and molecular pathways involved in development of congestive heart failure (CHF) following myxomatous mitral valve disease (MMVD) in dogs. The study is focused on a cohort of elderly age-matched dogs (n=34, age ~10 years) from a single breed – Cavalier King Charles Spaniels (CKCS) – with a high incidence of MMVD. The cohort comprises 19 dogs (10♀, 9♂) without MMVD-associated CHF, and 15 dogs (6♀, 9♂) with CHF caused by MMVD. I.e. we compare gene expression in breed and age matched groups of dogs, which only differ with respect to CHF status. We identify 56 genes, which are differentially expressed between the two groups. In this list of genes, we confirm an enrichment of genes related to the TNFβ signaling pathway, extracellular matrix organization, vascular development, and endothelium damage, which also have been identified in previous studies. However, the genes with the greatest difference in expression between the two groups are CNTN3 and MYH1. Both genes encode proteins, which are predicted to have an effect on the contractile activity of myocardial cells, which in turn may have an effect on valvular performance and hemodynamics across the mitral valve. This may result in shear forces with impact on MMVD progression.

overall_design: Total poly-A RNA isolated from canine mitral valves. The dataset comprise RNAseq data from case dogs with severe myxomatous mitral valve disease, which has progressed into congestive heart failure (CHF), and control dogs with milder myxomatous mitral valve disease, which has not reached a stage of CHF.

first: Susanna

last: Cirera

first: Merete

last: Fredholm

first: Fei

last: Gao

first: Maria

middle: U

last: Reimann

first: Signe

last: Cremer

first: Liselotte

last: Christiansen

first: Emil

last: Ibragimov

first: Lisbeth

last: Olsen


title: Single cell transcriptome analysis of intermediate neural progenitors (INPs) and type II neural stem cells (NSCII) from brat and control backgrounds isolated from Drosophila melanogaster larval brains

city: Plymouth

first: Claudia

last: Barros

state: Devon

address: The John Bull Building, Plymouth Science Park, 16 Research Way

institute: University of Plymouth

summary:
The analysis presented here aims at exposing single-cell transcriptome profiles of Drosophila larval brain type II neural stem cells (NSCII) and of their intermediate neural progenitor (INP) cell progeny during normal development and upon brain tumour initiation using the brain tumour (brat) mutant model.
We have used brains 24 hours after larval hatching (ALH), a developmental stage when brat INPs (b_INP) have transformed into brain tumour initiating cells, expressing aberrantly the self-renewal transcription factor Deadpan unlike their iINP control counterparts (c_iINP), but have not yet started to overproliferate. iINP will acquire expression of proneural Asense (Ase) becoming mature INPs (m_INPs), yet brat INPs never express Ase and will lead to massive tumour growth (Bello et al., 2008; Boone and Doe, 2008; Bowman et al., 2008). NSCIIs, adjacent smaller iINPs and one mature INP were individually harvested from live freshly dissected brains expressing membrane tagged GFP specifically in NSCII lineages, and single cell transcriptomes obtained as previously described (Bossing et al., 2012; Barros & Bossing, 2022). PCRs confirmed iINPs and INP samples to lack or show ase expression, respectively. Single cell cDNAs were hybridised on whole-genome microarrays in pairs and data processed as indicated below.
References:
Bello, B.C., Izergina, N., Caussinus, E., and Reichert, H. (2008). Amplification of neural stem cell proliferation by intermediate progenitor cells in Drosophila brain development. Neural Dev 3, 5.
Bowman, R.L., Wang, Q., Carro, A., Verhaak, R.G., and Squatrito, M. (2017). GlioVis data portal for visualization and analysis of brain tumor expression datasets. Neuro Oncol 19, 139-141.
Boone, J.Q., and Doe, C.Q. (2008). Identification of Drosophila type II neuroblast lineages containing transit amplifying ganglion mother cells. Dev Neurobiol 68, 1185-1195.
Bossing, T., Barros, C.S., Fischer, B., Russell, S., and Shepherd, D. (2012). Disruption of microtubule integrity initiates mitosis during CNS repair. Dev Cell 23, 433-440.
Barros C.S. & Bossing, T. (2022). Direct isolation of single cells from living brains of Drosophila melanogaster without dissociation for transcriptome analysis. STAR Protoc. Dec 16;3(4):101735.

overall_design: Single INPs and type II NSCs were isolated from brat mutant Drosophila larval brains. Single immature INPs (iINPs), one mature INP and type II NSCs were isolated from control Drosophila larval brains. Samples were hybridized as follows: single brat INP versus single brat NSCII pairs (n=3), single control iINP versus single control NSCII pairs (n=3), and one single control INP versus single control NSCII (n=1). Each single cell was independently harvested directly from live 24h ALH brain lobes.

first: Torsten

last: Bossing

first: Karolina

middle: J

last: Jaworek

first: Jon

last: Gil-Ranedo

first: Matthias

middle: E

last: Futschik

middle: S


title: Study Nocte's functions in transcription and translation in Drosophila eye discs

city: Baltimore

first: Weidong

last: Wang

state: MD

address: 251 Bayview Blvd BRC, Suite 100 Rm10B014

institute: National Institute of Aging

summary: Nocte is an RNA binding protein but its functions in Drosophila eye development is unknown. We found that knockdown of nocte by RNAi in Drosophila eyes leads to small and rough eye phenotypes. We detected nocte's functions at mRNA levels by doing RNA-seq with purified polyA mRNA. We detected nocte's functions in mRNA translation by doing Ribo-seq and total RNA-seq to calculate the translation efficiencies.

overall_design: For polyA RNA-seq, 20 pairs of late L3 eye discs were used in one repeat, and three repeats for WT and ey>nocte-RNAi eye discs were done. For Ribo-seq, 50 pairs of late L3 eye discs were used in one repeat, and three repeats for WT and ey>nocte-RNAi eye discs were done. The total RNAs from two repeats of WT and ey>nocte-RNAi samples for Ribo-seq were used for total RNA-seq. The samples in total RNA-seq were treated with rRNA depletion and submitted for RNA-seq.

first: Tianyi

last: Zhang

first: Yutong

last: Xue

first: Shuaikun

last: Su

first: Valerie

last: Altouma

first: Katherine

last: HO

first: Jennifer

last: Martindale

first: Seung

last: Lee

first: Weiping

last: Shen

first: Myriam

last: Gorospe


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer [ChIP-Seq]

city: Boston

first: Daniel

last: Temko

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

summary: Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity and treatment response, we combined functional and molecular profiling with computational analysis tools. Using these approaches, we defined transcriptional, epigenetic, and metabolic subtypes, and identified subtype-driving super-enhancers. Single cell RNA sequencing analyses revealed relative homogeneity of the three major transcriptional subtypes (luminal, basal and mesenchymal) within tumors. We found that mesenchymal TNBCs are more similar to mesenchymal neuroblastoma and rhabdoid tumors than to other TNBC subtypes, and the PRRX1 transcription factor serves as a key driver of these tumors. By directly regulating the transcription of mesenchymal genes, PRRX1 is sufficient for inducing the mesenchymal subtype but is not required for its maintenance.

overall_design: Duplicate H3K27ac ChIP-seq of 2 TNBC cell lines with TET-inducible expression of wild type or DNA-binding mutant PRRX1, with and without doxycycline treatment, at two time points

first: Bojana

last: Jovanović

first: Franziska

last: Michor

first: Kornelia

last: Polyak


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer [RNA-Seq]

overall_design: RNA-seq of two TNBC cell lines with and without TET-inducible expression of PRRX1-targeting shRNA's, with and without doxycycline treatment, at two time points


title: C-Terminal Binding Protein (CtBP) a critical regulator of ErbB2/3 signaling in PDAC

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: Pancreatic ductal adenocarcinoma (PDAC) remains among the most lethal of human cancers underscoring the need to identify new therapeutic vulnerabilities. Previously, we reported high expression of transcriptional co-regulators C-terminal binding proteins (CtBP) 1 and 2 in human PDAC, however their precise role in PDAC formation or progression remains unclear. Here, we have studied PDAC tumor dependency on CtBPs for growth and metastasis using an orthotopic syngeneic pancreatic tumor mouse model. CRISPR-based homozygous deletion of Ctbp2 dramatically decreased PDAC tumor growth, drastically reduced metastatic potential, and significantly prolonged survival. Interrogating differential gene expression of the orthotopic PDAC tumors from CtBP2 WT vs. CtBP2 KO cohorts, we identified significant downregulation of the EGFR-superfamily receptor ErbB3 in CtBP2 KO tumors, and further determined that CtBP regulates expression of both the ErbB2 and 3 EGFR superfamily genes in PDAC cells. We therefore hypothesized that CtBP regulation of physiologic ErbB2/3 signaling contributes, in part, to PDAC growth and metastasis. Indeed, we observed that CtBP2 KO cells exhibited severely attenuated activation of phospho-Akt after neuregulin stimulation of ErbB2/3, and we demonstrate that human PDAC cells also show CtBP dependence of ErbB2/3 expression. Our results suggest that a subset of PDAC tumors is dependent on physiologic ErbB2/3 signaling and could be targeted by pharmacologic inhibitors of ErbB2 and/or ErbB3. Providing proof of concept, the ErbB2-targeted multikinase inhibitor lapatinib, but not the ErbB1/EGFR targeted agent erlotinib, effectively killed ErbB3 expressing PDAC cells, while CtBP2 KO cells where ErbB3 expression was extinguished, were resistant to lapatinib. Taken together, our data suggests that ErBb2/3 targeted therapeutics can effectively target a critical PDAC dependency on physiologic ErbB2/3 signaling which is the result of CtBP’s oncogenic transcriptional program that drives PDAC tumor progression.

overall_design: We have studied the impact of Ctbp2 deletion in PDAC using an orthotopic syngeneic pancreatic tumor mouse model using a mouse PDAC cell line derived from a CKP (K-Ras G12D/ p53 null) PDAC tumor. Ctbp2 was then deleted homozygously in the CKP cell line using CRISPR/Cas9. RNA-seq was performed to determine gene expression differences between KO and WT Ctbp2 expressing cells.

first: Kranthi

last: Chougoni

first: Steven

last: Grossman


title: Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy [placenta-ncbi-cell-line_scRNA-seq_snRNA-seq]

status: Public on Nov 09 2023

city: Beijing

first: Hongmei

last: Wang

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: The human placenta plays vital roles in ensuring a successful pregnancy. Despite the growing body of knowledge about its cellular compositions and functions, however, there has been limited research on the heterogeneity of the billions of nuclei within the syncytiotrophoblast (STB), a multinucleated entity primarily responsible for placental function. Here, we conducted integrated snRNA-seq and snATAC-seq on human placentas from early and late pregnancy. Our findings demonstrate the dynamic heterogeneity and developmental trajectories of STB nuclei and their presence in human trophoblast stem cells (hTSCs)-derived STB. Furthermore, we identified transcription factor (TF) motifs that are biased towards diverse STB nuclear lineages through their associated gene regulatory networks. The role of these TFs in STB differentiation were confirmed in the hTSCs- and trophoblast organoid-derived STB. Together, our data provide valuable insights into the heterogeneity of human STB and represents a valuable resource for interpreting its associated pregnancy complications.

overall_design: To determine multinucleated STB features in vitro, two hTSC cell lines, which were derived from either human early blastocyst (hereinafter referred as hTSCs-BL) and or first-trimester placental CTBs (hereinafter referred as hTSCs-CT30), were cultured and differentiated to STB. we conducted snRNA-seq analysis of STB derived from both hTSCs-BL and hTSCs-CT30, along with scRNA-seq sequencing for the two hTSCs.

first: Meijiao


title: Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy [placenta-ncbi-placenta-villi_multiomic]

overall_design: To comprehensively understand the human placental nuclear repertoire and its regulatory mechanisms, we applied snRNA-seq and snATAC-seq techniques to nuclei isolated from six healthy placentas in early pregnancy (10X Genomics; 6-9 weeks of gestation), and six healthy placentas in late pregnancy (10X Genomics; 38-39 weeks of gestation). We took measures to eliminate potential sex-bias by collecting an equal number of placentas on each gender prior sequencing. Equal portions of intact placental nuclei from the same placenta were utilized for snRNA-seq and snATAC-seq


title: Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy [placenta-ncbi-cell-line_ChIPseq_cuttag]

overall_design: To determine whether there is a correspondence regulatory mechanisms exist between in vitro and in vivo STB, we differentiated two hTSC cell lines, which were derived from either human early blastocyst (hereinafter referred as hTSCs-BL) and or first-trimester placental CTBs (hereinafter referred as hTSCs-CT30) to syncytiotrophoblast (STB). Then ChIP-seq and CUT&Tag  experiments were performed with antibody CEBPB and FOSL2 for both hTSC cell lines and STB cell lines. We used IgG and/or input as controls.


title: SAR-096: Phase II clinical trial of ribociclib in combination with everolimus in advanced dedifferentiated liposarcoma (DDL), and leiomyosarcoma (LMS)

city: 3601 Spruce Street

first: Yan

last: Zhou

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

summary: Purpose: DDL and LMS are two common subtypes of soft tissue sarcoma, a rare group of diseases for which new treatments are needed. Chemotherapy remains the standard option for advanced disease. Targeting CDK4/6 in DDL and mTOR in LMS is of biologic interest. When combined, the CDK4 inhibitor ribociclib and the mTOR inhibitor everolimus, have shown synergistic growth inhibition in multiple tumor models, suggesting that this combination could be beneficial in patients.Methods: This was a single arm, open label, multi-center phase II study of the combination of ribociclib and everolimus. Patients were enrolled into one of two cohorts: DDL or LMS with intact Rb. The primary endpoint was progression free rate (PFR) at 16 weeks. Secondary endpoints included progression free (PFS) and overall survival, safety and biomarker analyses. Results: In the DDL cohort, 33.3% (95% CI 15.6%-55.3%) of patients were progression free at 16 weeks. Median PFS in this cohort was 15.4 weeks (95% CI, 8-36 weeks) with 2 partial responses. In the LMS cohort the PFR at 16 weeks was 29.2% (95% CI 12.6%-51.1%). Median PFS in this cohort was 15.7 weeks (95% CI 7.7-NA). Most common toxicities included fatigue (66.7%), anorexia (43.8%) and hyperglycemia (43.8%). Concordance between Rb testing methodologies was poor.Conclusions: The combination of ribociclib and everolimus demonstrates activity in DDL with prolonged stable disease (≥16 weeks) meeting the primary endpoint. Notably partial responses were observed. The primary endpoint was not reached in the LMS cohort. The combination was well tolerated with expected side effects.

overall_design: We have collected total RNAs of sarcoma patient samples which are either responders or non-responders. We want to study the gene expression changes between the two groups.

first: Sujana

last: Movva

first: Delia

last: Zumpano

first: Lori

last: Rink


title: γδ T cell-mediated cytotoxicity against patient-derived healthy and cancer cervical organoids

city: Kiel

first: Thomas

middle: F.

last: Meyer

address: Schwanenweg 20, Haus U27, 2 OG

department: Infektion Onkologie

institute: IKMB

summary:
Cervical cancer is a leading cause of death among women globally, primarily driven by high-risk papillomaviruses. However, the effectiveness of chemotherapy is limited, underscoring the potential of personalized immunotherapies. Patient-derived organoids, which possess cellular heterogeneity, proper epithelial architecture and functionality, and long-term propagation capabilities offer a promising platform for developing viable strategies.
In addition to αβ T cells and natural killer (NK) cells, γδ T cells represent an immune cell population with significant therapeutic potential against both hematologic and solid tumours.
To evaluate the efficacy of γδ T cells in cervical cancer treatment, we generated patient-derived healthy and cancer ectocervical organoids. Furthermore, we examined transformed healthy organoids, expressing HPV16 oncogenes E6 and E7. We analysed the effector function of in vitro expanded γδ T cells upon co-culture with organoids. Our findings demonstrated that healthy cervical organoids were less susceptible to γδ T cell-mediated cytotoxicity compared to HPV-transformed organoids and cancerous organoids.

overall_design: To identify the underlying pathways involved in this observed cytotoxicity, we performed bulk-RNA sequencing on the organoid lines, revealing differences in DNA-damage and cell cycle checkpoint pathways, as well as transcription of potential γδ T cell ligands. We validated these results using immunoblotting and flow cytometry. We also demonstrated the involvement of BTN3A1 and BTN2A1, crucial molecules for γδ T cell activation, as well as differential expression of PDL1/CD274 in cancer, E6/E7+ and healthy organoids. Interestingly, we observed a significant reduction in cytotoxicity upon blocking MSH2, a protein involved in DNA mismatch-repair.

first: Junxue

last: Dong

first: David

last: Holthaus

first: Christian

last: Peters

first: Stefanie

last: Koster

first: Marzieh

last: Ehsani

first: Alvaro

last: Quevedo-Olmos

first: Hilmar

last: Berger

first: Michal

last: Zarobkiewicz

first: Mandy

last: Mangler

first: Rajendra

last: Kumar Gurumurthy

first: Nina

last: Hedemann

first: Cindrilla

last: Chumduri

first: Dieter

last: Kabelitz

middle: F


title: Classical estrogen signaling in ciliated epithelial cells of the oviduct is nonessential for fertility in female mice

city: Columbia

first: Wipawee

last: Winuthayanon

state: Missouri

address: 1030 Hitt Street

department: OB/GYN & Women's Health

institute: University of Missouri

summary: Ciliary action performs a critical role in the oviduct (Fallopian tube), during pregnancy establishment through sperm and egg transport. The disruption of normal ciliary function in the oviduct affects oocyte pick-up and is a contributing factor to female infertility. Estrogen is an important regulator of ciliary action in the oviduct and promotes ciliogenesis in several species. Global loss of estrogen receptor 1 alpha (encoded by Esr1 gene) leads to infertility. Our laboratory has previously shown that ESR1 in the oviductal epithelial cell layer is required for female fertility. Here, we assessed the role of estrogen on transcriptional regulation of ciliated epithelial cells of the oviduct using single-cell RNA-sequencing analysis. We observed minor variations in ciliated cell genes in the proximal region (isthmus and uterotubal junction) of the oviduct. However, E2 treatment had little impact on the gene expression profile of ciliated epithelial cells. To assess the requirement of ESR1 specifically in ciliated cells for female fertility, we conditionally ablated Esr1 from ciliated epithelial cells of the oviduct (called ciliated Esr1d/d mice). Our studies showed that ciliated Esr1d/d females had fertility rates comparable to control females, did not display any disruptions in preimplantation embryo development or embryo transport to the uterus, and had comparable cilia formation to control females. However, we observed some incomplete deletion of Esr1 in the ciliated epithelial cells, especially in the ampulla region. Therefore, more studies are required to definitively determine ESR1 function in ciliated cells of the oviduct. Nevertheless, our data suggest that ESR1 expression in ciliated cells of the oviduct is dispensable for ciliogenesis, but nonessential for female fertility in mice. All genes expressed in scRNA-seq datasets are available for scientific community and separable at https://www.winuthayanon.com/genes/ve2h_cilia/ and https://www.winuthayanon.com/genes/ve2h_allclusters/

overall_design: Wild-type female mice were ovariectomized and treated with 17b-estradiol. After 2 h of injection, oviducts were collected and processed for single cell RNA-sequencing analysis.

first: Emily

last: McGlade

first: Kalli

middle: K

last: Stephens

first: Sarayut

first: Prashanth

last: Anamthathmakula

first: Michael

last: Holtzman


title: CRISPR screening in human trophoblast stem cells reveals both shared and distinct aspects of human and mouse placental development [ChIP-seq]

first: Eri

last: Kobayashi

summary: The placenta serves as the interface between the mother and fetus, facilitating the exchange of gases and nutrients between their separate blood circulation systems. Trophoblasts in the placenta play a central role in this process. Our current understanding of mammalian trophoblast development relies largely on mouse models. However, given the diversification of mammalian placentas, findings from the mouse placenta cannot be readily extrapolated to other mammalian species, including humans. To fill this knowledge gap, we performed CRISPR knockout (KO) screening in human trophoblast stem cells (hTSCs). We targeted genes essential for mouse placental development and identified more than 100 genes as critical regulators in both human hTSCs and mouse placentas. Among them, we further characterized in detail two transcription factors, DLX3 and GCM1, and revealed their essential roles in hTSC differentiation. Moreover, a gene function-based comparison between human and mouse trophoblast subtypes suggests that their relationship may differ significantly from previous assumptions based on tissue localization or cellular function. Notably, our data reveal that hTSCs may not be analogous to mouse TSCs or the extraembryonic ectoderm (ExE) in which in vivo TSCs reside. Instead, hTSCs may be analogous to progenitor cells in the mouse ectoplacental cone and chorion. This finding is consistent with the absence of ExE-like structures during human placental development. Our data not only deepen our understanding of human trophoblast development but also facilitate cross-species comparison of mammalian placentas.

overall_design: ChIP-seq for  DLX3 and GCM1 in undifferentiated and differentiated hTSCs.

first: Takahiro

last: Arima

first: Hiroaki

last: Okae


title: CRISPR screening in human trophoblast stem cells reveals both shared and distinct aspects of human and mouse placental development [HiChIP]

overall_design: HiChIP for H3K4me3  in undifferentiated and differentiated hTSCs.


title: Mature interleukin-36γ induces stratum corneum exfoliation in generalized pustular psoriasis by suppressing corneodesmosin

city: Fukuoka

first: Emi

last: Sato

state: Fukuoka

address: 7-45-1 Nanakuma, Jounan-ku

institute: Fukuoka University Faculty of Medicine

summary: Loss-of-function mutations in the IL36RN gene encoding IL-36 receptor antagonist (IL-36RA) cause familial generalized pustular psoriasis (GPP), which sometimes begins shortly after birth and is difficult to treat, and its effects on the epidermis are unclear. This study aimed to investigate the involvement of IL-36 receptor agonists in the epidermal formation of GPP. In this study, we found that IL-36 receptor agonists, especially mature IL-36γ, stimulate IL-8 and proIL-36γ production in the epidermis, while down-regulating the genes encoding epidermal cornified envelope-related proteins such as corneodesmosin. IL-36 receptor antagonists and monoclonal anti-IL-36γ antibodies counteract the effect of mature IL-36γ on corneodesmosin in keratinocytes in a dose-dependent manner. In the epidermis of generalized pustular psoriasis patients with IL36RN loss-of-function mutations, proIL-36γ is overproduced in the epidermis and corneodesmosin protein expression is markedly decreased in the region of giant subcorneal pustules called Kogoj’s spongiform pustules with high neutrophil infiltration. IL-8 induced by mature IL-36γ induces several neutrophils in the epidermis, and the newly produced proIL-36γ is cleaved to the mature form by neutrophil proteases. This newly produced mature IL-36γ was predicted to further suppress the gene expression of the granulosa-stratum-associated protein, corneodesmosin, leading to significant stratum corneum exfoliation and formation of giant subcorneal pustules. Overall, our results elucidate the mechanism underlying the formation of Kogoj’s spongiform pustules in generalized pustular psoriasis.

overall_design: Normal human 3D epidermis to which only solvent was added was used as a control and compared with (1) IL-36α-added group, (2) IL-36β-added group, and (3) IL-36γ-added group, respectively.

first: Hiroko

last: Imayoshi

first: Yuki

last: Tsutsui

first: Hiroki

last: Shimizu

first: Shinichi

last: Imafuku


title: Profiling whole-tissue metabolic reprogramming during cutaneous poxvirus infection and clearance

city: Bethesda

first: Katherine

last: Hornick

address: 10 Center Dr, Building 29B

department: Integrated Data Sciences Section (IDSS)

institute: NIAID

summary: Background Vaccinia virus (VACV) infection induces prominent changes in host cell metabolism. Little is known about the global metabolic reprogramming that takes place in the whole tissue during viral infection. Here, we performed an unbiased longitudinal metabolomics study in VACV-infected mice to investigate metabolic changes in the tissue during infection. We assessed metabolites in homogenized skin over time in the presence or absence of antigen-specific T cells using untargeted mass spectrometry. VACV infection induced several significant metabolic changes, including in the levels of nucleic acid metabolites (reflecting the impact of viral replication on the skin metabolome). Furthermore, monocyte- and antiviral T cell-produced metabolites, including itaconic acid, glutamine, and glutathione, were significantly increased following infection, highlighting the immune response’s contribution to the global skin metabolome. Additional RNA-Seq of infected skin tissue recapitulated transcriptional changes identified via metabolomics. Overall, our study reveals the metabolic balance of viral replication and the antiviral immune response in the skin and identifies metabolic pathways that could contribute to cutaneous poxvirus control in vivo.

overall_design: Ears were collected on indicated day post-infection (dpi) and immediately placed in buffer RLT (Qiagen). Tissues were homogenized, and RNA was isolated using Lysing Matrix S (1/8”) metal beads (MPBiomedicals) and a FastPrep-24 Instrument (MPBiomedicals). RNA was then purified using a Qiagen RNAEasy Mini Kit (Qiagen) according to the manufacturer’s protocol. An on-column DNAse digestion was performed prior to RNA elution. RNA concentration and purity were accessed using an Agilent TapeStation 4200. Samples were sequenced on a NovoSeq 6000 S1 using Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.

first: Pei

last: Luxin

first: Alan

last: Jarmusch

first: Kirsten

last: Overdahl

first: John

middle: B

last: Shannon

first: Heather

middle: D

last: Hickman


title: CRISPR screening in human trophoblast stem cells reveals both shared and distinct aspects of human and mouse placental development [RNA-seq]

overall_design:
We performed RNA-Seq of four WT, two DLX3 KO, two GCM1 KO, and two genetically unmodified clones of hTSCs.
To generate DLX3 KO and GCM1 KO hTSC clones, we employed CRISPR/Cas9 with sgRNAs that were designed to remove the DNA binding domains of DLX3 and GCM1.


title: The fungal pathogen Ustilago maydis targets the maize corepressor RELK2 to modulate host transcription for tumorigenesis

city: Köln

first: Gunther

last: Doehlemann

address: Zülpicher Straße 47a

institute: University of Cologne/ Universität zu Köln

summary:
Ustilago maydis is a biotrophic fungus that causes tumor formation on all aerial parts of maize. U. maydis secretes effector proteins during penetration and colonization to successfully overcome the plant immune response and reprogram host physiology to promote infection.
In this study, we functionally characterized the U. maydis effector protein Topless (TPL) interacting protein 6 (Tip6). We found that Tip6 interacts with the N-terminus of RELK2 through its two Ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs. We show that the EAR motifs are essential for the virulence function of Tip6 and critical for altering the nuclear distribution pattern of RELK2.
We propose that Tip6 mimics the recruitment of RELK2 by plant repressor proteins, thus disrupting host transcriptional regulation. We show that a large group of AP2/ERF B1 subfamily transcription factors are misregulated in the presence of Tip6.
Our study suggests a regulatory mechanism where the U. maydis effector Tip6 utilizes repressive domains to recruit the corepressor RELK2 to disrupt the transcriptional networks of the host plant.

overall_design: 9 Samples

first: Luyao

last: Huang

first: Bilal

last: Ökmen

first: Sara

middle: C

last: Stolze

first: Melanie

last: Kastl

first: Mamoona

last: Khan

first: Daniel

last: Hilbig

first: Hirofumi

last: Nakagami

first: Armin

last: Djamei


title: The circadian regulator PER1 promotes cell reprogramming by inhibiting inflammatory signaling from macrophages

city: Minneapolis

first: Nobuaki

last: Kikyo

state: MN

address: University of Minnesota, MTRF, Room 2-216, 2001 6th St SE

institute: University of Minnesota

summary: Fibroblasts can be reprogrammed to induced neurons (iNs) via transducion of Brn2, Ascl1, and Myt1l (BAM). To understand the roles of the circadain regulators Per1 and Per2 on the reprogramming, embryonic fibroblasts from wild type (WT), Per1-/-, and Per2-/- mice were transduced with the three genes and the cells were harvested on day 0, 2, and 4 after transduction for RNA-seq.

overall_design: Embryonic fibroblasts from wild type (WT), Per1-/-, and Per2-/- mice were transduced with the BAM genes and the cells were harvested on day 0, 2, and 4 after transduction for RNA-seq

first: Nobuko

last: Katoku-Kikyo

first: Seunghyun

last: Lim

first: Ce

last: Yuan

first: Jinsha

last: Koroth

first: Yasushi

last: Nakagawa

first: Elizabeth

last: Bradley


title: Single Cell RNA sequencing of mouse periodontitis gingiva

city: Los Angeles

first: Takeru

last: Kondo

state: California

address: 10824 Lindbrook Dr. #304

institute: UCLA School of Dentistry

summary: Purpose: The goal of this study was to characterize the gingival oral barrier immunity of mouse periodontitis gingiva. Method: A silk thread (ligature) was tied wround the mouse maxillary molar. Mouse palatal gingiva was harvested at 1 days after the ligature placement. Gingival cells were harvested and subjected to 10X Genomix scRNA-seq. Cell Ranger processed data were analysed.

overall_design: Gingival oral barrier cells were examined in periodontitis gingiva.

first: Ichiro

last: Nishimura


summary: Fibroblasts can be reprogrammed to induced neurons (iNs) via transducion of Ascl1, Brn2, and Myt1l. To understand the roles of the circadian regulators Per1 and Per2 on the reprogramming, embryonic fibroblasts from wild type (WT), Per1-/-, and Per2-/- mice were transduced with the three genes and cells were harvested for scRNA-seq on days 4, 7, and 10 after transduction.

overall_design: single-cell RNA-seq


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (PDX H3K27ac ChIP-Seq)

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

overall_design: H3K27ac ChIP-seq of 12 TNBC patient derived xenografts

first: Bojana

last: Jovanović

last: Temko

first: Franziska

last: Michor


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (PDX  RNA-Seq)

overall_design: RNA-seq of 15 TNBC patient derived xenografts


title: An epigenetic barrier sets the timing of human neuronal maturation

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: A challenge for understanding the development of brain circuits is to identify the factors that instruct neurons to accomplish each developmental step at the appropriate stage. Neuronal maturation follows an intrinsic species-specific developmental pace that is extremely protracted in humans and that is retained during human pluripotent stem cells (hPSCs) differentiations. Using a novel platform that synchronized the generation of cortical neurons from hPSC, we established morphological, functional, and molecular roadmaps of maturation. We found that the temporal unfolding of maturation programs proceeds gradually and is limited by the retention of complex epigenetic signatures. Loss-of-function of multiple such epigenetic factors at the neuron stage triggered precocious molecular and functional maturation. Remarkably, transient pharmacological manipulation of a subset of epigenetic factors, including EZH2, EHMT1/2 and DOT1L, at the progenitor cell stage can prime precursors to reach enhanced molecular and functional signatures of maturity as neurons. Our results indicate that the rate at which neurons mature is set well before neurogenesis through the establishment of an “epigenetic barrier” in progenitor cells that gets slowly erased in neurons, allowing the gradual onset of maturation programs.

overall_design:
Cleavage Under Targets and Release Using Nuclease (CUT&RUN) enriching for histone modifications in human pluripotent stem cell (hPSC)-derived neural progenitor cells and neurons. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) enriching for histone modifications in human pluripotent stem cell (hPSC)-derived neural progenitor cells treated with DMSO or inhibitors of chromatin modifiers.
RNA sequencing of WA09 (H9) human pluripotent stem cell (hPSC)-derived neurons at different stages of differentiation and treated with DMSO or inhibitors of chromatin modifiers.
RNA sequencing of MSK_SRF001 induced human pluripotent stem cell (hPSC)-derived neurons at day 37 of differentiation and treated with DMSO or inhibitors of chromatin modifiers.
RNA sequencing of induced human pluripotent stem cell (hPSC)-derived neurons at day 38 of differentiation and treated with DMSO or inhibitors of chromatin modifiers.

first: Gabriele

last: Ciceri

first: Lorenz

last: Studer


title: Single Cell Transcriptomics of human carotid artery plaques

status: Public on Nov 08 2023

city: München

first: Jessica

last: Pauli

state: Bayern

address: Biedersteiner Str. 29

department: Molecular Vascular Medicine

institute: TUM Universitätsklinikum (Klinikum rechts der Isar)

summary: To profile single-cell transcriptome and analyze the diversity of cell types present in human atherosclerotic tissue specimens (carotid artery, CAR), we carried out scRNA-seq from 10 different patients.

overall_design: scRNA-Seq

first: Lars

last: Maegdefessel

first: Sara

last: Schanda


title: Oligodendrocyte-derived IL-33 functions as a microglial survival factor during neuroinvasive flavivirus infection

city: Seattle

first: Joshua

last: Ames

state: WA

address: 750 Republican st

institute: University of Washington

summary: In order to recover from infection, organisms must balance robust immune responses to pathogens with the tolerance of immune-mediated pathology. This balance is particularly critical within the central nervous system, whose complex architecture, essential function, and limited capacity for self-renewal render it susceptible to both pathogen- and immune-mediated pathology.  Here, we identify the alarmin IL-33 and its receptor ST2 as critical for host survival to neuroinvasive flavivirus infection. We identify oligodendrocytes as the critical source of IL-33, and microglia as the key cellular responders. Notably, we find that the IL-33/ST2 axis does not impact viral control or adaptive immune responses; rather, it is required to promote the activation and survival of microglia. In the absence of intact IL-33/ST2 signaling in the brain, neuroinvasive flavivirus infection triggered aberrant recruitment of monocyte-derived peripheral immune cells, increased neuronal stress, and neuronal cell death, effects that compromised organismal survival. These findings identify IL-33 as a critical mediator of CNS tolerance to pathogen-initiated immunity and inflammation.

overall_design:
To study the contribution of Il33 to CNS immune responses to flavivirus infection, we used wildtype and IL33 knockout mouse model that were intracranially infected with the attenuated WNV-E218A strain.
At 7 days post infection, brains were collected for anti F4/80 MACS mediated isolation of microglia and peripheral monocyte derived macrophages for RNA-seq.
The RNA-seq data generated was used to perform a comparative analysis beween Il33 knockout and wildtype CNS immune responses to WNV-E218A infection.

first: Geoffrey

middle: T

last: Norris

first: Steven

last: Ziegler

first: Andrew

last: Oberst


title: Brain glucose induces tolerance of Cryptococcus neoformans to amphotericin B during meningitis

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

summary: In bacteria, antibiotic tolerance, the ability of a susceptible population to survive high doses of cidal drugs, has been shown to compromise therapeutic outcomes. In comparison, whether fungicide tolerance can be induced by host-derived factors during fungal diseases remains unproven. Here, through a systematic evaluation of metabolite-drug-fungal interactions in the leading fungal meningitis pathogen, Cryptococcus neoformans, we found that glucose, on which the brain depends for fuel, induces fungal tolerance to amphotericin B (AmB) in mouse brain tissue and patient cerebrospinal fluid via the fungal glucose repression activator Mig1. To explore the mechanisms underlying glucose-dependent AmB tolerance mediated by Mig1, we used time-series RNA-seq to evaluate dynamic gene expression in wildtype and mig1Δ fungi after exposure to AmB under both drug-tolerant (glucose) or drug-sensitive (galactose) conditions.

overall_design: 24 samples contain wild type, mig1△, three replicates

first: Lei

last: Chen

first: Xiuyun

last: Tian

first: Lanyue

last: Zhang

first: Wenzhao

last: Wang

first: Pengjie

last: Hu

first: Zhongyi

last: Ma

first: Yeqi

last: Li

first: Shibin

first: Zhenghao

last: Shen

first: Xin

last: Fan

first: Leixin

last: Ye

first: Weixin

last: Ke

first: Yao

last: Wu

first: Guanghou

last: Shui

first: Meng

last: Xiao

first: Guang-jun

last: He

first: Ying

last: Yang

first: Wenxia

last: Fang

first: Fan

last: Bai

first: Guojian

last: Liao

first: Min

first: Xiaorong

last: Lin

first: Chong

first: Linqi


title: Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy

first: Hongmei

last: Wang

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

overall_design: Refer to individual Series


title: Expression data from colorectal cancer cell lines with USP51 overexpression

status: Public on Nov 07 2023

city: Xi'an

first: mingchao

last: mu

address: 277 West Yanta Road

department: Department of General Surgery

institute: the First Affiliated Hospital of Xi’an Jiaotong University

summary: USP51 enhances colorectal cancer stemness and chemoresistance, and elevated USP51 expression predicts poorer survival in colorectal cancer patients. To probe the role of USP51, we conducted RNA-seq data analysis, comparing control and USP51-overexpressing SW480 and HCT116 cells.

overall_design: Analysis of RNA-seq data comparing control and USP51 overexpression in SW480 and HCT116 cells.

first: Mingchao

last: Mu

first: Junhui

last: Yu

first: Qin

last: Zhang

first: Jing


title: N6-methyladenosine RNA modification drives a rapid shift to cisplatin resistance in bladder cancer by regulating SLC7A11 expression via YTHDF3 [RIP-seq]

first: Emmanuelle

last: Hodara

state: CA

address: 1450 Biggy Street

institute: Keck School of Medicine of USC

type: Methylation profiling by high throughput sequencing

summary: Our study examines the role of m6A RNA modification in regulating gene expression of transcripts promoting cisplatin resistance in bladder cancer.

overall_design: MeRIP-seq of T24 vs T24R2 BC cell lines in 5 replicates (includes input ctrl and MeRIP samples)

first: Aubree

last: Mades

first: Tong

last: Xu

first: Daniel

last: Bsteh

first: Lisa

last: Swartz

first: Maheen

last: Iqbal

first: Peggy

last: Farnham

first: Suhn

last: Rhie

first: Amir

last: Goldkorn


title: Diurnal ChIP-Seq for Petunia hybrida

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

summary: To better understand how diurnal transcriptional regulation contributes to day/night cycles of volatile emission from the petunia flower, cross-linked chromatin from corolla in the morning (7AM) and evening (7PM) was immunoprecipitated with antibodies against 4 histone marks associated with trancriptional activity to determine islands enriched for the marks in morning and evening.

overall_design: Input or immunoprecipitated chromatin from formaldehyde cross-linked corolla tissue was used for library preparation and sequencing, at two time points, with two biological replicates for each ChIP (three input replicates)

middle: M

first: Natalia

last: Dudareva

first: Ying

last: Li


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (Cell lines Methylation)

city: Boston

first: Kornelia

last: Polyak

institute: Dana-Farber Cancer Institute

summary:
Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity and treatment response, we combined functional and molecular profiling with computational analysis tools.
Using these approaches, we defined transcriptional, epigenetic, and metabolic subtypes, and identified subtype-driving super-enhancers. Single cell RNA sequencing analyses revealed relative homogeneity of the three major transcriptional subtypes (luminal, basal and mesenchymal) within tumors. We found that mesenchymal TNBCs are more similar to mesenchymal neuroblastoma and rhabdoid tumors than to other TNBC subtypes, and the PRRX1 transcription factor serves as a key driver of these tumors. By directly regulating the transcription of mesenchymal genes, PRRX1 is sufficient for inducing the mesenchymal subtype but is not required for its maintenance.

overall_design: DNA methylation array profiling of 34 TNBC cell lines

first: Bojana

last: Jovanović

last: Temko

first: Franziska

last: Michor


title: Knocking out non-muscle myosin II in retinal ganglion cells promotes long-distance optic nerve regeneration

city: Tampa

first: Xuewei

last: Wang

state: FL

address: 4001 E Fletcher Ave, ALZ 339

department: Molecular Medicine

institute: University of South Florida


title: Diabetes-associated breast cancer has a distinct transcriptome and metabolome and shows DNA repair deficiency [RNAseq-MDA-MB-231_and_MDA-MB-468]

first: Stefan

last: Ambs

address: Building 37, Room 3050B

department: CCR

institute: NCI

summary: Diabetes commonly affects cancer patients. As a comorbidity, it may modify tumor biology and therapy response. Yet, we still lack an understanding of the diabetes-induced molecular changes in human breast tumors and their implication for therapy. The goal of this study was aimed to identify diabetes induced phenotypes and molecular signatures in breast cancer. Here, we investigated the effect of diabetes on breast cancer biology using a three-pronged approach that included analysis of orthotopic human tumor xenografts, patient tumors, and breast cancer cells exposed to diabetes and hyperglycemia. Diabetes and hyperglycemia induced a mesenchymal and stem cell-like phenotypes. Further Diabetes and hyperglycemia also associated with oxidative stress and both gene expression and mutational signatures of DNA repair deficiency. Breast cancer cells cultured under hyperglycemia acquired increased DNA damage and sensitivity to DNA damage response inhibitors. Based on these observations, diabetes-associated breast tumors may show an increased drug response to DNA repair pathway inhibitors that are cancer therapeutics.

overall_design: mRNA profiles of breast cancer cells (MDA-MB-231 and MDA-MB-468) grown under low (5mM) and high glucose (25mM) for 48 hrs were generated by deep sequencing, with 4 replicates, using Illumina NextSeq.

first: Gatikrushna

last: Panigrahi

first: Julián

last: Candia

first: Tiffany

last: Dorsey

first: Wei

last: Tang

first: Byun

last: Jung

first: Tsion-Zewdu

last: Minas

first: Amy

last: Zhang

first: Anuoluwapo

last: Ajao

first: Mayank

last: Tadon

first: Ashley

last: Cellini

first: Harris

last: Yfantis

first: Dean

last: Mann

first: Xin

middle: W

first: Huaitian

last: Liu

first: Christopher

middle: A

last: Loffredo

first: Ana

last: Napoles


title: The histone chaperone ANP32B regulates chromatin incorporation of the atypical human histone variant macroH2A

city: Badalona

first: David

last: Corujo

address: Ctra de Can Ruti, Camí de les Escoles

country: Spain

institute: Josep Carreras Leukaemia Research Institute

summary: Eukaryotic chromatin structure is highly conserved, with the canonical histone proteins revealing only small sequence changes across species. Yet, all vertebrates exhibit three much larger histone H2A variants, macroH2A. A distinctive feature of these atypical histones is the globular macrodomain module, which can bind metabolites and is connected to the histone fold through a flexible linker. MacroH2A variants impact heterochromatin organization, transcription regulation and establish a barrier for cellular reprogramming. However, the mechanisms of how these large H2A variants are incorporated into chromatin and the identity of any chaperones required for histone deposition have remained elusive. Here, we developed a split-GFP-based cellular readout for histone incorporation and conducted a genome-wide mutagenesis screen in haploid human cells to identify proteins that regulate macroH2A dynamics. We identified and validated the histone chaperone ANP32B as a regulator of macroH2A chromatin deposition. ANP32B associates with macroH2A in cells and in vitro binds to histones with low nanomolar affinity. In vitro nucleosome assembly assays show that ANP32B stimulates deposition of macroH2A-H2B and not of H2A-H2B onto tetraso me. In cells, depletion of ANP32B in cells strongly affects global macroH2A deposition, revealing ANP32B as a macroH2A chaperone. Our study highlights the power of haploid cell functional genomics coupled with cellular imaging to identify factors that are required for chromatin plasticity and diversity.

overall_design: CUT&RUN with non-targeting IgG antibodies and anti-macroH2A1 antibodies was performed on HepG2 cells transfected with either non-targeting control siRNAs or ANP32B-targeting siRNAs.

first: Imke

last: Mandemaker

first: Eevelyn

last: Fessler

first: Christiane

last: Kotthoff

first: Andreas

last: Wegerer

first: Clément

last: Rouillon

first: Marcus

last: Buschbek

first: Lucas

last: Jae

first: Francesca

last: Mattiroli

last: Ladurner


title: Enhancing sensitivity and versatility of Tn5-based single cell omics

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

institute: DKFZ


title: Diabetes-associated breast cancer has a distinct transcriptome and metabolome and shows DNA repair deficiency [RNAseq-Hs578T]

first: Stefan

last: Ambs

overall_design: mRNA profiles of breast cancer cells (Hs578T) grown under low (5mM) and high glucose (25mM) for 48 hrs were generated by deep sequencing, with 4 replicates, using Illumina NextSeq.

first: Gatikrushna

last: Panigrahi

first: Julián

last: Candia

first: Tiffany

middle: H

last: Dorsey

first: Wei

last: Tang

first: Byun

last: Jung

first: Tsion-Zewdu

last: Minas

first: Amy

last: Zhang

first: Anuoluwapo

last: Ajao

first: Mayank

last: Tadon

first: Ashley

last: Cellini

last: Wang


title: PARP inhibition induces cytotoxicity in mESCs by activating endogenous retroviruses.

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel


title: Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [PRO-seq]

city: Tel Aviv

first: Gil

last: Ast

state: Israel

address: Haim Levanon 55

country: Israel

institute: Tel Aviv University

summary: Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA processing machineries, have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. Although H1s have a minor effect on global gene expression levels, they are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation rate of RNA polymerase II. Thus, H1 variants determine splicing fate by modulating the RNA polymerase II elongation rate.

overall_design: Determine the H1-mediated RNA polymerase II elongation rate and its influence on alternative splicing by conducting and analyzing precision nuclear run-on (PRO-seq) experiments in both WT and H1 knockout cells, then integrate this information with our RNA-seq results

first: Corina

last: Pascal

first: Jonathan

last: Zonszain

first: Ofir

last: Hameiri

first: Luna

last: Tammer

first: Chen

last: Gargi Levi

first: Stav

last: Ben Salmon

first: Tamar

last: Levy

last: Hakim

first: Mireille

last: Eid

first: Vanessa

middle: R

last: Roy

first: Salima

last: Abu Rabe'a

first: Nana

last: Shalev

first: Liraz

last: Elbaz

first: Galit

last: Lev Maor

first: Albert

last: Jordan

first: Eran

last: Meshorer


title: Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (PDX Methylation)

first: Kornelia

last: Polyak

overall_design: DNA methylation array profiling of 15 TNBC patient derived xenografts

first: Bojana

last: Jovanović

first: Daniel

last: Temko

first: Franziska

last: Michor


title: NFIB dependent and independent mechanisms of metastasis in small cell lung cancer

city: Stanford

first: Julie

last: Ko

address: 265 Campus Drive G2065

institute: Stanford University


title: Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [RNA-seq]

first: Gil

last: Ast

overall_design: Comparative splicing and gene expression analysis of RNA-seq data for WT HEK293 cells and its KO and rescue derivatives. Including two biological replicates of 5-KO sample.

first: Corina

last: Pascal

first: Jonathan

last: Zonszain

first: Ofir

last: Hameiri

first: Luna

last: Tammer

middle: G

last: Levi

last: Salmon

last: Rabe'a

middle: L

last: Maor


title: Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H1 histone variants from WT HEK293 cells and 5-KO (H1.0,H1.2,H1.3,H1.4,H1.5) and H1 rescue in HEK293. The immunoprecipitation was done with either H1-specific antibody or antibody for HA-tag.

first: Chen

first: Stav

last: Ben Salmon

first: Tamar

last: Levy

last: Hakim

first: Mireille

last: Eid

first: Vanessa

last: Roy

last: Shalev

last: Elbaz


title: Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate.