title: Apparent loss of PRC2 chromatin occupancy as an artefact of RNA depletion

city: Clayton

first: Evan

last: Healy

state: VIC

address: 23 Innovation Way, Building 77,, Monash University

institute: Monash University

summary: RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence in favour and against this idea. RNase treatment of chromatin is a prevalent tool for the study of RNA-mediated regulation of chromatin modifiers, but the limitations of this approach remain unclear. One of the most studied chromatin modifiers in the context of RNA-mediated regulation is the H3K27me3 methyltransferase Polycomb Repressive Complex 2 (PRC2). RNase A treatment during chromatin immunoprecipitation (rChIP) reduces the occupancy of PRC2 on chromatin. This led to suggestions of an “RNA bridge" between PRC2 and chromatin. Here we show that RNase A treatment during chromatin immunoprecipitation leads to the apparent loss of all facultative heterochromatin, including both PRC2 and its H3K27me3 mark genome-wide. This phenomenon persists in mouse embryonic stem cells, human cancer cells and human-induced pluripotent stem cells. We track this observation to a global gain of chromatin that artificially reduces ChIP signals from facultative heterochromatin. Our results point to substantial limitations in RNase A treatment for mapping RNA-dependent chromatin occupancy and invalidate conclusions that were previously established for PRC2 based on this assay.

overall_design: ChIP sequecning for EZH2, SUZ12, RPB1, H3K27me3 and H3K27Ac in the presence or absence of RNase A treatment performed in mouse embryonic stem cells, K562 cells and human induced pluripotent stem cells. Independent replicates included.

first: Qi

last: Zhang

first: Emma

last: Gail

first: Samuel

last: Agius

first: Guizhi

last: Sun

first: Michael

last: Bullen

first: Varun

last: Pandey

first: Partha

middle: P

last: Das

first: Jose

last: Polo

first: Chen

last: Davidovich


title: SRF transcriptionally regulates the oligodendrocyte cytoskeleton during CNS myelination

status: Public on Feb 23 2024

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Genomic Landscape of Diploid and Aneuploid Microsatellite Stable Early Onset Colorectal Cancer

status: Public on Feb 21 2024

city: Scottsdale

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

country: USA

institute: Mayo Clinic Arizona

type: Genome variation profiling by genome tiling array

summary: We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 21 patients with early onset colorectal carcinoma (EOCRC). These included a fresh frozen sample obtained from a surgical resection and 20 archived formalin fixed paraffin embedded (FFPE) samples from a Mayo Clinic tissue bank. Our flow sorting methods are compatible with analyses of biopsies of interest including FFPE samples and frozen biopsies. Notably for this study we distinguished and sorted diploid and aneuploid tumors. We then profiled the exomes of tumor normal pairs for all 21 cases, the whole genome copy number for a subset of 6 samples, and telomere length in diploid and aneuploid nuclei from 9 cases. Additionally, we screened the 20 FFPE cases for EGFR expression with an established IHC assay.

overall_design: We applied DNA content based flow sorting to isolate the nuclei of clonal populations from early onset colorectal carcinoma biopsies. We coupled this strategy with oligonucleotide array CGH (aCGH) thereby obtaining high definition genomic profiles of clonal populations from each tumor. Whole exome sequencing of each flow sorted sample identified somatic pathogenic variants.

first: Yumei

last: Zhou

first: Xianfeng

last: Chen

first: Jun

first: Conner

middle: D

last: Kendrick

first: Ramesh

middle: K

last: Ramanathan

first: Rondell

last: Graham

first: Kimberlee

middle: F

last: Kossick

first: Lisa

middle: A

last: Boardman

middle: T


title: Transcriptional profiling of M. intracellulare under acidic and oxidative stress conditions

city: Jinju-si

first: Hyun-Eui

last: Park

state: Gyeongsangnam-do

address: 15, Jinju-daero 816beon-gil

department: College of Medicine

country: South Korea

institute: Gyeongsang National University

summary: Mycobacterium avium complex (MAC), including Mycobacterium avium and Mycobacterium intracellulare (MI), accounts for a significant portion of nontuberculous mycobacterial lung disease affecting immunocompromised and lung structural disease patients. Adapting pathogens to a host-induced hostile environment is critical to establishing infection and persistence within the host. However, the cellular and molecular mechanisms of stress response for MAC still need to be elucidated. In this study, we analyzed the transcriptional profile of MI under acidic and oxidative stress conditions using RNA-seq. At the transcriptome level, 80 genes were shown [FC] ≥2.0 and p <0.05 under oxidative stress with 10 mM hydrogen peroxide. In detail, 77 genes were upregulated, while 3 genes were downregulated. Also, 878 genes were shown [FC] ≥2.0 and p <0.05 under acidic stress with pH 4.5. Among these genes, 339 were upregulated, while 539 were downregulated. Functional analysis revealed the activation of several pathways, including nitrogen and sulfur metabolism, under acidic stress conditions. On the contrary, oxidative stress conditions activated DNA replication and repair pathways. Our data demonstrate the activation of nitrogen and sulfur metabolism in MAC infection, which could be crucial for persistence and survival under stress conditions encountered within the host during infection. In conclusion, this study suggests the importance of stress responses in MAC pathogenesis and identifies potential therapeutic target pathways.

overall_design: To elucidate the transcriptional changes of Mycobacterium intracellulare under host-induced stress, we conducted RNA-seq with Mycobacterium intracellulare under acidic and oxidative stress conditions.

first: Min-Kyoung

last: Shin


title: scRNA-seq analysis of tumor-infiltrating CD45+ cells from sitagliptin-treated mice

city: Beijing

first: Haidong

last: Tang

address: Shuangqing Road

country: China

institute: Tsinghua University

summary: Dendritic cell (DC)-mediated antigen presentation is essential for the priming and activation of tumor-specific T cells. However, few drugs that specifically manipulate DC functions are available. Here, we observed that DCs initiated a distinct transcriptional program during antigen presentation. We utilized a network-based approach to screen for DC-targeting therapeutics. Sitagliptin, an oral gliptin widely used for type 2 diabetes, was identified as a drug that targets DCs. In mouse models, sitagliptin inhibited tumor growth by enhancing DC-mediated antigen presentation, leading to better T cell activation.

overall_design: MC38-OVA tumor-bearing mice were fed control or sitagliptin diet. CD45+ cells were sorted from tumor tissues. ScRNA-seq was performed.


title: Single-cell RNA-sequencing and single-cell TCR-sequencing of tumour-infiltrating CD8+ T cells derived from mouse BRAFV600E melanoma [scRNA-Seq + TCR 10x]

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

summary: Single-cell RNA-sequencing and single-cell TCR-sequencing was used to characterize PGE2-mediated changes in the gene expression profile of tumor-infiltrating CD8+ T cells.

overall_design: Ptger2-/-Ptger4fl/fl, CD4CrePtger2-/-Ptger4fl/fl, GzmBCrePtger2-/-Ptger4fl/fl and C57BL/6 wildtype mice were subcutaneously injected with BRAFV600E tumour cells at their flanks. Tumours were harvested on day 11 post tumour cell inoculation and tumour-infiltrating CD8+ T cells were sorted by FACS. Each experimental group consisted of 4 biological replicates.

first: J

last: Böttcher

first: S

last: Lacher

first: G


title: Microbiota configuration dictates nutritional immune optimization

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: Mild or transient dietary restriction (DR) improves many aspects of health and aging. Emerging evidence from us and others has demonstrated that DR also optimizes the development and quality of immune responses. However, the factors and mechanisms involved remain to be elucidated. Here, we demonstrate that DR-induced optimization of immunological memory requires co-operation between memory T cells, the intestinal microbiota, and myeloid cells. Our data indicate that DR enhances the ability of memory T cells to recruit and activate myeloid cells in the context of a secondary infection. Concomitantly, DR promotes expansion of the commensal Bifidobacteria within the large intestine, which supplies the short-chain fatty acid acetate to myeloid cells. Acetate conditioning of the myeloid compartment during DR enhances their capacity to kill pathogens. Enhanced host protection during DR is abolished when Bifidobacteria expansion is prevented, indicating that microbiota configuration and function critically dictates immune responsiveness to this dietary intervention. Altogether, DR induces both memory T cells and the gut microbiota to produce essential, distinct factors that converge on myeloid cells to promote optimal pathogen control. These findings reveal how nutritional cues promote adaptation and co-operation between multiple immune cells and the gut microbiota, which synergize to optimize immunity and protect the collective metaorganism.

overall_design: Examiniation of T cells, monocyts and neutrophils during dietary restriction versus normal condition with RNA-seq and ATAC-seq

first: Nicholas

last: Collins


title: Global profiling of Nkx2.2 SD-domain mutant pancreas during development and adulthood compared to transcriptional profiling of SD-domain mutant expressing neural progenitors.

city: Aurora

first: Elena

last: Abarinov

state: Colorado

address: 1775 Aurora Ct

institute: University of Colorado at Denver

summary: The consolidation of unambiguous cell fate commitment relies on the ability of transcription factors (TFs) to exert tissue-specific regulation of complex genetic networks. The mechanisms by which TFs establish such precise control over gene expression, however, have remained elusive—especially in instances where a single TF operates in two or more discrete cellular systems. In this study, we demonstrate that  cell specific functions of NKX2.2 are driven by the highly conserved NK2-Specific Domain (SD). Mutation of the endogenous NKX2.2 SD domain prevents the developmental progression of beta cell precursors into mature, insulin-expressing beta cells, resulting in overt neonatal diabetes. Within the adult beta cell, the SD domain stimulates beta cell performance through the activation and repression of a subset of NKX2.2-regulated transcripts critical for beta cell function. These irregularities in beta cell gene expression may be mediated via SD domain-contingent interactions with components of the nuclear pore complex. In stark contrast to these pancreatic phenotypes, however, the SD domain is entirely dispensable for the development of NKX2.2-dependent cell types within the CNS. Together, these results reveal a previously undetermined mechanism through which NKX2.2 directs disparate transcriptional programs in the pancreas vs. neuroepithelium.

overall_design: Examination of total RNA profiles of E15.5 pancreata of wildtype and Nkx2.2SDmut animals, of wildtype and beta-specific Nkx2.2SDmut adult islets, and of mouse ES cell-derived spinal motor neuron progenitors expressing a wildtype copy of Nkx2.2 tagged by FLAG under the control of a doxycycline (DOX) inducible promotor (iNkx2.2), an SD-domain mutant copy of Nkx2.2 tagged by FLAG under the control of a doxycycline (DOX) inducible promotor (iSDmut), or no Nkx2.2 (pMN). Examination of the global DNA binding profile of Nkx2.2 in MIN6 cells. 2-4 replicates are provided for all  samples.

first: Vladimir

first: Joshua

last: Levine

first: Angela

middle: J

last: Churchill

first: Bryce

last: Hopwood

first: Cailin

last: Dieter

first: Michelle

last: Guney

first: Kristen

middle: L

last: Wells

first: Jessica

middle: M

last: Friel

first: Yuchun

last: Guo

first: Jennifer

last: Hammelman

first: David

last: Gifford

first: Mark

last: Magnuson

first: Hynek

last: Wichterle

first: Lori

last: Sussel


title: Genome wide CRISPR screen for Trametinib sensitivity in resistant MOLM13 cells using Y. Kosuke library

status: Public on Feb 22 2024

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

summary: Cas9-expressing trametinib resistant MOLM-13 cell lines (TM1) were generated using the Cas9-Blst (Addgene, #52962) and expanded for genome-wide loss-of-function screens using the Y. Kosuke library (Addgene, #67989) Following transduction, cells cultured in the presence of trametinib (100 nM) or DMSO after lentiviral infection.

overall_design: Performed comparisons of sgRNA read counts between Trametinib and DMSO treated cells at Day 14.

first: Anupriya

last: Agarwal

first: Rucha

middle: V

last: Modak

first: Shannon

last: McWeeney


title: MCAF2/ATF7IP2 directs meiosis-specific H3K9 methylation

city: Davis

first: Satoshi

middle: H

last: Namekawa

state: CA

address: One Shields Ave

department: Microbiology and Molecular Genetics

institute: University of California, Davis

summary: H3K9 tri-methylation (H3K9me3) has emerging functions in gene regulation in addition to its accumulation on constitutive heterochromatin at pericentromeres. It remains a mystery why and how H3K9me3 is dynamically regulated in male meiosis. Here, we identify a novel and critical regulator of H3K9 methylation and spermatogenic heterochromatin organization: the germline-specific protein MCAF2 (ATF7IP2). We show that MCAF2 amasses on autosomal and X pericentric heterochromatin in male germ cells. On the sex chromosomes, which undergo meiotic sex chromosome inactivation (MSCI), the DNA damage response pathway recruits MCAF2 to X pericentric heterochromatin, where it facilitates the recruitment of SETDB1, a histone methyltransferase that catalyzes H3K9me3. In the absence of MCAF2, germ cells are arrested in meiotic prophase, and the mutant analyses revealed that MCAF2 is required for the maintenance of MSCI, and for global activation of autosomal genes and retrotransposon-derived loci in meiosis; this reveals a regulatory function for MCAF2 that is counterintuitive to its association with repressive H3K9me3. Taken together, we propose that MCAF2 is a downstream effector of the DDR pathway in meiosis that coordinates the organization of heterochromatin and gene regulation through the spatial regulation of SETDB1-mediated H3K9me3 deposition.

overall_design: Whole cell lysates were collected from P14 Mcaf2ctrl or Mcaf2KO testes.

first: Kris

middle: G

last: Alavattam

first: Hironori

last: Abe

first: Jasmine

last: Esparza


title: SRF transcriptionally regulates the oligodendrocyte cytoskeleton during CNS myelination (ChIP-Seq)

first: Fabian

last: Kern

summary: Myelination of neuronal axons is essential for nervous system development. Myelination requires dramatic cytoskeletal dynamics in oligodendrocytes, but how actin is regulated during myelination is poorly understood. We recently identified serum response factor (SRF)—a transcription factor known to regulate expression of actin and actin regulators in other cell types—as a critical driver of myelination in the aged brain. Yet, a major gap remains in understanding the fundamental role of SRF in oligodendrocyte lineage cells. Here we show that SRF is required cell autonomously in oligodendrocytes for myelination during development. Combining ChIP-seq with RNA-seq identifies SRF-target genes in OPCs and oligodendrocytes that include actin and other key cytoskeletal genes. Accordingly, SRF knockout oligodendrocytes exhibit dramatically reduced actin filament levels early in differentiation, consistent with its role in actin-dependent myelin sheath initiation. Together, our findings identify SRF as a transcriptional regulator that controls the expression of cytoskeletal genes required in oligodendrocytes for myelination. This study identifies a novel pathway regulating oligodendrocyte biology with high relevance to brain development, aging, and disease.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for SRF in primary rat OPC and OL (Oligodendrocyte) culture cells.

first: Tal

last: Iram

first: Miguel

last: Garcia

first: Jeremy

last: Amand

first: Achint

last: Kaur

first: Micaiah

last: Atkins

first: Manasi

last: Iyer

first: Mable

last: Lam

first: Nicholas

last: Ambiel

first: Danielle

last: Jorgens

first: Andreas

last: Keller

first: Tony

last: Wyss-Coray

first: J

middle: B

last: Zuchero


title: Exogenous IL-2 delays the generation of memory precursor cells and is essential for the generation of memory cells with increased effector functions

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

country: France

institute: AltraBio

summary: To investigate the impact of paracrine IL-2 signals on memory precursor (MP) cell differentiation., we activated CD8 T cell in vitro in the presence or absence of exogenous IL-2 (ex-IL-2). We assessed the memory differentiation of activated T cells by transfer into virus-infected mice. Both conditions generated CD8 T cells that participate in the ongoing immune response and gave rise to similar memory cells. Conversely, when transferred into a naive host, T cells activated with ex-IL-2 generated a higher frequency of memory cells displaying increased functional memory traits. Single-cell RNA-seq analysis indicated that without ex-IL-2, cells rapidly acquire a MP signature, while in its presence they adopted an effector signature. This was confirmed at the protein level and in a killing assay. Overall, ex-IL-2 delays the transition into MP cells, allowing the acquisition of effector functions that become imprinted in their progeny. These findings may help to optimize the generation of therapeutic T cells.

overall_design:
To investigate the transcriptional changes that IL-2 could mediate over the course of in vitro activation, we activated F5 CD8 T cells for 3, 4 or 5 days in the absence or presence of ex-IL-2. Naive cells (=day 0) were used as a control (7 different conditions).
These cells were then isolated by Fluorescence-activated cell sorting (FACS) and analyzed using single-cell RNA-seq

first: Shaoying

last: Wang

first: Margaux

last: Prieux

first: Daphne

last: Laubreton

first: Manon

last: Zala

first: Maxence

last: Dubois

first: Jacqueline

last: Marvel


title: An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140 [RNA-seq]

status: Public on Feb 20 2024

city: Boulder

first: Edward

last: Chuong

state: CO

address: 3415 Colorado Ave.

institute: CU - Boulder

summary: Speckled Protein 140 (SP140) is a chromatin reader with critical roles regulating immune cell transcriptional programs, and SP140 splice variants are associated with immune diseases including Crohn’s disease, multiple sclerosis, and chronic lymphocytic leukemia. SP140 expression is currently thought to be restricted to immune cells. However, by analyzing human transcriptomic datasets from a wide range of normal and cancer cell types, we found recurrent cancer-specific expression of SP140, driven by an alternative intronic promoter derived from an intronic endogenous retrovirus (ERV). The ERV belongs to the primate-specific LTR8B family. The ERV drives expression of multiple cancer-specific isoforms, including a nearly full-length isoform that retains all the functional domains of the full-length canonical isoform and is also localized within the nucleus, consistent with a role in chromatin regulation. In a fibrosarcoma cell line, silencing the cancer-specific ERV promoter of SP140 resulted in increased sensitivity to interferon-mediated cytotoxicity and dysregulation of multiple genes. Our findings implicate aberrant ERV-mediated SP140 expression as a novel mechanism contributing to immune gene dysregulation in a wide range of cancer cells.

overall_design: Transcriptional profiling (RNA-seq) of a fibrosarcoma cancer cell line (HT1080) that was either untreated or treated with 10 U/mL IFNB for 4 hr. The HT1080 cell line stably expresses dCas9 and a gRNA targeting LTR8B element in first intron of SP140 or a GFP control.

first: Adam

last: Dziulko

first: Holly

last: Allen


title: An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140 [CUT&RUN]

overall_design: Epigenomic (CUT&RUN) profiling of a fibrosarcoma cancer cell line (HT1080) that was untreated.


title: Transcriptome data of B cells and T helper cells from patients with multiple sclerosis receiving methylprednisolone for the treatment of an acute relapse

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

summary: We analyzed the transcriptome profiles of CD19+ B cells and CD4+ T cells from the peripheral blood of patients with multiple sclerosis (MS) immediately before and after relapse therapy with high-dose methylprednisolone (MP). High-density Clariom D Arrays for human were used to quantify the transcript levels. This GEO entry provides the processed data from the gene-level and exon-level workflows.

overall_design:
Peripheral blood was taken from 16 MS patients before the first (T0) and after the last (T1) administration of MP (up to 2000 mg/day) for the treatment of an acute exacerbation. From 3 of the patients, a blood sample pair was obtained for both the initial course of MP (M1) as well as the escalating second course of MP (M2) for the same relapse. Therefore, a total of 19 relapse treatments were evaluated. Thirteen of these led to improvements of the affected functional systems (FS) and 6 did not.
CD19+ B cells were isolated from 13 blood sample pairs, while CD4+ T helper cells were isolated from 11 blood sample pairs, resulting in a total of 48 samples. Total RNA was extracted, labeled and hybridized to Clariom D microarrays to quantify the transcript levels.

first: Dirk

last: Koczan

first: Uwe

last: Zettl


title: Piezo1 channels restrain ILC2s and regulate the development of airway hyperactivity [yoda1]

city: Los Angeles

first: Benjamin

last: Hurrell

address: 1450 Biggy Street

institute: USC

summary: Mechanosensitive ion channels sense force and pressure in immune cells to drive the inflammatory response in highly mechanical organs. Here we report that Piezo1 channels repress group 2 innate lymphoid cells (ILC2s)-driven type 2 inflammation in the lungs. Piezo1 is induced on lung ILC2s upon activation, as genetic ablation of Piezo1 in ILC2s increases their function and exacerbates the development of airway hyperreactivity (AHR). Conversely, Piezo1 agonist Yoda1 reduces ILC2-driven lung inflammation. Mechanistically, Yoda1 inhibits ILC2 cytokine secretion and proliferation in a KLF2-dependent manner, as we further found that Piezo1 engagement reduces ILC2 oxidative metabolism. Consequently, in vivo Yoda1 treatment notably reduces the development of AHR in experimental models of ILC2-driven allergic asthma. Human circulating ILC2s express and induce Piezo1 upon activation, as Yoda1 treatment of humanized mice reduces human ILC2-driven AHR. Our studies define Piezo1 as a critical regulator of ILC2s and we propose the potential of Piezo1 activation as a novel therapeutic approach for the treatment of ILC2-driven allergic asthma.

overall_design: mRNA profiles of sorted mouse lung ILC2s treated either with PBS or Yoda1 were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.


title: Phase I Trial Evaluating Locoregionally-delivered IL13Rα2-targeting CAR T Cells in High-Grade Glioma

city: Phoenix

first: Nicholas

last: Banovich

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

summary: We report here a phase I trial (NCT02208362) evaluating locoregional delivery of IL13Rα2-targeted CAR T cells in 65 patients with recurrent high-grade glioma, the majority being recurrent glioblastoma (rGBM). Primary objectives were to evaluate safety and feasibility, and secondary objectives were to assess therapy-related cytokine dynamics, CAR T cell persistence and clinical outcomes. Feasibility and safety were established for three routes of locoregional CAR T cell administration [intratumoral (ICT), intraventricular (ICV) and dual ICT/ICV], with IL13Rα2-CAR T cells being well-tolerated with clinically manageable adverse events at all dose levels. Stable disease or better was achieved in 50% of patients, with two partial responses, one complete response (CR), and a second CR after additional CAR T cycles off protocol therapy.  Patients with rGBM treated on Arm 5, utilizing dual ICT/ICV delivery and an optimized manufacturing process exhibited the best overall survival of 10.2 months. . Central nervous system (CNS) increases in inflammatory cytokines, including IFNγ, CXCL9, and CXCL10, were associated with CAR T cell administration and bioactivity. Further, pre-treatment intratumoral CD3 T cell levels were positively associated with survival, suggesting an interplay between host immunity and CAR T cells as a determinant of outcomes. These findings advance our understanding of CAR T cell immunotherapy for malignant brain tumors. ClinicalTrials.gov Identifier: NCT02208362

overall_design: Single-cell sequencing of cryopreserved samples was carried out using the 10x Chromium platform. Single-cell RNA sequencing (sc-RNAseq) was carried out on excess available CAR T cell product samples from 62 of the 65 treated patients (40 Tcm, 22 Tn/mem). Additionally, expression levels of cell surface proteins of 27 CAR T product samples (14 Tcm, 13 Tn/mem) were quantified using CITEseq.

first: Christine

middle: E

last: Brown

first: Jonathan

middle: C

last: Hibbard

first: Darya

last: Alizadeh

first: M

middle: S

last: Blanchard

first: Heini

last: Natri

first: Dongrui

first: Julie

middle: R

last: Ostberg

first: Brenda

last: Aguilar

first: Jamie

last: Wagner

first: Jinny

last: Paul

first: Renate

last: Starr

first: Aleksandr

last: Filippov

first: Ammar

last: Chaudhry

last: Ressler

last: Kilpatrick

first: Paige

last: Myers-McNamara

first: Mike

last: Chen

first: Leo

first: Russell

last: Rockne

first: Joseph

last: Georges

first: Jana

last: Portnow

last: Barish

first: Massimo

last: D’Apuzzo

first: Stephen

last: Forman

first: Behnam

last: Badie


title: Denaturing purifications demonstrate that PRC2 and other widely-reported chromatin proteins do not appear to bind directly to RNA in vivo [ChIP-seq]

city: Pasadena

first: Jimmy

last: Guo

address: 1200 E California Blvd

institute: Caltech

summary: The Polycomb Repressive Complex 2 (PRC2) has been reported to bind to many RNAs and has become a central player in reports describing the mechanisms of how long non-coding RNAs (lncRNAs) regulate gene expression. Based largely on these observations of PRC2, many additional chromatin proteins have similarly been reported to bind RNA to enact their functions. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here we revisit the evidence supporting broad RNA binding by PRC2 and other chromatin proteins and show that many previously reported RNA-protein interactions do not represent in vivo interactions. We find that denaturing purification of in vivo crosslinked RNA-protein complexes leads to loss of detectable PRC2-RNA interactions. Similarly, we fail to detect in vivo RNA binding of other chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, WDR5, and others), despite accurately mapping bona fide RNA-protein binding sites across a range of proteins including several specific chromatin-associated proteins (SPEN, CHTOP, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP was used to map chromatin-associated proteins in HEK293T and mouse embryonic stem cells.

first: Mario

last: Blanco

first: Mitchell

last: Guttman


title: Isolation and Characterization of a Novel Mammary Adenocarcinoma, MCa-P1362, with Hormone Receptor Expression, Human Epidermal Growth Factor Receptor 2 Positivity, and Enrichment in Cancer and Mesenchymal Stem Cells

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: In this study, we conducted a detailed cellular and molecular characterization of MCa-P1362, a novel syngeneic Balb/c mouse model of metastatic breast cancer. MCa-P1362 cancer cells expressed estrogen receptors (ER), progesterone receptors (PR), and HER-2 receptors.

overall_design: The MCa-P1362 cell line was established from a spontaneous mammary tumor P1362 that arose in a female syngeneic Balb/c breeder in the Cox-7 animal facility at Massachusetts General Hospital.

first: Samir

last: Jana

first: Wende

last: Li

first: Shaye

last: Kibara

first: Zixiong

last: Wang

first: Peigen

last: Huang

first: Dennis

last: Jones


title: Investigating the role of SNU66 in 5' splice site maintenance

city: Santa Cruz

first: Alan

last: Zahler

address: 1156 High St.

department: MCD Biology

institute: UC Santa Cruz

summary: CryoEM modeling of the human pre-B complex suggests an interaction between SNU66(H734) and SNRP27(M141) at the base of the ACAGAGA box of U6. We had previously shown in C. elegans that SNRP-27(M141T) mutants alter 5'ss usage. Here we generate new alleles by CRISPR in snu-66 at the corresponding H765 location in C. elegans (H765G and H765L) and demonstrate that they have similar effects as SNRP-27(M141T) mutants on 5'ss selection globally.

overall_design: Alternative splicing analysis of snu-66(H765G), snu-66(H765L) and snrp-27(M141T) mutant strains at larval stage L3 compared to N2 wild type

first: Sol

last: Katzman

first: Kenna

last: Sarka


title: Foxp1 regulates the development of glutamatergic synaptic input onto spiny projection neurons expressing Drd2 [snRNA-seq]

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: Long-range glutamatergic inputs from the cortex and thalamus provide important motor and cognitive information to the striatum where they are integrated for learning and action planning. Genetic programs and transcription factors that orchestrate the development of these inputs are relatively unknown. The transcription factor, FOXP1, is crucial for the development of spiny projection neurons (SPNs) in the striatum. We investigated the cell-specific role of Foxp1 in the formation of glutamatergic inputs – including corticostriatal inputs. Embryonic Foxp1 deletion in dopamine receptor 2-expressing SPNs (D2 Foxp1cKO) leads to reduced transmission of corticostriatal excitatory inputs and decreased synaptically driven excitability. Postnatal deletion of Foxp1 also resulted in decreased glutamatergic inputs onto D2 SPNs. Single nuclei RNA sequencing of D2 Foxp1cKO striatum identified downregulated postsynaptic genes, consistent with the synaptic phenotype. Reinstating Foxp1 postnatally rescued electrophysiological deficits and expression of a subset of genes that were altered by embryonic deletion in D2 SPNs. Postnatal Foxp1 reinstatement could also rescue behavioral phenotypes. In summary, we demonstrate that FOXP1 regulates the development of corticostriatal circuitry. Further, changes at multiple levels of brain function resulting from loss of Foxp1 are rescued with postnatal Foxp1 reinstatement, indicating a therapeutic approach for individuals with FOXP1 syndrome.

overall_design: We used single nuclei RNA sequencing (snRNA-Seq) in juvenile (P18) mouse striatum to test the effects of loss of Foxp1 in D2 SPNs and study gene expression changes with postnatal reinstatment of Foxp1 in striatum.

first: Nitin

last: Khandelwal

first: Ashwinikumar

last: Kulkarni

first: Newaz

last: Ahmed

first: Matthew

last: Harper

first: Jay

last: Gibson


title: RNA sequencing of murine in vitro differentiated and repetitively activated, antigen-experienced TCF1+CD8+ T cells after PGE2 treatment and stimulation [bulk RNA-Seq]

first: Gustavo

last: de Almeida

summary: RNA sequencing was used to characterise PGE2-mediated changes in the gene expression profile of in vitro differentiated and repetitively activated antigen-experienced TCF1+CD8+ T cells.

overall_design: In vitro differentiated and repetitively activated antigen-experienced TCF1+CD8+ T cells were pre-incubated with or without PGE2 (100 ng/mL) for 1 hour at 37°C. Subsequently, the cells were stimulated for an additional 4 hours with low dose IL-2 (85 U/ml) or the combination of low dose IL-2 and aCD3/CD28 beads.

first: J

last: Böttcher

first: S

last: Lacher

first: G

middle: P


title: PGE2 curtails IL-2-dependent effector expansion from tumour-infiltrating stem-like CD8+ T cells to promote cancer immune escape

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

overall_design: Refer to individual Series


title: Gene expression analysis at single cell level from the CNS of mice that recieved B-NHL and treated with either Non Transduced (NT) or CD19 Chimeric Antigen Receptor (CAR) T cells

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

institute: Freiburg Medical Center

summary: Microglia constitute the myeloid compartment of the Central Nervous System (CNS). scRNA sequencing was employed to decipher diverse microglia populations and other cell types from the cortex.

overall_design: Cell populations frrom the cortex of the mice were isolated and enriched for microglia by flourescent activated cell sorting (FACS) and analyzed using sn RNA sequencing

first: Robert

last: Zeiser

first: Janaki

last: Manoja Vinnakota

first: Chintan

last: Chhatbar


title: Protozoan-Derived Cytokine-Transgenic Macrophages Reverse Hepatic Fibrosis.

city: Anhui

first: Ying

last: Chen

state: China

address: No. 81 Meishan Road, Hefei

institute: Anhui Medical University

summary: Macrophage therapy for liver fibrosis is on the cusp of meaningful clinical utility. Due to the heterogeneities of macrophages, it is urgent to develop safer macrophages with a more stable and defined phenotype for the treatment of liver fibrosis. Herein, a new macrophage-based immunotherapy using macrophages stably expressing a pivotal cytokine from Toxoplasma gondii, a parasite that infects ≈ 2 billion people is developed. It is found that Toxoplasma gondii macrophage migration inhibitory factor-transgenic macrophage (Mφtgmif) shows stable fibrinolysis and strong chemotactic capacity. Mφtgmif effectively ameliorates liver fibrosis and deactivates aHSCs by recruiting Ly6Chi macrophages via paracrine CCL2 and polarizing them into the restorative Ly6Clo macrophage through the secretion of CX3CL1. Remarkably, Mφtgmif exhibits even higher chemotactic potential, lower grade of inflammation, and better therapeutic effects than LPS/IFN-γ-treated macrophages, making macrophage-based immune therapy more efficient and safer. Mechanistically, TgMIF promotes CCL2 expression by activating the ERK/HMGB1/NF-κB pathway, and this event is associated with recruiting endogenous macrophages into the fibrosis liver. The findings do not merely identify viable immunotherapy for liver fibrosis but also suggest a therapeutic strategy based on the evolutionarily designed immunomodulator to treat human diseases by modifying the immune microenvironment.

overall_design: mRNA profiles of mouse leukemia cell of monocyte macrophage RAW264.7 (Mφ), Mφ stably expressing LV-ZsGreen (LV-Mφ), Mφ stably expressing LV-TgMIF-ZsGreen (TgMIF-Mφ), LPS and IFN-γ treated Mφ(LPS/IFNγ-Mφ). Two or three independent experiments were performed for each condition.

first: Jie

last: Wang

last: Zhou

first: Qi

last: Fang

first: Haijian

last: Cai

first: Zhuoran

last: Du

first: Ran

last: An

first: Deng

last: Liu

first: Xuepeng

first: Xinxin

first: Fangmin

last: Li

last: Yan

first: Lijian

first: Jian


title: The 3’ UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Staphylococcus aureus is an adaptable human pathogen causing life-threatening endocarditis and bacteraemia. Methicillin-resistant S. aureus (MRSA) is alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteraemia and vancomycin treatment failure is often associated with vancomycin-intermediate S. aureus strains termed VISA. The regulatory 3’ UTR of vigR mRNA contributes to vancomycin tolerance in the clinical VISA isolate JKD6008 and upregulates the lytic transglycosylase IsaA. Using MS2-affinity purification coupled with RNA sequencing (MAPS), we find that the vigR 3' UTR also interacts with mRNAs involved in carbon metabolism, amino acid biogenesis, cell wall biogenesis, and virulence. The vigR 3' UTR was found to repress dapE, a succinyl-diaminopimelate desuccinylase required for lysine and cell wall peptidoglycan synthesis, suggesting a broader role in controlling cell wall metabolism and vancomycin tolerance. Deletion of the vigR 3' UTR increased VISA virulence in a wax moth larvae model, and we find that an isaA mutant is completely attenuated in the larvae model. Sequence and structural analysis of the vigR 3' UTR indicates that the UTR has expanded through the acquisition of Staphylococcus aureus repeat insertions (STAR repeats) that partly contribute sequence for the isaA interaction seed and may functionalise the 3’ UTR. Our findings reveal an extended regulatory network for vigR, uncovering a novel mechanism of regulation of cell wall metabolism and virulence in a clinical S. aureus isolate.

overall_design: We have used MS2 affinity pull-downs (MAPS, PMID: 25891076) to capture and sequence mRNAs interacting with the 3'UTR of the vigR transcript from Staphylococcus aureus JKD6008. The experiment used the aTc-inducible vector pRAB11 to express the vigR 3'UTR fused to a 5' MS2 RNA sequence. The same vector expressing MS2 RNA but lackign the vigR 3'UTR was used as a control. The MS2 fusion and control plasmods transformed into Staphylococcus aureus JKD6009 ∆vigR-3'UTR and grown in BHI media to an OD of 3.0. Biological duplictes were induced for 15 mins with 0.4uM aTc and processed for MAPS as per PMID: 25891076.

first: Daniel

last: Mediati

first: David

last: Lalaouna


title: Network-based screening identifies sitagliptin as an antitumor drug targeting dendritic cells

city: Beijing

first: Haidong

last: Tang

address: Shuangqing Road

institute: Tsinghua University

summary: Dendritic cell (DC)-mediated antigen presentation is essential for the priming and activation of tumor-specific T cells. However, few drugs that specifically manipulate DC functions are available. Here, we observed that DCs initiated a distinct transcriptional program during antigen presentation. We utilized a network-based approach to screen for DC-targeting therapeutics. Sitagliptin, an oral gliptin widely used for type 2 diabetes, was identified as a drug that targets DCs. In mouse models, sitagliptin inhibited tumor growth by enhancing DC-mediated antigen presentation, leading to better T cell activation.

overall_design: cDC1 and cDC2 cells were isolated from MC38-EGFP tumor tissues by FACS. Cells were further divided into EGFP- and EGFP+ based on their EGFP signals. RNAseq was performed.


title: Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells

status: Public on Feb 19 2024

city: Hanover

first: Paula

middle: F.

last: Zamora

state: NH

address: 74 College st

institute: Geisel School of Medicine at Dartmouth

summary: Phage therapy is a therapeutic approach to treat multidrug resistant infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. Using a panel of Pseudomonas aeruginosa phages and human airway epithelial cells derived from a person with cystic fibrosis, we determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.

overall_design: We sought to determine whether respiratory epithelial cells can sense and respond to purified lytic phages. We conducted RNA sequencing of RNA derived from phage-treated CF AECs. To enrich for phage-positive cells, CFBE41o- cells were exposed to fluorescently labeled OMKO1, LPS-5, PSA04, and PSA34 for 24 h and were then subjected to cell sorting using flow cytometry.

middle: F

first: Thomas

last: Reidy

first: Catherine

last: Armbruster

first: Ming

last: Sun

first: Daria

last: Van Tyne

first: Paul

last: Turner

first: Jonathan

last: Koff

first: Jennifer

last: Bomberger


title: An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140

first: Edward

last: Chuong


title: Cooperative role of Lymphotoxin Beta Receptor and Tumor Necrosis Factor Receptor p55 in murine liver regeneration

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)


title: Piezo1 channels restrain ILC2s and regulate the development of airway hyperactivity [piezo1KO]

first: Benjamin

last: Hurrell

overall_design: mRNA profiles of sorted mouse lung ILC2s lacking or not Piezo1 were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.


title: Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

institute: Max Planck Institute of Neurobiology.


title: Sustained antidepressant effects of ketamine metabolite involve GABAergic inhibition-mediated molecular dynamics in aPVT glutamatergic neurons

city: Kyoto

first: Shusaku

last: Uchida

state: Kyoto

address: 53 Kawaharamachi, Sakyo-ku

country: Japan

institute: Kyoto University

summary: We performed high-throughput profiling of gene expression in the anterior paraventricular nucleus of thalamus of stress-vulnerable BALB/c mice subjected to social defeat stress. BALB/c mice were subjected to 5-day of social defeat stress and then injected with saline or (2S,6S)-HNK. Seven days after the drug injection, mice were euthanized for tissue collection. We then conducted the transcriptomics analysis. Our study provided insights into the understanding of the molecular mechanisms underlying the sustained antidepresssant effects of (2S,6S)-HNK.

overall_design: BALB/c mice were subjected to 5-day of social defeat stress (smSDS). Total 3 groups were set up: non-stressed (NS_Saline), social defeat stres swith saline (smSDS_Saline), and smSDS with (2S,6S)-HNK (smSDS_SHNK). Three replicates were used for each group.


title: Spatial enhancer activation determines inhibitory neuron identity (ChIP-seq of MEIS transcription factors)

summary: The mammalian telencephalon contains a tremendous diversity of GABAergic projection neuron and interneuron types, that originate in a germinal zone of the embryonic basal ganglia. How genetic information in this transient structure is transformed into different cell types is not yet fully understood. Using a combination of in vivo lineage tracing, CRISPR perturbation and ChIP-seq in mice, we found that the transcription factor MEIS2 favors the development of projection neurons through genomic binding sites in regulatory enhancers of projection neuron specific genes. MEIS2 requires the presence of the homeodomain transcription factor DLX5 to direct its functional activity towards these sites. In interneurons, the activation of projection neuron specific enhancers by MEIS2 and DLX5 is repressed by the transcription factor LHX6. When MEIS2 carries a mutation associated with intellectual disability in humans, it is less effective at activating enhancers involved in projection neuron development. This suggests that GABAergic differentiation may be impaired in patients carrying this mutation. Our research has uncovered a mechanism by which the selective activation of enhancers plays a crucial role in the establishment of neuronal identity, as well as in potential pathological mechanisms

overall_design: MEIS ChIP-seq of ganglionic eminences

first: Elena

last: Ddvoretskova

first: May

last: Ho

first: Volker

last: Kittke

first: Ilaria

last: Vitali

middle: D

last: Lam

first: Irene

last: Delgado

first: Chao

last: Feng

first: Miguel

last: Torres

first: Juliane

last: Winkelmann


summary: The mammalian telencephalon contains distinct GABAergic projection neuron and interneuron types, originating in the germinal zone of the embryonic basal ganglia. How genetic information in the germinal zone determines cell types is unclear. Here we use a combination of in vivo CRISPR perturbation, lineage tracing and ChIP-sequencing analyses and show that the transcription factor MEIS2 favors the development of projection neurons by binding enhancer regions in projection-neuron-specific genes during mouse embryonic development. MEIS2 requires the presence of the homeodomain transcription factor DLX5 to direct its functional activity toward the appropriate binding sites. In interneuron precursors, the transcription factor LHX6 represses the MEIS2-DLX5-dependent activation of projection-neuron-specific enhancers. Mutations of Meis2 result in decreased activation of regulatory enhancers, affecting GABAergic differentiation. We propose a differential binding model where the binding of transcription factors at cis-regulatory elements determines differential gene expression programs regulating cell fate specification in the mouse ganglionic eminence.

overall_design: Transcriptomic and barcode-lineage tracing of developing mouse forebrain cell subtypes of ganglionic eminences

first: Daniel


title: Radiotherapy induces persistent innate immune reprogramming of microglia into a priming state

city: Groningen

first: Takuya

last: Oshima

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences of Cells & Systems

country: Netherlands

institute: University Medical Center Groningen

summary: More than half of all brain tumour survivors experience debilitating and often progressive cognitive decline after treatment with radiotherapy. Microglia, the tissue-resident macrophages of the brain, have been implicated in this decline. In response to various insults microglia can develop innate immune memory (IMM), which can either enhance (priming) or repress (tolerance) the response to subsequent inflammatory challenges. Here, we investigated whether radiation can affect the IMM of microglia by irradiating the brains of rats and later exposing them to a second inflammatory   challenge. Transcriptomic profiling of microglia isolated from irradiated rats showed a stronger immune response to a second inflammatory insult demonstrating that radiation can lead to long-lasting molecular reprogramming of microglia. Transcriptomic analysis of post-mortem non-tumour brain tissue of glioblastoma patients indicates that radiation-induced microglial priming is conserved in humans. Targeting microglial priming after radiotherapy or avoiding further inflammatory insults could decrease progressive radiotherapy-induced cognitive decline.

overall_design: Bulk RNA sequencing analysis of FACS-isolated microglia from the whole brains of rats (sham-)irradiated with 14 Gy X-rays with following i.p. injection of PBS vehicle or lipopolysaccharide (LPS) 6 weeks later . N =  4 per condition.

first: Daniëlle

last: Voshart

first: Yuting

last: Jiang

first: Gideon

last: van der Linden

first: Anna

last: Ainslie

first: Luiza

last: Reali Nazario

first: Fleur

last: van Buuren-Broek

first: Ayla

last: Scholma

first: Hilmar

last: van Weering

first: Nieske

last: Brouwer

first: Jeffrey

last: Sewdihal

first: Uilke

first: Rob

last: Coppes

first: Inge

last: Holtman

first: Bart

last: Eggen

first: Susanne

last: Kooistra

first: Lara

last: Barazzuol


title: Single-cell RNA sequencing identifies response of renal lymphatic endothelial cells to acute kidney injury

city: Bryan

first: Joseph

middle: M.

last: Rutkowski

address: 8447 Riverside Parkway

department: Medical Physiology

institute: Texas A&M University School of Medicine

summary: Background: The inflammatory response to acute kidney injury (AKI) likely dictates future renal health. Lymphatic vessels are responsible for maintaining tissue homeostasis through transport and immunomodulatory roles. Due to the relative sparsity of lymphatic endothelial cells (LECs) in the kidney, past sequencing efforts have not characterized these cells and their response to AKI. Methods: Here we characterized murine renal LEC subpopulations by single-cell RNA sequencing and investigated their changes in cisplatin AKI 72 hours post injury. Data was processed using the Seurat package. We validated our findings by qPCR in LECs isolated from both cisplatin-injured and ischemia reperfusion injury, by immunofluorescence, and confirmation in in vitro human LECs. Results: We have identified renal LECs and their lymphatic vascular roles that have yet to be characterized in previous studies. We report unique gene changes mapped across control and cisplatin injured conditions. Following AKI, renal LECs alter genes involved in endothelial cell apoptosis and vasculogenic processes as well as immunoregulatory signaling and metabolism. Differences between injury models were also identified with renal LECs further demonstrating changed gene expression between cisplatin and ischemia reperfusion injury models, indicating the renal LEC response is both specific to where they lie in the lymphatic vasculature and the renal injury type. Conclusions: In this study, we uncover lymphatic vessel structural features of captured populations and injury-induced genetic changes. We further determine LEC gene expression is altered between injury models. How LECs respond to AKI may therefore be key in regulating future kidney disease progression.

overall_design: Renal LECs were isolated from 5 male C57BL6/J mice treated with saline or cisplain (20mg/kg) 72 hours post injury. Renal LECs were isolated through dual magnetic enrichment of the markers CD31 and PDPN. A total of 10 kidneys were used per condition. Magnetic beads were cleaved after magnetic enrichment. LEC enrichment was confirmed by flow cytometry of CD45- Live Population expression of Cd31+, Pdpn+, and Lyve1+ marker presence.

first: Heidi

middle: A

last: Creed

first: Saranya

last: Kannan

first: Brittany

last: Tate

first: Priyanka

last: Banerjee

first: Brett

last: Mitchell

first: Sanjukta

last: Chakraborty


title: Targeting DNMT3A-mediated oxidative phosphorylation to overcome ibrutinib resistance in mantle cell lymphoma

city: Madison

first: Lixin

last: Rui

state: WI - Wisconsin

address: 1111 Highland Ave R.4060

department: Medicine

institute: University of Wisconsin-Madison

summary: The use of Bruton tyrosine kinase (BTK) inhibitors such as ibrutinib has achieved a remarkable clinical response in mantle cell lymphoma (MCL). Acquired drug resistance, however, is significant and impacts long-term survival of MCL patients. Here we demonstrate that DNMT3A is involved in ibrutinib resistance. We found that DNMT3A expression is upregulated upon ibrutinib treatment in ibrutinib-resistant MCL cells. Genetic and pharmacological analyses revealed that DNMT3A mediates ibrutinib resistance independent of its DNA-methylation function. Mechanistically, DNMT3A induces the expression of MYC target genes through interaction with the transcription factors MEF2B and MYC, thus mediating metabolic reprogramming to oxidative phosphorylation (OXPHOS).  Targeting DNMT3A by a low dose of decitabine inhibits the growth of ibrutinib-resistant lymphoma cells both in vitro and in a patient-derived xenograft mouse model. These findings suggest that targeting DNMT3A-medited metabolic reprogramming to OXPHOS with decitabine provides a potential therapeutic strategy to overcome ibrutinib resistance in relapsed/refractory MCL.

overall_design: To generate DNMT3A KO clones, Z138 cell line was transduced with CAS9-RFP and sgDNMT3A (2 guides) whose expression can be induced by doxycycline. Uninduced clones are preserved in different vials. For every experiment, uninduced cells were freshly thawn to use. For RNA-sequencing, 3 biological replicates were performed, that means cells frozen in different vials were  induced on 3 different day.  For each biological replicate, 2 technical duplicates were performed. Their total RNA are then pooled for analysis. For ChIP-seq, Z138 WT was used and DNMT3A KO in Z138 clone 7 was used as negative control.

first: Nguyet

last: Hoang


title: Human antigen R (HuR) SUMOylation controls senescence response in liver cancer

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The clinical management of liver cancer is challenged by the reduced availability of drugs targeting key signaling pathways and their modest benefits to patients. Senescence induction may represent a strategy for cancer treatment, especially as a combination therapy. The posttranslational modification (PTM) of proteins critically influences many biological processes, including gene expression, cell proliferation, differentiation and apoptosis, tumor progression, and drug resistance. Herein, we newly discovered that the RNA-binding protein (RBP) Human antigen R (HuR), a hub in liver cancer, is SUMOylated in the tumor sections of patients with hepatocellular carcinoma (HCC) in contrast to the surrounding tissue, as well as in human cell line and mouse models of the disease. SUMOylation of HuR promotes major cancer hallmarks, namely proliferation and invasion, whereas the absence of HuR SUMOylation results in a senescent phenotype with dysfunctional mitochondria and endoplasmic reticulum (ER). Mechanistically, SUMOylation induces a structural rearrangement of the RNA recognition motifs (RRMs) that modulates HuR binding affinity to its target mRNAs further modifying the transcriptomic profile towards hepatic tumor progression.

overall_design: Profiling of RNAs interaction with SUMOylated and non-SUMOylated HuR by performing a V5-tagged HuR immunoprecipitation followed by the isolation and sequencing of the bound RNAs (RIP-Seq) in the human hepatoma HuH-7 cell line stably overexpressing WT HuR or expressing HuR(K120/182R) SUMOylation mutant.

first: Sofia

last: Lachiondo-Ortega

first: Jorge

last: Simon

first: Fernando

last: Lopitz-Otsoa

first: Teresa

last: Delgado

first: Krystyna

last: Mazan-Mamczarz

first: Naroa

last: Goikoetxea-Usandizaga

first: Ruba

last: Al-Abdulla

first: Carmen

last: Fernandez-Rodriguez

first: Mikel

last: Azkargorta

first: Alejandro

last: Velázquez-Cruz

first: Joris

last: Guyon

first: César

last: Martín

first: Juan

last: Zalamea

first: Leire

last: Egia-Mendikute

first: Marina

last: Serrano-Maciá

first: Irene

last: González-Recio

first: Asís

last: Palazón

first: Luis

last: Martínez-Cruz

first: Ana

last: Aransay

first: Nicola

last: Abrescia

first: Félix

last: Elortza

first: Amaia

last: Lujambio

first: Jesus

last: Banales

first: Matias

last: Avila

first: Jose

middle: J

last: Marin

first: Thomas

last: Daubon

first: Antonio

last: Díaz-Quintana

last: Díaz-Moreno

first: Myriam

last: Gorospe

first: Manuel

last: Rodríguez

first: María

middle: L

last: Martínez-Chantar


title: CGRP sensory neurons promote tissue healing by modulating neutrophils and macrophages

status: Public on Feb 18 2024

city: Clayton

first: Mikaël

last: Martino

state: VICTORIA

address: 15 Innovation Walk, Clayton, VIC

department: Australian Regenerative Medicine Institute

institute: Monash University

summary: Since the immune system plays a critical role in orchestrating tissue healing, regenerative strategies that control immune components have proven effective. This is particularly relevant when immune dysregulation resulting from conditions such as diabetes or advanced age impairs tissue healing following injury. Nociceptive sensory neurons play a crucial role as immunoregulators, exerting both protective and harmful effects depending on the context. However, how neuro-immune interactions impact tissue repair and regeneration after acute injury is unclear. Here, we show that Nav1.8+ nociceptor ablation impairs skin wound repair and muscle regeneration after acute tissue injuries. Nociceptor endings grow into injured skin and muscle tissues and signal to immune cells through the neuropeptide calcitonin gene-related peptide (CGRP) during the healing process. CGRP acts via receptor activity modifying protein 1 (RAMP1) on neutrophils and macrophages to inhibit recruitment, accelerate death, enhance efferocytosis, and polarise macrophages towards a pro-repair phenotype. CGRP effects on neutrophils and macrophages are mediated via thrombospondin-1 release and its subsequent autocrine/paracrine effects. In mice without nociceptors and diabetic mice with peripheral neuropathies, delivering an engineered version of CGRP accelerated wound healing and promoted muscle regeneration. Harnessing neuro-immune interactions holds potential to treat non-healing tissues where dysregulated neuro-immune interactions impair tissue healing.

overall_design: To understand  the molecular mechanisms by which CGRP modulates neutrophils and macrophages, we performed RNA-seq analysis on bone marrow-derived neutrophils and macrophages stimulated/treated with CGRP (1 nM) or saline control for 4 hours in vitro.

middle: M

first: Yen-Zhen

last: Lu

first: Bhavana

last: Nayer


title: UV cross-linking RIP-seq of VSV-GFP-infected HEK293T cells overexpressed PTENα

first: Zeliang

last: Yang

address: No.38 Xueyuan Road,Haidian

institute: Peking University Health Science Center

summary: To determine whether PTENα directly binds to viral RNA or host mRNA, we performed UV cross-linking RNA immunoprecipitation (RIP) sequencing of HEK293T cells transfected with vector encoding PTENα under VSV-GFP (green fluorescent protein-expressing vesicular stomatitis virus) infection

overall_design: Five 10cm2 dishes of HEK293T cells at 70% confluency were transfected with 10μg of FLAG-PTENα plasmid per dish. At 24 hours after transfection, cells were stimulated with VSV-GFP (MOI = 0.01). 14 hours later, cells were irradiated with 254nm UV wavelength of 400mJ/cm2 energy. Then, cells were collected and resuspended with co-IP lysis buffer under RNase Inhibitor treatment (1U/μl). After rotation at 4℃ for 15 min, the lysates were centrifuged at 13000 × g and the pellets were discarded. After saving 1/20 of the sample as input, the supernatant was incubated with ANTI-FLAG M2 beads and rotated at 4℃ for 2 hours to enrich the RNA-protein complex. Next, the beads were washed with IP washing buffer four times, and treated with DNase I (2U/μl) and RNase Inhibitor (1U/μl) at 22℃ for 15 min. Finally, the protein-RNA complexes were digested with Proteinase K (0.5mg/mL) and 0.1% SDS at 56℃ for 15 min and the bound RNA was separated using TRIzol reagent.

first: Xin

last: Zhang

first: Dan


title: Effect ofhepatocyte-specific Chrebp knockout on model of high-fructose diet during pregnancy

city: Tianjin

first: Jiaqi

last: Li

state: None Selected

address: No.94 Weijin Road, Nankai District

institute: Nankai university

summary: During pregnancy, a high-fructose diet (HFrD) exacerbates gestational insulin resistance and is associated with an increased risk of gestational diabetes. The relationship between liver ChREBP and gestational insulin resistance remains unknown. To address this question, we fed pregnant hChrebp-KO mice and wild-type mice a high-fructose diet, and on the 17th day of pregnancy, we extracted liver tissue from the mice and conducted comparative transcriptomic analysis to elucidate the role of liver ChREBP in gestational insulin resistance."

overall_design: We analyzed 6 female liver tissue samples (3 samples from hChrebp-KO mice fed with HFrD-diet during pregnancy named “KPF group”, 3 samples from wild-type mice fed with HFrD-diet during pregnancy named “WPF group”,).


title: Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line [ATAC-seq]

city: Oxford

first: Siim

last: Pauklin

state: United Kingdom

address: Botnar Research Centre,

country: United Kingdom

institute: University of Oxford

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest and most metastatic cancers in human. PDACs respond poorly to therapies, partly due to cancer stem cells (CSCs) that self-renew, survive chemotherapies, metastasise and replenish the tumor. Factors secreted by tumor cells mediate autocrine/paracrine crosstalk with surrounding cells contributing to the stem cell niche but are still insufficiently characterised. Here we used quantitative SILAC proteomics to identify secreted factors enriched in CSC secretome compared to non-CSCs. Our data uncovered factors that mediate the crosstalk between CSCs and non-CSCs as well as genes mediating the gene expression circuitries regulating CSC proliferation.

overall_design: To investigate the differences of chromatin accessibility between PDAC CSCs (A13A_P_Ctrl samples) and non-CSCs (A13A_Adh_Ctrl samples) in A13A PDAC cell line. We grew CSCs (A13A_P_Ctrl samples) in 3D condition in suspension as tumor spheres for 7 days from single cell suspension, and non-CSCs (A13A_Adh_Ctrl samples) in 2D condition on petri dishes until 80% confluency before collecting samples for total RNA isolation in triplicates.


title: Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line

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

overall_design: Refer to individual Series


title: Three-dimensional chromatin landscapes in MLLr AML

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

department: Molecular Medicine

institute: UT health San Antonio


title: Human transcriptomic response to periprosthetic joint infection

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: Periprosthetic joint infection (PJI), a devastating complication of total joint replacement, is of incompletely understood pathogenesis and may sometimes be challenging to clinically distinguish from other causes of arthroplasty failure. We characterized human gene expression in 93 specimens derived from surfaces of resected arthroplasties, comparing transcriptomes of subjects with infection- versus non-infection-associated arthroplasty failure. Differential gene expression analysis confirmed 28 previously reported potential biomarkers of PJI, including bactericidal/permeability increasing protein (BPI), cathelicidin antimicrobial peptide (CAMP), C-C-motif chemokine ligand 3 (CCL3), 4(CCL4), and C-X-C-motif chemokine ligand 2 (CXCL2), colony stimulating factor 2 receptor beta (CSF2RB), colony stimulating factor 3 (CSF3), alpha-defensin (DEFA4), Fc fragment of IgG receptor 1B (CD64B), intercellular adhesion molecule 1 (ICAM1), interferon gamma (IFNG), interleukin 13 receptor subunit alpha 2 (IL13RA2), interleukin 17D (IL17D), interleukin 1 (IL1A, IL1B, IL1RN), interleukin 2 receptors (IL2RA, IL2RG), interleukin 5 receptor (IL5RA), interleukin 6 (IL6), interleukin 8 (IL8), lipopolysaccharide binding protein (LBP), lipocalin (LCN2), lactate dehydrogenase C (LDHC), lactotransferrin (LTF), matrix metallopeptidase 3 (MMP3), peptidase inhibitor 3 (PI3), and vascular endothelial growth factor A (VEGFA), and identified three novel molecules of potential diagnostic use for detection of PJI, namely C-C-motif chemokine ligand CCL20, coagulation factor VII (F7), and B cell receptor FCRL4. Comparative analysis of infections caused by staphylococci versus bacteria other than staphylococci and Staphylococcus aureus versus Staphylococcus epidermidis showed elevated expression of interleukin 13 (IL13), IL17D, and MMP3 in staphylococcal infections, and of IL1B, IL8, and platelet factor PF4V1 in S. aureus compared to S. epidermidis infections. Pathway analysis of over-represented genes suggested activation of host immune response and cellular maintenance and repair functions in response to invasion of infectious agents. The data presented provides new potential targets for diagnosis of PJI and for differentiation of PJI caused by different infectious agents.

overall_design: Human host RNA from sonicate fluids collected from resected implants of arthroplasty failure individuals were analyzed for gene expression.

first: Thao

last: Masters

middle: V

first: Mrunal

last: Dehankar

first: Kerryl

last: Greenwood-Quaintance

first: Matthew

last: Abdel

first: Jay

middle: N

last: Mandrekar

first: Robin

last: Patel


title: Metabolic rewiring promotes anti-inflammatory effects of glucocorticoids

city: Berlin

first: Artur

last: Wilhelm

address: Virchowweg 11

department: Rheumatology and clinical immunology

institute: Charite Berlin

summary: Glucocorticoids represent the mainstay of therapy for a broad spectrum of immune-mediated inflammatory diseases (IMIDs). However, molecular mechanisms underlying their anti inflammatory mode of action have remained incompletely understood. Here we show that the anti-inflammatory properties of glucocorticoids involve a reprogramming of the mitochondrial metabolism of macrophages, which results in an increased and sustained production of the anti-inflammatory metabolite itaconate and a consequent inhibition of the inflammatory response. The glucocorticoid receptor interacts with parts of the pyruvate dehydrogenase complex where glucocorticoids provoke an increase in activity and allow an accelerated and paradoxical flux of the tricarboxylic acid (TCA) cycle in otherwise pro-inflammatory macrophages. This glucocorticoid-mediated rewiring of mitochondrial metabolism potentiates TCA cycle-dependent production of itaconate throughout the inflammatory response, thereby interfering with the production of pro-inflammatory cytokines. Artificial block of the TCA cycle or genetic deficiency in aconitate decarboxylase 1, the rate-limiting enzyme of itaconate synthesis, in contrast, interferes with the anti-inflammatory effects of glucocorticoids and accordingly abrogates their beneficial effects during a diverse range of preclinical models of IMIDs. Our findings provide important additional insights into the anti-inflammatory properties of glucocorticoids and have substantial implications for the future design of novel classes of anti-inflammatory drugs.

overall_design: To investigate the anti inflammatory effect of glucocortidcoids we performed RNA sequencing of LPS treated bone marrow derived macrophages in the absence and presence of glucocorticoids. Additionally, we performed RNA sequencing of IRG1 Knockout mice using the same conditions.

first: Jean-Phillipe

last: Auger

first: Max

last: Zimmermann

first: Maria

last: Faas

first: Ulrich

last: Stifel

first: David

last: Chambers

first: Brenda

last: Krishnacoumar

first: R. Verena

last: Taudte

first: Charlotte

last: Grund

first: Gitta

last: Erdmann

first: Carina

last: Scholtysek

first: Stefan

last: Uderhardt

first: Oumaima

last: Ben Brahim

first: Mónica

last: Pascual Maté

first: Cornelia

last: Stoll

first: Martin

last: Böttcher

first: Katrin

last: Palumbo-Zerr

first: Matthew SJ

last: Mangan

last: Dzamukova

first: Markus

last: Kieler

first: Melanie

last: Hofmann

first: Stephan

last: Blüml

first: Gernot

last: Schabbauer

first: Dimitrios

last: Mougiakakos

first: Uwe

last: Sonnewald

first: Fabian

last: Hartmann

last: Simon

first: Arnd

last: Kleyer

first: Anika

last: Grüneboom

first: Susetta

last: Finotto

first: Eicke

last: Latz

first: Jörg

first: Georg

last: Schett

first: Jan

last: Tuckermann

first: Gerhard

last: Krönke


title: Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line [RNA-seq]

first: Siim

last: Pauklin

overall_design: To investigate the differences of gene expression between PDAC CSCs and non-CSCs in A13A PDAC cell line. We grew CSCs 3D condition in suspension as tumor spheres for 7 days from single cell suspension, and non-CSCs in 2D condition on petri dishes until 80% confluency before collecting samples for total RNA isolation in triplicates.


first: Artur

last: Wilhelm

overall_design: To investigate the time dependant anti inflammatory effect of glucocortidcoids we performed RNA sequencing of LPS treated bone marrow derived macrophages in the absence and presence of glucocorticoids of Wildtype mice at 4h and 24h post stimulation

first: Jean-Phillipe

last: Auger

first: Max

last: Zimmermann

first: Maria

last: Faas

first: Ulrich

last: Stifel

first: David

last: Chambers

first: Brenda

last: Krishnacoumar

first: R. Verena

last: Taudte

first: Charlotte

last: Grund

first: Gitta

last: Erdmann

first: Carina

last: Scholtysek

first: Stefan

last: Uderhardt

first: Oumaima

last: Ben Brahim

first: Mónica

last: Pascual Maté

first: Cornelia

last: Stoll

first: Martin

last: Böttcher

first: Katrin

last: Palumbo-Zerr

first: Matthew SJ

last: Mangan

last: Dzamukova


title: Transcriptomic Analysis of THP-1 Cells  Electroporated with GFP-EV or GFP-SARS-CoV-2-ORF6

city: Los Angeles

first: Tianhao

last: Duan

state: CA

address: 1450 Biggy ST

department: Department of Medicine

institute: Keck school of medicine of University of Southern California

summary: SARS-CoV-2 ORF6 plays a pivotal role as an accessory protein in modulating the innate immune signaling pathway during SARS-CoV-2 infection. Our study presents a comprehensive analysis of transcriptomes within innate immune cells overexpressing SARS-CoV-2-ORF6. This transcriptomic analysis facilitates rapid exploration of biological networks regulated by ORF6 and allows for a detailed examination of its multifaceted roles across diverse innate immune signaling pathways.

overall_design:
To explore the role of SARS-CoV-2 ORF6 in regulating the inflammatory signaling pathway, we transfected THP-1 cell lines with GFP control or GFP-ORF6 plasmids using electroporation.
Next, we conducted gene expression profiling analysis by utilizing RNA-seq data derived from two THP-1 cell lines that were stimulated with Pam3CSK4 for four hours.
Comparison of gene expression profiles using RNA-seq data from two THP-1 cell lines.

first: Rongfu

last: Wang


title: Single cell RNA sequencing on pancreatic islet infiltrating T cells from NOD mice.

city: Pittsburgh

first: Alok

last: Joglekar

state: PA

address: Assembly 3045, 5051 Center Ave

department: Immunology

institute: University of Pittsburgh

summary: CD4+ T cells recognize peptide antigens presented on class II Major Histocompatibility Complex (MHC-II) molecules to carry out their function. The remarkable diversity of T cell receptor (TCR) sequences and lack of antigen discovery approaches for MHC-II make profiling the specificities of CD4+ T cells challenging. We have expanded our platform of Signaling and Antigen-presenting Bifunctional Receptors to encode MHC-II molecules presenting covalently linked peptides (SABR-IIs) for CD4+ cell antigen discovery. SABR-IIs can present epitopes to CD4+ T cells and induce signaling upon their recognition, allowing a readable output. Here, we demonstrate that SABR-IIs libraries presenting endogenous and non-contiguous epitopes can be used for antigen discovery. Using SABR-II libraries in conjunction with single cell RNA sequencing, we de-convoluted multiple highly expanded TCRs from pancreatic islets of Non-Obese Diabetic (NOD) mice and identified novel Hybrid Insulin Peptide targets. We compounded antigen discovery by incorporating computational TCR similarity prediction metrics followed by experimental validation. Finally, we showed SABR-IIs presenting epitopes in class II Human Leukocyte Antigen (HLA-II) alleles can be used for antigen discovery for human CD4+ T cells. Taken together, we have developed a rapid, flexible, scalable, and versatile approach for de novo identification of CD4+ T cell ligands from single cell RNA sequencing data using experimental and computational approaches.

overall_design: Pancreatic islets from NOD mice were isolated after perfusion with collagenase. The islet-infiltrating T cells were FACS sorted and subjected to 10x Genomics GEX and VDJ sequencing. The overall goal is profile the T cell repertoires in these pre-diabetic mice.

first: Paul

last: Zdinak

first: Stephanie

last: Grebinoski

first: Jishnu

last: Das


title: Blimp-1 and c-Maf regulate common and unique immune gene networks to protect against distinct pathways of pathobiont-induced colitis [scRNA-Seq]

city: London

first: Anne

last: OGarra

address: 1 Midland Road

institute: Francis Crick Insititue

summary: Using single-cell RNA-seq of colon lamina propria leukocytes (LPL), together with ATAC-seq, ChIP-seq and RNA-seq from colon LPL and sorted CD4+ T from colon lamina propria during oral infection with the pathobiont Helicobacter hepaticus we show that Blimp-1 and c-Maf both positively regulate Il10 gene expression, but also cooperate to negatively regulate a large network of proinflammatory effector genes in T cells. While T cell-specific deletion of either Prdm1, Maf or both transcription factors did not result in overt inflammation of the colon at steady state, H. hepaticus infection resulted in mild/moderate colitis in both the Prdm1fl/flCd4Cre and Maffl/flCd4Cre single T cell-specific transcription factor deficient mice, while the double knockout Prdm1fl/flMaffl/flCd4Cre infected mice suffered severe colitis and showed a massive increase in T cell effector genes in colonic LPL. Blimp-1 and c-Maf cooperate to negatively regulate genes including Ifng, Csf2, Il23r, Stat4, Il18r1 and Il2rg, and deletion of both these transcription factors in T cells translated to an exacerbated pathogenic TH1, IFN-g+GM-CSF+ effector cell response. c-Maf, additionally negatively regulated Il17a expression which was elevated in the LPL as assessed by bulk RNA-seq and scRNA-Seq analysis in the H. hepaticus infected Maffl/flCd4Cre mice.

overall_design: scRNA-seq  of colon lamina propria leukocytes was perfomed in samples from mice with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 Maf on Day 14 following infection with Helicobacter hepaticus

first: Marisol

last: Alvarez-Martinez

first: Luke

last: Cox

first: Claire

last: Pearson

first: William

last: Branchett

first: Probir

last: Chakravarty

first: Xuemei

last: Wu

first: Hubert

last: Slawinski

first: Alaa

last: Al-Dibouni

first: Vasileios

last: Samelis

first: Leona

last: Gabrysova

first: Simon

last: Priestnall

first: Alejandro

last: Suarez-Bonnet

first: James

last: Briscoe

first: Fiona

last: Powrie

last: O'Garra


title: Blimp-1 and c-Maf regulate common and unique gene networks to protect against distinct pathways of pathobiont-induced colitis [RNA-Seq]

overall_design: RNA-seq  of colon lamina propria CD4+ T cells isolated from mice with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 Maf on Day 14 following infection with Helicobacter hepaticus


title: Blimp-1 and c-Maf regulate common and unique immune gene networks to protect against distinct pathways of pathobiont-induced colitis [ATAC-Seq]

overall_design: ATAC-seq  of colon lamina propria CD4+ T cells isolated from mice with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 Maf on Day 14 following infection with Helicobacter hepaticus


title: Blimp-1 and c-Maf regulate common and unique immune gene networks to protect against distinct pathways of pathobiont-induced colitis


title: Integrative spatial analysis reveals a multi-layered organization of glioblastoma

city: Rehovot

first: Itay

last: Tirosh

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Glioma contains malignant cells in diverse states. Here, we combine spatial transcriptomics with novel computational approaches to uncover the organization of glioma cellular states. We find three prominent modes of organization. First, cells in any given state tend to be spatially clustered, with local environments that are each enriched with one major cellular state. Second, specific pairs of states preferentially reside in proximity across multiple scales. Third, the pairwise interactions that we detect collectively define a global architecture composed of five layers. Hypoxia appears to drive this 5-layered organization, as it is associated with a long-range organization that extends from the hypoxic core to the infiltrative edge of the tumor. Accordingly, tumor regions distant from any hypoxic foci are less organized. In summary, we provide a conceptual framework for the organization of gliomas and highlight the role of hypoxia as a potential long-range tissue organizer.

overall_design: 13 IDH-WT human glioblastoma samples spatially annotated by the surgeon during navigation-guided tumor resection and 6 IDH-mutant glioma samples profiled by 10X Visium spatial transcriptomics.

first: Alissa

last: Greenwald

first: Noam

middle: G

last: Darnell

first: Rouven

last: Hoefflin


title: RNA-Seq and Ribo-Seq analyses of the study "tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa"

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

summary: The success of bacterial pathogens depends on the coordinated expression of virulence determinants. Regulatory circuits that drive pathogenesis are complex, multilayered, and incompletely understood. Here, we reveal that alterations in tRNA modifications define pathogenic phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. We demonstrate that the enzymatic activity of GidA leads to the introduction of a carboxymethylaminomethyl modification in selected tRNAs. Modifications at the wobble uridine base (cmnm5U34) of the anticodon drives translation of transcripts containing rare codons. Specifically, in P. aeruginosa the presence of GidA-dependent tRNA modifications modulates expression of genes encoding virulence regulators, leading to a cellular proteomic shift toward pathogenic and well-adapted physiological states. Our approach of profiling the consequences of chemical tRNA modifications is general in concept. It provides a paradigm of how environmentally driven tRNA modifications govern gene expression programs and regulate phenotypic outcomes responsible for bacterial adaption to challenging habitats prevailing in the host niche.

overall_design: Pseudomonas aeruginosa UCBPP-PA14 mutant strains were planktonically cultured in LB to an OD600 of 0.4 (ribo seq experiment) or 2 (RNA seq experiment).domonas aeruginosa UCBPP-PA14 wild type and mutants strains cultivated in LB

first: Jonas

last: Krueger

first: Matthias

last: Preusse

first: Nicolas

middle: O

last: Trinler

first: Yannick

last: Frommeyer

first: Sebastian

last: Doberenz

first: Anne

last: Lorenz

first: Svenja

last: Grobe

first: Mathias

last: Müsken

first: Sarah

last: Svensson

first: Ann-Janine

last: Imsiecke

first: Siegfried

last: Weiss

first: Volkhard

last: Kaever

first: Andreas

last: Pich

first: Cynthia

last: Sharma

first: Zoya

last: Ignatova

last: Haeussler


title: Gli1 labels progenitors during chondrogenesis in postnatal mice

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

institute: Sichuan University

summary: Skeletal growth promoted by endochondral ossification is tightly coordinated by self-renewal and differentiation of chondrogenic progenitors. Emerging evidence has shown that multiple skeletal stem cells (SSCs) participate in cartilage formation. However, as yet, no study has reported the existence of common long-lasting chondrogenic progenitors in various types of cartilage. Here, we identified Gli1+ chondrogenic progenitors (Gli1+ CPs), which were distinct from SSCs, were responsible for the lifelong generation of chondrocytes in the growth plate, vertebrae, ribs, and other cartilage. The absence of Gli1+ CPs led to cartilage defects and dwarfishness phenotype in mice. Furthermore, we found that the BMP signal played an important role in self-renewal and maintenance of Gli1+ CPs. The deletion of Bmpr1α caused the exhaustion of Gli1+ CPs, consequently disrupting columnar cartilage. Collectively, our data demonstrate that Gli1+ CPs are common long-term chondrogenic progenitors in multiple types of cartilage and are essential to maintain cartilage homeostasis.

overall_design: Primary chondrocytes were stained with anti-CD45, anti-CD31 and anti-Ter119 primary antibody as described previously. Cell sorting was performed on a FACS Aria III cell sorter (BD Biosciences) to collect CD45-CD31-Ter119-tdTomato+ and CD45-CD31-Ter119-tdTomato- populations. The total RNA sample from each population was extracted separately using TRIzol and the RNeasy mini kit (Qiagen, Germany).

first: Boer

last: Li

first: Yu

last: Shi


title: Transcriptomic profiling of MC38 tumor cells and cancer-associated fibroblasts on murine MC38 liver metastasis sections by NanoString GeoMX DSP

city: Austin

first: Ningling

last: Kang

state: Minnesota

address: 801 16th Ave NE

institute: The Hormel Institute


title: RNA-sequencing analysis of liver tissue from mice subjected to high-fructose or normal diets during pregnancy.

first: Jiaqi

summary: During pregnancy, a high-fructose diet (HFrD) exacerbates gestational insulin resistance and is associated with an increased risk of gestational diabetes. The relationship between liver ChREBP and gestational insulin resistance remains elusive. To address this question, we fed pregnant mice either a high-fructose diet or a normal diet. On the 17th day of pregnancy, we extracted liver tissue from the mice and conducted comparative transcriptomic analysis to elucidate the alterations in liver ChREBP during gestational insulin resistance.

overall_design: We analyzed 6 WT female liver tissue samples (3 fed with HFrD-diet during pregnancy named “PF group”, 3 fed with normal diet during pregnancy named “PC group”).


title: Effect of recombinant murine Lipocalin-2 (LCN2) on murine macrophages

city: Freiburg

first: Robert

last: Zeiser

address: Hugstetter Straße 53

department: Interdisziplinäres Tumorzentrum

institute: University Medical Center Freiburg

summary: We analyzed if LCN2 modulates the activity of phosphotyrosine kinases in LPS/IFNg-stimulated primary murine macrophages (BMDMs)

overall_design: From start of differentiation, murine BMDMs were treated with LCN2 or vehicle (n=5 biological replicates per group), then treated with LPS and IFNg for 16 hours prior to cell collection

first: Marie

last: Czech


title: Transcriptomic profiling of the cancer-associated fibroblasts (CAFs) on murine MC38 liver metastasis sections by NanoString GeoMX DSP

summary: To study how targeting Glut1 influences the transcriptome of cancer-associated fibroblasts (CAFs), the transcriptome of control CAFs and that of Glut1-deficient CAFs on murine MC38 liver metastasis sections were obtained and compared with the NanoString GeoMx DSP

overall_design: Two months old Glut1F/F mice (control mice) and Glut1F/FPRβ-CreERT2 mice (conditional Glut1 knockout mice) were received implantation of MC38 murine colorectal cancer cells by portal vein injection. Cryo-sections of MC38 liver metastases were fixed with formalin, hybridized with NanoString mouse whole transcriptome atlas, followed by immunofluorescence staining with anti-desmin to label CAFs, anti-CD45 for immune cells, and SYTO 13 for cell nuclei. Regions of Interest (ROIs) were selected for data requisition and analysis. CAFs (Desmin+ CD45-) within a ROI were collected for transcriptomic profiling and MC38 cancer cells (Desmin- CD45-) within a same ROI were collected for transcriptomic profiling as well. Segments 17-20 were ROIs from Glut1F/FPRβ-CreERT2 mice and 21-26 were from Glut1 F/F mice. 20 sequencing data were generated for the CAFs due to dual-indexing primers-based sequencing.

first: Yuanguo

last: Wang


title: Transcriptomic profiling of MC38 tumor cells on murine MC38 liver metastasis sections by NanoString GeoMX DSP

summary: To study how targeting Glut1 in CAFs influences the transcritome of adjacent cancer cells, MC38 adjacent to control CAFs and Glut1-deficient CAFs were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP

overall_design: Two months old Glut1F/F mice (control mice) and Glut1F/FPRβ-CreERT2 mice (conditional Glut1 knockout mice) were received implantation of MC38 murine colorectal cancer cells by portal vein injection. Cryo-sections of MC38 liver metastases were fixed with formalin, hybridized with NanoString mouse whole transcriptome atlas, followed by immunofluorescence staining with anti-desmin to label CAFs, anti-CD45 for immune cells, and SYTO 13 for cell nuclei. Regions of Interest (ROIs) were selected for data requisition and analysis. CAFs (Desmin+ CD45-) within a ROI were collected for transcriptomic profiling and MC38 cancer cells (Desmin- CD45-) within a same ROI were collected for transcriptomic profiling as well. Segments 17-20 were ROIs from Glut1F/FPRβ-CreERT2 mice and 21-26 were from Glut1 F/F mice. 20 sequencing data were generated for MC38 cancer cells due to dual-indexing primers-based sequencing.


title: RNA-Seq analysis for the study "tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa"

first: Susanne

last: Häußler

overall_design: RNA-Seq profiles of gidA and ladS mutants in Pseudomonas aeruginosa were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500

first: Jonas

last: Krueger

first: Matthias

last: Preusse

first: Nicolas Oswaldo

last: Trinler

first: Sebastian

last: Doberenz

first: Anne

last: Lorenz

first: Adrian

last: Kordes

first: Svenja

last: Grobe

last: Svenson


title: Loss of EIF4G2 Mediates Aggressiveness in Distinct Endometrial Cancer Subpopulations with Adverse Outcomes in Patients

first: Tsviya

last: Olender

department: Molecular Genetics

institute: The Weizmann Institute

summary: Low EIF4G2 protein expression was shown to have a poor OS of endometrial patients. Control and EIF4G2KD HEC-1A cells were sorted using CD133 merker to CD133+ and CD133- populations. These populations were taken to RNAseq and MS analysis to explore the mechanism.

overall_design: HEC-1A endomertial cell line was KD with shRNA for EIF4G2 (DAP5) or shGFP (shNT) as control. The control and EIF4G2KD cells were subjected to sorting according to CD133 into CD133+ (p) and CD133- populations. The four populations were sorted as N=4 in independent experiments and save in the appropriate buffer according to the manufacturers protocol  (Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen)). mRNA was isolated and subjected to MARSseq2.0 protocol.

first: Sara

last: Meril

first: Chen

last: Lior

first: Marcela

last: Bahlsen

first: Maya

last: Muhlbaur

first: Alon

last: Savidor

first: Shani

last: Bialik

first: Yehuda

last: Ben David

first: Ruth

last: Scherz-Shouval

first: Adi

last: Kimchi


title: A genome-wide genetic screen uncovers novel determinants of human pigmentation

status: Public on Feb 17 2024

city: Stanford

first: Tomasz

last: Swigut

address: 265 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University

summary: To study the differentially expressed genes in lightly and darkly pigmented human skin melanocytes, we isolated melanocytes from light and dark skin samples and performed RNA-seq using Illumina platform.

overall_design: comparative gene expression analysis of degron depleted KLF6 in MNT-1 cells

first: Joanna

last: Wysocka


title: Chromatin accessibility profile of splenic LCMV-specific memory B cells following type I or II interferon blockade in acute versus chronic LCMV infection

first: Kim

last: Good-Jacobson

state: Victoria

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

institute: Monash University

summary: Dynamics of interferon signalling impact the adaptive immune response. We used ATAC sequencing (ATAC-seq) to analyze chromatin accessibility in memory B cells from mice infected with acute or chronic LCMV infection, treated with type I or type II interferon blocking antibodies.

overall_design: Splenic LCMV-specific memory B cells from LCMV-infected mice were isolated by fluorescence-activated cell sortings (FACS) and analysed using ATAC-seq.

first: Lucy

last: Cooper

first: Christopher

last: Scharer


title: Blimp-1 and c-Maf regulate common and unique immune gene networks to protect against distinct pathways of pathobiont-induced colitis [bulk tissue RNA-seq]

first: Anne

last: OGarra

summary: Using single-cell RNA-seq and bulk tissue RNA-seq of colon lamina propria leukocytes (LPL), together with ATAC-seq, ChIP-seq and RNA-seq from colon LPL and sorted CD4+ T from colon lamina propria during oral infection with the pathobiont Helicobacter hepaticus we show that Blimp-1 and c-Maf both positively regulate Il10 gene expression, but also cooperate to negatively regulate a large network of proinflammatory effector genes in T cells. While T cell-specific deletion of either Prdm1, Maf or both transcription factors did not result in overt inflammation of the colon at steady state, H. hepaticus infection resulted in mild/moderate colitis in both the Prdm1fl/flCd4Cre and Maffl/flCd4Cre single T cell-specific transcription factor deficient mice, while the double knockout Prdm1fl/flMaffl/flCd4Cre infected mice suffered severe colitis and showed a massive increase in T cell effector genes in colonic LPL. Blimp-1 and c-Maf cooperate to negatively regulate genes including Ifng, Csf2, Il23r, Stat4, Il18r1 and Il2rg, and deletion of both these transcription factors in T cells translated to an exacerbated pathogenic TH1, IFN-g+GM-CSF+ effector cell response. c-Maf, additionally negatively regulated Il17a expression which was elevated in the LPL as assessed by bulk RNA-seq and scRNA-Seq analysis in the H. hepaticus infected Maffl/flCd4Cre mice.

overall_design: RNA-seq analysis (in 2-5 biological replicates) of colon lamina propria leukocytes isolated from mice with Cd4Cre-mediated deletion of either Prdm1, Maf or both Prdm1 Maf on Day 14 following infection with Helicobacter hepaticus in the presence anti-IL-10R blocking mAb or matched isotype control

first: Marisol

last: Alvarez-Martinez

first: Luke

last: Cox

first: Claire

last: Pearson

first: William

last: Branchett

first: Probir

last: Chakravarty

first: Xuemei

last: Wu

first: Hubert

last: Slawinski

first: Alaa

last: Al-Dibouni

first: Vasileios

last: Samelis

first: Leona

last: Gabryšová

first: Simon

last: Priestnall

first: Alejandro

last: Suárez-Bonnet

first: James

last: Briscoe

first: Fiona

last: Powrie

last: O’Garra


title: Accelerated Aging and Microsatellite Instability in Recessive Dystrophic Epidermolysis Bullosa-Associated Cutaneous Squamous Cell Carcinoma

city: Boston

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary: Recessive dystrophic epidermolysis bullosa (RDEB) is a severely debilitating disorder caused by mutations in COL7A1 and is characterized by extreme skin fragility, chronic inflammation and fibrosis. A majority of RDEB patients develop squamous cell carcinoma (SCC), a highly aggressive skin cancer with limited treatment options currently available. In this study, we utilized a novel approach leveraging WGS and RNA-seq across three different tissues in a single RDEB patient to gain insight into possible mechanisms of RDEB-associated SCC progression and to identify potential novel therapeutic options. As a result, we identified PLK-1 as a possible candidate for targeted therapy and discovered microsatellite instability and accelerated aging as factors potentially contributing to the aggressive nature and early onset of RDEB SCC.

overall_design: Paired end RNA-seq from one SCC tumor sample and one blister-adjacent skin sample from the same RDEB patient

first: Catherine

last: Lee


title: Chromatin accessibility profile at the single cell level of splenic LCMV-specific B cells in acute versus chronic LCMV infection [scATAC-seq]

first: Kim

last: Good-Jacobson

summary: Chronic viral infection disrupts memory B cell development. We used single cell ATAC sequencing (scATAC-seq) to analyze chromatin accessibility in antigen-specific B cells responding to acute versus chronic LCMV infection.

overall_design: Splenic LCMV-specific B cells from LCMV-infected mice were isolated by fluorescence-activated cell sortings (FACS) and analysed using scATAC-seq.

first: Lucy

last: Cooper

first: David

last: Powell


title: Cardiomyocyte-specific adenylyl cyclase type-8 overexpression induces cell-autonomous activation of RelA and non-cell-autonomous myocardial and systemic inflammation

status: Public on Feb 16 2024

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

institute: NIA-IRP, NIH

summary: Using a model of cardiac AC8 overexpression that lead to accelerated cardiac aging, fibrosis and immune system overactivation, this study used scRNA-seq to investigate the signaling pathways dysregulated in cardiac cells to have a better understanding of the biological processes invoved in cardiac aging.

overall_design: A single cell suspension was made from fresh cardiac tissue obtained from AC8 overexpressing mice and littermate controls, An equal number of FACS-sorted CD45+CD31- (leukocytes), CD45-CD31- (resident mesenchymal cells), and CD45-CD31+ (endothelial cells) cells were mixed and processed to generate single-cell cDNA libraries using the 10X Genomics platform Cells were sequenced at a target read depth of 75,000 reads/cell using a NovaSeq 6000 sequencer (Illumina). Single-cell counts were generated from unaligned reads by sequence alignment and de-multiplexing using Cell Ranger from 10x Genomics.

first: Vikas

last: Kumar

first: Kevin

middle: C

last: Bermea

first: Dhaneshwar

first: Amit

last: Singh

first: Anjali

last: Verma

first: Mary

last: Kaileh

first: Ranjan

last: Sen

first: Edward

last: Lakatta

first: Adamo

last: Luigi


title: Splenic LCMV-specific B cells in acute versus chronic LCMV infection

city: Clayton

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

overall_design: Refer to individual Series