title: Targeting YES1 Disrupts Mitotic Fidelity and Potentiates the Response to Taxanes  in Triple-Negative Breast Cancer

city: CLEVELAND

first: Ruth

last: Keri

state: OH

address: 10900 Euclid Ave

institute: Cleveland Clinic

summary: Triple negative breast cancer (TNBC) is a heterogeneous disease with limited therapeutic options. Two commonalities of TNBCs are a failure to express receptors for hormone or HER2-targeted therapies and high levels of chromosomal instability (CIN), both of which generate considerable therapeutic challenges. Focusing on the Src Family Kinases (SFKs), we found that treatment of TNBC cells with pan-SFK inhibitors causes abnormal nuclear phenotypes and DNA double strand breaks that are characteristic of excessive CIN, suggesting that SFKs may provide a vulnerability for treating TNBC. While prior clinical studies found that pan-SFK inhibition causes dose-limiting toxicities and minimal efficacy, we asked whether targeting individual family members may provide more specificity and hence, greater impact. Analysis of public datasets revealed that YES1 is one of the most highly expressed SFKs in basal/TNBC breast cancer and that its expression is associated with poor patient outcomes. Genomic and pharmacologic targeting of YES1 in TNBC cells further demonstrated that its sustained activity is essential for normal mitoses, including centrosome composition and bipolar spindle formation, as well as chromosome stability. We then determined if the ability of YES1 inhibition to induce mitotic defects and profound CIN could be leveraged to potentiate the efficacy of taxanes, cornerstone drugs for TNBC that also induce CIN. Combining paclitaxel with the selective YES1 inhibitor, CH695355, synergistically inhibited growth of several TNBC models both in vitro and in vivo. Moreover, YES1 inhibition re-sensitized taxane-resistant TNBC cells to paclitaxel. Elevated tumor expression of YES1 was also associated with worse overall survival of TNBC patients treated with combined taxanes/anthracyclines. Mechanistically, YES1 suppression leads to a loss of FOXM1 expression, a transcription factor whose disruption has also been reported to induce CIN, but has not yet been effectively therapeutically targeted. Together, these studies demonstrate that the SFK family member, YES1, is a novel and essential regulator of genome stability in TNBC. More broadly, these results suggest that YES1 may be a therapeutically targetable vulnerability that could potentiate the efficacy of mitotic inhibitors to induce maladaptive CIN and improve the treatment of TNBC.

overall_design: RNA-seq study of MDA-MB-231 and SUM159 cells transfected with DMSO or YES1i (CH6953755) in technical (4) replicates.

first: Natasha

last: Ingles-Martinez

first: Katrina

last: Piemonte

first: Kristen

middle: L

last: Weber-Bonk

first: Mitchell

last: Valentine

first: Parth

last: Majmudar

first: Salendra

last: Singh


title: Nucleocytoplasmic β‐Catenin expression contributes to neuroendocrine differentiation in muscle invasive bladder cancer

status: Public on Jul 16 2024

city: İZMİR

first: Serap

last: Erkek Özhan

state: BALÇOVA

address: İzmir Biyotıp ve Genom Merkezi (IBG), Dokuz Eylül Üniversitesi Sağlık Yerleşkesi, Mithatpaşa Caddesi No:58/5

country: Turkey

institute: Izmir Biomedicine and Genome Center

type: Expression profiling by high throughput sequencing

summary: Muscle invasive bladder cancer (MIBC) is highly heterogeneous, both at the molecular level and in terms of clinical progression. Several molecular classifications have been proposed to understand this heterogeneity and contribute to diagnosis and treatment. Although the neuroendocrine-like subtype is the most aggressive and exhibits the worst survival rate when compared to other subtypes, molecular mechanisms underlying neuroendocrine differentiation have not yet been understood. The nuclear localization of β-catenin is known to be associated with the activation of the Wnt/β-catenin pathway, and it is linked to disease progression and aggressiveness in various cancer types. To decipher the mechanisms underlying the neuroendocrine differentiation of bladder cancer, we determined β-catenin expression profiles of 169 T2-stage primary MIBC samples. Immunohistochemistry analysis revealed increased expression of the most widely used NE markers SYP, CGA, and CD56 in β-catenin positive MIBC tumors. As a result of our transcriptomic analysis, we observed higher expression of neuroendocrine differentiation-related genes, and lower expression of basal differentiation and urothelial differentiation-related genes in β-catenin positive MIBC tumors. Furthermore, we applied a molecular consensus classifier to β-catenin positive and negative samples, and the NE score was significantly higher in β-catenin positive MIBC compared to others. By comparing transcriptome proﬁles, we reveal that β-catenin positive MIBC harbor unique gene modules and gene expression profiles that are divergent from the β-catenin negative MIBC. GO term and KEGG pathway analyses showed that various neurogenesis-related pathways as well as regulation of gene expression and chromatin remodeling were significantly enriched at β-catenin positive MIBC. Our results collectively revealed that β-catenin expression contributes to neuroendocrine differentiation of bladder cancer.

overall_design: mRNA-seq for primary muscle-invasive bladder tumors

first: Burcu

last: Akman

first: Ahmet

last: Bursalı

first: Gökhan

last: Karakülah


title: Foxa-deficiency Restricts Hepatitis B Virus Biosynthesis Through Epigenic Silencing [NanoSting]

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

summary: In the HBV transgenic mouse model of chronic infection, the forkhead box protein A/hepatocyte nuclear factor 3 (Foxa/HNF3) family of pioneer transcription factors are required to support postnatal viral demethylation and subsequent HBV transcription and replication. Liver-specific Foxa-deficient mice with hepatic expression of only Foxa3 do not support HBV replication but display biliary epithelial hyperplasia with bridging fibrosis. However, liver-specific Foxa-deficient mice with hepatic expression of only Foxa1 or Foxa2 also successfully restrict viral transcription and replication but display only minimal alterations in liver physiology. These observations suggest that the level of Foxa activity, rather than the combination of specific Foxa genes, is a key determinant of HBV biosynthesis. Together, these findings suggest that targeting Foxa activity could lead to HBV DNA methylation and transcriptional inactivation, resulting in the resolution of chronic HBV infections which are responsible for approximately one million deaths annually worldwide.

platform_organism:
Mus musculus
Hepatitis B virus

overall_design: HBV transgenic mouse RNA from liver was subjected to Nanostring gene expression analysis to determine transcript levels in various Foxa-deficient mouse strains.

first: Rachel

last: Matrenec

first: Claudia

middle: E

last: Oropeza

first: Eddie

last: Dekoven

first: Carly

first: Cecilia

middle: S

last: Chau

first: Stefan

middle: J

last: Green

first: Klaus

middle: H

last: Kaestner

first: Alan


title: Foxa-deficiency Restricts Hepatitis B Virus Biosynthesis Through Epigenic Silencing [Bisulfite-Seq]

type: Methylation profiling by high throughput sequencing

overall_design: Protein-free HBV transgenic mouse DNA from liver was subjected to bisulfite treatment, PCR amplification and sequencing to determine HBV DNA methylation status.

last: McLachlan


title: Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria

city: Madrid

first: Alvaro

last: San Millan

address: Darwin, 3

department: Biotecnología Microbiana

country: Spain

institute: Centro Nacional de Biotecnología-CSIC

summary: Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveil that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded IS1 elements. Specifically, IS1-mediated gene inactivations expedite the adaptation rate of clinical strains in vitro and foster within-patient adaptation in the gut. We decipher the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings propose that plasmid-mediated IS transposition represents a crucial mechanism for swift bacterial adaptation.

sample_organism:
Citrobacter freundii
Escherichia coli
Klebsiella pneumoniae

overall_design: We performed differential expression analysis to analyze the transcription of IS1 in a subset of clinical enterobacterial strains carrying and not carrying the carbapenem-resistance plasmid pOXA-48. We sequenced three biological replicates per strain and condition (carrying and not carrying pOXA-48), except for strains CF13, K209p and K209 that we sequenced two replicates due insufficient RNA Integrity number (RIN).

first: Jorge

last: Sastre-Dominguez

first: Javier

last: DelaFuente

first: Laura

last: Toribio-Celestino

first: Cristina

last: Herencias

first: Pedro

last: Herrador-Gomez

first: Coloma

last: Costas Romero

first: Rafael

last: Canton

first: Jeronimo

last: Rodriguez-Beltran

first: Alfonso

last: Santos-Lopez


title: Foxa-deficiency Restricts Hepatitis B Virus Biosynthesis Through Epigenic Silencing

first: Mark

last: Maienschein-Cline

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

overall_design: Refer to individual Series


title: Longitudinal changes in DNA methylation associated with clozapine use in treatment-resistant schizophrenia from two international cohorts

status: Public on Jul 17 2024

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

summary: 126 Peripheral whole blood samples from 26 individuals across two independent cohorts were collected prior to clozapine initiation,  4-12 weeks after initiation, and a 6 months after initiation.

overall_design: Bisulphite converted DNA from the 126 samples were hybridised to either the Illumina Infinium HumanMethylation450 BeadChip (KCL samples) or the Illumina Infinium HumanMethylationEPIC BeadChip (UMC)

middle: M

first: Amy

last: Gillespie

first: Eilis

last: Hannon

first: Grant

last: McQueen

first: Kyra

middle: V

last: Sendt

first: Alessia

last: Avila

first: John.

last: Lally

first: Alice

last: Egerton

first: Cynthia

last: Okhuijsen-Pfeifer

first: Martea

last: van der Horst

first: Alkomeit

last: Hasan

last: Dempster

first: Joe

last: Burrage

first: Jan

last: Bogers

first: Dan

last: Cohen

first: Marcos

last: Boks

first: Jurjen

last: Luykx

first: Jonathan

last: Mill

first: James

last: MacCabe


title: The PP2A regulator IER5L supports prostate cancer progression

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: Prostate cancer exhibits high prevalence and accounts for a high number of cancer-related deaths. The discovery and characterization of molecular determinants of aggressive prostate cancer represents an active area of research. The Immediate Early Response (IER) family of genes, which regulate Protein Phosphatase 2A (PP2A) activity, has emerged among the factors that influence cancer biology. Here, we show that the less studied member of this family, Immediate Early Response 5 like (IER5L), is upregulated in aggressive prostate cancer. Interestingly, the upregulation of IER5L expression exhibits a robust association with metastatic disease in prostate and is recapitulated in other cancer types. In line with this observation, IER5L silencing reduces foci formation, migration and invasion ability in a variety of human and murine prostate cancer cell lines. In vivo, using zebrafish and immunocompromised mice models, we demonstrate that IER5L is required for prostate cancer tumor growth, dissemination, and metastasis. Mechanistically, we characterize the transcriptomic and proteomic landscapes of IER5L-silenced cells. This approach allowed us to identify DNA replication and monomeric G protein regulators as downstream programs of IER5L through a pathway that is consistent with the regulation of PP2A. In sum, we report the alteration of IER5L in prostate cancer and beyond and provide biological and molecular evidence of its contribution to tumor aggressiveness.

overall_design: Total RNA sequencing of PC3 prostate cancer cell lines tranduced with Scramble or IER5L shRNA. 4 individual biological replicates per condition have been analyzed.

first: Jana

last: Crespo

first: Natalia

last: Martín-Martín

first: Saioa

last: Garcia-Longarte

first: Onintza

last: Carlevaris

first: Ianire

last: Astobiza

first: Amaia

last: Zabala-Letona

first: Marc

last: Guiu

first: Mikel

last: Azkargorta

first: Nuria

last: Macias-Camara

first: Monika

last: Gonzalez-Lopez

first: Phuong

last: Doan

first: Félix

last: Elortza

first: Isabel

last: Mendizabal

first: Jukka

last: Westermack

first: Roger

middle: R

last: Gomis

last: Ercilla

first: Arkaitz

last: Carracedo


title: DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency

city: Paris

first: Julien

last: Richard Albert

address: 15 Rue Hélène Brion

country: France

institute: Institut Jacques Monod, CNRS, Université de Paris

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To formally assess how 5mC shapes the H3K27me3 landscape, we profiled the epigenome of naive and differentiated cells in the presence and absence of the DNA methylation machinery.

overall_design: Whole genome bisulphite sequencing and H3K27me3 and H3K36me3 CUT&Tag was performed on mouse embryonic stem cells and epiblast-like cells. H3K27me3 CUT&Run was performed on epiblast-like cells treated by TET1 site-directed epigenome editing.

first: Teresa

last: Urli

first: Ana

last: Monteagudo-Sánchez

first: Anna

last: Le Breton

first: Amina

last: Sultanova

first: Angélique

last: David

first: Margherita

last: Scarpa

first: Mathieu

last: Schulz

first: Maxim

last: Greenberg


title: GCN2 is a determinant of the response to WEE1 kinase inhibition in small-cell lung cancer

city: Stanford

first: Alexandros

last: Drainas

state: California

address: 265 Campus Drive

department: Pediatrics and Genetics

institute: Stanford

summary: Patients with small-cell lung cancer (SCLC) are in dire need of more effective therapeutic options. Frequent disruption of the G1 checkpoint in SCLC cells creates a greater dependency of these cells on the G2/M checkpoint to maintain genomic integrity. Indeed, in pre-clinical models, inhibiting the G2/M kinase WEE1 shows promise in inhibiting SCLC growth. However, toxicity and acquired resistance limit the clinical effectiveness of this strategy. Here we conducted CRISPR/Cas9 knockout screens to identify genes influencing the response of SCLC cells to WEE1 kinase inhibition. These screens uncovered a role for the GCN2 amino acid-sensing pathway in modulating the response of SCLC cells to WEE1 inhibition. Rapid activation of GCN2 upon WEE1 inhibition triggers a stress response. Pharmacological activation of the GCN2 pathway synergizes with WEE1 inhibition. Thus, activation of the GCN2 amino acid-sensing pathway represents a novel approach for augmenting the efficacy of WEE1 inhibitors in SCLC.

overall_design: Triplicate of small cell lung cancer cells, NCI-H82 and NJH29, treated with AZD1775 or DMSO for 24 hours. The experiment was designed to investigate the transcrption profile between treatment and control conditions after 24 hours.

middle: P

last: Sage


title: Thymic epithelial organoids mediate T cell development [Bulk RNA-seq]

city: Lausanne

first: Tania

last: Hübscher

address: Station 15

department: SV IBI

country: Switzerland

institute: EPFL

summary: Although the advent of organoids opened unprecedented perspectives for basic and translational research, immune system-related organoids remain largely underdeveloped. Here we established organoids from the thymus, the lymphoid organ responsible for T cell development. We identified conditions enabling thymic epithelial progenitor cell proliferation and development into organoids with diverse cell populations and transcriptional profiles resembling in vivo thymic epithelial cells (TECs) more closely than traditional TEC cultures. Contrary to these two-dimensional cultures, thymic epithelial organoids maintained thymus functionality in vitro and mediated physiological T cell development upon reaggregation with T cell progenitors. The reaggregates showed in vivo-like epithelial diversity and ability to attract T cell progenitors. Thymic epithelial organoids are the first organoids originating from the stromal compartment of a lymphoid organ. They provide new opportunities to study TEC biology and T cell development in vitro, paving the way for future thymic regeneration strategies in ageing or acute injuries.

overall_design: Gene expression profiling analysis of bulk RNA-seq data from: freshly extracted (in vivo) TEC, TEC cultured in 2D and TEC organoids

first: L

middle: F

last: Lorenzo-Martín

first: Thomas

last: Barthlott

first: Lucie

last: Tillard

first: Jakob

last: Langer

first: Katrin

last: Hafen

first: Paul

last: Rouse

first: C

middle: C

last: Blackburn

first: Georg

last: Holländer

first: Matthias

last: Lutolf


title: Thymic epithelial organoids mediate T cell development [scRNA-seq]

overall_design: Single-cell RNA-seq of organoid reaggreagte fetal thymic organ culture (ORFTOC) and fetal thymic organ culture (FTOC) labeled with HTOs


title: Knock-down of LPAR6 in mouse embryonic fibroblats

city: Houston

first: Bogdan

last: Czerniak

state: TX

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

summary: Analyses of the whole genome mRNA gene expression profiling performed on Lpar6+/+ and  Lpar6-/- mouse embryonic fibroblasts (MEFs). The Lpar6-/- MEFs showed higher proliferation rate. The  LPAR6 knock-down cells displayed NFkB and STAT3 pathway actvation and downregulation of AHR and TRIM24 pathway.

overall_design: Total RNA obtained from Lpar6+/+ and  Lpar6-/- mouse embryonic fibroblasts

first: Sangkyou

last: Lee

first: Tadeusz

last: Majewski


title: Inhibiting phosphatidylcholine remodeling in adipose tissue increases insulin sensitivity [RNA-Seq]

city: Brooklyn

first: Xian-Cheng

last: Jiang

state: New York

address: 450 Clarkson Ave

department: Cell Biology

institute: SUNY Downstate Medical Center

summary: Cell membrane phosphatidylcholine composition is regulated by lysophosphatidylcholine acyltransferase (LPCAT); changes in membrane phosphatidylcholine saturation are implicated in metabolic disorders. Here, we identified LPCAT3 as the major isoform of LPCAT in adipose tissues and created adipocyte-specific Lpcat3-knockout mice to study adipose tissue lipid metabolism. Transcriptome sequencing and plasma adipokine profiling were used to investigate how LPCAT3 regulates adipose tissue insulin signaling. LPCAT3 deficiency reduced polyunsaturated phosphatidylcholines in adipocyte plasma membranes, increasing insulin sensitivity. LPCAT3 deficiency influenced membrane lipid rafts, which activated insulin receptors and AKT in adipose tissue, and attenuated diet-induced insulin resistance. Conversely, higher LPCAT3 activity in adipose tissues from ob/ob, db/db, and high-fat diet-fed mice reduced insulin signaling. Adding polyunsaturated phosphatidylcholines to mature human or mouse adipocytes in vitro worsened insulin signaling. We suggest that targeting LPCAT3 in adipose tissues to manipulate membrane phospholipid saturation is a new strategy to treat insulin resistance.

overall_design: We collected sWAT isolated from 2-month-old CD-fed wild-type and LPCAT3-AKO mice for RNA sequencing, and SVF for scRNA sequencing.

first: Mulin

last: He

first: Victoria

last: Tung

first: Oleg

last: Evgrafov


title: Targeting YES1 Disrupts Mitotic Fidelity and Potentiates the Response to Taxanes in Triple-Negative Breast Cancer

city: Cleveland

first: Ruth

last: Keri

state: Ohio

address: 9620 Carnegie Ave

institute: Cleveland Clinic Foundation

overall_design: RNA-seq study of MDA-MB-231 and SUM159 cells transfected with non-targeting sgRNA (NTS) or sgRNA targeting YES1 (sgYES) in technical (4) replicates.

first: Piemonte

last: Katrina

first: Ingles-Martinez

last: Natasha

first: Weber-Bonk

last: Kristen

first: Valentine

last: Mitchelle

first: Majmudar

last: Parth

first: Singh

last: Salendra

first: Keri

middle: A

last: Ruth


title: Arid5a directs autoimmune inflammation through an IL-17 signaling pathway [human]

status: Public on Jul 15 2024

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5051 Centre Avenue, 4051

department: Microbiology and Immunology

institute: University of Pittsburgh

summary: Using Arid5a deficient mice to study the role of the RNA-binding protein Arid5a in models of autoimmunity, namely autoimmune glomerulonephritis

overall_design: Identification of Arid5a target transcripts using RIP-seq

first: Sarah

last: Gaffen

first: Yang

last: Li

first: Isha

last: Mehta


title: Arid5a directs autoimmune inflammation through an IL-17 signaling pathway [mouse]


title: Assessing the impact of loss of IRF2 on TASOR2 localization

city: Cambridge

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: The HUSH complex preserves genome integrity through the epigenetic repression of invasive genetic elements. However, despite our understanding of HUSH as an obligate complex of three subunits, only loss of MPP8 or Periphilin, but not TASOR, triggers interferon signaling following derepression of endogenous retroelements. Here we resolve this paradox by characterising a second HUSH complex which shares MPP8 and Periphilin but assembles around TASOR2, an uncharacterized paralog of TASOR. Whereas HUSH represses LINE-1 retroelements marked by the repressive histone modification H3K9me3, HUSH2 is recruited by the transcription factor IRF2 to repress interferon-stimulated genes. Mechanistically, HUSH-mediated retroelement silencing sequesters the limited pool of the shared subunits MPP8 and Periphilin, preventing TASOR2 from forming HUSH2 complexes and hence relieving the HUSH2-mediated repression of interferon-stimulated genes. Thus, competition between two HUSH complexes intertwines retroelement silencing with the induction of an immune response, coupling epigenetic and immune aspects of genome defense.

overall_design: CUT&RUN for TASOR2 was performed in wild-type or IRF2 knockout K562 cells. TASOR2 knockout cells served as a negative control.

first: Joshua

last: Danac


title: Regression of Post-Prandial Cardiac Hypertrophy in Burmese Pythons is Mediated by FoxO1

city: Boulder

first: Dakota

last: Hunt

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado Boulder

summary: As ambush-hunting predators that consume large prey after long intervals of fasting, Burmese pythons evolved with unique adaptations for regulating organ structure and function. Among these is cardiac hypertrophy that develops within three days following a meal (1, 2), which we previously showed was initiated by circulating growth factors (3). Post-prandial cardiac hypertrophy in pythons also rapidly regresses with subsequent fasting (2); however, the molecular mechanisms that regulate the dynamic cardiac remodeling in pythons during digestion are largely unknown. In this study, we employed a multi-omics approach coupled with targeted molecular analyses to examine remodeling of the python ventricular transcriptome and proteome throughout digestion. We found that forkhead box protein O1 (FoxO1) signaling was suppressed prior to hypertrophy development and then activated with regression, which coincided with decreased and then increased expression, respectively, of FoxO1 transcriptional targets involved in protein degradation. To define the molecular mechanistic role of FoxO1 in hypertrophy regression, we used cultured mammalian cardiomyocytes treated with post-fed python plasma. Hypertrophy regression both in pythons and in vitro coincided with activation of FoxO1-dependent autophagy; however, introduction of a FoxO1-specific inhibitor prevented both regression of cell size and autophagy activation. Finally, to determine if FoxO1 activation could induce regression, we generated an adenovirus expressing a constitutively active FoxO1. FoxO1 activation was sufficient to prevent and reverse post-fed plasma-induced hypertrophy, which was partially prevented by autophagy inhibition. Our results indicate that modulation of FoxO1 activity contributes to the dynamic ventricular remodeling in post-prandial Burmese pythons.

overall_design: To identify factors associated with the regression of cardiac mass in Burmese pythons, we performed bulk RNA sequencing on poly-A-enriched left ventricle tissue samples from fasted, 1-day post-fed (DPF), 4DPF, and 6DPF python ventricles. Snakes were fasted for 28 days and then fed pythons received rodent meals equivalent to 25% of their body mass. 1DPF represents an actively hypertrophing timepoint, 4DPF represents an early regression timepoint, while 6DPF represents a later regression timepoint. We then performed differential gene expression and pathway enrichment analysis to genes and pathways changing between group and across the postprandial resposne.

first: Hunt

last: Dakota

first: Martin

last: Thomas


title: Assessing the impact of loss of HUSH or HUSH2 subunits on the transcriptome

overall_design: dCas9-KRAB K562 cells were transduced with at least two independent CRISPRi sgRNAs targetting each of TASOR, TASOR2, MPP8 or Periphilin. An sgRNA targeting AAVS1 served as a negative control. Total RNA was harvested seven days after transduction.


title: Profiling the genome-wide distribution of TASOR2 upon expression of a LINE-1 reporter or Vpx

overall_design: CUT&RUN for TASOR2 was performed in wild-type, L1-expressing, or Vpx-expressing K562 cells. TASOR2 knockout cells were used as negative controls.


title: Profiling the genome-wide distribution of HUSH2 subunits

overall_design: CUT&RUN for TASOR2, MPP8, or Periphilin was performed in wild-type or TASOR2 knockout K562 cells. Rabbit IgG was used as a matched isotype control.


title: CITE-seq of CAR-NK cells

city: Frankfurt am Main

first: Katharina

last: Imkeller

address: Heinrich-Hoffmann-Str. 7

country: Germany

institute: University Hospital Frankfurt

summary: Primary chimeric antigen receptor (CAR) natural killer (NK) cells show strong cytotoxic efficacy against acute myeloid leukemia (AML) in vivo. However, NK cell-mediated tumor killing is often impaired by tumor-mediated immune cell inactivation. Here, we report a novel strategy to overcome NK cell inhibition caused by the immune checkpoint NKG2A, which interacts with HLA-E expressed on AML blasts. We generated AML-specific CD33-directed CAR (CAR33)-KLRC1ko-NK cells with CRISPR/Cas9-based gene editing of the NKG2A-encoding KLRC1 gene. Single-cell multi-omic analyses revealed a higher proportion of activated cells in CAR33-NK- and CAR33-KLRC1ko-NK pools, which were preserved following AML-cell contact. This activated state of the CAR33-KLRC1ko-NK cells has been translated into improved antileukemic activity in vitro and in vivo against AML cell lines and primary blasts. This dual modification of primary NK cells has the potential to bypass the suppressive effect not only of AML but also in a broad range of other cancer identities.

overall_design:
For single cell sequencing analysis, the cryopreserved (genetically modified) NK cells from three different donors were thawed and seeded at 2x106 cells/ml in a 48-well plate in 750µl in NK-MACS® medium supplemented with 1% NK-MACS® Supplements, 5% human plasma, 1% Pen/Strep, 500 U/ml IL-2 (Miltenyi Biotec or Novartis) as well as 50 ng/ml IL-15 (CellGenix) per well. Three days later cells were harvested and co-cultivated with OCI-AML2 cells in 6cm dishes at an E:T ratio of 1:1. OCI-AML2 cells were previously stained with Cell Trace CFSE proliferation kit (Invitrogen) according to manufacturer’s protocol. As a control, NK cells were cultured without contact to AML cells. After two hours the plated cells were harvested, and an Fc-block was performed using hIgG antibodies (University Hospital Frankfurt). Subsequently cells were stained with an anti-NKG2A-PE antibody (Clone Z199, Beckman Coulter, Brea, CA, USA), CD33-CAR-detection reagent (CD33-protein-biotin + anti-biotin-APC (Clone RE746, Miltenyi Biotec) depending on the cell type and each condition was labeled with a different SampleTag from a human Single Cell Sample Multiplexing Kit (BD Biosciences, Franklin Lakes, NJ, USA). Subsequently, cells were stained with 7-AAD (BD Biosciences) to exclude dead cells and were sorted using a BD FACSAria™ machine. NK cells were sorted as follows: NT-NK as CFSE-, KLRC1ko-NK as CFSE-/NKG2A-, CAR33-NK as CFSE-/CAR+ and CAR33-KLRC1ko-NK cells as CFSE-/NKG2A-/CAR+ cells. Afterwards, single cell sequencing was performed using a BD Rhapsody™ Single-cell analysis system (BD Biosciences).

**RAW data not provided due to patient privacy**

first: Tobias

last: Bexte

first: Nawid

last: Albinger

first: Ahmad

last: Al Ajami

first: Philipp

last: Wendel

first: Leon

last: Buchinger

first: Alec

last: Gessner

first: Jamal

last: Alzubi

first: Vinzenz

last: Särchen

first: Meike

last: Vogler

first: Hadeer Mohamed

last: Rasheed

first: Beate Anahita

last: Jung

first: Sebastian

last: Wolf

first: Raj

last: Bhayadia

first: Thomas

last: Oellerich

first: Jan-Henning

last: Klusmann

first: Olaf

last: Penack

first: Nina

last: Möker

first: Toni

last: Cathomen

first: Michael

last: Rieger

first: Evelyn

last: Ullrich


title: Assessing the impact of loss of IRF2 on the transcriptome

first: Iva

last: Tchasovnikarova

overall_design: dCas9-KRAB K562 cells were transduced with at two independent CRISPRi sgRNAs targetting IRF2. An sgRNA targeting AAVS1 served as a negative control. Total RNA was harvested seven days after transduction.

first: Joshua

last: Danac


title: Profiling the genome-wide distribution of HUSH subunits

overall_design: CUT&RUN for TASOR, MPP8 or Periphilin was performed in wild-type or TASOR knockout K562 cells. MPP8 knockout and Periphilin knockout cells were used as negative controls.


title: DNA methylation profiles of SMARCB1-deficient T cell lymphomas

city: Ulm

first: Anja

last: Fischer

address: Albert-Einstein-Allee

department: Institute for Human Genetics

institute: University Medical Center Ulm

summary: Peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) is a heterogeneous group of malignancies with poor outcome. Here we have identified a subgroup of SMARCB1 deficient PTCL-NOS, which is characterized by the lack of the SMARCB1 protein and is more common in young patients. Human and murine Smarcb1-negative PTCL-NOS from a corresponding mouse model show similar DNA methylation profiles, with hypermethylation of T-cell-related genes and hypomethylation of genes involved in myeloid development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: DNA methylation profiles of PTCL-NOS patients (n = 5) showing SMARCB1/INI1 protein loss in immunohistochemnistry (IHC), Cd4-cre::Smarcb1fl/fl mice (n = 5) and corresponding control groups including non-neoplastic samples isolated from the spleen (n = 5) and splenic Cd3+ sorted cells (n = 5) were generated using Illumina Infinium MethylationEPIC and Mouse Methylation BeadChips, respectively.

last: Albert

first: Natalia

last: Moreno

first: Selina

last: Glaser

first: Reiner

last: Siebert

first: Kornelius

last: Kerl


title: Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

city: San Francisco

first: Scot

last: Federman

state: CA

address: 499 Illinois St

institute: UCSF

summary: Kidney failure, the decrease of kidney function below a threshold necessary to support life, is a major cause of morbidity and mortality in humans. Kidney function is highly heritable; yet, the cellular and molecular mechanisms which contribute to differences in human kidney function remain obscure. We performed a genome wide association study (GWAS), identifying 430 loci affecting kidney function in middle-aged adults. To investigate which cell types are affected by these loci, we integrated the GWAS with human kidney candidate cis-regulatory elements (cCREs), identified using scATAC-seq. 56% of kidney function heritability localized to kidney tubule epithelial cCREs and an additional 7% to kidney podocyte cCREs. Thus, most of the heritable differences in adult kidney function is due to altered gene expression in these two cell types. Using enhancer assays, allele-specific scATAC-seq and machine learning, we found that many kidney function variants alter cCRE chromatin accessibility and function. Using CRISPRi, we determined which genes some of these cCREs regulate, implicating NDRG1, CCNB1 and STC1 in human kidney function. This work provides an experimental approach to identify the variants, regulatory elements and genes involved in human traits and disease.

overall_design: HRCEs (Lonza, CC-2554) from 4 donors grown in renal epithelial growth media (Lonza, CC-3190) were transduced with lentivirus encoding dCas9-mCherry-ZIM3. Three days later cells were transduced with lentivirus encoding the sgRNA library and blue fluorescent protein (BFP). Nine days after guide transduction mCherry, BFP double-positive cells from each donor were sorted.

first: Gabriel

middle: B

last: Loeb

first: Pooja

last: Kathail

first: Richard

last: Shuai

first: Ryan

last: Chung

first: Reinier

last: Grona

first: Sailaja

last: Peddada

first: Volkan

last: Sevim

first: Karl

last: Mader

first: Audrey

last: Chu

first: Jonathan

last: Davitte

first: Juan

last: Du

first: Alexander

last: Gupta

first: Chun

last: Ye

first: Shawn

last: Shafer

first: Laralynne

last: Przybyla

first: Radu

last: Rapiteanu

first: Nilah

last: Ioannidis

first: Jeremy

last: Reiter


title: PARP1 knockout mice

city: Grand Forks

first: Yaroslava

last: Karpova

state: ND

address: 501 Columbia Road

department: Biomedical Sciences

institute: University of North Dakota

summary: Poly(ADP-ribose) polymerase 1 (PARP1) is a highly conserved nuclear protein in multicellular organisms that modulates chromatin opening, and by doing so, it plays a significant role in gene expression regulation during development and differentiation.  Despite its significance, all reported Parp1 total knockout mice strains are viable and fertile with no developmental anomalies. It was previously believed that functional redundancy with other PARP family members explain such a controversy. PARP2 is the main candidate to fulfill PARP1 functions in Parp1 knockout mice. Indeed, Parp1 Parp2 double knockout mice are arrested early in development and unable to proceed through gastrulation. However, while PARP2 has similar catalytic domain to PARP1, it lacks other domains that play important regulatory roles, thus making the lack of developmental problems in Parp1 mice total knockouts highly unlikely. To address this question, we checked the best investigated and publicly available Parp1 knockout mice strain. We found that Parp1 is still expressed in these mice, based on the presence of its mRNA transcript. Contrary to prior assumptions, we identified persistent mRNA expression in knockout mice, albeit at reduced levels. Detailed transcript analysis revealed an alternatively spliced PARP1 variant lacking exon two with introduced artificial cassette. Subsequent protein analysis confirmed the existence of a truncated PARP1 protein in knockout mice. We established embryonic stem cell lines from knockout mice and revealed the presence of pADPr. The decreased level of pADPr was detected in knockout ES cells with Western Blotting analysis, but immunofluorescence staining didn’t detect any difference in distribution or level of pADPr in nuclei of knockout ES cells compared to control ones. Moreover, in double Parp1 Parg mutant ES cells the accumulation of pADPr greatly exceeded its amount in normal and even in hypomorph Parg mutant ES cells, suggesting the presence of functionally active PARP1. Therefore, our findings challenge the conventional understanding of PARP1 depletion effects.

overall_design: To check the presence of Parp1 on mRNA level in knockout mice we performed RNAseq analysis in testis of control and knockout mice.

first: Alexei

last: Tulin


title: IGF2BP3 promotes mRNA degradation through internal m7G modification [RNA-Seq]

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

country: China

institute: CAS Center for Excellence in Molecular Cell Science, CAS

summary: Recent studies have suggested that mRNA internal m7G and its writer protein METTL1 are closely related to cell metabolism and cancer regulation. Here, we identify that IGF2BP family proteins IGF2BP1-3 can preferentially bind internal mRNA m7G. Such interactions, especially IGF2BP3 with m7G, could promote the degradation of m7G target transcripts in cancer cells. IGF2BP3 is more responsive to changes of the m7G modification, while IGF2BP1 prefers m6A to stabilize the bound transcripts. We also demonstrate that p53 transcript, TP53, is m7G-modified at its 3’UTR in cancer cells. In glioblastoma, the methylation level and the half lifetime of the modified transcript could be modulated by tuning IGF2BP3, or by site-specific targeting of m7G through a dCas13b-guided system, resulting in modulation of cancer progression and chemosensitivity.

overall_design: mRNA half-time in HepG2 cells

first: Chang

last: Liu

first: Chuan

last: He


title: Glial ferritin maintains self-renewal and proliferation of neural stem cells by supplying iron in Drosophila

city: Nanjing

first: Su

last: Wang

state: Jiangsu

address: 2 Sipailou Road

department: School of Life Science and Technology

institute: Southeast University

summary: Stem cell niche is critical for regulating the behavior of stem cells. Drosophila neural stem cells (Neuroblasts, NBs) are encased by glial niche cells closely, but it still remains unclear whether glial niche cells can regulate the self-renewal and differentiation of NBs. Here we show that ferritin produced by glia, cooperates with Zip13 to transport iron into NBs for the energy production, which is essential to the self-renewal and proliferation of NBs. The knockdown of glial ferritin encoding genes causes energy shortage in NBs, which leads to the low proliferation and premature differentiation of NBs. Moreover, the level of glial ferritin production is affected by the status of NBs, establishing a bicellular iron homeostasis. In this study, we demonstrate that glial cells are indispensable to maintain the self-renewal of NBs, unveiling a novel role of the NB glial niche during brain development.

overall_design: To identify the biological processes related to Fe-S clusters in NB lineages, we performed transcriptome analysis of sorted NB lineages from glial ferritin knockdown as well as the control groups.

first: Zhixin

last: Ma

first: Xiaojing

last: Yang


title: Regulation of MYC by CARD14 in Human Epithelium is a Determinant of Epidermal Homeostasis and Disease II

status: Public on Jul 13 2024

city: Cincinnati

first: Stanley

last: DeVore

address: 3333 Burnett Ave

department: Division of Asthma Research

institute: CCHMC

summary: Caspase recruitment domain family member 14 (CARD14) and its variants are associated with both atopic dermatitis (AD) and psoriasis, but their mechanistic impact on skin barrier homeostasis is largely unknown. CARD14 is known to signal via NFκB, however, CARD14-NFκB signaling does not fully explain the heterogeneity of CARD14-driven disease. Herein, we describe a direct interaction between CARD14 and MYC and show that CARD14 signals through MYC in keratinocytes to coordinate skin barrier homeostasis. CARD14 directly binds MYC and influences barrier formation in a MYC-dependent fashion, and this mechanism is undermined by disease-associated CARD14 variants. These studies establish a paradigm that CARD14 activation regulates skin barrier function by two distinct mechanisms including activating NFκB to bolster the antimicrobial (chemical) barrier and stimulating MYC to bolster the physical barrier. Finally, we show that CARD14-dependent MYC signaling occurs in other epithelia expanding the impact of our findings beyond the skin.

overall_design: To determine differentially-activated pathways by hypomorphic CARD14 variants (R820W, N737H, I593T) vs WT CARD14, we transfected CARD14-deficient KO HaCat keratinocytes with plasmids expressing GFP-tagged CARD14 constructs. We subsequently sorted cells for positive GFP expression and performed RNA-sequencing and subsequent analysis of two independent experiments.

first: Matthew

last: Schuetz

first: Lauren

last: Alvey

first: Henry

last: Lujan

first: David

last: Ochayon

first: Lindsey

last: Williams

first: Wan

last: Chang

first: Alyssa

last: Filuta

first: Brandy

last: Ruff

first: Arjun

last: Kothari

first: Jennifer

last: Hahn

first: Eric

last: Brandt

first: Latha

last: Satish

first: Krishna

last: Roskin

first: Andrew

last: Herr

first: Jocelyn

last: Biagini

first: Lisa

last: Martin

first: Denz

last: Cagdas

first: Sevgi

last: Keles

first: Joshua

middle: D

last: Milner

first: Dorothy

last: Supp

first: Gurjit

middle: K

last: Hershey


title: Regulation of MYC by CARD14 in Human Epithelium is a Determinant of Epidermal Homeostasis and Disease I

first: Stanley

last: DeVore

overall_design: To determine differentially-activated pathways by WT CARD14 (vehicle- and mepazine-treated) vs R820W CARD14 (vehicle- and mepazine-treated) vs CARD14-deficiency, we utilized HaCat keratinocytes CRISPR-edited to harbor the desired genotype and cultured them with the MALT1 inhibitor mepazine or vehicle. We then performed RNA-sequencing and subsequent analysis of three independent experiments.

first: Matthew

last: Schuetz

first: Lauren

last: Alvey

first: Henry

last: Lujan

first: David

last: Ochayon

first: Lindsey

last: Williams


title: IGF2BP3 promotes mRNA degradation through internal m7G modification [seq_Ribo]

first: Xiaoyang

last: Dou

overall_design: Ribo-seq in HepG2 cells

first: Chang

last: Liu

first: Yutao

last: Zhao

first: Chuan

last: He


title: Aged Mouse Muscle and Serum: Sedentary or Exercised Animals with or without Nicotinamide N-methyltransferase Inhibitor Treatment

first: Stan

last: Watowich

state: Texas

address: 2450 Holcombe Blvd, Suite J

institute: Ridgeline Therapeutics

summary: Epigenomic profiling mouse gastrocnemius muscle and serum in aged female mice with/without exercise, with/without nicotinamide N-methyltransferase inhibitor treatment

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Four-condition experiment. Muscle samples were analyzed two ways: All groups cross-compared (Sedentary Saline-treated mice [n=9]), Sedentary Nicotinamide N-methyltransferase Inhibitor (NNMTi)-treated mice [n=9], Progressive Weighted Wheel Running (PoWeR) Saline-treated mice [n=10], and PoWeR NNMTi-treated mice [n=7]), or a subset of groups cross-compared (Sedentary Saline-treated mice [n=9] vs. PoWeR Saline-treated mice [n=10]).


title: Expression data from adult C10 G58R OMA1 KD mouse liver.

city: Bethesda

first: Narendra

last: Derek

state: MD

address: 35 Convent Drive, Room 2A215

department: National Institute of Neurological Disorders and Stroke

institute: National Institutes of Health

summary:
Mitochondrial dysfunction causes devastating disorders, including mitochondrial myopathy. Here, we identified that diverse mitochondrial myopathy models elicit a protective mitochondrial integrated stress response (mt-ISR), mediated by OMA1-DELE1 signaling. The response was similar following disruptions in mtDNA maintenance, from knockout of Tfam, and mitochondrial protein unfolding, from disease-causing mutations in CHCHD10 (G58R and S59L). The preponderance of the response was directed at upregulating pathways for aminoacyl-tRNA biosynthesis, the intermediates for protein synthesis, and was similar in heart and skeletal muscle but more limited in brown adipose challenged with cold stress. Strikingly, models with early DELE1 mt-ISR activation failed to grow and survive to adulthood in the absence of Dele1, accounting for some but not all of OMA1’s protection. Notably, the DELE1 mt-ISR did not slow net protein synthesis in stressed striated muscle, but instead prevented loss of translation-associated proteostasis in muscle fibers. Together our findings identify that the DELE1 mt-ISR mediates a stereotyped response to diverse forms of mitochondrial stress and is particularly critical for maintaining growth and survival in early-onset mitochondrial myopathy.
This experiment used the Clariom_S_Mouse Microarray from Affymetrix/Applied Biosystems to analyze the effect of knocking down OMA1 by ASO in CHCHD10 G58R mouse model of mitochondrial myopathy/cardiomyopathy.

overall_design: 12 total samples were analyzed. Genes with an FDR≤0.05 and a fold-change ≥2 were selected.

first: Lin

last: Hsin-Pin


title: Pachytene piRNAs govern male meiosis I by spatial restriction of gene expression [piRNA_RNAIP]

status: Public on Jul 12 2024

first: Jacob

middle: Manuel

last: Ortega

address: 6550 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Pachytene piRNAs control male fertility across metazoans, yet mechanisms through which they govern meiosis I in pachytene remain unclear. We demonstrate, in C. elegans, that homolog pairing, and crossover formation are compromised in the absence of piRNA function. We identify several protein coding genes as targets of piRNAs including Polo like kinase 3 (PLK-). Pachytene piRNAs spatially restrict and exclude PLK-3 expression from meiosis I. Expansion of PLK-3 expression into the pachytene region, upon loss of piRNAs, is reflected in meiotic defects, which are partially rescued by removal of ectopic PLK-3. Pachytene piRNAs regulate PLK-3 through both translational repression and post-transcriptional degradation establishing the spatiotemporal control of gene expression. Given the conserved role of pachytene piRNAs, we propose that these mechanisms may be applicable to mammals.

overall_design: To measure differences in levels of piRNAs bound to PRG-1 between wild type and prg-1(∆PAZ-domain) mutant adult hermaphrodite C. elegans, we profiled small RNA samples for piRNAs derived from PRG-1 RNA IP samples animals of the following genotypes [replicates]: Wild Type [x2] and prg-1(∆PAZ-domain) [x2]. Average total piRNA reads between genotypes were normalized to total reads mapping to the C. elegans genome and their abundance was compared.

first: Lamia

last: Wahba

last: Seemann

first: Shin-Yu

last: Chen

first: Andrew

last: Fire

first: Swathi

last: Arur


title: Simultaneous profiling of full-length RNA transcripts and chromatin accessibility within single cells of human retinal organoids

city: guangzhou

first: yuhua

last: xiao

state: guangdong province

address: jinsui load

department: zhongshan Ophthalmic  center

institute: Sun Yat-sen University

summary: Single-cell multi-omics sequencing can integrate transcriptome and epigenome to analyze the complex mechanisms underlying neuron development and regeneration, but most current methods are based on second-generation short-read sequencing, which has low efficiency in detecting RNA structural heterogeneity. Long-length sequencing can analyze RNA structures, but the throughput and the number of transcripts detected at the single-cell level are very low, and single-cell level epigenome profiling has not been accomplished either. Therefore, there is currently a lack of an effective method that can integrate RNA splicing and epigenetic modification to analyze the molecular mechanism of neural development. This study developed a single-cell multi-omics assay based on short-read sequencing for the simultaneous detection of single-cell full-length RNA isoforms and DNA accessibility. The accuracy of its resolution in RNA transcript structure can reach 94.5%, and the sensitivity of detecting single-cell gene expression is twice that of third-generation sequencing. And it can detect over 10,000 single nuclei at one run, enabling the effective integrated analysis of single-cell RNA isoforms and DNA accessibility at high throughput. We used this method to construct a multidimensional cell atlas of human retinal organoids, and found that gene expression and differential choices of isoforms of multiple fate-determining factors were significantly associated with chromatin accessibility. This method provides a new technical method for dissecting the multidimensional molecular mechanism of fate determination in neural cell development and regeneration.

overall_design: Perform  scRCAT-seq2  test  using  hESCs  cells,  and  refer  to  SIRV-set  3  as  the  control  to  verify  the  method  for  single-cell  full-length  transcriptome  analysis  based  on  short-read  sequencing.  Test  the  single-cell  multi-omics  analysis  method  based  on  short-read  sequencing  using  D45 human retinal organoids,  and  simultaneously  detect  single-cell  full-length  RNA  isoforms  and  DNA  accessibility.

first: Shuyao

last: Zhang

first: Xinzhi

last: Mo

first: Yuhua

last: Xiao

first: Youjin

last: Hu


title: MP3-seq: Massively parallel measurement of protein-protein interactions by sequencing

city: Seattle

first: Alyssa

last: La Fleur

state: WA

address: Campus Box 352500 185 Stevens Way

institute: University of Washington

summary: Abstract: Protein-protein interactions (PPIs) regulate many cellular processes, and engineered PPIs have cell and gene therapy applications.  Here we introduce massively parallel protein-protein interaction measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast-two-hybrid approach for measuring PPIs.  In MP3-seq, DNA barcodes are associated with specific protein pairs, and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength.  We show that MP3-seq is highly quantitative and scales to over 100,000 interactions.  We apply MP3-seq to characterize interactions between families of rationally designed heterodimers and to investigate elements conferring specificity to coiled-coil interactions. Finally, we predict coiled heterodimer structures using AlphaFold-Multimer (AF-M) and train linear models on physics simulation energy terms to predict MP3-seq values.  We find that AF-M-based models could be valuable for pre-screening interactions, but that measuring interactions experimentally remains necessary to rank their strengths quantitatively.

overall_design: The interactions of barcoded synthetic designed heterodimers were measured using a high throughput yeast two hybrid assay. Protein pairs were subject to an interaction dependent growth selection step. Expression plasmids were subsequently extracted and resulting barcodes were counted using an Illumina Next Seq (NGS) , and pre and post selection barcodes were processed using DeSeq2 to get a measure of PPI strength.

first: Alexander

last: Baryshev

first: Benjamin

last: Groves

first: Cirstyn

last: Michel

first: David

last: Baker

first: Ajasja

last: Ljubetič

first: Georg

last: Seelig


title: BEAM: a combinatorial recombinase toolbox for binary gene expression and mosaic genetic analysis

first: Luciano

middle: Custo

last: Greig

address: 490 Illinois St

department: Ophthalmology

institute: University of California, San Francisco

summary: We describe a system for mosaic genetic analysis termed BEAM, which relies on exogenous DNA delivery in combination with sparse recombinase activation to generate two genetically distinct, non-overlapping populations of cells for comparative analysis. Following transfection or viral transduction, combinatorial recombinase activity generates two distinct populations of cells labeled with either green or red fluorescent protein. BEAM relies on recombinase-dependent signal amplification and delayed reporter expression to enable sharper delineation of control and experimental cells, and to improve reliability of relative to existing methods. We applied BEAM to a variety of known phenotypes to illustrate its advantages for identifying temporally or spatially aberrant phenotypes, for revealing changes in cell proliferation or death, and for controlling for procedural variability. In addition, we used BEAM to test the cortical protomap hypothesis at the individual radial unit level, revealing that area identity is cell-autonomously specified in adjacent radial units.

overall_design: BEAM plasmids were electroporated into the developing cerebral cortex of Couptf1-fl/fl mice at E14.5 and somatosensory cortex was collected at P3. The tissue was dissociated and RFP- and GFP-labeled cells were FACS purified. We then performed RNAseq gene expression analysis, and identified differentially expressed transcripts

first: Mollie

last: Woodworth

first: Stephanie

last: Lim

first: Alexandros

last: Poulopoulos

first: Jeffrey

last: Macklis


title: Alternative sources of molybdenum for Methanococcus maripaludis and their implication for the evolution of molybdoenzymes

city: Bozeman

first: Eric

last: Boyd

address: 1 Montana State University

institute: Montana State University

summary: Molybdoenzymes are essential in global nitrogen, carbon, and sulfur cycling. To date, the only known bioavailable source of molybdenum (Mo) is molybdate. However, in the sulfidic and anoxic (euxinic) habitats that predominate in modern subsurface environments and that were pervasive prior to Earth's widespread oxygenation, Mo occurs as soluble tetrathiomolybdate ion and molybdenite mineral that is not known to be bioavailable. This presents a paradox for how organisms obtain Mo to support molybdoenzymes in these environments. Here, we show that tetrathiomolybdate and molybdenite sustain the high Mo demand of a model anaerobic methanogen, Methanococcus maripaludis, grown via Mo-dependent formate dehydrogenase, formylmethanofuran dehydrogenase, and nitrogenase. Cells grown with tetrathiomolybdate and molybdenite have similar growth kinetics, Mo content, and transcript levels of proteins involved in Mo transport and cofactor biosynthesis when compared to those grown with molybdate, implying similar mechanisms of transport and cofactor biosynthesis. These results help to reconcile the paradox of how Mo is acquired in modern and ancient anaerobes and provide new insight into how molybdoenzymes could have evolved prior to Earth's oxygenation.

overall_design: Methanococcus maripaludis was grown in triplicate reacters without any molybenum source, with molybdate, and with molybdenite. Total RNAs were extracted from all 9 reactors and subjected to RNA-seq analysis.

first: Payne

last: Devon

first: Keller

last: Lisa

first: Larson

last: James

first: Bothner

last: Brian

first: Colman

last: Daniel

first: Boyd

last: Eric


title: Pachytene piRNAs govern male meiosis I by spatial restriction of gene expression [piRNA_hermaphrodite]

city: Houston

first: Jacob

last: Ortega

overall_design: To measure differences in piRNA levels between wild type and prg-1 mutant adult hermaphrodite C. elegans, we profiled small RNA samples for piRNAs derived from animals of the following genotypes [replicates]: Wild Type [x3], prg-1(RNase dead) [x3], and prg-1(∆PAZ-domain) [x3]. Average total piRNA reads between genotypes were normalized to total reads mapping to the C. elegans genome and their abundance was compared.

first: Lamia

last: Wahba

last: Seemann

first: Shin-Yu

last: Chen

first: Andrew

last: Fire

first: Swathi

last: Arur


title: Intratumoral radiation dose heterogeneity augments antitumor immunity in mice and primes responses to checkpoint blockade

city: Madison

first: Zachary

middle: Scott

last: Morris

state: Wisconsin

address: 1111 Highland Ave., WIMR Tower 1, Room 3131

department: Human Oncology

institute: University of Wisconsin-Madison

summary: The immunologic effects of radiation (RT) are influenced by dose and each may be optimized over a unique dose range. We hypothesized that delivering a heterogenous dose of RT would enhance anti-tumor immunity compared to homogenous RT in combination with immune checkpoint blockade (ICI). Using a point source, we delivered a spectrum of dose (~2-32 Gy) to the primary tumor and observed superior systemic immunity in models of metastatic cancer compared to low (2 Gy), moderate (8 Gy), or high (20 Gy) dose homogenous RT. Heterogeneity in RT dose resulted in spatial heterogeneity in gene expression and immune cell infiltration. Moreover, heterogenous RT optimally engaged multiple immune signaling pathways with diverse dose response relationships whereas responses to homogenous RT treatment groups were limited. Single cell RNAseq demonstrated unique enrichment of immune cell populations between each homogenous RT dose group, with several of these dose-dependent changes also represented in the heterogeneously treated tumors, with engagement of both lymphoid and myeloid compartments. This optimized activation of multiple immune mechanisms with distinct dose-dependent profiles within a single tumor may underlie a greater capacity of RT heterogeneity to augment anti-tumor immune response when combined with ICI, as compared to homogenous dose RT.

overall_design: B78 melanoma cells were engrafted by subcutaneous flank injection of C57BL/6 and FVBn mice. Sham sample received mock treatment and is control sample. BT samples received subcutaneous brachytherapy with 192Ir high dose rate source prescribed as 2 Gy to the proximal edge of the tumor. ICI samples received Anti-CTLA-4 and anti-PD-L1 immune checkpoint inhibitors. External beam external beam radiation therapy (EBRT) was performed in vivo prescribed to either 2, 8, or 20 Gy along with ICI treatment. At day 10, tumor-infiltrating leukocytes were isolated from tumor single-cell suspensions via CD45+ FACs.

first: Justin

last: Jagodinsky

first: Jessica

last: Vera

first: Won

last: Jin

first: Amanda

middle: G

last: Shea

first: Paul

last: Clark

first: Raghava

middle: N

last: Sriramaneni

first: Thomas

last: Havighurst

first: Ishan

last: Chakravarthy

first: Raad

last: Allawi

first: KyungMann

last: Kim

last: Harari

last: Sondel

first: Michael

last: Newton

first: Marka

last: Crittenden

last: Gough

last: Miller

first: Irene

last: Ong


title: Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair [RNA-seq]

city: St. Louis

first: Monica

last: Chang-Panesso

state: MO

address: 600 S. Euclid Ave CB 8126

department: Medicine / Nephrology

institute: Washington University in St. Louis

summary: In this dataset, we study the role of FOXM1 in human primary renal tubular epithelial cells (hRPTECs) by first performing Foxm1 knockdown with an siRNA approach and then performing bulk RNA sequencing. We also sought to identify FOXM1 binding sites on hRPTECs using Cut&Run. These studies will help better understand the role of Foxm1 in acute kidney injury and repair.

overall_design: Bulk RNA-sequencing in hRPTECs after FOXM1 siRNA knockdown.

first: Yoshiharu

last: Muto

first: Benjamin

last: Humphreys


title: Supplementation of ACBP/DBI for the Experimental Treatment of Anorexia Nervosa

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

institute: Centre de Recherche des Cordeliers

summary: Total liver RNA extracts from adult female mice (8-week-old) subjected to CRS (chronic restraint stress) or CDDP (cisplatin) induced anorexia with or without ACBP/DBI delivery to investigate the impact of ACBP/DBI on anorexia-induced transcriptomic alterations.

overall_design: ALZET osmotic pumps containing ACBP/DBI (2.5 mg/mL) or PBS were transplanted into eight-week-old female C57BL/6 J mice. Anorexia was induced by CRS or CDDP fourty-eight hours or seventy-two hours later respectively (Goups: CTR=PBS / CDDP / CRS / ACBP / CDDP+ACBP / CRS+ACBP)

first: Hui

last: Chen

first: Vincent

last: Carbonnier

first: Isabelle

last: Martins


title: Spatial gene expression profile of the brain from WT and Sema6d-/- mice

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Sema6D is highly expressed in the brain. We used spatial transcriptional analysis to reveal the roles of Sema6D in the brain.

overall_design: The brains of WT and Sema6d-/- mice were dissected and analyzed by Visium spatial transcriptomics.

first: Yoshimitsu

last: Nakanishi

first: Mayuko

last: Izumi

first: Sujin

last: Kang

first: Atsushi

last: Kumanogoh


title: Hepatic lipopolysaccharide binding protein uncouples inflammation from fibrosis in MAFLD

city: Los Angeles

first: Tamer

last: Sallam

address: 650 Charles E. Young Dr. South

institute: UCLA

summary: MAFLD is a heterogenous spectrum disorder affecting 20% of the population. Inflammatory processes contribute to various stages of MAFLD and thought to instigate hepatic fibrosis. For this reason, targeting inflammation has been heavily nominated as an approach to mitigating liver fibrosis. Lipopolysaccharide binding protein is a secreted protein that plays an established role in innate immune responses. In a murine model of MAFLD, we used a liver-specific deletion of LBP model to study its role in hepatic inflammation. Single nucleus RNA-seq were applied to investigate the role of LBP in hepatic cell composition.

overall_design: The nuclei were isolated using frozen liver from WT and LBP-KO male mice that fed with FPC diet for 16 weeks. The snRNA-seq were applied to investigate the cell composition in the liver.

first: Dan

last: Wang

first: Zhengyi

last: Zhang

first: Ya

last: Cui


first: Zachary

last: Morris

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

overall_design: Refer to individual Series


title: Gene expression profile of the amygdala from WT and Sema6d-/- mice at single cell level

summary: Sema6D is highly expressed in the amygdala. We used single nucleus RNA sequencing (snRNA-seq) to analyze the roles of Sema6D in the amygdala.

overall_design: The amygdalae of WT and Sema6d-/- mice were dissected and analyzed using snRNA-seq.


title: IGF2BP3 promotes mRNA degradation through internal m7G modification [MeRIP-Seq]

first: Xiaoyang

last: Dou

summary: Recent studies have suggested that mRNA internal m7G and its writer protein METTL1 are closely related to cell metabolism and cancer regulation. Here, we identify that IGF2BP family proteins IGF2BP1-3 can preferentially bind internal mRNA m7G. Such interactions, especially IGF2BP3 with m7G, could promote the degradation of m7G target transcripts in cancer cells. IGF2BP3 is more responsive to changes of the m7G modification, while IGF2BP1 prefers m6A to stabilize the bound transcripts. We also demonstrate that p53 transcript, TP53, is m7G-modified at its 3’UTR in cancer cells. In glioblastoma, the methylation level and the half lifetime of the modified transcript could be modulated by tuning IGF2BP3, or by site-specific targeting of m7G through a dCas13b-guided system, resulting in modulation of cancer progression and chemosensitivity.

overall_design: m6A MeRIP-seq in HepG2 cells

first: Chang

last: Liu

first: Chuan

last: He


title: Identifying the role of FOXM1 in human primary renal tubular epithelials using bulk RNA-seq and Cut&Run to understand its role in acute kidney injury and repair [CUT&RUN]

first: Monica

last: Chang-Panesso

overall_design: Cut&Run on human primary RPTECs

first: Yoshiharu

last: Muto

first: Benjamin

last: Humphreys


title: An axonal guidance cue Semaphorin 6D orchestrates systemic metabolism and myelopoiesis through tuning sympathetic innervation (epididymal white adipose tissue)

summary: The goal of this study is to characterize the molecular basis for enhanced catabolism in Sema6d-/- mice fed a high fat diet.

overall_design: WT and Sema6d-/- mice were fed with either control or high fat diet for 3 months. Adipocytes were sorted from the epididymal white adipose tissue.


title: IGF2BP3 promotes mRNA degradation through internal m7G modification [PARCLIP]

overall_design: PARCLIP in HepG2 cells

first: Yutao

last: Zhao


title: Transcriptomic Profiling of Neutrophils in SARS-CoV-2 Infected Mice

city: Helsinki

first: Tomas

last: Strandin

address: Haartmaninkatu 3

department: Virology

country: Finland

institute: University of Helsinki

summary: The severity of COVID-19 is linked to excessive inflammation. Neutrophils represent a critical arm of the innate immune response and are major mediators of inflammation, but their role in COVID-19 pathophysiology remains poorly understood. We conducted transcriptomic profiling of neutrophils obtained from SARS-CoV-2 infected mice, in comparison to non-infected healthy controls. In addition, we investigated the inflammasome formation potential in neutrophils from mice upon SARS-CoV-2 infection. Transcriptomic analysis of polymorphonuclear cells (PMNs), consisting mainly of mature neutrophils, revealed a striking type I interferon (IFN-I) gene signature in infected mice. Furthermore, IFN-I emerged as a priming stimulus for neutrophil inflammasomes, which was confirmed in a COVID-19 mouse model. These findings underscore the crucial role of neutrophil inflammasomes in driving inflammation during severe COVID-19. Altogether, these findings open promising avenues for targeted therapeutic interventions to mitigate the pathological processes associated with the disease.

overall_design: Experimental procedures were approved by the Animal Experimental Board of Finland (license number ESAVI/28687/2020). Female BALB/c mice (7 to 8 weeks old) were transferred to a biosafety level-3 facility and acclimatized for 7 days. Mice were inoculated intranasally with SARS-CoV-2 MaVie strain or PBS (mock-infected control). Four separate experiments were conducted, involving various groups of mice that were infected, treated, and euthanized at different time points (2 and 4 days post-infection). Neutrophils were isolated from lung tissues for RNA sequencing. The sequencing libraries were prepared using the Illumina Stranded with RiboZero library preparation method, and sequencing was performed on the Illumina NextSeq platform. The study aims to understand the transcriptomic changes in neutrophils during SARS-CoV-2 infection and their role in inflammation associated with severe COVID-19.


overall_design: B78 melanoma cells were engrafted by subcutaneous flank injection of C57BL/6 and FVBn mice. BT+ICI samples received subcutaneous brachytherapy with 192Ir high dose rate source prescribed as 2 Gy to the proximal edge of the tumor and anti-CTLA-4 and anti-PD-L1 immune checkpoint inhibitors. BT+ICI treated tumors were harvested three days  post-radiation treatment.

first: Justin

last: Jagodinsky

first: Jessica

last: Vera

first: Won

middle: J

last: Jin

first: Amanda

last: Shea

first: Paul

last: Clark

first: Raghava

last: Sriramaneni

first: Thomas

last: Havighurst

first: Ishan

last: Chakravarthy

first: Raad

middle: H

last: Allawi

first: KyungMann

last: Kim

last: Harari

last: Sondel

first: Michael

last: Newton

first: Marka

last: Crittenden

last: Gough

last: Miller

first: Irene

last: Ong

middle: S


title: Enhanced HRG production following rt-PA treatment modulate neutrophil immune activity and hemorrhagic transformation in ischemic stroke

city: Tianjin

first: Wei

last: Jiang

address: 154 Anshan Road，Heping District

institute: Tianjin Medical University General Hospital

summary: Intravenous thrombolysis (IVT) with recombinate tissue plasminogen activatior (rt-PA) remains the primary approach for the treatment of acute ischemic stroke (AIS). Based on the short half-life of rt-PA, it is speculated that the coagulative/fibrinolytic cascade induced by alteplase administration might have subsequent longer effect on immune modulation. The exact role of Histidine-rich glycoprotein (HRG), which was found elevated following thrombolysis in this study, on affecting the innate immunity and hemorrhagic transformation (HT) following thrombolysis was investigated in this study. RNA sequencing was performed to show different expressed genes under HRG treatment and revealing the potential regulating pathway.

overall_design: To investigate the effect of HRG on human peripheral blood neutrophils,fresh blood samples were obtained from patients diagnosed with ischemic stroke.Neutrophils isolated from human peripheral blood were cultured with PBS, rt-PA, and rt-PA+HRG for 2.5 hours,then comparative gene expression profiling analysis of RNA-seq date for neutrophils under these three treatments.

first: Yuexin

last: Zhao

first: Rongrong

last: Liu

first: Kaibin

last: Shi


title: RAD52 resolves replication-transcription collisions to mitigate R-loop induced genome instability

status: Public on Jul 11 2024

city: New York

first: Nils

last: Weinhold

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Collisions of transcription and replication machinery on the same DNA strand can pose a significant threat to genomic stability. These collision occur in part due to of RNA-DNA hybrids termed R-loops, in which a newly synthesized RNA molecule hybridizes with the DNA template strand. This study investigated the novel role of RAD52, a known DNA repair factor, in preventing collisions by managing R-loop formation and resolution. We show that RAD52 deficiency increases R-loop accumulation, exacerbating collisions and resulting in elevated DNA damage. Further, RAD52's ability to interact with the transcription machinery, coupled with its capacity to facilitate R-loop dissolution, highlights its role in preventing collisions. Lastly, we provide the first evidence of an increased mutational burden at conserved R-loop sites in human tumor samples. In summary, this study underscores the importance of RAD52 in orchestrating the delicate balance between replication and transcription processes to prevent collisions and maintain genome stability.

overall_design: In HeLa cells: ChIP-seq of RNA Pol II (Rpb1), gH2AX and S9.6 in untreated (siNT) andd RAD52-depleted (si52) cells; ChIP-seq of RAD52 in untreated (siNT) cells.

first: Simon

last: Powell


title: An axonal guidance cue Semaphorin 6D orchestrates systemic metabolism and myelopoiesis through tuning sympathetic innervation

first: Daisuke

last: Motooka

summary: The goal of this study is to characterize the molecular basis for enhanced myelopoiesis in Sema6d-/- mice fed a high fat diet.

overall_design: WT and Sema6d-/- mice were fed with either control or high fat diet for 3 months. Hematopoietic stem cells and multipotent progenitors were sorted from the bone marrow.

first: Yoshimitsu

last: Nakanishi

last: Okuzaki


title: Syngeneic mouse model of YES-driven metastatic and proliferative hepatocellular carcinoma.

city: Montreal

first: Sylvain

last: Meloche

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute of Research in Immunology and Cancer

summary: Hepatocellular carcinoma (HCC) is a disease of high unmet medical need that has become a global health problem. The development of targeted therapies for HCC has been hindered by the incomplete understanding of HCC pathogenesis and the limited number of relevant preclinical animal models. We have recently unveiled a novel YES-dependent oncogenic signaling pathway in HCC. To model this subset of HCC, we have established a series of syngeneic cell lines from liver tumors of transgenic mice expressing activated YES. The resulting HepYF cell lines were enriched for expression of stem cell/progenitor markers, proliferated rapidly and were characterized by high SRC-family kinase activity and activated mitogenic signaling pathways. Transcriptomic analysis indicated that HepYF cells are representative of the most aggressive proliferation class G3 subgroup of HCC. HepYF cells formed rapidly growing metastatic tumors upon orthotopic implantation into syngeneic hosts.

overall_design: We compared the transcriptomes of primary mouse hepatocytes and cancer cells isolated from murine liver tumors expression activated Yes Y537F.


title: Transcriptome changes of SyMSCs and AdMSCs before and after the injection into rat OA knees

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

institute: Institute of Science Tokyo

summary: To clarify similarities/differences in factors produced by SyMSCs and AdMSCs under OA environment, we performed RNA sequencing for SyMSCs and AdMSCs before and after the injection into rat OA knees.

overall_design: Human SyMSCs and AdMSCs were collected the next day of injection into knees of pMx rats.

first: Seiya

last: Matsuta


title: Identification of genes important during atrial myocardial morphogenesis

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Atrial cardiomyocytes undergo complex cellular behaviours after 72 hours post fertilization to build muscle structures.  We aimed to identify the genes involved during this process, and therefore we seqeunced the RNA from 48 and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis after 72 hpf.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 48 and 72 hours post fertilization wild-type zebrafish atrial cardiomyocytes.

first: Marga

last: Albu

first: Alessandra

last: Gentile

first: Felix

last: Gunawan

first: Yanli

last: Xu

first: Khrievono

last: Kikhi

last: Guenther

first: Didier

last: Stainier


title: miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue [miRNA]

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Acute kidney injury (AKI) is an important contributor to the development of chronic kidney disease (CKD). We performed miRNA and mRNA sequencing on biobanked human kidney tissues obtained in the routine clinical care of patients with the diagnoses of AKI and minimal change disease (MCD), in addition to nephrectomized (Ref) tissue from individuals without known kidney disease. From all renal biopsy samples, 2 cryosections (10 μM) including the entire cross-section of the tissue were placed directly into PicoPure RNA extraction buffer. RNA was isolated using the PicoPure isolation kit. Total RNA was evaluated for quantity and quality using an Agilent Bioanalyzer. Approximately 100 ng of total RNA was used for library construction with QIASeq miRNA Library Kit. Each resulting indexed library was quantified and its quality assessed by Qubit and Agilent Bioanalyzer. The libraries were then loaded onto an Illumina NextSeq 500 for 75 bp single-read sequencing to a depth of 15-20M reads per library. Sequence reads were uploaded to the Qiagen GeneGlobe Data Analysis Center (https://www.qiagen.com/us/resources/geneglobe) for quality control, alignment and expression quantification. Reads were mapped to different databases for mature, hairpin, noncoding RNA, mRNA and other RNA using bowtie v1.2. Read counts and UMI counts for each RNA category (mature, hairpin, piRNA, tRNA, rRNA, mRNA and otherRNA) were calculated for each sample, using miRbase V21 for miRNA, and piRNABank for piRNA.

overall_design: Bulk 10 um thickness specimens from cross-sectional human kidney biopsies or nephrectomies embedded in OCT underwent small RNA sequencing. Biopsy subjects had AKI or minimal change disease, nephrectomy subjects had no known kidney disease.

first: Danielle

last: Janosevic

first: Thomas

last: De Luca

first: Ricardo

middle: M

last: Ferreira


title: miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue [mRNA, minimal change disease]

summary: Acute kidney injury (AKI) is an important contributor to the development of chronic kidney disease (CKD). We performed miRNA and mRNA sequencing on biobanked human kidney tissues obtained in the routine clinical care of patients with the diagnoses of AKI and minimal change disease (MCD), in addition to nephrectomized (Ref) tissue from individuals without known kidney disease. From all renal biopsy samples, 2 cryosections (10 μM) including the entire cross-section of the tissue were placed directly into PicoPure RNA extraction buffer. RNA was isolated using the PicoPure isolation kit. Total RNA was evaluated for quantity and quality using an Agilent Bioanalyzer. Approximately 10 ng of total RNA were used for each sample’s library preparation. Ribosomal RNA was removed using RiboGone – Mammalian Kit protocol. After rRNA depletion, double-stranded cDNA was synthesized and amplified using the SMARTer Universal Low Input RNA Kit protocol. The cDNA was sheared by Covaris, and the library was prepared and barcoded following the Ion Plus Fragment Library Kit protocol. Each resulting barcoded library was quantified and quality assessed by Agilent Bioanalyzer. Multiple libraries were pooled in equal molarity. Finally, 8 μL of 100 pM pooled libraries were loaded into lanes of an Illumina HiSeq 4000. At least 30M reads per library were generated.

overall_design: Bulk 10 um thickness specimens from cross-sectional human kidney biopsies embedded in OCT underwent RNA sequencing.


title: Response to lupus antibodies of a human cardiac tissue model composed of cardiomyocytes and myofibroblasts

first: Richard

last: Friedman

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

summary: RNASeq study of  how a human cardiac tissue model composed of cardiomyocytes and myofibroblast responds to lupus antibodies

overall_design:
a. Tissue model treated with antibodies from healthy subjects (n=3).
b. Tissue model treated with antibodies from subjects with lupus but not myocarditis (n=3)
c. Tissue model treated with antibodies from subjects with lupus and myocarditis but with a preserved left ventricular ejection fraction (n=4)
d. Tissue model treated with antibodies from subjects with lupus and myocarditis but with a reduced  left ventricular ejection  fraction (n=4)

first: Sharon

last: Fleischer

first: Trevor

middle: R

last: Nash

first: Manuel

last: Tamargo

first: Roberta

middle: I

last: Lock

first: Margaretha

last: Morsink

first: Vanessa

last: Li

first: Morgan

last: Lamberti

first: Pamela

middle: L

last: Graney

first: Martin

last: Liberman

first: Youngbin

last: Kim

middle: Z

last: Zhuang

first: Jaron

last: Whitehead

first: Rajesh

last: Soni

first: Laura

last: Geraldino-Pardilla

first: Robert

last: Winchester

first: Gordana

last: Vunjak-Novakovic


title: Gene expression profile at single cell level of human pulmonary arteries (PA) of 2 healthy and 3 pulmonary hypertension associated with pulmonary fibrosis (PFPH) affected lungs

city: Graz

first: Francesco

last: Valzano

address: Neue Stiftingtalstraße 6, 8010 Graz

country: Austria

institute: Ludwig Boltzmann Institute for lung vascular research

summary: Dysfunction of pulmonary arterial endothelial cells (PAECs) is associated with the development and progression of vascular pathology. However, it remains unknown how pulmonary hypertension (PH) affects cellular composition and transcriptomic profile of pulmonary endothelium. Here, we have undertaken a single-cell, compartment specific approach to characterise alterations in PAECs  associated with two different types of PH, i.e., pulmonary arterial hypertension (PAH) and pulmonary hypertension associated with pulmonary fibrosis (PHPF). Our unbiased analysis showed that endothelium of medium / small caliber pulmonary arteries is composed of three subsets of endothelial cells (ECs). The analysis of healthy and PH endothelium revealed that the three populations are persistently represented in remodelled arteries. Additionally, an exploratory analysis of human aorta (AO) and coronary arteries (CA) endothelium revealed that, although similar gene expression patterns were noticeable, PAECs subpopulations proportions differs significantly from pulmonary arteries (PA) endothelium. To address whether EC heterogeneity is a prime feature of human endothelium, we also performed a similar analysis in a murine model of hypoxia, revealing that similar EC populations were evident in this animal model. Comparative analysis of EC subpopulations in healthy and PH EC identified a common genetic deregulation accompanying vascular remodelling. Even though murine EC displayed some similarities with human EC subpopulations, the intense re-programming associated with hypoxia associated vascular remodelling displayed significant differences compared to the human disease. Finally, in depth comparative analysis of PAH and PHPF EC highlighted the development of disease-specific transcriptomic alterations in the three populations. Therefore, characterisation of transcriptomic differences in the endothelial bed of PAH and PHPF patients can facilitate identification of novel, disease-specific therapeutic targets.

overall_design: Using droplet-based single cell RNA sequencing we analyzed 3 pulmonary arteries (PA) from lungs affected with pulmonary hypertension associated with pulmonary fibrosis(PHPF_1, PHPF_2, PHPF_3) against PA from 2 healthy controls (Donor_4, Donor_5). Clustering, dimensionality reduction, trajectory inference and pseudotime, as well as transcription factor analyses were performed and select marker gene were examined for specific segregation of PA media layer using immunofluorescence in both the conditions.

first: Izabela

last: Borek

first: Slaven

last: Crnkovic

first: Anna

last: Birnhuber

first: Helene

last: Thekkekara Puthenparampil

first: Mike

middle: P

last: Morley

first: Panja

last: Böhm

first: Konrad

last: Hoetzenecker

first: Walter

last: Klepetko

first: Edward

middle: E

last: Morrisey

first: Leigh

last: Marsh

first: Grazyna

last: Kwapiszewska


title: Pan-Cancer Single-Cell Dissection Reveals Phenotypically Distinct B Cell Subtypes

city: Beijing

first: Yu

last: Yang

state: Beijing

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

department: Academy for Advanced Interdisciplinary Studies

institute: Peking University

summary: Characterizing the compositional and phenotypic characteristics of tumor-infiltrating B cells (TIBs) is important for advancing our understanding of their role in cancer development. Here, we establish a comprehensive resource of human B cells by integrating single-cell RNA sequencing data of B cells from 649 patients across 19 major cancer types. We demonstrate substantial heterogeneity in their total abundance and subtype composition and observe immunoglobulin G (IgG)-skewness of antibody-secreting cell isotypes. Moreover, we identify stress-response memory B cells and tumor-associated atypical B cells (TAABs), two tumor-enriched subpopulations with prognostic potential, shared in a pan-cancer manner. In particular, TAABs, characterized by a high clonal expansion level and proliferative capacity as well as by close interactions with activated CD4 T cells in tumors, are predictive of immunotherapy response. Our integrative resource depicts distinct clinically relevant TIB subsets, laying a foundation for further exploration of functional commonality and diversity of B cells in cancer.

overall_design:
We generated scRNA-seq data from cancer patients to investigate tumor-infiltrating B cells across multiple cancer types.
***The submitter declares that raw data have been submitted to China's Genome Sequence Archive (GSA, https://ngdc.cncb.ac.cn/gsa/) and can be accessed with the HRA000321 accession number***

first: Xueyan

last: Chen

first: Dongfang

last: Wang

first: Zemin

last: Zhang


title: KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

institute: Universite Paris Saclay

overall_design: Refer to individual Series


title: Systemically primed central memory T cells source intranasally boosted tissue-resident memory T cells against melanoma lung metastasis

status: Public on Jul 10 2024

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

summary: Tissue resident memory T (TRM) cells mediate the frontline protection against melanoma lung metastasis. We utilized scRNA-seq to investigate the underlying molecular mechanism of central memory T (TCM) to lung TRM development in the prime-boost vaccinaiton regimen.

overall_design: We immunized groups of C57BL/6 mice with DNA vaccine DNA-OVA i.m./EP plus live-attenuated influenza-vectored vaccine LAIV-HK68-OVA i.n. regimen and extracted total cells from lungs, MLN, and spleen at 21 days post DNA-OVA prime immunization (termed Day 0), 2 days, 4 days, and 30 days post LAIV-HK68-OVA booster vaccination for single-cell RNA sequencing (scRNA-seq).

first: Haoran

last: Xu

first: Zhiwei


title: guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel [ChIP-Seq]

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: Since the introduction of next generation sequencing technologies, the field of epigenomics has evolved rapidly. However, most commonly used assays are enrichment-based methods and thus only semi-quantitative. Nucleosome occupancy and methylome sequencing (NOMe-seq) allows for quantitative inference of chromatin states with single locus resolution, but this requires high sequencing depth and is therefore prohibitively expensive to routinely apply to organisms with large genomes. To overcome this limitation, we introduce guidedNOMe-seq, where we combine NOMe profiling with large scale sgRNA synthesis and Cas9-mediated region-of-interest (ROI) enrichment. To facilitate quantitative comparisons between multiple samples, we additionally develop an R package to standardize differential analysis of NOMe-seq data. We extensively benchmark guidedNOMe-seq in a proof-of-concept study, dissecting the interplay of ChAHP and CTCF on chromatin. In summary we introduce a cost-effective, scalable, and customizable targeted enrichment extension to the existing NOMe-seq protocol allowing genome-scale quantification of nucleosome occupancy and transcription factor binding at single allele resolution.

overall_design: ChIP-seq was performed in biological replicates for Ctcf and endogenously tagged Adnp in wild-type mouse ES cells.

first: Michaela

last: Schwaiger

first: Lucas

last: Kaaij


title: guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel [guidedNOMe-seq]

overall_design: Two sets for guidedNOMe-seq datasets were generated. First, at steady state using biological duplicates of wt, Adnp-/- and Ctcf-FKBP12(F36V) mouse ES cells and second during an Adnp depletion and recovery time-course in Adnp-Avi-3xFLAG-FKBP12(F36V)-mNeonGreen mouse ES cells by dTAG13 treatment for 12h followed by a wash-out for 24h.


title: "Hepatocyte growth factor has a unique function in keratinocytes that differs from IL-17A and TNF-aand may contribute to the severity of hidradenitis suppurativa.”

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: The goal is To examine the effects of four cytokines, HGF, IL-17A, TNF-a, and IL-22, on keratinocytes and compare them to the transcriptomes of HS skin. To examine the expression and localization of HGF, lesional skin samples from patients with HS were investigated by immunohistochemical staining and single cell data analysis. Transcriptome analysis of RNA from keratinocytes stimulated with each cytokine was performed and compared to those of HS lesions.

overall_design: Primary normal human adult epidermal keratinocytes were purchased and cultured using EpiLife medium with Growth Supplements and Antibiotic-Antimycotic Solution . When the cells reached 80% confluence, they were trypsinized and resuspended in the medium at 2 ×105cells/ml, and 1 ml was added to each well of the 12-well plates.  After overnight starvation, the cells were stimulated with recombinant human IL-17A (200 ng/ml), IL-22 (50 ng/ml), TNF-a (10 ng/ml), and HGF (100 ng/ml)  for 24 hours.

first: Naomi

last: Shishido


title: Transcriptomic analysis of the nickel response in roots and shoots in the nickel hyperaccumulator Leucocroton havanensis (Euphorbiaceae) endemic from Cuba.

city: Auzeville Tolosane

first: Sylvain

last: MERLOT

address: 24, chemin de Borde Rouge

department: Biological Sciences

institute: CNRS

summary: The goal of this study was to produce a reference transcriptome for the nickel hyperaccumulator Leucocroton havanensis endemic from Cuba and use this transcriptome as a reference to identify genes responding to the presence or the absence of nickel in both roots and shoots of this species

overall_design: To perform this analysis, Leucocroton havanensis plantlets were grown in vitro on a medium without or with nickel for 6 weeks after germination. Roots and shoots were then collected collected separatly to extract RNA. cDNA were then sequenced by Illumina paired-end sequencing. One repetition per sample was used in this study .

first: Dubiel

middle: A

last: Gonzalez

first: Vanesa

last: Garcia de la Torre

first: Ludivine

last: Soubigou-Taconnat

last: Merlot

first: Rosalina

last: Berazaín


title: Benefit of adjuvant chemotherapy on recurrence free survival per consensus molecular subtype in stage III colon cancer

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: In this study, we evaluated the added value of CMS in predicting both prognosis and benefit of adjuvant chemotherapy in stage III CC patients.

overall_design: Multicenter observational cohort study in stage III CC patients diagnosed between 2005 and 2018.

first: Simone

last: Weerd

first: Jan Paul

last: Medema


title: KMT2C deficiency enhances HSC mobilization and granulocyte bias in response to G-CSF

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

summary: single cell RNA-seq/CITE-seq analysis of bone marrow cells from wild type and Kmt2c-deleted mice

overall_design: Lin-Kit+ cells were isolated, stained with barcoded antibodies and processed with 10x genomics ver3.1 and feature barcode kits

first: Jeffrey


title: Atrial fibrillation variant-to-gene prioritization through cross-ancestry eQTL and single-nucleus multiomic analyses (bulk RNA-seq)

status: Public on Jul 09 2024

first: Guillaume

last: Lettre

address: 5000 Belanger

institute: Montreal Heart Institute

summary: Atrial fibrillation (AF) is the most common arrhythmia in the world, and is linked to significant morbidity and mortality. Despite advances in the treatment and management of AF, important challenges remain for patients. Human genetics can provide strong therapeutic candidates, but the identification of the causal genes and their functions is difficult. Here, we apply an AF fine-mapping strategy that leverages results from a cross-ancestry genome-wide association study (GWAS), expression quantitative trait loci (eQTLs) from left atrial appendages (LAA) obtained from two cohorts with distinct ancestry (European and East Asian), and a paired RNAseq and ATACseq LAA single-nucleus assay (sn-multiome). We found that AF-associated LAA eQTLs are largely consistent across ancestries. At ten AF loci, our co-localization and fine-mapping analyses implicated 14 genes. Furthermore, by integrating our LAA sn-multiome data and other epigenomic datasets with our fine-mapping results, we identified four primary candidate causal AF variants, including rs7612445 at GNB4 and rs242557 at MAPT, for which we propose molecular mechanisms of AF-association at the cellular level. Finally, we showed that the repression of the strongest AF-associated eQTL gene, LINC01629, in human embryonic stem cell-derived cardiomyocytes using CRISPR inhibition results in the dysregulation of pathways linked to genes involved in the development of atrial tissue and the cardiac conduction system (e.g. HCN4, PITX2 and TBX5).

overall_design: The H1-dCas9-KRAB hESC lines were infected with Non-Targeting Control (NTC) and LINC01629 gRNAs, then differentiated into cardiomyocytes and matured for 60 days before harvesting for bulk RNAseq.

first: Francis

last: Leblanc


title: Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [ATAC-seq]

city: Montréal

first: Platon

last: Megagiannis

state: QC

address: 3801 Rue University

department: Neurology and Neurosurgery

institute: McGill University

summary: Reactive changes of glial cells during neuroinflammation impact brain disorders and disease progression. Elucidating the mechanisms that control reactive gliosis may help understand brain pathophysiology and improve outcomes. Here, we report that adult ablation of the ASD-associated CHD8 in astrocytes attenuates reactive gliosis via remodeling chromatin accessibility, changing gene expression. Conditional Chd8 deletion in astrocytes, but not microglia, suppresses reactive gliosis by impeding astrocyte proliferation and morphological elaboration. Astrocyte Chd8 ablation alleviates lipopolysaccharide-induced neuroinflammation and septic-associated hypothermia in mice. Astrocytic CHD8 plays an important role in neuroinflammation by altering the chromatin landscape, regulating metabolic and lipid-associated pathways, and astrocyte-microglia crosstalk. Moreover, we show that reactive gliosis can be directly mitigated in vivo using an AAV-mediated Chd8 gene editing strategy. These findings uncover a role of ASD-associated CHD8 in the adult brain, which may warrant future exploration of targeting epigenetic pathways in reactive gliosis and neuroinflammation in injury and neurological diseases.

overall_design: Bulk tissue RNA seq from cortex samples of mice with astrocyte specific Chd8 cKO after LPS or Saline injections, compared to controls. This designed was chosen to probe for transcriptional changes after Chd8 cKO in astrocytes at the baseline and during neuroinflammation

first: Yuan

last: Mei

first: Tony

last: Kwan

first: Trey

last: Ideker

first: Yang

last: Zhou


title: Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [bulk RNA-seq]