title: Profiling Sox4 binding sites and histone post-translational modifications in adult hepatocytes (CUT&RUN II)

first: Takeshi

last: Katsuda

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

summary: Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event. To investigate the effect of Sox4 on the change of chromatin landscape of hepatocytes, we exogenosly expressed Sox4 in adult hepatocytes, and profiled its binding sites in a genome wide manner by CUT&RUN-seq. We also profiled histone post-translational modifications of H3K4me1, H3K4me3, H3K27ac and H3K27me3 to explore the influence of Sox4 on the epigenetic landscape of hepatocytes.

overall_design: Mice were injected with adeno-associated viruses (AAVs) packaged with mouse Sox4 (AAV8-TBG-HA-Sox4-P2A-Cre), and hepatocytes were harvested 18 hours post injection (18 hpi) and 4 days post injection (4 dpi) by a standard 2-step liberase digestion method followed by a Percoll enrichment step.

first: Jonathan

last: Sussman

first: Ben

middle: Z

last: Stanger


title: Influence of Sox4 on chromatin accessibility of adult hepatocytes [EV and Sox4]

status: Public on Nov 28 2023

city: Philadelphia

state: PA

country: USA

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event To investigate the effect of Sox4 on the change of chromatin landscape of hepatocytes, we performed ATAC-seq of exogenously Sox4-expressed hepatocytes.

overall_design: Mice were injected with adeno-associated viruses (AAVs) packaged with mouse Sox4 (AAV8-TBG-HA-Sox4-P2A-Cre) or empty virus (AAV8-TBG-Cre), and hepatocytes were harvested 4 days post injection by a standard 2-step liberase digestion method followed by a Percoll enrichment step.


title: Profiling Sox4 binding sites and histone post-translational modifications in adult hepatocytes (CUT&RUN I)


title: MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch

status: Public on Nov 29 2023

city: Odense

first: Simon

middle: Toftholm

last: Jakobsen

state: Syddanmark

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: The transcription factor MYC is overexpressed in most cancers, where it drives multiple hallmarks of cancer progression. MYC is known to promote oncogenic transcription by binding to active promoters. In addition, MYC has also been shown to invade distal enhancers when expressed at oncogenic levels, but this enhancer binding has been proposed to have low gene-regulatory potential. Here, we demonstrate that MYC directly regulates enhancer activity to promote cancer type-specific gene programs predictive of poor patient prognosis. MYC induces transcription of enhancer RNA through recruitment of RNA polymerase II (RNAPII), rather than regulating RNAPII pause-release, as is the case at promoters. This process is mediated by MYC-induced H3K9 demethylation and acetylation by GCN5, leading to enhancer-specific BRD4 recruitment through its bromodomains, which facilitates RNAPII recruitment. We propose that MYC drives prognostic cancer type-specific gene programs through induction of an enhancer-specific epigenetic switch, which can be targeted by BET and GCN5 inhibitors.

overall_design: ChIP-seq during MYC inhibition using KJ-PYR-9, BRD4 inhibition with JQ1 and GCN5 KD in BT549, MCF7, T47D and MDA-MB-231 breast cancer cell lines. ChIP-seq during MYC inhibition using KJ-PYR-9, MYCMI6 and MYCi975  in BT549 or  Fulvestrant treatment in MCF7 breast cancer cell lines.

middle: T

first: Rikke

middle: A

last: Jensen

first: Tina

last: Ravnsborg

first: Christian

middle: D

last: Vaagenso

first: Maria

middle: S

last: Madsen

first: Robin

last: Andersson

first: Ole

middle: N

first: Rasmus

last: Siersbæk

first: Majken


title: Influence of Sox4 on transcriptomic changes in adult hepatocytes

type: Expression profiling by high throughput sequencing

summary: Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. An earlier work in our laboratory nominated Sox4 as an initiation factor of this reprogramming event. To investigate the effect of Sox4 on the transcriptomic changes in hepatocytes, we performed RNA-seq of Sox4-overexpressed (OE) hepatocytes.

overall_design: Mice were injected with adeno-associated viruses (AAVs) packaged with mouse Sox4 (AAV8-TBG-HA-Sox4-P2A-Cre) or empty vector (AAV8-TBG-Cre). Hepatocytes were harvested 4 days post injection by a standard 2-step liberase digestion method followed by a Percoll enrichment step.


title: TFAM deficiency in dendritic cells leads to mitochondrial dysfunction and enhanced antitumor immunity through cGAS-STING pathway

status: Public on Nov 30 2023

city: Chengdu

first: tianqi

last: lu

address: qinglong

country: China

institute: The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University

summary: To investigate the role of TFAM knockout in the regulation of dendritic cell function, we cultured bone marrow-derived dendritic cells from wild type or Tfamflox/flox Cre-lyz2 mice, which were stimulated by tumor supernatant from LLC and harvested for RNA-seq analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from wildtype or Tfamflox/flox Cre-lyz2 BMDCs treated with or without LLC  tumor supernatant (TS) were carried out.

first: Hao

last: Zeng

first: Ziqi

last: Zhang


title: The endogenous retrovirus Mtv8 which resides within the V kappa locus does not influence the mouse immunoglobulin repertoire

status: Public on Nov 27 2023

city: Chicago

first: Helen

last: Beilinson

state: IL

address: 924 E 57TH ST

department: Microbiology

institute: University of Chicago

summary: The vast diversity of mammalian adaptive antigen receptors allows for robust and efficient immune responses against a wide number of pathogens. The  antigen receptor repertoire is built during the recombination and hypermutation of B and T cell receptor (B-, TCR) loci. V(D)J recombination rearranges these antigen receptor loci which are organized as an array of separate V, (D), and J gene segments. Which gene segments are recombined, and thus which particular antigen receptors are present in the host repertoire, depends on the three-dimensional architecture of the recombining locus. The endogenous retrovirus (ERV) mouse mammary tumor provirus (Mtv8) resides on mouse chromosome 6 interposed within the large array of light chain kappa (IgK) V gene segments. It was unknown, however, whether Mtv8 influences the BCR repertoire, as ERVs can contribute to changes in genomic architecture by driving high levels of local transcription. We generated Mtv8-deficient mice to determine if the ERV influenced V(D)J recombination and found no significant difference in the peripheral BCR repertoire of Mtv8-deficient mice compared to wildtype controls. Thus, Mtv8, the endogenous retrovirus in the Igk locus, does not influence BCR repertoires.

overall_design: To investigate the role of Mtv8 in shaping the murine Ig repertoire, we used CRISPR/Cas9 to generate Mtv8-deficient C57BL/6J mice (KO). From WT and KO mice, we isolated splenic CD19+ cells using MACS and isolated RNA using guanidine thiocyanate extraction and CsCl gradient centrifugation. We then generated immunoglobulin libraries using the NEBNext Immune Sequencing Kit, specifically enriching for B cell receptor chains during the first PCR step. Libraries were sequenced by paired-end 300 bp sequencing on an Illumina MiSeq. Processing of data was performed using the pRESTO NEBNext Immune Sequencing Kit Workflow on Galaxy and subsequent analyses were performed in R.

first: Beilinson

last: Helen A.

first: Erickson

last: Steven A.

first: Golovkina

last: Tatyana


title: Enhancing chimeric antigen receptor T cell therapy by modulating the p53 signaling network with Δ133p53α

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

summary: Chimeric antigen receptor (CAR) T cell dysfunction is a major barrier to achieving lasting remission in hematologic cancers, especially in chronic lymphocytic leukemia. We have shown previously that Δ133p53α, an endogenous isoform of the human TP53 gene, decreases in expression with age in human T cells, and that reconstitution of Δ133p53α in poorly functional T cells can rescue proliferation. Although Δ133p53α lacks a transactivation domain, it can form heterooligomers with full length p53 and modulate the p53-mediated stress response. Here, we show that constitutive expression of Δ133p53α, potentiates the anti-tumor activity of CD19-directed CAR T cells, and limits dysfunction under conditions of high tumor burden and metabolic stress. We demonstrate that Δ133p53α-expressing CAR T cells exhibit a robust metabolic phenotype, maintaining the ability to execute effector functions and continue proliferating under nutrient limiting conditions, in part due to upregulation of critical biosynthetic processes and improved mitochondrial function. Importantly, we show that our strategy to constitutively express Δ133p53α improves the anti-tumor efficacy of CAR T cells generated from CLL patients that previously failed CAR T cell therapy. More broadly, our results point to the potential role of the p53-mediated stress response in limiting the prolonged antitumor functions required for complete tumor clearance in patients with high disease burden, suggesting that modulation of the p53 signaling network with Δ133p53α may represent a translationally viable strategy for improving CAR T cell therapy.

overall_design: To understand the impact of Δ133p53α on CAR T cell function, we harvested RNA from CAR T cells isolated on day 3.5 of in vitro co-culture with nalm6 leukemia cells. To understand whether there are differences prior to co-culture we also harvested RNA from CAR T cells isolated from CAR product. All Δ133p53α-CAR T cells were compared to WT control CAR T cells which transduced with mCherry. All samples were collected across three healthy human donors.

first: Roselle

last: Christopher

first: Hui

last: Linhui

first: Carl

last: June


first: Simon

last: Jakobsen

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

overall_design: Refer to individual Series


title: The Rtf1/Prf1-dependent histone modification axis and Rpb1 C-terminal domain phosphorylation counteract multi-drug resistance in fission yeast [RNA-seq]

city: Montreal

first: Jason

last: Tanny

state: Quebec

address: 3655 Prom Sir William Osler room 132

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

summary: RNA polymerase II (RNAPII) transcription elongation directs an intricate pattern of histone modifications. Formation of this pattern involves a highly conserved regulatory axis, key components of which are the elongation factor Rtf1, monoubiquitylation of histone H2B (H2Bub1), and methylation of histone H3 on lysine 4 (H3K4me). Direct contact between Rtf1 and the ubiquitylation complex Rad6-Bre1 stimulates H2Bub1, which in turn promotes H3K4me by stimulating the activity of the Set1C/COMPASS methyltransferase complex. Previous studies have defined the molecular basis for these regulatory relationships, but it remains unclear how they regulate chromatin and transcription in vivo. We found that mutations affecting multiple components of the Rtf1-H2Bub1-H3K4me axis in the model eukaryote Schizosaccharomyces pombe caused resistance to the ribonucleotide reductase inhibitor hydroxyurea (HU). Resistance correlated with a reduced effect of HU on dNTP pools, bypass of the S-phase checkpoint in the presence of HU, and blunting of the transcriptional response to HU treatment. Mutations in the C-terminal repeat domain (CTD) of the RNAPII large subunit Rpb1 led to a similar spectrum of phenotypes. Moreover, all the HU resistant mutants we identified also exhibited resistance to several azole class antifungal agents. Our results suggest a novel, shared gene regulatory function of the Rtf1-H2Bub1-H3K4me axis and the Rpb1 CTD in controlling fungal drug tolerance.

overall_design: To investigate the basis for hydroxyurea (HU) resistance in S. pombe mutants affecting the Rtf1/Prf1 histone modification axis, we compared the response to HU in wild-type and HU-resistant mutants.

first: Jennifer

middle: J

last: Chen

first: Calvin

last: Moy

first: Viviane

last: Page

first: Cian

last: Monnin

first: Ziad

middle: W

last: El-Hajj

first: Daina

last: Z Avizonis

first: Rodrigo

last: Reyes-Lamothe

middle: C


title: Antitumor effects of intravenous natural killer cell infusion in an orthotopic glioblastoma xenograft murine model and gene expression profile analysis

city: Kashihara

first: Takayuki

last: Morimoto

state: Nara prefecture

address: 840 Shijo-Cho

department: Department of Neurosurgery

country: Japan

institute: Nara Medical University

summary: Despite standard multimodality treatments, including maximal safe resection, te-mozolomide, radiotherapy, and tumor-treating fields, patients with glioblastoma (GBM) face dismal prognosis. Natural killer cell (NKC)-based immunotherapy appears to be a promising approach to treat GBM. We previously reported a novel technique to derive ex vivo-expanded highly activated NKCs from human peripheral blood mononuclear cells, which exhibited no-table antitumor effects against GBM cells. In this study, we performed preclinical evaluation of these NKCs in an in vivo orthotopic xenograft murine model, which was established by sub-cutaneously implanting U87MG cells in nonobese diabetes/severe combined immunodefi-ciency/IL2rγ null (NOG) mice. In this model, administering NKCs via the retro-orbital sinus prolonged the overall survival of NOG mice, indirectly indicating the growth inhibitory ef-fects of NKCs. In addition, we performed a comprehensive analysis of differentially ex-pressed genes using microarray, focusing on the expression of NKC activating receptor lig-ands, NKC inhibitory receptor ligands, chemokines, and chemokine receptors, between intra-cranial tumors treated with NKCs and non-treated intracranial tumors. We also performed differential gene expression analysis between the internal and external layers of intracranial tumors. Our findings provide crucial insights into NKC-based immunotherapy for patients with GBM.

overall_design: In this study, we performed preclinical evaluation of these NKCs in an in vivo orthotopic xenograft murine model, which was established by subcutaneously implanting U87MG cells in nonobese diabetes/severe combined immunodeficiency/IL2rγ null (NOG) mice. In this model, administering NKCs via the retro-orbital sinus prolonged the overall survival of NOG mice, indirectly indicating the growth inhibitory effects of NKCs. In addition, we performed a comprehensive analysis of differentially expressed genes using microarray, focusing on the expression of NKC activating receptor ligands, NKC inhibitory receptor ligands, chemokines, and chemokine receptors, between intracranial tumors treated with NKCs and non-treated intracranial tumors. We also performed differential gene expression analysis between the in-ternal and external layers of intracranial tumors.

first: Tsutomu

last: Nakazawa

first: Ryosuke

last: Matsuda

first: Fumihiko

last: Nishimura

first: Mitsutoshi

last: Nakamura

first: Shuichi

last: Yamada

first: Ichiro

last: Nakagawa

first: Young-Soo

last: Park

first: Takahiro

last: Tsujimura

first: Hiroyuki

last: Nakase


title: Hypermethylation leads to the loss of HOXA5, resulting in JAG1 expression and NOTCH signaling for renal fibrosis

city: AUGUSTA

first: Qingqing

last: Wei

state: Georgia

address: 1460 Laney Walker Blvd.

department: Cellular Biology & Anatomy

institute: Augusta University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation has been implicated in renal fibrosis. In this study, we demonstrated the induction of DNA methyltransferases and global DNA methylation in fibrotic kidneys, and further proved the beneficial effects of their inhibitor 5-Aza in renal fibrosis. HOXA5 was shown to be down-regulated in fibrotic kidneys through hypermethylation, and this down-regulation led to JAG1 expression and consequent activation of NOTCH signaling for renal fibrogenesis. These findings unveil DNA methylation and related genes, such as HOXA5, as potential therapeutic targets in renal fibrotic disease.

overall_design: To investigate the differentially methylated genes in kidney fibrosis, C57BL/6 mice were subjected to unilateral ureter obstruction for 7 days (UUO7D with daily-saline injection), UUO 7D with daily-5'Aza injection, and sham operation. The genomic DNA from the kidney cortex and outer medulla were extracted for bisulfite sequencing.

first: Xiao

last: Xiao

first: Huidong

last: Shi

first: Zheng

last: Dong


title: A study of genetic variants associated with skin traits in the Vietnamese population

status: Public on Nov 26 2023

city: Hanoi

first: Tham

middle: H

last: Hoang

address: Floor 9th, 458 Minh Khai

country: Viet Nam

institute: Vingroup Big Data Institute

summary: Background: Most skin-related traits have been studied in Caucasian genetic backgrounds. A comprehensive study on skin-associated genetic effects on underrepresented populations such as Vietnam is needed to fill the gaps in the field.  Objectives: We aimed to develop a computational pipeline to predict the effect of genetic factors on skin traits using public data (GWAS catalogs and whole-genome sequencing (WGS) data from the 1000 Genomes Project-1KGP) and in-house Vietnamese data (WGS and genotyping by SNP array). Also, we compared the genetic predispositions of 25 skin-related traits of Vietnamese population to others to acquire population-specific insights regarding skin health.    Results: The skin-related genetic profile of Vietnamese cohorts was similar at most to East Asian cohorts (JPT: Fst=0.036, CHB: Fst=0.031, CHS: Fst=0.027, CDX: Fst=0.025) in the population study. In addition, we identified pairs of skin traits at high risk of frequent co-occurrence (such as skin aging and wrinkles (r = 0.45, p =1.50e-5) or collagen degradation and moisturizing (r = 0.35, p = 1.1e-3)).

overall_design: Methods: Vietnamese cohorts of whole-genome sequencing (WGS) of 1008 healthy individuals for the reference and 96 genotyping samples (which do not have any skin cutaneous issues) by Infinium Asian Screening Array-24 v1.0 BeadChip were employed to predict skin-associated genetic variants of 25 skin-related and micronutrient requirement traits in population analysis and correlation analysis. Simultaneously, we compared the landscape of cutaneous issues of Vietnamese people with other populations by assessing their genetic profiles.


title: Deficiency of ASGR1 promotes liver injury by increasing GP73-mediated hepatic endoplasmic reticulum stress

city: xianyang

first: leng

last: xiangkai

state: shanaxi

address: No.22, Xinong Road, Yangling National Agricultural High-tech Industry Demonstration Zone

institute: Northwest A&F University

summary: Liver injury is a core pathological process in the majority of liver diseases, yet the genetic factors predisposing individuals to its initiation and progression remain poorly understood. Here we show that asialoglycoprotein receptor 1 (ASGR1), a lectin specifically expressed in the liver, is downregulated in patients with liver fibrosis or cirrhosis and male mice with liver injury. ASGR1 deficiency exacerbates while its overexpression mitigates acetaminophen-induced acute and CCl4-induced chronic liver injuries in male mice. Mechanistically, ASGR1 binds to an endoplasmic reticulum stress mediator GP73 and facilitates its lysosomal degradation. ASGR1 depletion increases circulating GP73 levels and promotes the interaction between GP73 and BIP to activate endoplasmic reticulum stress, leading to liver injury. Neutralization of GP73 not only attenuates ASGR1 deficiency-induced liver injuries but also improves survival in mice received a lethal dose of acetaminophen. Collectively, these findings identify ASGR1 as a potential genetic determinant of susceptibility to liver injury and propose it as a therapeutic target for the treatment of liver injury.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for livers of WT and Asgr1-/- mice.

first: Zhe

last: Zhang

first: Xiangkai

last: Leng

first: Yuanyuan

last: Zhai

first: Jiangwei

last: Wu

first: Zhiwei

last: Sun

first: Junying

first: Junfeng

last: Lu

first: Kun

last: Liu

first: Bo

last: Xia

first: Qi

last: Gao

first: Miao

last: Jia

first: Chengqi

last: Xu

first: Yina

last: Jiang

first: Xiaogang

first: Kaishan

last: Tao


title: Transcriptome Analysis of Rabies virus-infected Mice Salivary Glands

city: Changchun

first: xin

last: guo

state: Jilin

address: College of Veterinary Medi- 7 cine, Jilin University, Changchun 130062, China.

institute: Jilin university

summary: Rabies is a fatal zoonotic disease posing a threat to the public health globally. Rabies virus (RABV) is excreted in the saliva of infected animals, and is primarily transmitted through bite contact. Salivary glands play an important role for virus propagation. However, the significance of salivary glands is less studied in RABV pathogenic mechanisms. To identify functionally important genes in the salivary glands, we employed RNA sequencing (RNA-seq) to establish and analyze mRNA expression profiles in parotid tissue infected with two RABV strains, CVS-11 and PB4. We map the transcriptome changes in response to RABV infection in parotid tissue for the first time. This work provides new clues to the study of RABV-affected salivary gland function and RABV transmission mechanisms in parotid tissue. And the salivary gland-enriched transcripts could be potential targets of interest for rabies disease control.

overall_design: 36 mice were assigned to three groups (mock, CVS-11- and PB4-infected groups), each group contained 12 mice. Within each group, 4 mice constituted one biological replicate. We employed RNA sequencing (RNA-seq) to establish and analyze mRNA expression profiles in uninfected mice parotid tissue (mock group) and parotid tissue infected with two RABV strains, CVS-11 and PB4.

first: Xin

last: Guo

first: Yidi

first: Maolin

first: Ye

last: Feng


title: The role of the antifolate methotrexate in LPS response in human macrophages

status: Public on Nov 25 2023

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

summary: Macrophage phenotypic and functional heterogeneity derives from tissue-specific transcriptional signatures shaped by the local microenvironment. M-CSF drives the generation of human monocyte-derived macrophages with a potent anti-inflammatory activity upon stimulation. One-carbon metabolism (OCM) is a complex network of biosynthetic pathways that includes de novo biosynthesis of purines and thymidylate, amino acid metabolism, and methylation reactions. We explored the molecular impact of blocking OCM with high-doses of the anti-folate methotrexate (MTX) on the gene expression profile in M-CSF-primed human monocyte derived macrophages during LPS activation.

overall_design: mRNA profiles of human untreated or MTX treated monocyte-derived macrophages exposed to 10 ng/ml LPS for 3h. Monocytes were cultured for 7 days containing M-CSF (10 ng/ml) to generate M-CSF-polarized macrophages (M-MØ). M-CSF was added every two days. Methotrexate (MTX, 5 uM) was added once on monocytes inmediatly before the initation of the M-CSF differentiation process.  On day 7, M-MØ and MTX-M-MØ were exposed to LPS (10 ng/ml) for 3h.

first: Clara

last: Lorente-Sorolla

first: Mónica

last: Torresano

middle: P

last: Kröger


title: Effect of PAI-1 knockdown on gene expression in SK-OV-3 cells, and effect of platelets on gene expression in SK-OV-3 cells.

city: Dublin

first: Tanya

middle: E

last: Kelly

email: kellyt9@tcd.ie, kellyt14@tcd.ie

address: James' Street

department: Histopathology and Morbid Anatomy

country: Ireland

institute: Trinity College Dublin School of Medicine

summary:
To investigate the role of PAI-1 (SERPIN E1) in ovarian cancer, we performed several in vitro assays using SK-OV-3 cells in which PAI-1 had been knocked down by siRNA, treated with platelets, or both.
We then performed a comparative gene expression analysis using RNA-Seq data from untreated cells, PAI-1 siRNA knockdown or negative control, each with and without incubation with healthy donor platelets.

overall_design: Comparative gene expression profiling analysis of RNA-Seq data from untreated cells, PAI-1 siRNA knockdown or negative control, each with and without incubation with healthy donor platelets.

first: Karsten

last: Hokamp

first: John

last: O'Leary

first: Sharon

last: O'Toole


title: High-throughout sequencing of liver cancer cells treated Flavokawain C

status: Public on Nov 23 2023

city: wenzhou

first: Jin

last: Yuepeng

state: Zhejiang Province

address: Chashan Street, Ouhai District, Wenzhou City

institute: Wenzhou Medical University First Affiliated Hospital

summary: The high-throughput sequencing technology was performed after the treatment of humanliverl cancer cells HUH-7 with  Flavokawain C  synthesized by ourselves, to explore the expression of genes related to cell proliferation, adhesion, migration and invasion of human liver cancer cells HUH-7  after the treatment of the active compound and to find an interesting target gene.

overall_design: Human liver cancer cells HUH-7  were treated with Flavokawain C at the concentration of 10 µM for 48 hours.

first: Yuepeng

last: Jin

first: Xiaohui

last: Zheng


title: Comparing the relative transcription levels of genes in Pichia pastoris at different stages of growth

status: Public on Nov 22 2023

city: Hangzhou

first: Qi

last: Shen

state: Zhejiang

address: Chaowang road 118

institute: Zhejiang university of technology

summary: It is widely accepted that the expression levels of certain genes undergo significant changes with the cellular growth state. The promoters of these genes may serve as potential candidates for constructing the desired biphasic expression system. Therefore, we performed RNA-Seq analysis of Pichia pastoris during early, mid, and late logarithmic growth phases.

overall_design: Logarithmic phase (OD600 value 2-3) of Pichia pastoris GS115 cells (50 μL) were inoculated into 50 mL of YPD medium (1% yeast extract, 2% peptone, and 2% dextrose). The cells were grown under the condition of 30°C with shaking (250-300 rmp). The cells were collected at 24, 36, and 48 hours. Comparative gene expression profiling analysis of RNA-seq data for cells collected at different time points.

first: Ya-Ping

last: Xue

first: Yu-Guo


title: Environmental regulation of male fertility is mediated through Arabidopsis bHLH89, 91 and 10

city: Loughborough

first: Zoe

last: Wilson

address: Sutton Bonington Campus

department: Plant Sciences

country: United Kingdom

institute: University of Nottingham

summary: Formation of functional pollen and successful fertilisation relies upon the spatial and temporal regulation of anther and pollen development. This process responds to environmental cues to maintain optimal fertility despite climatic changes. Arabidopsis transcription factors bHLH10,-89,-91 were previously thought to be functionally redundant in their control of male reproductive development, however here we show that they play distinct roles in the integration of light signals to maintain pollen development under different environmental conditions. Combinations of the double and triple bHLH10,-89,-91 mutants were analysed under normal (200μmol/m2/s) and low (50μmol/m2/s) light conditions to determine the impact on fertility. Transcriptomic analysis of a new conditionally sterile bhlh89,91 double mutant shows differential regulation of genes related to sexual reproduction, hormone signal transduction and lipid storage and metabolism under low-light. Here we have shown that bHLH89 and bHLH91 play a role in regulating fertility in response to light, suggesting they function in mitigating environmental variation to ensure fertility is maintained under environmental stress.

overall_design: To elucidate the genetic basis of conditional sterility in the Arabidopsis thaliana bhlh89,91 double mutant here we present an RNA-Seq, comparing floral transcriptomic changes under normal (200μmol/m2/s) and low (50μmol/m2/s) intensity light conditions to wild-type Col-0.

first: Jordan

middle: K

last: Robson


title: TREX1 is required for microglial cholesterol homeostasis and subsequent oligodendrocyte maturation during brain development [bulk RNA-seq]

city: La Jolla

first: Alysson

last: Muotri

state: California

address: 2880 Torrey Pines Scenic Drive, Room 3005

institute: University of California - San Diego

summary: Three Prime Repair Exonuclease 1 (TREX1) gene mutations have been associated with Aicardi-Goutières Syndrome (AGS) – a rare, severe pediatric autoimmune disorder that primarily affects the brain and has a poorly understood etiology. Microglia are brain-resident macrophages indispensable for brain development and implicated in multiple neuroinflammatory diseases. However, the role of TREX1 – a DNase that cleaves cytosolic nucleic acids, preventing viral- and autoimmune-related inflammatory responses – in microglia biology remains to be elucidated. Here, we leverage a model of human embryonic stem cell (hESC)-derived engineered microglia-like cells, bulk and single-cell transcriptomics, optical and transmission electron microscopy, and three-month-old assembloids composed of microglia and regionalized neural organoids to interrogate TREX1 functions in human microglia. Our analyses suggest that TREX1 influences cholesterol metabolism, leading to an active microglial morphology with increased phagocytosis in the absence of TREX1. Notably, regulating cholesterol metabolism with an HMG-CoA reductase inhibitor, FDA-approved atorvastatin, rescues these microglial phenotypes. Functionally, TREX1-deficient microglia selectively affect oligodendrocyte maturation and myelination in assembloids. Together, these results suggest routes for therapeutic intervention in pathologies such as AGS based on microglia-specific molecular and cellular mechanisms.

overall_design: Samples represent independent differentiations of H9 human embryonic stem cell (hESC)-derived microglia-like cells. Two microglia genotypes were tested: control (CTRL) and CRISPR-edited TREX1 mutant (KO) microglia, and two isogenic pairs were used (CTRL1 with KO1 and CTRL2 with KO2). Two biological replicates were generated for each line. We extracted RNA and performed bulk RNA-seq to characterize these a microglia-like cells and interrogate the role of human TREX1 variants in microglial biology.

first: Gabriela

last: Goldberg


title: Shaping immune landscape of colorectal cancer by cholesterol metabolites [BALB/c]

city: Shanghai

first: Haochen

last: Yang

state: Shanghai

address: 320 Yue-yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Cancer immunotherapies have achieved unprecedented success in clinic, but they remain largely ineffective in some major types of cancer, such as colorectal cancer with microsatellite stability (MSS CRC) (Picard et al., 2020). It is therefore important to study tumor microenvironment of resistant cancers for developing new intervention strategies. In this study, we identify a metabolic cue that determines the unique immune landscape of MSS CRC. Through secretion of distal cholesterol precursors, which directly activate RORgt, MSS CRC cells can polarize T cells toward Th17 cells that have well-characterized pro-tumor functions in colorectal cancer. Analysis of large human cancer cohorts revealed an asynchronous pattern of the cholesterol biosynthesis in MSS CRC, which is responsible for the abnormal accumulation of distal cholesterol precursors. Inhibiting the cholesterol biosynthesis enzyme Cyp51 by ketoconazole, a clinically approved drug, reduced the levels of intratumoral distal cholesterol precursors and suppressed tumor progression through a Th17-modulation mechanism in preclinical MSS CRC models. Our study therefore reveals a novel immune-modulation mechanism of oncometabolites and an invention strategy for the difficult-to-treat MSS CRC.

overall_design: Cyp51-KO or sg-Ctrl CT26 tumors were harvested at day 26 post orthotopic injection in BALB/c mice.

first: Yibing

last: Bai

first: Tongzhou

last: Li

first: Qingshu

last: Wang

first: Weiqiang

last: You

first: Zhigang

first: Zheng-Jiang

last: Zhu

first: Chenqi

last: Xu


title: Accurate stress response silencing by an E3 ligase complex mutated in neurodegenerative disease

city: Berkeley

first: Diane

middle: L

last: Haakonsen

state: CA

address: 1951 Oxford St

department: MCB

institute: UC Berkeley

summary: Stress response pathways detect and alleviate many adverse conditions to safeguard cell and tissue homeostasis, yet their prolonged activation induces apoptosis and disrupts organismal health. How stress responses are turned off at the right time and place remains poorly understood. Here, we report a ubiquitin-dependent mechanism to silence the cellular response to mitochondrial protein import stress. Critical to this process is the silencing factor of the integrated stress response (SIFI), a large E3 ligase complex mutated in ataxia that degrades both unimported mitochondrial precursors and stress response components. By recognizing bifunctional substrate motifs that equally encode protein localization and stability, the SIFI complex can rapidly turn off a general stress response after a specific stress has been resolved. Pharmacological stress response silencing sustains cell survival even if stress resolution failed, which underscores the importance of signal termination and provides a roadmap for treating neurodegenerative diseases caused bymitochondrial import defects.

overall_design: Comparative gene expression profiling analysis of RNA-seq  data for wt 293T and ΔUBR4 cells depleted with sgTIMM8A (or sgCNTL) and treated with an inducer of the integrated stress response (sodium arsenite) or an inhibitor of the integrated stress response (ISRIB).

first: Michael

last: Heider

first: Andrew

last: Ingersoll

first: Kayla

last: Vodehnal

first: Samuel

last: Witus

first: Takeshi

last: Uenaka

first: Marius

last: Wernig

last: Rapé


title: Single-cell joint profiling of multiple epigenetic proteins and gene transcription

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

summary: we first develop uCoTarget, utilizing a split-pool barcoding strategy for realizing ultrahigh-throughput single-cell joint profiling of multiple epigenetic proteins. We then develop uCoTargetX, an expansion of uCoTarget to simultaneously measure transcriptome and multiple epigenome targets.

overall_design: K562 and Kasumi cells were colleced and submited to uCoTarget for co-profiling H3K4me3 and H3K27me3. Different T5 barcodes were used to identify K562 and Kasumi, which were then splitted and pooled for 4 rounds to realize single-cell resolution. H1 and K562 Cells were colleced and used for uCoTargetX experiments.

first: Qianhao

first: Chen C

first: Aibin

last: He


title: The Rtf1/Prf1-dependent histone modification axis and Rpb1 C-terminal domain phosphorylation counteract multi-drug resistance in fission yeast [ChIP-seq]

first: Jason

last: Tanny

overall_design: To investigate the basis for hydroxyurea (HU) resistance in S. pombe mutants affecting the Rtf1/Prf1 histone modification axis, we compared RNAPII ChIP-seq profiles in wild-type and HU-resistant mutants.

first: Jennifer

last: Chen

first: Calvin

last: Moy

first: Viviane

last: Page

first: Cian

last: Monnin

first: Ziad

last: El-Hajj

first: Daina

last: Z Avizonis

first: Rodrigo

last: Reyes-Lamothe


title: Benefits of diazoxide/dibenozylmethane (DZ/DIB) co-treatment on hippocampal gene expression in Female Fisher transgenic 344-AD rats.

city: New York

first: Kelechi

last: Ndukwe

state: NY

address: 695 Park Ave, New York, NY 10065

department: Biology

institute: Hunter College City University of New York Graduate Center

summary: Alzheimer’s disease (AD) is the major cause of dementia prevalent in older adults and with a high incidence in females; thus, Identification of early biomarkers is important for preventive interventions. To show potential early biomarkers, we carried out RNA-Sequencing analysis for 4-month(pre-pathology) TgF344-AD rats, a transgenic Alzheimer’s model that exhibits age-dependent AD progression. Our study showed two potential early biomarker genes (early growth response 2 (EGR2) and histone H2AA (HISIT1H2AA)) for AD, in the hippocampus of 4-month TgF344-AD females compared to wild-type littermates. Furthermore, due to the multifactorial cause for AD, we tested the therapeutic benefit of a multi-target approach using a co-treatment with diazoxide (DZ), a potassium channel activator, and dibenzoylmethane (DIB), which inhibits eIF2α-P activity, on TgF344-AD female. Our results strongly support the DZ/DIB-treatment as potential strategy to mitigate AD pathology due to its multi-target approach.

overall_design:
To show the potential early hippocampal biomarker gene expression.   Hippocampi of Five (4-month-old) TgF344-AD rats and Five (4-month-old) Wild-type female rats were analyzed for gene expression by RNAseq
To show the effects of diazoxide/dibenozylmethane (DZ/DIB) co-treatment on gene expression levels, Hippocampi of Six (4-month old) TgF344-AD DZ/DIB -treated rats and Four (4-month old) untreated TgF344-AD Female rats were analyzed for gene expression by RNAseq
At 4 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis.
For DZ/DIB treated rats, treatment began at age (52 days) and ended at 4-month. WT1 – WT5 (Untreated Wild-type rats), Tg1 – Tg5 (Untreated transgenic AD rats); Tg-1- Tg-5 (Untreated transgenic AD rats) and Tg-C1-Tg-C6 (transgenic AD rats treated with the drugs diazoxide and dibenozylmethane)
For the early biomarker experiment, the gene expression for the transgenic rats was compared to that of the Wild-type group (Tg1-5/WT1-5). For the effects of DZ/DIB, the gene expression for the DZ/DIB treated rats was compared to that of the untreated transgenic rats (Tg-C1-6/ Tg-1-5)

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submitter states that fastq files are no longer available.
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first: Charles

last: Wallace

first: Giovanni

last: Oliveros

first: Osama

last: Chaudry

first: Lei

last: Xie

first: Peter

last: Serrano

first: Patricia

last: Rockwell

first: Maria

last: Figueiredo-Pereira


title: IL-4 drastically decreases deuterosomal and multiciliated cells via alteration in progenitor cell differentiation

status: Public on Nov 21 2023

city: Seoul

first: Hyung-Ju

last: Cho

address: 50-1, Yonsei-ro, Seodaemun-gu,

department: Otorhinolaryngology

country: South Korea

institute: Yonsei University College of Medicine

summary: Allergic inflammation affects the epithelial cell populations resulting in goblet cell hyperplasia and decreased ciliated cells. In this study, we aimed to investigate the effect of allergic inflammation in nasal epithelial cell transcriptomes at the single-cell level. We performed scRNAseq in cultured primary human nasal epithelial (HNE) cells and in vivo nasal epithelium. The transcriptomic features and epithelial cell subtypes were determined under IL-4 stimulation, and cell-specific marker genes and proteins were identified. We confirmed that cultured HNE cells were similar to in vivo epithelial cells through scRNAseq. Cell-specific marker genes were utilized to cluster the cell subtypes, and FOXJ1+ -ciliated cells were sub-classified into multiciliated and deuterosomal cells. PLK4 and CDC20B were specific for deuterosomal cells, and SNTN, CPASL, and GSTA2 were specific for multiciliated cells. IL-4 altered the proportions of cell subtypes, resulting in a decrease in multiciliated cells and loss of deuterosomal cells. The trajectory analysis revealed deuterosomal cells as precursor cells of multiciliated cells and deuterosomal cells function as a bridge between club and multiciliated cells. A decrease in deuterosomal cell marker genes was observed in nasal tissue samples with type 2 inflammation.The effects of IL-4 appear to be mediated through the loss of the deuterosomal population, resulting in the reduction in multiciliated cells. This study also newly suggests cell-specific markers that might be pivotal for investigating respiratory inflammatory diseases.

first: Youn

last: Chung

first: Sungmin

last: Moon

first: Ju

last: Seo

first: Miran

last: Kang

first: Jae

last: Nam

first: Sang-Nam

last: Lee

first: Chang-Hoon

last: Kim

first: Augustine

middle: M

last: Choi

first: Joo-Heon

last: Yoon


title: The Integrated Stress Response effector GADD34 is repurposed by neurons to promote stimulus-induced translation

city: New York City

first: Mauricio

middle: Martins

last: Oliveira

address: 4 Washington Place, room 621

institute: New York University

summary: Neuronal protein synthesis is required for long-lasting plasticity and long-term memory consolidation.  Dephosphorylation of eukaryotic initiation factor 2α is one of the key translational control events that is required to increase de novo protein synthesis that underlies long-lasting plasticity and memory consolidation. Here, we interrogate the molecular pathways of translational control that are triggered by neuronal stimulation with brain-derived neurotrophic factor (BDNF), which results in eIF2α dephosphorylation and de novo protein synthesis. Primary rodent neurons exposed to BDNF displayed elevated translation, but not transcription, of GADD34, which facilitates eIF2α dephosphorylation and subsequent de novo protein synthesis. Furthermore, GADD34 requires G-actin generated by cofilin to dephosphorylate eIF2α and enhance protein synthesis. Finally, GADD34 is required for BDNF-induced translation of synaptic plasticity-related proteins. Overall, we provide evidence that neurons repurpose GADD34, an effector of the Integrated Stress Response, as an orchestrator of rapid increases in eIF2-dependent translation in response to plasticity-inducing stimuli.

overall_design: Wild type or GADD34flfl primary neurons were transduced either with mock virus or Cre-carrying virus. They were also co-transduced with AAV5.Camk2a.TRAP virus. After 14 days, neurons were exposed for 1h to either vehicle or BDNF and ribosomes purified for sequencing of translatome.

first: Eric

last: Klann


title: Molecular and clinical analyses of PHF6 mutant myeloid neoplasia provide clues as to their pathogenesis and therapeutic targeting.

city: Cleveland

first: Yasuo

last: Kubota

state: Ohio

address: 9500 Euclid Ave

department: Translational Hematology & Oncology

institute: Cleveland Clinic

summary: PHF6 mutations (PHF6MT) are identified in various myeloid neoplasms (MN). However, little is known about the precise function and consequences of PHF6 in MN. Our comprehensive genomic analyses focused on three main findings. Firstly, we revealed a different pattern of genes correlating with PHF6MT in male and female cases. When analyzing male and female cases separately, in only male cases, RUNX1 and U2AF1 were co-mutated with PHF6. In contrast, female cases revealed co-occurrence of ASXL1 mutations and X-chromosome deletions with PHF6MT. Next, proteomics analysis revealed a direct interaction between PHF6 and the pioneer transcription factor RUNX1. Both proteins co-localize in active enhancer regions that define the context of lineage differentiation. Finally, we demonstrated a negative prognostic role of PHF6MT, especially in association with RUNX1. The negative effects on survival were additive as PHF6MT cases with RUNX1 mutations had worse outcomes when compared to cases carrying single mutation or wild-type.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PHF6 in THP1 cells.

first: Maciejewski

last: Jaroslaw

first: Przychodzen

last: Bartlomiej

first: Kubota

last: Yasuo

first: Visconte

last: Valeria


title: Investigating the role of Hmo1 in transcription by Pol I in yeast.

status: Public on Nov 20 2023

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

summary: The purpose of this study was to investigate the role of the yeast protein, high mobility group protein (Hmo1), in rRNA synthesis. For over twenty years, Hmo1 has been proposed to be an activator of transcription by Pol I, but its regulatory mechanism remains largely undefined. Therefore, we used native elongating transcript sequencing (NET-seq) to explore the role of this factor in transcription by Pol I. Our NET-seq results demonstrated that in cells lacking Hmo1 (hmo1D), Pol I occupancy was significantly increased across the rDNA template, indicating an increased pause propensity in these cells. These data suggest that Hmo1 is an important transcription elongation factor for Pol I.

overall_design:
Triplicate NET-seq libraries were generated for wild-type (WT) and hmo1△ yeast strains.

Please note that the WT samples (in GSE216460/PRJNA893665) were re-analysed in the current study:
GEO accession title SRA accessions Biosample accession
========= ==== ========== =============
GSM6674347 WT yeast, untreated, rep1 SRR22028427/SRX18009711 SAMN31430711
GSM6674348 WT yeast, untreated, rep2 SRR22028426/SRX18009712 SAMN31430710
GSM6674349 WT yeast, untreated, rep3 SRR22028425/SRX18009713 SAMN31430709

first: David

last: Schneider


title: Effects of Follicle Stimulating Hormone on Adipose Tissue Metabolic Health After Loss of Ovarian Function

status: Public on Nov 18 2023

city: Aurora

first: Paul

last: MacLean

state: CO

department: Endocrinology, Metabolism, & Diabetes

institute: University of Colorado Anschutz Medical Campus

summary: Loss of ovarian function imparts increased susceptibility to obesity and metabolic disease. These effects are largely attributed to decreased estradiol (E2), but the role of increased follicle stimulating hormone (FSH) in modulating energy balance has not been fully investigated. Previous work that inhibited FSH activity in mice suggested this hormone may play a part in modulating body weight and energy expenditure after ovariectomy.  We used an alternate approach to experimentally isolate the individual and combined contributions of FSH and E2 in mediating energy imbalance and changes in tissue-level metabolic health.  Female Wistar rats were ovariectomized and given the GnRH antagonist degarelix to suppress FSH production. E2 and FSH were then added back individually and in combination for a period of 3 weeks.  Energy balance, body mass composition, and transcriptomic profiles of individual tissues were obtained.  In contrast to previous studies, ablation and replacement of FSH in our paradigm had no effect on body weight, body composition, food intake, or energy expenditure.  We did, however, observe organ-specific effects of FSH that produced unique transcriptomic signatures of FSH in retroperitoneal white adipose tissue. These included reductions in biological processes related to lipogenesis and carbohydrate transport.  Additionally, rats administered FSH had reduced liver triglyceride concentration (p<0.001), which correlated with FSH-induced changes at the transcriptomic level.  While not appearing to modulate energy balance after loss of ovarian function in rats, FSH may still impart tissue-specific effects in the liver and white adipose tissue that might affect the metabolic health of those organs.

overall_design: RNA was extracted from snap-frozen retroperitoneal white adipose tissue from individual ovariectomized rats receiving either degarelix-only (n=6) or degarelix+FSH (n=5) and subjected to RNA sequencing.

first: Andrew

last: Libby


title: Whole-genome analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans

city: College Station

first: Yuchao

last: Jiang

state: TX

address: 3143 TAMU

institute: Texas A&M University

summary: We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers (CPD) photoproducts in the Caenorhabditis elegans (C. elegans) genome. We focus on the C. elegans ortholog of the human XPC-deficient strain (xpc-1) and its exclusive use of transcription-coupled repair. We provide evidence demonstrating the utility of xpc-1 XR-seq as a remarkable tool for detecting nascent transcription and identifying new transcripts. The integration of epigenetic markers, chromatin states, and non-coding RNA annotations supports the robust detection of intergenic nascent transcription by XR-seq. Overall, our results provide a comprehensive view of the transcription-coupled repair landscape in C. elegans, highlighting their potential contributions to our understanding of DNA repair mechanisms and non-coding RNA biology.

overall_design: We employed XR-seq to evaluate genome-wide excision repair dynamics in xpc-1 C. elegans at distinct time points following UV exposure, specifically at 5 minutes, 1 hour, 8 hours, 16 hours, 24 hours, and 48 hours post-treatment. We also carried out poly(A) RNA-seq of wildtype and xpc-1 C. elegans.

first: Cansu

last: Kose

first: Laura

last: Lindsey-Boltz

first: Aziz

last: Sancar


title: Selected Spt5-Pol II inhibitors effectively relieve Huntington’s disease neuropathology and slow down its progression in mice [INCPMPM-17698]

city: Rehovot

first: Rivka

last: Dikstein

address: 234 Herzel

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Huntington’s disease (HD) is an incurable inherited disorder caused by repeat expansion in the huntingtin gene (Htt). The mutant protein causes neuronal degeneration leading to severe motor and psychological abnormalities. Selective downregulation of the mutant Htt by targeting Spt4/Spt5 or the Spt5-PolII transcription elongation complexes was proposed as a potential therapy. We report the identification of SPI-24 and SPI-77 small molecule inhibitors of Spt5-PolII that selectively lower mutant Htt. In the BACHD mouse model of HD, direct delivery to the striatum, subcutaneous injection and oral administration of these inhibitors diminished mutant Htt levels, ameliorated mitochondrial dysfunction and restored BDNF expression. Prolonged treatment attenuated motor and anxious-like phenotypes of HD mice and delayed disease deterioration. SPI-24 long-term treatment had no side-effects or global changes in gene expression. Mechanistically, SPIs reduce Spt5 and PolII occupancies of mutant Htt. Thus, SPIs can be an effective therapeutic strategy for HD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for brain cells derived from BACHD mice treated for long term with either DMSO or SPI-24

first: Anat

last: Bahat

first: Elad

last: Itzhaki

first: Benjamin

last: Weiss

first: Michael

last: Tolmasov

last: Tsoory

first: Yael

last: Kuperman

first: Alexander

last: Brandis

first: Khriesto

last: Shurrush


title: Selected Spt5-Pol II inhibitors effectively relieve Huntington’s disease neuropathology and slow down its progression in mice

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

overall_design: Refer to individual Series


title: Mouse Insulinoma 6 (MIN6) transcriptome data at 2.8mM and 25mM extracellular glucose concentrations.

status: Public on Nov 15 2023

city: New Delhi

first: Firdos

last: Firdos

state: New Delhi

address: Hauz khas

department: Kusuma School of Biological Sciences

country: India

institute: Indian Institute of Technology, Delhi

summary:
To investigate whether the upregulated proteins identified through transcriptome studies have any possible direct interaction with intracellular and unphosphorylated glucose.

To investigate whether enhanced insulin secretion is at the cost of other secretory proteins.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of MIN6 cells at hypoglycemic (2.8mM) and hyperglycemic (25mM) extracellular glucose concentrations.

first: Aditya

last: Mittal


title: 8-Cl-Ado and 8-NH2-Ado Synergize with Venetoclax to Target the Methionine-MAT2A-SAM Axis in Acute Myeloid Leukemia

status: Public on Nov 09 2023

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Background: Targeting the metabolic dependencies of acute myeloid leukemia (AML) cells is a promising therapeutical strategy. In particular, the cysteine and methionine metabolism pathway (C/M) is significantly altered in AML cells compared to healthy blood cells. Moreover, methionine has been identified as one of the dominant amino acid dependencies of AML cells. Methods: Through RNA-seq, we found that the two nucleoside analogs 8-chloro-adenosine (8CA) and 8-amino-adenosine (8AA) significantly suppress the C/M pathway in AML cells, and methionine-adenosyltransferase-2A (MAT2A) is one of most significantly downregulated genes. Additionally, mass spectrometry analysis revealed that Venetoclax (VEN), a BCL-2 inhibitor recently approved by the FDA for AML treatment, significantly decreases the intracellular level of methionine in AML cells. Based on these findings, we hypothesized that combining 8CA or 8AA with VEN can efficiently target the Methionine-MAT2A-S-adenosyl-methionine (SAM) axis in AML. Results: Our results demonstrate that VEN and 8CA/8AA synergistically decrease the SAM biosynthesis and effectively target AML cells both in vivo and in vitro. Conclusions: These findings suggest the promising potential of combining 8CA/8AA and VEN for AML treatment by inhibiting Methionine-MAT2A-SAM axis and provide a strong rationale for our recently activated clinical trial.

overall_design: AML cells MV4-11 and KG-1a were treated with 1 uM 8-chloro-adenosine or 1 uM 8-amino-adenosine for 8h or 24h, and the total RNA was extracted for RNA seq.

first: Jiamin

last: Guo

first: Min-Hsuan

last: Chen

first: Xiwei

last: Wu

first: Steven

middle: T

last: Rosen


title: High-content CRISPR screens link coronary artery disease genes to endothelial cell programs [Bulk RNA-seq]

status: Public on Nov 14 2023

city: Stanford

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

institute: Stanford University

summary: Genome-wide association studies (GWAS) have discovered thousands of risk loci for common, complex diseases, each of which could point to genes and gene programs that influence disease. For some diseases, it has been observed that GWAS signals converge on a smaller number of biological programs, and that this convergence can help to identify causal genes. However, identifying such convergence remains challenging: each GWAS locus can have 2-20 candidate genes, the cellular programs a gene participates in are difficult to define in an unbiased fashion, and it remains unclear which genes and programs would be likely to influence disease risk. Here, we explored a new approach to address this challenge, by creating an unbiased catalog of gene programs and their regulators in endothelial cells to link variants to functions for coronary artery disease (CAD). To do so, we applied CRISPRi-Perturb-seq to knock down all expressed genes within 500 Kb of all CAD GWAS loci (2,285 genes in total) and measure their effects on the transcriptome using single-cell RNA-seq. We used consensus non-negative matrix factorization to define 60 gene expression programs—including core cellular programs, such as ribosome biogenesis, and endothelial cell-specific programs, such as flow response and angiogenesis—and link these programs to upstream regulators including transcription factors, chromatin regulators, metabolic enzymes, and signaling cascades. By combining this gene-to-program catalog with variant-to-gene maps, we find that candidate CAD genes converge onto 6 interrelated gene programs, together involving known and novel genes in 39 of 229 CAD GWAS loci. Analysis of these programs revealed that the cerebral cavernous malformations (CCM) complex—whose potential connection to CAD has not been previously explored—acts upstream to regulate other CAD genes involved in cytoskeletal organization, extracellular matrix remodeling, and cell migration. The strongest regulator of these programs is TLNRD1, a highly conserved but poorly studied gene that we show acts in the CCM pathway and regulates actin organization and endothelial cell barrier function. Together, our study nominates new genes that likely influence risk for CAD, identifies convergence of CAD risk loci into certain gene programs in endothelial cells, and demonstrates a generalizable strategy to catalog gene programs to connect disease variants to functions.

overall_design: RNA-seq libraries were made from CRISPRi TeloHAEC (TeloHAEC with doxycycline-inducible KRAB-dCAS9-BFP) that were transduced with lentiviral single guide RNA vectors, selected for blast resistance, and treated with doxycycline to induce CRISPRi machinery and silence the sgRNA-targeted promoters. For some libraries, cells were grown under laminar flow for 48 hours. For others, cells were nucleofected with Cas9-DNA complexes with control guides, or guides targeting MAP3K3.

first: Gavin

middle: R

last: Schnitzler

first: Helen

last: Kang

first: Vivian

last: Lee-Kim

first: X

last: Ma

first: Tony

last: Zeng

first: Shamsudheen

last: Vellarikkal

first: Ronghao

last: Zhou

first: Katherine

first: Oscar

last: Sias-Garcia

first: Alex

last: Bloemendal

first: Glen

last: Munson

first: Philine

last: Guckelberger

first: Tung

last: Nguyen

first: Drew

last: Bergman

first: Deepak

last: Atri

first: Nathan

last: Cheng

first: Brian

last: Cleary

first: Eric

last: Lander

first: Hilary

last: Finucane

first: Rajat

last: Gupta


city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

summary: Gene expression profiles of Ccl21a+ and Rank+ E17 thymic epithelial cells (TECs) were compared using Ccl21a-tdTomato-KI Rank-Venus-Tg mice

overall_design: tdTom+Venus-, tdTom-Venus+, and tdTom-Venus- cells within CD45- EpCam+ thymic epithelial cells (TECs) from E17 embryos were isolated and their RNAs were extracted for bulk sequencing analysis

first: Izumi

last: Ohigashi

first: Andrea

last: White

first: Sevilay

last: Turan

first: Graham

last: Anderson

first: Yousuke

last: Takahama


title: Ex Vivo Expansion Potential of Murine Hematopoietic Stem Cells: A Rare Property Only Partially Predicted by Phenotype

status: Public on Nov 08 2023

city: Lund

first: Qinyu

last: Zhang

address: Box 188

department: Department of Molecular Hematology

country: Sweden

institute: Lund University

summary: The scarcity of hematopoietic stem cells (HSCs) restricts their use in both clinical settings and experimental research. Here, we examined a recently developed method for expanding rigorously purified murine HSCs ex vivo. Input HSCs displayed varying potential for ex vivo self-renewal, with alternative outcomes revealed by single cell multimodal RNA- and ATAC-seq profiling. While most HSC progeny offered only transient in vivo reconstitution, these cells efficiently rescued mice from lethal myeloablation. The amplification of functional HSC activity allowed for long-term multilineage engraftment in unconditioned hosts that somewhat surprisingly associated with a return of HSCs to quiescence. Thereby, our findings identify several key considerations for ex vivo HSC expansion, with major implications also for assessment of normal HSC activity.

overall_design: To gain a deeper understanding of the cells generated in ex vivo HSC cultures, we collected cells from the entire culture or EPCR+ cells and isolated nuclei for single cell multiome sequencing

first: Rasmus

last: Olofzon

first: Anna

last: Konturek-Ciesla

first: Ouyang

last: Yuan

first: David

last: Bryder


title: Effect of inhibition of LDHA using FX11 on gene expression in CT2A glioma cells

city: CHICAGO

first: Peiwen

last: Chen

state: IL

address: 303 East Superior Street, Suite 6-512

institute: Northwestern University

summary:
To investigate the role of LDHA in regulating gene expression in glioma cells, we treated CT2A glioma cells with LDHA inhibitor FX11.
We then performed gene expression profiling analysis using data obtained from RNA-seq of control and FX11-treated cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Control and FX11-treated cells.

first: Fatima

last: Khan


title: Selected Spt5-Pol II inhibitors effectively relieve Huntington’s disease neuropathology and slow down its progression in mice [INCPMPM-16068]

first: Rivka

last: Dikstein

overall_design: Comparative gene expression profiling analysis of RNA-seq data for brain cells derived from BACHD mice treated for short term with either DMSO or SPI-24 or SPI-77

first: Anat

last: Bahat

first: Elad

last: Itzhaki

first: Benjamin

last: Weiss

first: Michael

last: Tolmasov

last: Tsoory

first: Yael

last: Kuperman

first: Alexander

last: Brandis

first: Khriesto

middle: A

last: Shurrush


title: Concentrations of 27 cytokines and chemokines in the culture medium of HUVECs

status: Public on Nov 07 2023

city: Nanjing

first: Ying

last: Wang

address: Guangzhou Road

institute: NanJing Medical University

summary: Culture medium of HUVECs was collected and analyzed with the Bio-Plex Pro™ Human Cytokine 27-plex Panel.

overall_design: Culture medium was sequentially mixed with fluorescence-labeled capture beads and highly specific monoclonal antibodies. The mixture was then resuspended and irradiated. Concentrations of 27 cytokines and chemokines in the mixture were detected using the Luminex™ 200™ instrument system (Luminex, Austin, TX, USA). Data were analyzed with the xPONENT® software.

first: Xue

first: Qinghuai

last: Liu


title: An epigenetic barrier in neural progenitor cells and early neurons sets the timing of human neuronal maturation

status: Public on Nov 06 2023

first: Ryan

last: Walsh

address: 430 E 67th St

department: Developmental Biology

institute: MSKCC

summary: A challenge for understanding the development of brain circuits is to identify the factors that instruct neurons to accomplish each developmental steps 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: Neural induction of WA09 (H9) hPSC was completed using the dual SMAD inhibition protocol and WNT inhibition on Matrigel coated dishes. hPSC-derived neurons were maintained on poly-L-ornithine and Laminin/ Fibronectin coated plates in Neurobasal medium supplemented with B27, L-glutamine and DAPT,  dissociated at d27 using Accutase and Papain and processed for scRNAseq.

first: Gabriele

last: Ciceri

first: Hyunwoo

last: Cho

first: Meghana

last: Kshirsagar

first: Arianna

last: Baggiolini

first: Kelly

last: Aromolaran

first: Peter

last: Goldstein

first: Richard

last: Koche

first: Christina

middle: S

last: Leslie

first: Lorenz

last: Studer


title: Two-motif model illuminates DICER cleavage preferences

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Homo sapiens
synthetic RNA

platform_organism:
Homo sapiens
synthetic RNA


title: Synergistic roles of DYRK1A and GATA1 in trisomy 21 megakaryopoiesis

status: Public on Nov 04 2023

city: Philadelphia

first: Eric

last: Wafula

state: PA

address: 2714-2720 South Street

department: DBHi

institute: Children's Hospital of Philadelphia

summary: Patients with Down syndrome (DS, trisomy 21, T21) are at increased risk of transient abnormal myelopoiesis (TAM) and acute megakaryoblastic leukemia (ML-DS). Both TAM and ML-DS require prenatal somatic mutations in GATA1, resulting in the truncated isoform GATA1s.  The mechanism by which individual chromosome 21 (HSA21) genes synergize with GATA1s for leukemic transformation is challenging to study, in part due to limited human cell models with wild type GATA1 or GATA1s. HSA21-encoded DYRK1A is overexpressed in ML-DS and may be a therapeutic target. To determine how DYRK1A influences hematopoiesis in concert with GATA1s, we used gene editing to disrupt all 3 alleles of DYRK1A in isogenic T21 induced pluripotent stem cells (iPSCs) with and without the GATA1s mutation. Unexpectedly, hematopoietic differentiation revealed that DYRK1A loss combined with GATA1s leads to increased megakaryocyte proliferation and decreased maturation. This proliferative phenotype was associated with upregulation of D-type cyclins and hyperphosphorylation of Rb to allow E2F release and de-repression of its downstream targets. Notably, DYRK1A loss had no effect in T21/wtGATA1 megakaryocytes. These surprising results suggest that increased DYRK1A expression may be protective against TAM and ML-DS and that DYRK1A inhibition would not be a therapeutic option for GATA1s-associated leukemias.

overall_design: To investigate the role of DYRK1A in TAM and ML-DS, we used CRISPR/Cas9 gene editing to knock out all isoforms of human DYRK1A in isogenic T21 iPSC lines with wtGATA1 or GATA1s. We then performed gene expression profiling analysis using data obtained from RNA-seq for flow cytometry-purified CD43+/41+/235+ hematopoietic progenitors and CD41+/CD42b+ megakaryocytes from T21/GATA1s/DYRK1A+/+/+ and T21/GATA1s/DYRK1A-/-/-.

last: Sit

first: Kaoru

last: Takasaki

first: Hyun

last: An

first: Yan

last: Xiao

first: Christian

last: Hurtz

last: Gearhart

first: Zhe

last: Zhang

first: Paul

last: Gadue

first: Deborah

last: French

first: Stella

last: Chou


title: Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals

status: Public on Nov 13 2023

first: Jianhua

last: Chen

state: Jiangsu

address: 101 Longmian Road

institute: Nanjing Medical University State Key Laboratory of Reproductive Medicine

summary: In order to explore the regulatory role of the RBP we predicted on alternative splicing, an experiment was carried out.

overall_design: Using effective siRNAs, Eif4a3 was selected as an example and its expression was decreased in mouse zygotes via microinjection. Blastocysts were collected on the fifth day, with 3 samples from each of the Negative Control group (NC) and the Eif4a3-knockdown (Eif4a3-KD) group, each sample containing 5 embryos. The embryos were then placed in SMART lysate and sent to LC-Bio Technologies (Hangzhou) Co., Ltd for Smart-seq2 sequencing, which was conducted using the Illumina NovaseqTM 6000 150PE platform.

first: Yanni

last: He

first: Liangliang

first: Ruizhi

last: Feng


title: A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Refer to individual Series

Grant ID:    NIH T32 AI007512
Grant title: Molecular Basis of Allergic and Immunologic Disease
Affiliation: Children's Hospital
Name:        Yeguang Hu


title: The time integral of BMP signaling determines fate in a stem cell model for early human development

status: Public on Nov 03 2023

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

summary: The study aimed to identify genes integrating BMP signaling, whose transcript levels rise or fall approximately linearly over the course of BMP4-driven differentiation, and whose rate of change is proportional to the level of BMP signaling.

overall_design: RNA seq of hESCs treated with a high dose of BMP4 concurrent with WNT inhibition, collected at 0, 4, 12, 20, 28, and 42 hours after differentiation with no inhibition of BMP signaling or at 5 hours with varying levels of inhibition of BMP signaling with the receptor inhibitor LDN-193189.

first: Seth

last: Teague

first: Idse

last: Heemskerk

first: Craig

last: Johnson


title: Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute


title: Black Carbon Impacts on Paraburkholderia xenovorans Strain LB400 Cell Enrichment and Activity: Implications toward Lower-Chlorinated Polychlorinated Biphenyls Biodegradation

city: Iowa City

first: Timothy

last: Mattes

address: 4105 Seamans Center

institute: University of Iowa

summary: Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging approach to remove PCBs from sediment, but development of aerobic biofilms on BC for long-term, sustained LC-PCBs remediation is poorly understood. This work aimed to characterize cell enrichment and activity of biphenyl- and benzoate-grown Paraburkholderia xenovorans strain LB400 on various BCs. Biphenyl dioxygenase gene (bphA) abundance on four BC types demonstrated corn kernel biochar hosted at least four orders of magnitude more attached cells per gram than other feedstocks, and microscopic imaging revealed the attached live cell fraction was >1.5X more on corn kernel biochar than GAC. BC characteristics (i.e., sorption potential, surface area, pH) drove cell attachment differences. Reverse transcription qPCR indicated BC feedstocks significantly influenced bphA expression in attached cells. The bphA transcript-per-gene ratio of attached cells was >10-fold more than suspended cells, confirmed by transcriptomics. RNA-seq also demonstrated significant upregulation of biphenyl and benzoate degradation pathways on attached cells, revealing biofilm formation potential and cell-cell communication pathway connections. These novel findings demonstrate aerobic PCB-degrading cell abundance and activity could be tuned by adjusting BC feedstocks/ attributes to improve LC-PCBs biodegradation.

overall_design: To investigate the impacts of black carbon feedstocks on LB400 cell attachment and activity, we performed qPCR and Rt-qPCR of targeted gene (bphA) abundance and expression, and RNA-seq of both suspended and attached cells growing in three black carbons. These three black carbons include small corn kernel biochar, large corn kernel biochar, and granular activated carbon.

first: Qin

last: Dong

first: Gregory

last: LeFevre


title: Targeting Arginine Methylation Suppresses Cancer Stem Cell Maintenance and Elicits cGAS-mediated anti-Cancer Immunity

city: Monrovia

first: Ling

last: Li

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

summary: Current anti-cancer therapies cannot eliminate all the cancer cells, which hijack normal arginine methylation as a means to promote their own maintenance via unknown mechanisms. Herein, we show that targeting protein arginine methyltransferase 9 (PRMT9), whose activities are elevated in leukemia stem cells (LSCs) from patients with acute myeloid leukemia (AML), eliminates disease via cancer-intrinsic mechanisms and cancer-extrinsic Type-I Interferon (IFN-I)-associated immunity. PRMT9 ablation in AML cells decreased arginine methylation of regulators of RNA translation and the DNA damage response, suppressing cell survival. Notably, PRMT9 inhibition promoted DNA damage and activated cGAS, which underlies the IFN-I response. Genetically activating cGAS in AML cells blocked leukemogenesis. We also report synergy of a PRMT9 inhibitor with anti-PD1 in eradicating PRMT9-proficient cancers, including AML and lymphoma. We conclude that PRMT9 governs LSCs survival and immune evasion, and that combining a PRMT9 inhibitor with an immune checkpoint inhibitor represents a novel anti-cancer strategy.

overall_design: BM and spleen cells in Ctrl or Prmt9-KD MA9mice administered Dox in drinking water over 7 days were collected for analysis.

first: Haojie

first: Xin

first: Lei

first: Wei

first: Yi-Chun

last: Lin

first: Song-Bai

last: Liu

first: Huafeng

last: Wang

first: Victor

last: Huang

first: Min

first: Yinghui

last: Zhu

first: Dandan

last: Zhao

first: Lucy

last: Ghoda

first: Rui

last: Su

first: Jianjun

first: Ritin

last: Sharma

first: Patrick

last: Pirrotte

first: Xiwei

last: Wu

first: Weidong

last: Hu

last: Han

first: Binghui

last: Shen

first: Ya-Huei

last: Kuo

first: Jie

last: Jin

first: Amandeep

last: Salhotra

first: Jeffrey

first: Guido

last: Marcucci

first: L

middle: Y

last: Luo


first: Ling

last: Li

address: 1218 S 5TH AVE, MONROVIA

overall_design: Molm13 and THP1 cells with Ctrl or Prmt9-KD administered by Dox induction were collected for analysis.

first: Haojie

last: Dong

first: Xin

last: He

first: Lei

last: Zhang

first: Wei

last: Chen

first: Yi-Chun

last: Lin

first: Song-Bai

last: Liu

first: Huafeng

last: Wang

first: Victor

first: Min

first: Yun


title: MTOR modulation induces selective perturbations in histone methylation which influence the anti-proliferative effects of mTOR inhibitors [ChIP-Seq]

status: Public on Nov 02 2023

city: Montreal

first: HaEun

last: Kim

state: Quebec

address: 3999 ch de la Cote-Sainte-Catherine

institute: McGill

summary: Emerging data suggest a significant cross-talk between metabolic and epigenetic programs. However, the relationship between the mechanistic target of rapamycin (mTOR) which is a pivotal regulator of cellular metabolism, and epigenetic modifications remains poorly understood. We thus explored the impact of modulating mTOR signaling on histone methylation, a well-known epigenetic modification. Our results show that constitutive mTORC1 activation caused by abrogation of TSC2 increases H3K27me3 but not H3K4me3 or H3K9me3, via 4E-BPs-mediated induction of EZH2 protein levels. Surprisingly, mTOR inhibition also induced H3K27me3 independently of TSC2. This coincided with reduced EZH2 and increased EZH1 protein levels. Notably, the ability of mTOR inhibitors to induce H3K27me3 levels was positively correlated with their anti-proliferative effects. Collectively, our findings demonstrate that both activation and inhibition of mTOR selectively increase H3K27me3 by distinct mechanisms, whereby the ability of mTOR inhibitors to induce H3K27me3 influences their anti-proliferative effects.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27me3 after mTOR inhibition (Ink128, rapamycin and serum starvation) vs Stimulation (vehicle)

first: Benjamin

last: Lebeau

first: David

last: Papadopoli

first: Predrag

last: Jovanovic

first: Mariana

last: Russo

first: Daina

last: Avizonis

first: Massahiro

last: Morita

first: Josie

last: Ursini-Siegal

first: Lynne-Marie

last: Postovit

first: Ivan

last: Topisirovic

first: Michael

last: Witcher


title: Cas-SF01, an engineered Cas12i nuclease is an efficient genome editing tool in mammalian cells and plants

status: Public on Nov 05 2023

city: Shenzhen

first: Weilong

last: Yang

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

summary: The type V-I CRISPR-Cas system is becoming increasingly attractive for its potential utility in gene editing. However, natural nucleases often exhibit low efficiency, limiting their application. Here, we utilized structure-guided rational design and combinatorial protein engineering to optimize an uncharacterized Cas12i nuclease, Cas12i3. Accordingly, we developed Cas-SF01, a Cas12i3 variant that exhibits significantly improved gene-editing activity in mammalian cells and plants. Cas-SF01 displays comparable or superior editing performance compared to SpCas9 or recently engineered Cas12 nucleases. Further analysis of PAM recognition showed that Cas-SF01 has an expanded PAM range and effectively recognizes NTTN and noncanonical NATN and TTVN PAMs. Additionally, we identified an amino acid substitution, D876R, that markedly reduced the off-target effect while maintaining high on-target activity, leading to the development of Cas-SF01HiFi (high-fidelity Cas-SF01). Finally, we demonstrated that Cas-SF01 has robust gene-editing activity in both the monocot plant rice and dicot plant pepper. Our results suggest that Cas-SF01 can serve as a robust gene-editing platform with high efficiency and specificity for future genome editing applications across different organisms.

overall_design: to investigate the off-target effect of the Cas12i3 nuclease, we established the GUIDE-Seq experiment of two gene targetes in 293T cell.

first: Zhiqiang

last: Duan

first: Yafeng

last: Liang


title: MTOR modulation induces selective perturbations in histone methylation which influence the anti-proliferative effects of mTOR inhibitors

overall_design: Refer to individual Series


title: Immunomodulatory effect of cisplatin and carboplatin in human and mouse cell line in vitro

city: SOUTH SAN FRANCISCO

first: Kobe

last: Yuen

state: California

address: 1 DNA WAY

department: Oncology Biomarker Development

institute: Genentech

summary: The Phase 3 1L urothelial carcinoma (IMvigor130) trial revealed more favorable effects on overall survival with atezolizumab combined with gemcitabine and cisplatin (GemCis) than with atezolizumab combined with gemcitabine and carboplatin (GemCarbo). This study investigates the immunomodulatory effects of cisplatin vs carboplatin as a potential explanation for these clinical observations. GemCis compared with GemCarbo ± atezolizumab induced transcriptional changes in circulating immune cells, including upregulation of antigen presentation and T-cell activation programs. In vitro experiments demonstrated that cisplatin, compared with carboplatin, exerted direct immunomodulatory effects on cancer cells, promoting dendritic cell activation and antigen-specific T cell killing. These results underscore the key role of immune modulation in cisplatin's efficacy in urothelial carcinoma and highlight the potential importance of specific chemotherapy backbones for immune checkpoint blockade combination therapies.

overall_design: To profile the impact of cisplatin and carboplatin on the whole transcriptomes of tumor cells, human bladder cancer cells (5637 and RT112) and murine colon cancer cells (MC38) were treated with cisplatin (5 µM), carboplatin (35 µM), or dimethyl sulfoxide control for 24 hours. In addition, we collected 5637 cells that had been treated for 24 hours with cisplatin (5 µM) or carboplatin (35 µM) in the presence or absence of an ATR inhibitor (1 µM) to evaluate the role of DNA damage sensor ATR in cisplatin- or carboplatin-mediated transcriptome changes.

first: Deepali

last: Rishipathak

first: Aaron

last: Rapaport


title: Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease

status: Public on Nov 01 2023

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

summary: SVA retrotransposons remain active in humans and contribute to individual genetic variation. Polymorphic SVA alleles harbor gene-regulatory potential and can cause genetic disease. However, how SVA insertions are controlled and functionally impact human disease is unknown. Here, we dissect the epigenetic regulation and influence of SVAs in cellular models of X-linked dystonia-parkinsonism (XDP), a neurodegenerative disorder caused by an SVA insertion at the TAF1 locus. We demonstrate that the KRAB zinc finger protein ZNF91 establishes H3K9me3 and DNA methylation over SVAs, including polymorphic alleles, in human neural progenitor cells. The resulting mini-heterochromatin domains attenuate the cis-regulatory impact of SVAs. This is critical for XDP pathology; removal of local heterochromatin severely aggravates the XDP molecular phenotype, resulting in increased TAF1 intron retention and reduced expression. Our results provide unique mechanistic insights into how human polymorphic transposon insertions are recognized, and their regulatory impact constrained by an innate epigenetic defense system.

overall_design:
In this study we used XDP patient and unaffected individual (Control) derived neural progenitor cells (NPCs) and induced pluripotent stem cell (iPSCs).  RNA sequencing data with TRIM28 CRISPRi, ZNF91 CRISPRi, DNMT1 CRISPR cut, ZNF91&DNMT1 CRISPRi samples is included. In all the CRISPR experiments LacZ was used as a non-targeting control. In most cases four replicates were generated for both CRISPRi and CRISPRi control (LacZ). Except for XNES1_DNMT1_LZ, CNES1_DNMT1_ZF91_KD, CNES1_DNMT1_LZ, CNES1_DNMT1_KO and XNES1_ZF91lacZ where we have three replicates.  CUT&RUN analysis was done in both ZNF91-CRISPRi and TRIM28-CRISPRi, including CRISPRi-Ctrl (lacZ). Data is provided for one replicate per condition.

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Raquel

last: Garza

first: Vivien

last: Horvath

first: Marie

last: Jönsson

first: Pia

last: Johansson

first: Anita

last: Adami

first: Georgia

last: Christoforidou

first: Ofelia

last: Karlsson

first: Laura

middle: C

last: Vallmanya

first: Patricia

last: Gerdes

first: Ninoslav

last: Pandiloski

first: Christopher

last: Douse


title: Gut-Liver Microphysiological Systems Revealed Arachidonic Acid as a Potential Crosstalk Factor Modulating Drug Metabolism

city: Bunkyo

first: Dhimas

middle: Agung

last: Kurniawan

state: Tokyo

address: Hongo

department: Chemical System Engineering

institute: The University of Tokyo

summary: Coculture of hepatocytes with small intestine cells using MPS have been shown to enhance hepatic drug metabolism, yet the crosstalk mechanism is still unclear. Coculture of PXB-cells and iPS-derived intestine cells in MPS with perfusion and direct oxygenation were conducted to investigate this crosstalk. Analysis on albumin secretion, CYP enzyme actvity and differentially expressed genes confirmed that perfusion and direct oxygenation enhanced PXB-cells. Upregulation of "epoxygenase P450 pathway" GO terms indicated involvement of Arachidonic Acid (ARA) in the crosstalk mechanism. This is further confirmed by comparing the effect of ARA and coculture toward PXB-cells CYP enzymes activity. We hypothesize that some stimulus from PXB-cells resulted made iPS-derived intestine cells released ARA in form of lipoprotein, which is then taken in by PXB-cells and enhanced CYP activity.

overall_design: PXB-cells were cultured in normal 24-well tissue culture plate (TCPS), MPS with perfusion only (MPS O2[-]) and MPS with perfusion + direct oxygenation (MPS O2[+]). To observe crosstalk, RNA-seq was performed by comparing cocultured and monocultured PXB-cells


title: Mitophagy and mitochondrion-related expression profiles in response to physiological and pathological hypoxia in the corneal epithelium

city: Wuhan

first: Ming-Feng

last: Wu

address: 1277 Jiefang Avenue

institute: Wuhan Union Hospital

summary: To study the responses to physiological and pathological hypoxia,  we performed gene expression profiling analysis of RNA-seq data for murince corneal epithelial cells preconditioned under 3 oxygen levels.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for corneal epithelial cells preconditioned under under 21% O2, 8% O2 and 1% O2.

first: Hua-Tao

last: Xie

first: Ming-Chang

last: Zhang

first: Xi

last: Peng

first: Jiang-Lan

last: Zhao


title: Single-cell RNA sequencing reveals human leukocyte responses in humanized mice with contusive spinal cord injury

city: Brisbane

first: Jacky

state: QLD

address: The University of Queensland

country: Australia

institute: The University of Queensland

summary: Next-generation humanized mouse models and single-cell RNA sequencing approaches enable in-depth studies into human immune cell biology. Here we used NSG-SGM3 mice engrafted with human umbilical cord haematopoietic stem cells to investigate how human immune cells respond to and/or are changed by traumatic spinal cord injury (SCI). Our behavioural studies firstly show that the benefits of immunocompromise on SCI recovery are lost with the introduction of human immune cells into these mice. Using flow cytometry and scRNAseq, we then describe the composition of their circulating immune cell repertoire, and how the human immune cell population transcriptionally changes following injury. Through comparisons of SCI with naïve and sham-operated mice, we also provide insight into the transcriptional signature of human leukocytes in association with SCI-induced systemic immune depression syndrome (SCI-IDS). We further highlight the local activating influence of the spinal cord lesion microenvironment by comparing the transcriptomes of circulating versus infiltrated human cells. We lastly applied an integrated bioinformatics approach to determine where immune responses in humanized NSG-SGM3 mice appear congruent to the native responses of human SCI patients, and where they diverge. Collectively, our study provides a valuable resource and methodological framework for the use of these mice in translational research.

overall_design: To investigate human white blood cell responses to spinal cord injury, we generated humanized NSG-SGM3 mice, performed a contusive T9 spinal cord injury and sacrificed at 7 days post-injury. We collected human immune cells from the blood and spinal cords of spinal cord injured mice, as well as from the blood of naive and sham controls, and performed scRNA-seq on human white blood cells. This data was used to conduct  gene expression profiling analysis to determine how human immune cells are changed with injury and between compartments.

first: Ellen

last: Gillespie

middle: F

last: Grice

first: Isabel

middle: G

last: Courtney

first: Hong

middle: W

last: Lao

first: Woncheol

last: Jung

first: Sonny

last: Rankomuth

first: David

last: Brown

first: James

last: Walsham

first: Kristen

last: Radford

first: Quan

middle: H

last: Nguyen

first: Marc

middle: J

last: Ruitenberg


title: MTOR modulation induces selective perturbations in histone methylation which influence the anti-proliferative effects of mTOR inhibitors [RNA-Seq]

first: HaEun

last: Kim

overall_design: Comparison of mRNA levels using RNA-seq after mTOR inhibition (Ink128, rapamycin and serum starvation) vs Stimulation (vehicle)

first: Benjamin

last: Lebeau

last: Papadopoli

first: Predrag

last: Jovanovic

first: Mariana

last: Russo

first: Daina

last: Avizonis

first: Massahiro

last: Morita

first: Josie

last: Ursini-Siegal

first: Lynne-Marie

last: Postovit

first: Ivan

last: Topisirovic

first: Michael

last: Witcher


title: Targeting the mevalonate or Wnt pathways to overcome CAR T-cell resistance in TP53-mutant AML cells

status: Public on Oct 31 2023

city: Zurich

first: Roman

middle: Raffael

last: Schimmer

state: Zurich

address: Raemistrasse 100

department: Department of Medical Oncology and Hematology

country: Switzerland

institute: University Hospital Zurich and University of Zurich

summary: TP53-mutant acute myeloid leukemia (AML) and myelodysplastic neoplasms (MDS) are characterized by chemotherapy resistance and represent an unmet clinical need. Chimeric antigen receptor (CAR) T-cell therapy might be a promising therapeutic option for TP53-mutant AML/MDS. However, the impact of TP53 deficiency in AML cells on the efficacy of CAR T-cells is unknown. We here show that CAR T-cells engaging TP53-deficient leukemia cells exhibit a prolonged interaction time, upregulate exhaustion markers, and are unable to control AML cell outgrowth in vitro and in vivo compared to TP53 wildtype cells. Transcriptional profiling revealed that the mevalonate pathway is upregulated in TP53-deficient AML cells under CAR T-cell attack, while CAR T-cells engaging TP53-deficient AML cells downregulate the Wnt pathway. In vitro rational targeting of either of these pathways rescues AML cell sensitivity to CAR T-cell-mediated killing.  We thus demonstrate that TP53 deficiency confers resistance to CAR T-cell therapy and identify the mevalonate pathway as a therapeutic vulnerability of TP53-deficient AML cells engaged by CAR T-cells, and the Wnt pathway as a promising CAR T-cell therapy-enhancing approach for TP53-deficient AML/MDS.

overall_design: To investigate whether, and if so, how TP53 deficiency in AML cells might confer resistance to CAR T-cell therapy, we took advantage of a recently developed, CRISPR/Cas9-engineered TP53 isogenic AML cell line (MOLM13-TP53) with either TP53+/+ or TP53-/- mutational status. Anti-CD33 CAR T-cells and MOLM13-TP53+/+ or MOLM13-TP53-/- cells were co-incubated for six days, sorted from each other by flow cytometry, and subjected to high-throughput sequencing using a NovaSeq 6000 Sequencing System (Illumina®), the SUSHI bioinformatics pipeline, and gene set enrichment software of UCSD and Broad.

first: Jan

last: Mueller

first: Christian

last: Koch

first: Florin

last: Schneiter

first: Jonas

last: Fullin

first: Veronika

last: Lysenko

last: Pellegrino

first: Nancy

last: Klemm

first: Norman

last: Russkamp

first: Renier

last: Myburgh

first: Laura

last: Volta

first: Alexandre

middle: P

last: Theocharides

first: Kari

last: Kurppa

middle: L

last: Ebert

first: Timm

last: Schroeder

first: Markus

last: Manz

first: Steffen

last: Boettcher


title: Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome [RNA-Seq]

city: Bethesda

first: Avindra

last: Nath

state: Maryland

address: 10 Center Drive

institute: NIH/NINDS

summary: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling disorder that may occur following an infection, yet the clinical phenotype is poorly defined, the pathophysiology is unknown, and no disease-modifying treatments are available. We used rigorous criteria to recruit a cohort of post-infectious ME/CFS (PI-ME/CFS) volunteers (n=17) with matched healthy controls (n=21) to conduct deep clinical and biological phenotyping using an extensive battery of tests. Among the many physical and cognitive complaints, one defining feature of PI-ME/CFS was an alteration of effort preference, rather than physical or central fatigue, due to dysfunction of integrative brain regions potentially associated with central catechol pathway dysregulation, with consequences on autonomic functioning and physical deconditioning. Immune profiling suggested chronic antigenic stimulation with increase in naïve and decrease in switched memory B-cells. Alterations in gene expression profiles of peripheral blood mononuclear cells and metabolic pathways were consistent with cellular phenotypic studies and demonstrated differences according to sex. Together these clinical abnormalities and biomarker differences provide unique insight into the underlying pathophysiology of PI-ME/CFS, which may guide future intervention.

overall_design:
Muscle RNA Sequencing:
RNA was extracted from muscle samples using the TRIzol protocol 63. The integrity of the RNA was verified using a standard quality metric denominated RNA integrity number (RIN) value using the Agilent 4200 TapeStation system and the concentration was measured using the DeNovix DS-11 spectrophotometer. Five hundred nanograms of RNA were used to prepare the RNA sequencing libraries using the NEBNext Ultra II Directional RNA Library Prep Kit and sequenced using the Illumina NovaSeq 6000 sequencer. Reads were demultiplexed using bcl2fastq v. 2.20.0.
Participants:
A total of 27 post-infectious Myalgic encephalomyelitis/chronic fatigue syndrome (PI-ME/CFS) volunteers underwent research evaluation at the National Institutes of Health (NIH) Clinical Center. Two participants withdrew after providing informed consent and completing a history and physical exam without undergoing any research investigations. Of the remaining 25 PI-ME/CFS participants, four were found to have previously undiagnosed medical conditions that were related to ME/CFS symptoms. This included one case each of desmoplastic small round cell tumor, atypical inflammatory myositis, primary biliary cholangitis, and parkinsonism. Of the remaining 21 PI-ME/CFS participants, four participants were determined not to have a demonstrable infectious association to their ME/CFS symptoms during the case adjudication process (Table S2C). Details about the case adjudication process can be reviewed below in Supplement, Methods. A total of 17 adjudicated PI-ME/CFS volunteers completed the initial deep phenotyping measurements; eight of these volunteers also completed the exercise stress measurements.
A total of 25 healthy volunteers (HVs) were recruited to serve as comparator volunteers. Of these, one volunteer withdrew prior to completing deep phenotyping measurements. Three volunteers were excluded after evaluation related to asymptomatic medical conditions were identified. One had leukodystrophy, another had pleocytosis in the cerebrospinal fluid, and the third had early onset dementia. A total of 21 healthy volunteer comparators completed the initial deep phenotyping measurements; nine of these comparators also completed the exercise stress measurements.
contributor: The CHI Consortium

first: Brian

last: Walitt

first: Komudi

last: Singh

first: Mark

last: Hallett

first: Steve

last: Jacobson

first: Kong

last: Chen

first: Yoshimi

middle: E

last: Akahata

first: Richard

last: Apps

first: Jennifer

last: Barb

first: Patrick

last: Bedard

first: Robert

last: Brychta

first: Ashura

last: Buckley

first: Peter

middle: D

last: Burbelo

first: Brice

last: Calco

first: Brianna

last: Cathay

first: Li

first: Jinguo

first: Foo

last: Cheung

first: Snigdha

last: Chigurupati

first: Lisa

middle: M

last: Chin

first: Benjamin

last: Coleman

first: Amber

middle: B

last: Courville

first: Madeleine

last: Deming

first: Bart

last: Drinkard

last: Feng

first: Luigi

last: Ferrucci

first: Scott

last: Gabel

first: Angelique

last: Gavin

first: David

last: Goldstein

first: Shahin

last: Hassanzadeh

first: Sean

last: Horan

first: Silvina

last: Horovitz

first: Kory

last: Johnson

first: Anita

last: Govan

first: Kristine

last: Knutson

first: Joy

last: Kreskow

first: Samuel

last: LaMunion


title: Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression

city: Beijing

first: Xiangzheng

last: Liu

address: Tsinghua University, Haidian  District, Beijing

institute: Tsinghua University

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