title: Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis [Prox1 OE iHep Timecourse scRNA-seq]

overall_design: scRNA-seq of MEFs ± Prox1 overexpression, harvested after 2, 7, or 14 days of 4in1-driven reprogramming to induced hepatocytes. Barcoded hashtag oligos (HTOs) were used to label cells from different biological replicates of the same condition for pooling into single GEM wells. This information was not used for biological analysis.


title: Cooperation between the Hippo and MAPK pathway activation drives acquired resistance to TEAD inhibition IV

status: Public on Dec 17 2024

city: San Fransisco

first: Xiaosai

last: Yao

state: CA

address: 1 DNA Way

department: Oncology Bioinformatics

country: USA

institute: Roche/Genentech

summary: TEAD transcription factors (TEAD1-4) serve as the primary effectors of the Hippo signaling pathway in various cancers. There has been significant progress in the development of therapeutic strategies aimed at disrupting the interaction of TEAD with its coactivators YAP/TAZ. However, targeted therapy leads to the emergence of resistance which poses a barrier to achieving complete cures. Currently, the underlying mechanism of resistance to TEAD inhibition in cancers remains unexplored. We uncover that upregulation of the AP-1 transcription factors, along with restored YAP/TEAD activity, drives resistance to GNE-7883, a pan-TEAD and allosteric TEAD inhibitor. Acute GNE-7883 treatment abrogates YAP binding and attenuates FOSL1 activity but compensation by increased MAPK pathway activity remains insufficient for cell survival. In contrast, TEAD inhibitor resistant cells are able to restore YAP and TEAD occupancy and acquire additional FOSL1 binding sites, leading to increased chromatin accessibility at AP-1 motifs. Resistant cells undergo transcriptional reprogramming to acquire a mesenchymal-like cell state and sustained MAPK activity. We uncover a dependence on the MAPK pathway in the TEAD inhibitor resistant cells, further highlighting the key role of MAPK pathway inhibitors, such as Cobimetinib and Belvarafenib to mitigate resistance mechanisms to TEAD inhibition in Hippo pathway dependent cancers. This study describes a clinically relevant interplay between the Hippo and MAPK pathway in cancers and offers a promising avenue to address TEAD inhibitor resistance in the clinic.

overall_design: To investigate the mechanism involved in TEAD acquired resistance, we developed TEADi resistant cell lines. We then performed exome-sequencing of the parental (sensitive) cell line and the GNE7883-resistant clone (CL3).

first: Thijs

middle: J

last: Hagenbeek

first: Sayantannee

last: Paul

first: Anwesha

last: Dey

first: Julien

last: Tremblay


title: Cooperation between the Hippo and MAPK pathway activation drives acquired resistance to TEAD inhibition I

type: Expression profiling by high throughput sequencing

overall_design: To investigate the mechanism involved in TEAD acquired resistance, we developed TEADi resistant cell lines. We then performed gene expression profiling using data obtained from TEAD inhibitor sensitive cells incubated with DMSO or TEAD inhibitor GNE-7883 and TEAD inhibitor resistant cells incubated with DMSO or TEAD inhibitor GNE-7883.


title: Single-cell gene expression profile of lymphotoxin-beta receptor-expressing myeloid cells from interleukin-33-treated mouse pancreatic tumor

city: New York

first: Masataka

last: Amisaki

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary: We investigated the single-cell level genetic profiles of fluorescence activated cell sorting-purified lymphotoxin-beta receptor-expressing CD11b-positive myeloid cells from interleukin-33-treated mouse pancreatic tumors delived from orthotopic injection of mouse KPC pancretic tumor cell line.

overall_design: Examining single cell RNA profiles of fluorescence activated cell sorting-purified lymphotoxin-beta receptor (LTBR)-positive and LTBR-negative myeloid cells (live, CD45+, CD11b+) from mouse pancreatic tumor


title: Replication Fork-Associated RNA-DNA Hybrids Safeguard Genomic Stability in Transcriptionally Active Regions

status: Public on Dec 18 2024

city: Beijing

first: Jiadong

last: Wang

address: 38 College Road, Haidian District

department: Department of Radiation Medicine

country: China

institute: Peking University Health Science Center

type: Genome binding/occupancy profiling by high throughput sequencing

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Cooperation between the Hippo and MAPK pathway activation drives acquired resistance to TEAD inhibition II

overall_design: To investigate the mechanism involved in TEAD acquired resistance, we developed TEADi resistant cell lines. In order to map interaction between YAP1, TEAD1 and FOSL1 and their DNA binding sites, we performed chromatin profiling (CUT&RUN) from TEAD inhibitor sensitive cells incubated with DMSO or TEAD inhibitor GNE-7883 and TEAD inhibitor resistant cells incubated with TEAD inhibitor GNE-7883.


title: TGM2-mediated histone serotonylation promotes HCC progression via MYC signalling pathway [RNA-Seq]

status: Public on Dec 16 2024

city: Wuhan

first: Tian Ci

state: Hubei

address: No. 1095 Jiefang Avenue, Wuhan, China

department: Hepatic Surgery Center

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Hepatocellular carcinoma (HCC) is a formidable malignancy with limited effective therapeutic avenues. This study was designed to investigate the role of transglutaminase 2 (TGM2) in promoting HCC progression and assess its potential as a target for therapeutic intervention in HCC treatment.TMG2 expression was positively related to a higher AFP level, poor differentiation, and a later BCLC stage. Tgm2 deficiency or H3Q5ser inhibition notably restrained HCC progression. Mechanism research revealed that TGM2-mediated H3Q5ser modifications promote HCC progression via MYC pathway signaling. Furthermore, transcriptional intermediary factor 1 beta (TIF1-β/TRIM28) mediated the recruitment of TGM2 by MYC to facilitate H3Q5ser modifications on MYC targets. Finally, targeting the TGM2 transglutaminase activity significantly suppressed HCC progression in preclinical models.

overall_design: Mechanistic study of TGM2 inhibition with GK921 exposes drug targetable vulnerabilities in HCC. MHCC-97H cells were exposed to DMSO and/or GK921 (2μM). Following 24 hours exposure, RNA was extracted from these cells and then subjected to RNA sequence analysis.

first: Renshun

last: Dong

first: Tianci

first: Bixiang

last: Zhang

first: Xuewu


title: Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation in Vibrio cholerae

city: Bloomington

first: Ankur

last: Dalia

state: IN

address: 1001 E Third St. BB469A

institute: Indiana University

summary: Transcriptional regulators are a broad class of proteins that alter gene expression in response to environmental stimuli. Transmembrane transcriptional regulators (TTRs) are a subset of transcriptional regulators in bacteria that can directly regulate gene expression while remaining anchored in the membrane. Whether this constraint impacts the ability of TTRs to bind their DNA targets remains unclear. Vibrio cholerae uses two TTRs, ChiS and TfoS, to activate horizontal gene transfer by natural transformation in response to chitin by inducing the tfoR promoter (PtfoR). While TfoS was previously shown to bind and regulate PtfoR directly, the role of ChiS in PtfoR activation remains unclear. Here, we show that ChiS directly binds PtfoR upstream of TfoS, and that ChiS directly interacts with TfoS. By independently disrupting ChiS-PtfoR and ChiS-TfoS interactions, we show that ChiS-PtfoR interactions play the dominant role in PtfoR activation. Correspondingly, we show that in the absence of ChiS, recruitment of the PtfoR locus to the membrane is sufficient for PtfoR activation when TfoS is expressed at native levels. Finally, we show that the overexpression of TfoS can bypass the need for ChiS for PtfoR activation. All together, these data suggest a model whereby ChiS both (1) recruits the PtfoR DNA locus to the membrane for TfoS and (2) directly interacts with TfoS to increase its local concentration near the membrane-proximal promoter. This work furthers our understanding of the molecular mechanisms that drive chitin-induced responses in V. cholerae and more broadly highlights how the membrane-embedded localization of TTRs can impact their activity.

overall_design: ChIP-seq of ChiS to identify its binding sites in the Vibrio cholerae genome


title: Transcriptional survey of the light-induced anthocyanin pathway in non-GM purple tomatoes

city: San Giuliano Terme

first: Silvia

last: Gonzali

state: Pisa

address: Via Guidiccioni n. 8/10

department: Institute of Plant Sciences

country: Italy

institute: Sant'Anna School of Advance Studies

summary: Tomato MicroTom plants of the genotypes Aft/Aft x atv/atv (Aft/atv) and Aft/Aft x atv/atv x hp2/hp2 (Aft/atv/hp2) were used. Fruits showing purple anthocyanin pigmentation in the skin were collected at at the mature green (MG) and mature red (MR) stages to compare the transcriptomes of exocarp and mesocarp between the two developmental stages and the two genotypes with the objective to highlight the mechanisms through which light induces anthocyanin synthesis in tomato skin and impede it in mesocarp and other internal parts of the fruits.

overall_design: Aft/atv and Aft/atv/hp2 plants were cultivated in a growth chamber with 23°/20°C of day/night temperature, 12h photoperiod, 150 µmol photons m-2 s−1, and 40% relative humidity. Fruit samples were collected at MG and MR stages and divided into exocarp and mesocarp. Four biological replicates were collected for each of the following sample: 1. Aft/atv MG exocarp, 2. Aft/atv MG mesocarp, 3. Aft/atv/hp2 MG exocarp, 4. Aft/atv/hp2 MG mesocarp, 5. Aft/atv MR exocarp, 6. Aft/atv MR mesocarp, 7. Aft/atv/hp2 MR exocarp, 8. Aft/atv/hp2 MR mesocarp. Each sample was subjected to qPCR and gene expression analysis starting from same amount of total RNA.

first: Jacopo

last: Menconi


title: IL-1β sensitizes to atrial fibrillation acting through resident macrophages and caspase-1 expression

city: Rio de Janeiro

first: Mariana

last: Boroni

state: RJ

address: Rua André Cavalcanti 37

country: Brazil

institute: Instituto Nacional de Câncer

summary: Atrial fibrillation (AF), a common cardiac arrhythmia, is more prevalent in patients with elevated interleukin (IL)-1β levels. Our study shows that 15-day IL-1β injections sensitize mice to AF, inducing fibrosis, β-pleated protein accumulation in the atria, and systemic inflammation resembling AF patients. Increased caspase-1 and IL-1β maturation in the left atrium and elevated Il1b and Casp1 transcription in resident macrophages—dependent on IL-1 receptor (IL-1R)—indicate a positive feedback loop. IL-1β shortened action potentials (APs), accelerating AP and Ca2+ transient restitution, and AF sensitivity required shortened APs, caspase-1, and IL-1R. Cre-Lox knockout models revealed IL-1β signaling relies on IL-1R in macrophages, not cardiomyocytes. While Ccr2-/- mice, lacking recruited macrophages, remained AF-susceptible, mice with IL-1R deletion in cardiac resident macrophages were protected. We present a novel IL-1β-driven AF etiology mediated by IL-1R in cardiac resident macrophages and caspase-1, offering insights into therapeutic targets and distinct AF etiologies.

overall_design: Mice were injected or not with IL-1b or saline for 15 consecutive days. Atrial from both groups were analyzed by RNAsec.

first: Oscar

last: Moreno-Loaiza

first: Pedro

last: Nicolau-Neto

first: Marco

middle: A

last: Pretti

first: Martin

middle: H

last: Bonamino

first: Emiliano

last: Medei


title: Neoadjuvant HER2 inhibition induces ESR1 DNA methylation alterations resulting in clinically relevant ER expression changes in breast cancer

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

type: Methylation profiling by genome tiling array

summary: Divergent estrogen receptor (ER) and HER2 status with breast cancer disease progression has important consequences for clinical management and long-term survival.  Molecular subtype expression is dynamic and influenced by therapeutic intervention and the metastatic environment.   HER2 status, ER expression levels and global DNA methylation was assessed in pre-treatment biopsies, in post-treatment samples in patients with residual disease and, where relevant, in metastatic tumour samples.  Mapping of the methylation landscape revealed global gains in hypomethylation following treatment (n=7 matched tumours, 16 samples) in contrast to hypermethylation on metastasis (n=5 matched tumours, 14 samples). Differential methylation of key signalling pathways, including estrogen response, epithelial to mesenchymal transition and PI3K/AKT/mTOR, is conserved between post-treatment and metastasis. However, where core pathway genes were hypomethylated following treatment, there was a shift to hypermethylation on metastasis, facilitating alterations in the tumour phenotype.  This study unlocks DNA methylation as a key process in breast cancer progression providing vital insights into the effects of targeted HER2 treatment. This work provides a clear rationale to develop combined HER2 inhibitor and endocrine therapeutic strategies to enhance long-term survival in HER2 positive patients.

overall_design: We undertook a clinical study of neoadjuvant HER2 inhibitor treated patients (n=161) to determine the consequence of treatment and metastatic environment on receptor subtype.  HER2 status, ER expression levels and global DNA methylation was assessed in pre-treatment biopsies, in post-treatment samples in patients with residual disease and, where relevant, in metastatic tumour samples (total, n = 22)

first: Gordon

last: Daly

first: Gavin

last: Dowling

first: Mihaela

last: Ola


title: TGM2-mediated histone serotonylation promotes HCC progression via MYC signalling pathway [Cut & Tag]

first: Tian Ci

overall_design: H3K4me3 and H3K4me3Q5ser Cut&Tag for MHCC-97H cells treated with TGM2 inhibitor (GK921) and DMSO control.

first: Renshun


title: Tau accumulation induces microglial state alterations in Alzheimer’s disease model mice (snRNA-seq, part 2)

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: Unique microglial states have been identified in Alzheimer’s disease (AD) model mice and postmortem AD brains. Although it has been well documented that amyloid-β accumulation induces the alteration of microglial states, the relationship between tau pathology and microglial states remains incompletely understood because of a lack of suitable AD models. In the present study, we generated a novel AD model mouse by the intracerebral administration of tau purified from human brains with primary age-related tauopathy into AppNL-G-F/MAPT double knock-in (dKI) mice.

overall_design: DAPI positive cell nuclei were isolated from the hippocampi of the double knock-in model mice with or without tau administration and analyzed using single-nucleus RNA sequencing (snRNA-seq).


title: Characterizing the function of SMARCB1 deficient and proficient SWI/SNF in Epithelioid Sarcoma cell lines by tetON re-expression and small molecule inhibition (BRM014)

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: Several isogenic tetON SMARCB1 re-expressing Epithelioid Sarcoma cell lines alongside bulk empty (MCS) vector transduced controls were submitted to DOX (re-expression) and BRMO014 (inhibition of SWI/SNF)

overall_design: Epithelioid Sarcoma cell lines cultured for 4 days in standard cell culture (DOX+/-) or (BRM014/DMSO).

first: Jia xiang

last: Jin

first: Fabia

last: Fuchslocher

middle: G

last: Grünewald


title: Genomic analyses reveal high diversity and rapid evolution of Pichia kudriavzevii within a neonatal intensive care unit in Delhi, India

city: Nutley

first: Neeraj

last: Chauhan

state: New Jersey

address: 111 ideation way

institute: Center for Discovery and Innovation, Hackensack Meridian Health

summary: Pichia kudriavzevii causes life-threatening infections in immune compromised hosts including hospitalized neonates. This pathogen is resistant to fluconazole while uncommon, strains resistant to multiple antifungal drugs voriconazole, amphotericin B and echinocandins have been reported in healthcare environments. Understanding how P. kudriavzevii spread, persist, and adapt to healthcare settings could help us develop better management strategies. In this study, whole genome sequencing identifies multiple outbreaks of bloodstream infections caused by P. kudriavzevii in a single neonatal intensive care unit (NICU) over five years. Interestingly, two genetically diverse clusters of P. kudriavzevii population showed frequent loss of heterozygosity (LOH) events between two temporal samples. The first outbreak cluster (during 2015-16) showed LOH at chromosomes 1, 4 and 5 and the other outbreak cluster (year 2020) exhibited marked LOH at chromosome 2.  The circulation of two separate strain clusters of P. kudriavzevii suggests nosocomial transmission in the NICU in different time periods. Further, to evaluate the gene expression difference between isolates from two clusters, we compared the transcriptomic profiles of three isolates of cluster I and II and exhibiting distinct fluconazole MICs.  While no difference was found at the azole target gene ERG11 or the ATP-binding cassette (ABC) transporter genes, differences in transcript abundance were found between the two isolates in genes coding for cell division and filamentation, repressor of ABC gene, FCR1 and ERG5 gene involved in ergosterol biosynthesis pathway. Our study indicates significant diversity, persistence, and rapid evolution of P. kudriavzevii within a single NICU.

overall_design: We performed RNA-seq analysis of logarithmically growing Candida krusei isolates in the Yeast Extract Peptone Dextrose broth medium (YPD; 1% yeast extract, 2% peptone, and 2% dextrose) at 30°C. We sequenced VPCI 06/P/16, VPCI 218/P/20 and VPCI 261/P/20 strains in biological duplicates.

first: Raju

last: Shivarathri

first: Kusum

last: Jain

first: Barsha

last: Kalita

first: Jianping

last: Xu

first: Anuradha

last: Chowdhary


title: Comparative transcriptomic profile reveals candidate genes manipulated by type III effectors of Pantoea agglomerans pv betae leading to gall formation in Beta vulgaris

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Pantoea agglomerans pv. betae (Pab) induces tumor-like galls in beet and gypsophila, a process mediated by the secretion of effector proteins via Pab's type III secretion system (T3SS). However, the molecular mechanisms underlying Pab-induced gall formation remain largely unexplored. This study delves into the cellular architecture and transcriptional profile of Pab-mediated galls, comparing host responses to wild-type Pab and a T3SS-inactive mutant, hrcC-. Morphological analysis using scanning electron microscopy and cross-sectional visualization of infected beet leaf tissues revealed that Pab-induced gall-like structures are linked to cell hyperplasia and tissue ruptures, contingent on T3SS activity. Comparative transcriptome analysis of wild-type Pab and hrcC- Pab-infected beet leaves at 12 and 48 hours unveiled significant transcriptional reprogramming, with nearly 2,000 differentially expressed genes as of 48 hours post inoculation. Enrichment analyses identified the upregulation of pathways related to signal transduction, defense, carbohydrate metabolism, and cell wall modulation in wild-type Pab-infected leaves compared to controls. Particularly notable was the significant upregulation of numerous genes associated with cell wall loosening by wild-type Pab, suggesting an initial rearrangement of cell wall architecture facilitating gall formation. Furthermore, transcriptome analysis demonstrated that wild-type Pab suppresses the expression of the betalain biosynthetic gene DOPA 4,5-DIOXYGENASE, leading to reduced betalain accumulation in infected tissues compared to the mutant strain. These findings offer fresh insights into the transcriptional and physiological manipulation of host tissue during the early stages of Pab-induced gall formation.

overall_design: Total RNA was isolated with the RNeasy Plant Mini Kit (QIAGEN) from mock, PabhrcC-, and PabWT inoculated leaves at 12 hpi and 48 hpi (three biological replicates for each treatment, in total 18 samples were collected).

first: Priya

last: Gupta

first: Hanita

last: Zemach

first: Isaac

last: Barash

first: Doron

last: Teper

first: Guido

last: Sessa


title: Tau accumulation induces microglial state alterations in Alzheimer’s disease model mice (Spatial Transcriptomics)

last: Motooka

overall_design: Cellular mRNA in the tau-injected dKI (Tau-dKI) brain was captured on thousands of spots (each 55 μm in diameter) using oligonucleotides with spatial barcodes.


title: Osteocyte Connexin 43 Hemichannels Influence Bone Marrow Mesenchymal Stromal Cell Fate through Prostagladin E2

city: San Antonio

first: JINGRUO

last: ZHANG

state: TEXAS

address: 8403 Floyd Curl Dr

institute: UT HEALTH SAN ANTONIO

summary: Inhibiting Connexin 43 (Cx43) hemichannels in osteocytes led to a significant increase in adipogenesis and a decrease in osteogenesis in bone marrow mesenchymal stromal cells.

overall_design: Bone marrow mesenchymal stromal cells (BM-MSCs) were isolated from three groups: the WT group and two transgenic mouse models, R76W (inhibiting osteocyte Cx43 gap junctions) and Δ130–136 (blocking osteocyte Cx43 hemichannels and gap junctions). Subsequently, single-cell RNA sequencing was conducted on the sorted BM-MSCs to unravel their transcriptomic profiles.

first: Jingruo

last: Zhang

first: Jean

middle: X

last: Jiang


title: Tau accumulation induces microglial state alterations in Alzheimer’s disease model mice (snRNA-seq, part 1)

first: Daisuke


title: The tumor immune microenvironment and therapeutic efficacy of trastuzumab deruxtecan in gastric cancer

city: Tokyo

first: Makito

last: Koga

address: 1-2-58 Hiromachi, Shinagawa-ku

institute: Daiichi Sankyo

summary: Trastuzumab deruxtecan (T-DXd), an anti-HER2 antibody-drug conjugate with a topoisomerase I inhibitor connected by a cleavable linker, has been approved for patients with HER2-positive gastric or gastroesophageal junction tumors. This biomarker study assessed HER2 expression and immune cell infiltration in relation to the therapeutic response to T-DXd. This retrospective analysis included samples from patients treated with T-DXd in three clinical trials. We performed RNA sequencing and multiplex immunohistochemistry on archival tumor samples obtained at baseline, during treatment, and after treatment. Flow cytometry was performed on tumor infiltrating immune cells freshly isolated from tumor tissues. Samples from 28 patients were included in this study. ERBB2 mRNA levels and CD20+ cell infiltration in tumors were significantly higher at baseline in responders than in nonresponders. Patients were classified into three biological groups based on their baseline tumor/stroma-infiltrating immune cell densities. Two groups reported similar response rates, but a trend was observed toward a shorter progression-free-survival in the group with more immunosuppressive regulatory T cells and programmed death-ligand 1 (PD-L1) expression at baseline. T-DXd treatment tended to increase the levels of tumor-infiltrating CD8+ T cells and PD1+CD8+ T cells, particularly in responders. Gene expression signatures of CTL and helper T cells increased during treatment, whereas signatures related to hypoxia, MYC targets, collagen formation, and interleukin-10 were downregulated. Our data suggest that HER2 expression levels and baseline tumor microenvironment (TME) characteristics correlate with T-DXd efficacy. Furthermore, this treatment may modulate TME immune profiles. Further validation using a larger sample size is warranted.

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Shigehiro

last: Koganemaru

first: Shohei

last: Koyama

first: Fumitaka

last: Suto

first: Koichiro

last: Inaki

first: Yusuke

last: Kuwahara

first: Takeo

last: Arita

first: Tsuyoshi

last: Hirata

first: Hiroki

last: Goto

first: Naoya

last: Wada

first: Maki

last: Kobayashi

first: Tomoko

last: Shibutani

first: Tatsuya

last: Okabayashi

first: Kenji

last: Nakamaru

first: Akihito

last: Kawazoe

first: Yousuke

last: Togashi

first: Hiroyoshi

last: Nishikawa

first: Kohei

last: Shitara


title: Plasma cell infiltration and tissue destruction are hallmarks of Epstein-Barr virus infection in periodontitis

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Expression profiling by microarray was performed to delineate the EBV effect on the transcriptome of gingival tissues from periodontitis patients and healthy volunteers. The transcriptome analysis revealed numerous genes that were differentially expressed in periodontitis only when EBV was present. The most upregulated genes were related to inflammatory/immune response, B and plasma cell markers. Conversely, major downregulation was reported for genes related to epithelial tissue organization and structural support. The results provide new significant insights regarding EBV physiopathology in the gum, assigning a direct etiopathogenetic contribution to EBV in periodontitis.

overall_design: A total of 16 participants were selected for transcriptomic analyses corresponding to 4 healthy EBV-negative (H_NEG), 4 healthy EBV-positive (H_EBV), 4 periodontitis EBV-negative (P_NEG) and 4 periodontitis EBV-positive (P_EBV) tissues.

first: L

last: Tonoyan

first: C

last: Mounier

first: J

last: Fassy

first: B

last: Mari

first: A

last: Doglio

first: K

first: P

last: Barbry


title: YTHDF2 promotes ATP synthesis and immune evasion in B cell malignancies

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: RNA epigenetics plays crucial roles in physiological and pathological processes. As the most abundant methylation of mRNA, 0.2-0.7% of the total adenosine, m6A is dynamically deposited co-transcriptionally by the methyltransferase complex, reversely removed by demethylases recognized and directly regulated by “reader” proteins. As the first identified m6A ‘reader’ protein, YTHDF2 recognizes and destabilizes m6A modified mRNAs by inducing mRNA decay or degradation in P-body and plays indispensable oncogenic or tumor suppressive roles in multiple malignant contexts by mediating distinct m6A modified mRNAs. Here, we report that YTHDF2 promotes the development of B cell malignancies by facilitating energy supplements and immune evasion. RNA-sequencing (RNA-seq) data reveal that a set of ATP production- and immune response-related genes are consistently and significantly dysregulated upon YTHDF2 knockdown (KD) in both B cell acute lymphoblastic leukemia (B-ALL) patient-derived xenotransplant (PDX) cells (IAH8R) and diffuse large B cell lymphoma (DLBCL) cells (SU-DHL-4). RNA immunoprecipitation sequencing (RIP-seq) of either wildtype or mutant YTHDF2 proteins identify target genes directly bind to YTHDF2 dependent on the RNA binding pockets. Methylation RIP-seq (MeRIP-seq) assays identify either m6A-moidfied genes or m5C-modified mRNAs, which is further confirmed by bisulfite-converted mRNA sequencing (BS-RNA-seq) in malignant B cells. Mechanically, we find that YTHDF2 enhances ATP synthesis by sustaining mRNA stabilities of target genes as an m5C reader protein by interacting with PABPC1, a well-know m5C-modified mRNA stabilizer. Further RNA-seq upon PABPC1 KD and RIP-seq assays for PABPC1 reveal the overlapped genes which are also regulated and bound with YTHDF2 via m5C modification. Strikingly, RNA-seq and m6A-MeRIP-seq data show that YTHDF2 promotes immune evasion by destabilizing CD19 and MHC-II molecules (e.g., HLA-DMA and HLA-DMB) in an m6A-dependent manner. Single cell RNA-seq (scRNA-seq) data further reveal the immune microenvironment and cell proportions in bone marrow of Ythdf2 conditional KO mouse models (Ythdf2fl/fl). Our proof-of-concept study discovers that a YTHDF2 selective inhibitor (e.g. CCI-38) significantly inhibits cell metabolism and immune evasion in malignant B cells (KOPN-8) by RNA-seq. Collectively, our data show that YTHDF2 promotes ATP synthesis and immune evasion and serves as a promising therapeutic target in B cell malignancies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
[Dataset 1] 22 samples. Duplicates for RNA-seq samples in B-ALL PDX cells (IAH8R) and DLBCL cells (SU-DHL-4) upon YTHDF2 KD or PABPC1 KD by two different shRNAs compared to controls (shNS) respectively. Duplicates for RNA-seq samples when treated with CCI-38 or DMSO in malignant B cells (KOPN-8).
[Dataset 2] 10 samples. Duplicates for BS-seq or MeRIP-seq against m6A or m5C.
[Dataset 3] 13 samples. Duplicates for RIP-seq samples in malignant B cells carrying CRISPR-Cas9 and sgRNA target endogenous YTHDF2, which were further overexpressed with flag tagged wildtype or mutant YTHDF2 proteins (synonymous substitution for sgRNA sequence). 2-3 replicates for RIP-seq samples in IAH8R cells with forced expression of flag tagged PABPC1.
[Dataset 4] 1 single cell RNA-seq sample. We employ a conditional Ythdf2 knockout mouse (Ythdf2fl/fl) carrying Mx1-Cre or not, and intravenously treat the mice with poly I:C each other day for a total of 5 times. Freshly collected bone marrow cells are stained with a specific Total seq type C harshtag for each mouse (2 wildtype bone marrow, 2 Ythdf2 knockout bone marrow). After staining with featured barcodes, equal numbers of cells are mixed together and proceed to 10X Genomics single cell platform and collect 10000 cells for the next library preparation and sequencing.

first: Zhenhua

first: Lu

last: Yang

first: Xiaolan

last: Deng


title: Trps1 regulates mouse zygotic genome activation and preimplantation embryo development via the PDE4D/AKT/CREB signaling pathway

status: Public on Dec 15 2024

city: Fuzhou

first: sun

middle: jian

last: dong

address: 1 North Road, Xuefu

institute: Fujian medical university

summary: Despite zygotic genome activation (ZGA) is crucial for early embryonic development, its regulatory mechanism is still unclear in mammals. In the present study, we demonstrate that TRPS1, a maternal factor, plays an essential role in mouse early embryogenesis by regulating the transition from 2-cell to 4-cell embryos during preimplantation development. The absence of Trps1 could leads to impaired ZGA through AKT/CREB signaling pathway. Furthermore, our findings suggest that TRPS1 may modulate the transcription of Pde4d to influence AKT and CREB phosphorylation. Interestingly, compared to Trps1 knockdown alone, co-injection of Trps1 siRNA and Pde4d mRNA significantly enhances the development rate of 4-cell embryos. Collectively, these results indicate a negative involvement of Trps1 in mouse preimplantation embryo development by targeting the PDE4D/AKT/CREB pathway to regulate ZGA.

overall_design: Cleavage Under Targets and Tagmentation sequencing (CUT&Tag-seq) for TRPS1 in mouse 2-cell embryo

first: Jiangxia

last: Jiang

first: Weiwei

last: Xu

first: Jiandong

last: Sun

first: Yue

last: Liu

first: Shie

last: Wang


title: Cooperation between the Hippo and MAPK pathway activation drives acquired resistance to TEAD inhibition [multiome-seq]

city: San Fransisco

first: Xiaosai

last: Yao

institute: Roche/Genentech

summary: TEAD transcription factors (TEAD1-4) serve as the primary effectors of the Hippo signaling pathway in various cancers. There has been significant progress in the development of therapeutic strategies aimed at disrupting the interaction of TEAD with its coactivators YAP/TAZ. However, targeted therapy leads to the emergence of resistance which poses a barrier to achieving complete cures. Currently, the underlying mechanism of resistance to TEAD inhibition in cancers remains unexplored. We uncover that upregulation of the AP-1 transcription factors, along with restored YAP/TEAD activity, drives resistance to GNE-7883, a pan-TEAD and allosteric TEAD inhibitor. Acute GNE-7883 treatment abrogates YAP binding and attenuates FOSL1 activity but compensation by increased MAPK pathway activity remains insufficient for cell survival. In contrast, TEAD inhibitor resistant cells are able to restore YAP and TEAD occupancy and acquire additional FOSL1 binding sites, leading to increased chromatin accessibility at AP-1 motifs. Resistant cells undergo transcriptional reprogramming to acquire a mesenchymal-like cell state and sustained MAPK activity. We uncover a dependence on the MAPK pathway in the TEAD inhibitor resistant cells, further highlighting the key role of MAPK pathway inhibitors, such as Cobimetinib and Belvarafenib to mitigate resistance mechanisms to TEAD inhibition in Hippo pathway dependent cancers. This study describes a clinically relevant interplay between the Hippo and MAPK pathway in cancers and offers a promising avenue to address TEAD inhibitor resistance in the clinic.

overall_design: To investigate the mechanism involved in TEAD acquired resistance, we developed TEADi resistant cell lines. We then performed single-cell multiome sequencing (ATACseq + scRNAseq)  of the parental (sensitive) cell line and the GNE7883-resistant clone (CL3) challenged with GNE7883 or DMSO.

first: Thijs

last: Hagenbeek

first: Sayantannee

last: Paul

first: Anwesha

last: Dey

first: Julien

last: Tremblay


title: Insulin-like Growth Factor Binding Protein 7 identified in aged dental pulp by single-cell RNA sequencing

city: Guangzhou

first: Zhongchun

last: Tong

address: Lingyuan West Road 56#

department: Hosiptal of Stomatology

institute: Sun Yat- Sen University

summary: Dental pulp plays a crucial role for dental health, and dental pulp aging influences their regenerative and reparative function. However, the underlying molecular mechanisms of dental pulp aging are not exhaustively understood, and thereby an in-depth and complete understanding of the aged dental pulp is of foremost importance. This study aimed to explore the heterogeneity of young and aged dental pulp tissue using single-cell RNA sequencing (scRNA-seq).

overall_design: A total of 24,158 cells  were sequenced from dental pulp samples of 8 patients, and categorized into 8 main clusters, including fibroblast, endodothelial cell, monocyte, T cell, B cell, mesenchymal stem cells, Schwann cell, and non myelinating ScC. We investigated the communication between all cell types of in young and aged dental pulps by CellChat software. We established H2O2-induced DPF senescence model, and IGFBP7 was further validated the H2O2-induced DPF senescence model.

first: Jie

last: Wu

first: Qimei

last: Gong

first: Yifang

last: Yuan

first: Shengchao

first: Wenkai


title: Identification of the thyroid genes whose expressions are altered by neonatal irradiation in rats

city: Hiroshima

first: Nariaki

last: FUJIMOTO

state: Hiroshima

address: 1-2-3 Kasumi

department: RIRBM

institute: Hiroshima University

summary: Childhood radiation is a risk factor for thyroid cancer, which became well-known after the Chornobyl nuclear plant accident, where childhood thyroid cancer cases significantly increased afterward. The mechanisms of thyroid cancer susceptibility to radiation exposure at young ages, however, have not yet been understood. Our previous investigations demonstrated that neonatal exposure to X-rays induced long-term mRNA expression changes in the thyroid cancer-related marker genes in rats. Then, we searched for the genes whose expressions were altered by neonatal radiation exposure in male Wistar rats exposed to X-rays.

overall_design: Male Wistar rats at 1 week and 4 months old were subjected to cervical X-irradiation at 4 Gy. After 8 weeks, total RNAs were extracted from the thyroid and applied to RNA-seq analysis to identify the genes that only neonatal irradiation alters the mRNA expressions.

last: Fujimoto


title: Single-cell RNA-seq analysis of additional mouse  prostates

city: New York

first: Michael

middle: M

last: Shen

address: 1130 St. Nicholas Avenue

institute: Columbia University Irving Medical Center

summary: Single-cell RNA-seq analysis of wild-type mouse prostates

first: Luis

last: Aparicio

first: Laura

last: Crowley

first: John

middle: R

last: Christin

first: Caroline

last: Laplaca

first: Hanina

last: Hibshoosh

first: Raul

last: Rabadan


title: Stimulating the regenerative capacity of the human retina with proneural transcription factors in 3D cultures

status: Public on Dec 13 2024

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

summary: Retinal diseases often lead to degeneration of specific retinal cell types with currently limited therapeutic options to replace the lost neurons. Previous studies have reported that overexpression of ASCL1 or combinations of proneural factors in Müller glia (MG) induces regeneration of functional neurons in the adult mouse retina. Recently, we applied the same strategy in dissociated cultures of fetal human MG and although we stimulated neurogenesis from MG, our effect in 2D cultures was modest and our analysis of newborn neurons was limited. In this study, we aimed to improve our MG reprogramming strategy in a more intact retinal environment. For this purpose, we used an in vitro culture system of human fetal retinal tissue and adult human postmortem retina. To stimulate reprogramming, we used lentiviral vectors to deliver constructs with a glial-specific promoter (HES1) driving ASCL1 alone or in combination with additional developmental transcription factors such as ATOH1 and NEUROD1. Combining IHC, scRNA-seq and electrophysiology, we show for the first time that human MG can generate new neurons even in adults. This work constitutes a key step towards a future clinical application of this regenerative medicine approach for retinal degenerative disorders.

overall_design: Human fetal retinospheres were infected with three different lentiviral constructs containing a glial specific promoter (HES1) driving the expression of transcription factors (ASCL1 alone) or (NEUROD1-ASCL1) and a fluorescent protein (GFP). The control vector contains the HES1 promoter driving the expression of the fluorescent protein. Infected cells were then FACS-sorted prior to single cell RNA sequencing.

first: Juliette

last: Wohlschlegel

first: Faith

last: Kierney

first: Kayla

middle: L

last: Arakelian

first: Guillaume

last: Luxardi

first: Naran

last: Suvarnpradip

first: Dawn

last: Hoffer

first: Fred

last: Rieke

first: Ala

last: Moshiri

first: Thomas

last: Reh


title: Thymic mimetic cells in humans [scRNA-seq]

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We profiled a subset of medullary thymic epithelial cells in humans by scRNA-seq to investigate mechanisms of T cell tolerance.

overall_design: scRNA-seq of human thymic mimetic cells

first: Brooke

last: Huisman

first: Daniel

last: Michelson

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Cooperation between the Hippo and MAPK pathway activation drives acquired resistance to TEAD inhibition

first: Xiaosai

last: Yao

address: 1 DNA Way

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

overall_design: Refer to individual Series


title: ID3 defines T cells with stem-like potential and sustains their response to chronic infection

status: Public on Dec 14 2024

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: Memory CD8+ T cells and precursors of exhausted T (Tpex) cells are important therapeutic targets due to their stem-like potential that allows them to self-renew while also giving rise to large numbers of effector T cells that can provide protection from infection or uncontrolled tumor growth. Identifying T cells with stem-like potential and understanding their molecular regulation is therefore critical to improve a wide range of T cell-focused therapies ranging from vaccination to checkpoint inhibitor and chimeric antigen receptor T cell therapies. Here, we identify memory T cells based on expression of the transcriptional regulator ID3 while lacking expression of the chemokine receptor CXCR6 with superior stem-like potential to sustain T cell responses during chronic infection. Mechanistically, ID3 regulated a transcriptional network including Myb, Sell and cKit that promoted T cell stemness that was specifically required during ongoing T cell receptor stimulation. T cells lacking ID3 were unable to sustain a long-term response to chronic infection but capable of efficiently responding to acute infection. Overall, we identify a critical role for ID3 in promoting functional and long-lasting T cell responses specifically to chronic infections and highlight ID3-expressing stem-like memory T cells as a promising immunotherapeutic target to improve immune responses in chronic infections or tumors.

overall_design: RNA sequencing of ID3GFP+ (Tpex) or ID3GFP- (Tex) from control or ID3KO P14 T cells obtained from day 5 LCMV Docile infected mice.

first: Amania

last: Sheikh

first: Sarah

middle: S

last: Gabriel

first: David

last: Chisanga

first: Justine

last: Seow

first: Lifen

last: Wen

first: Minh-Hanh

middle: T

last: Nguyen

first: Chun-Hsi

last: Su

first: Carlson

last: Tsui

last: Burn

first: Laura

middle: K

last: Mackay

first: Jan

last: Schroeder

first: Axel

last: Kallies

last: Utzschneider


title: Progressively Differentiated Tfh13 Cells are Stabilized by JunB to Mediate Allergen Germinal Center Responses

first: Cody

last: Nelson

address: 221 Longwood Ave

institute: Brigham and Women's Hospital

summary: Allergic diseases are common and affect a large proportion of the population.  IL-13-expressing follicular T (Tfh13) cells are a newly identified population of Tfh cells that have been associated with high affinity IgE responses.  However, the origins, developmental signals, transcriptional programming and precise functions of Tfh13 cells are unknown.  Here, we examined the developmental signals for Tfh13 cells and found a direct and progressive differentiation pathway marked by the production of IL-21.  These two pathways differed in kinetics and extrinsic requirements. However, both pathways converged, forming transcriptionally similar Tfh13 cells that express the transcription factor JunB as a critical stabilizing factor.  Using an intersectional genetics-based Tfh13-DTR model to perturb these cells, we found that Tfh13 cells were essential to drive broad germinal center responses and allergen-specific IgG and IgE.  Moreover, we found that IL-21 is a broad positive regulator of allergen germinal center B cells and synergizes with IL-13 produced by Tfh13 cells to amplify allergic responses.  Thus, Tfh13 cells orchestrate multiple features of allergic inflammation.

overall_design: Various subsets of lymph node T follicular helper cells in duplicate

first: Peter

last: Sage

first: Pragya

last: Chandrakar

last: S Nelson

first: Manuel

last: Podesta


title: Thymic mimetic cells in humans [bulk RNA-Seq]

first: CBDM

last: Lab

summary: We profiled thymic epithelial cell subsets in humans by bulk RNA-seq to investigate mechanisms of T cell tolerance.

overall_design: Bulk RNA-seq of human mTEC subsets

first: Daniel

last: Michelson

first: Brooke

last: Huisman

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Hydroxychloroquine prevents resistance and potentiates antitumor effect of SHP2 inhibition in NF1-associated Malignant Peripheral Nerve Sheath Tumors

status: Public on Dec 12 2024

city: Portland

first: Pengtao

last: Dang

address: 2720 S Moody Ave

institute: Oregon Health & Science University

summary: Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas and the primary cause of mortality in patients with neurofibromatosis type 1 (NF1). These malignancies develop within pre-existing benign lesions called plexiform neurofibromas (PNs). PNs are solely driven by biallelic NF1 loss eliciting RAS pathway activation and respond favorably to MEK inhibitor therapy. MPNSTs harbor additional mutations and respond poorly to MEK inhibition. Our analysis of genetically engineered and orthotopic patient-derived xenograft MPNST tumor models indicates that MEK inhibition has poor anti-tumor efficacy. By contrast, upstream inhibition of RAS through the protein-tyrosine phosphatase SHP2 reduced downstream signaling and suppressed NF1 MPNST growth, although resistance eventually emerged. To investigate possible mechanisms of acquired resistance, kinomic analyses of resistant tumors was performed, and data analysis identified enrichment of activated autophagy pathway protein kinases. Combining SHP2 inhibition with hydroxychloroquine resulted in durable responses in NF1 MPNSTs in both genetic and orthotopic xenograft mouse models. Our studies could be rapidly translated into a clinical trial to evaluate SHP2 inhibition in conjunction with hydroxychloroquine as a novel treatment approach for NF1 MPNSTs.

overall_design: Shp099 treated (21 day, 5 day) vs Vehicle Controls

first: Sameer

last: Farouk Sait

first: Chi

last: Zhang


title: Single-cell transcriptome and TCR sequencing reveals immune cell heterogeneity in the submandibular gland of SS mice

first: Jin-Fen

last: Ma

address: 382 East Central Road, University Town

institute: South China University of Technology

summary: In this study, we analyzed the submandibular gland and submandibular gland-draining lymph nodes of P40-/-CD25-/- (SS mice) and P40-/-CD25+/- (control mice) using single-cell transcriptome and TCR sequencing of leukocytes. A total of 24,115 cells were obtained for analysis, of which 9,897 cells were from the submandibular gland and 14,218 cells were from the draining lymph nodes. We found that tissue-resident CD8+T cells (CD8+Trm) in the submandibular gland of SS mice expanded massively and highly expressed PD-1. These CD8+Trm cells, which highly express PD-1, exhibit clonal expansion and cytotoxicity. In addition, shared TCR analysis found that potential CD8+Trm precursor cells in the draining lymph nodes exhibited a Gzmk+Pdcd1+ phenotype. In summary, we found that PD-1+CD8+Trm cells in the submandibular gland of SS mice are potentially pathogenic and their precursors also express PD-1.

overall_design: The submandibular glands and their draining lymph nodes were taken from 4 SS mice and 4 control mice around 12 weeks old. After cell isolation, CD45+ leukocytes were labeled and sorted by flow cytometry. 10X single-cell transcriptome sequencing and TCR sequencing were performed, respectively.

first: Jinfen

first: Caiyue

last: Gao

first: Zhexiong

last: Lian


title: Duodenal-derived organoids from MASH patients exhibit altered digestive homeostasis.

city: Brussels

first: Alia

last: Hadefi

address: 808 route de lennik

department: Gastroenterology

country: Belgium

institute: CUB Hopital Erasme

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive disease linked to conditions like fibrosis, cirrhosis, and liver cancer, often resulting in higher mortality rates, primarily due to cardiovascular events. While MASH is closely tied to metabolic syndrome, recent research underscores the importance of the gut-liver axis in its pathogenesis, an aspect less explored in human studies. To address this gap, duodenal epithelial organoids were generated from both MASH and healthy (controls) subjects. Organoid formation efficiency was similar between controls derived epithelial organoids (CDEOs) and MASH derived epithelial organoids (MDEOs) groups. Variability in growth patterns was observed, with MDEOs frequently exhibiting cystic spheroid morphology. MASH-derived organoids displayed altered homeostasis and digestive potential in the duodenal epithelium. Despite potential lineage bias, MDEOs retained their lipid metabolic capacity, possibly mediated by lipid oxidation in stem/progenitor cells. Notably, cell adhesion components were misexpressed in MASH-derived organoids, indicating significant intrinsic alterations in cell-cell adhesion potential compared to controls. However, MDEOs maintained transepithelial electric resistance and leak pathway integrity, indicating that the intestinal epithelial barrier remained functionally intact in MDEOs under tested conditions. This study sheds light on the intricate dynamics of duodenal epithelial alterations in MASH, highlighting potential therapeutic avenues for restoring intestinal homeostasis.

overall_design: mRNA profiles of duodenum derived organoids from healthy human (controls) and metabolic dysfnction-associated steatohepatitis (MASH) patients

first: Morgane

last: Leprovots

first: Gilles

last: Dinsart

first: Maryam

last: Marefati

first: Marjorie

last: Vermeersch

last: Monteyne

first: David

last: Pérez-Morga

first: Anne

last: Lefort

first: Frédérick

last: Libert

first: Laurine

last: Verset

first: Claire

last: Liefferinckx

last: Moreno

first: Jacques

last: Devière

first: Eric

last: Trépo

first: Marie-Isabelle

last: Garcia


title: Deciphering the role of PGRMC2 in the human endometrium during the menstrual cycle and in vitro decidualization using an in vitro approach

city: Valencia

first: Francisco

last: Domínguez

state: SPAIN

address: Avenida Fernando Abril Martorell, 106

country: Spain

institute: IVI Foundation

summary: The endometrial response to progesterone is mediated by the classical and non-classical progesterone receptors. We previously demonstrated that PGRMC1 is critical for endometrial function, embryo implantation, and future placentation, however, the role(s) of PGRMC2, which is structurally similar to PGRMC1, have not been studied in the human endometrium.

overall_design:
To reveal PGRMC2 function during the decidualization process, we specifically knocked down PGRMC2 with siRNAs in four hEnSC before in vitro decidualization.
In vitro decidualization of hEnSCs was induced using co-treatment of cAMP and medroxyprogesterone 17-acetate progestin for four days, and evaluated by measuring prolactin by ELISA and F-actin immunostaining.
After decidualization, we performed a RNA-seq of four PGRMC2 silencing d-hEnSC and four scramble d-hEnSC. The common differentially expressed genes (DEGs) and proteins (DEPs) were considered for downstream functional enrichment analysis.

first: Yassmin

last: Medina-Laver

first: Roberto

last: Gonzalez-Martin

last: Dominguez


title: Thymic mimetic cells in humans

first: CBDM

last: Lab


title: Stem-like potential of T cells in infection and cancer is regulated by ID3

city: Parkville

first: Jan

last: Schroeder

address: Peter Doherty Institute Melbourne

department: DMI

institute: University of Melbourne

overall_design: RNA sequencing of CD62L+cKIT- or CD62L-cKIT- from control or ID3KO P14 T cells obtained from day 12 LCMV Docile infected mice.

first: Catarina

last: Gago da Graça

first: Amania

last: Sheikh

first: Dane

last: Newma

first: Lifen

last: Wen

first: Sining

last: Li

first: Jian

last: Shen

first: Yuqi

last: Zhang

first: Sarah

last: Gabriel

last: Chisanga

first: Justine

last: Seow

first: Annika

last: Poch

first: Lisa

last: Rausch

first: Minh-Hanh

last: Nguyen

first: Jayendra

last: Singh

first: Chun-His

last: Su

first: Leonie

last: Cluse

first: Carlson

last: Tsui

first: Thomas

last: Burn

first: Laura

last: Mackay

first: Ajithkumar

last: Vasanthakumar

last: Bending

first: Wei

last: Shi

first: Weiguo

last: Cui

last: Schröder

first: Ricky

middle: W

last: Johnstone

first: Axel

last: Kallies

first: Daniel

last: Utzschneider


title: Identification and characterization of a human MORC2 DNA binding region that is required for gene silencing

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

institute: Whitehead Institute

summary: The eukaryotic microrchidia (MORC) protein family are DNA gyrase, Hsp90, histidine kinase, MutL (GHKL)-type ATPases involved in gene expression regulation and chromatin compaction. The molecular mechanisms underlying these activities are incompletely understood. Here, we studied the full-length human MORC2 protein biochemically. We identified a DNA binding site in the C-terminus of the protein, and we observe that this region can be phosphorylated in cells. DNA binding by MORC2 reduces its ATPase activity and MORC2 can entrap multiple DNA substrates between its N-terminal GHKL and C-terminal coiled coil 3 dimerization domains. Finally, we observe that the MORC2 C-terminal DNA binding region is required for gene silencing in cells. Together, our data provide a model to understand how MORC2 engages with DNA substrates to mediate gene silencing.

overall_design:
The eukaryotic microrchidia (MORC) protein family are DNA gyrase, Hsp90, histidine kinase, MutL (GHKL)-type ATPases involved in gene expression regulation and chromatin compaction. We identified a DNA binding site in the C-terminus of the protein. Here we generated dox-inducible GFP, GFP-MORC2, and GFP-MORC2 DNA-binding mutants and performed RNA-sequencing. We show that the MORC2 C-terminal DNA binding region is required for gene silencing in cells. Our data provide a model to understand how MORC2 engages with DNA substrates to mediate gene silencing.
Here we generated dox-inducible GFP, GFP-MORC2, and GFP-MORC2 DNA-binding mutants and performed RNA-sequencing. Biological replicates were defined as replicate doxycycline inductions of GFP transgenes. N=3 biological replicates were performed for each overexpression

first: Nikole

last: Fendler

first: Seychelle

last: Vos


title: ID3 and c-Kit define the stem-like potential of T cells and their response to chronic infection and cancer

first: Jan

last: Schroeder

overall_design: Single cell RNA sequencing of P14 T cells obtained from day 21 LCMV Armstrong or clone13 infected mice; RNA sequencing of CD62L+, CD62L-Kit-, Kit+ ID3GFP+P14 T cells obtained from day 5 LCMV Docile infected mice.

first: Amania

last: Sheikh

first: Sarah

last: Gabriel

first: David

last: Chisanga

first: Justine

last: Seow

first: Lifen

last: Wen

last: Nguyen

first: Chun-Hsi


title: HSPA8 dampens SCAP/INSIG split and SREBP activation by reducing PKR-mediated INSIG phosphorylation

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

summary: Lipid accumulation in the renal tubules is a major determinant of diabetic kidney disease (DKD), and activation of SREBPs plays a central role in this process.  Our study aimed to explore whether HSPA8, a molecular chaperone, is the master regulator of INSIG/SREBPs function in DKD. Here, we showed that tubular epithelial cell (TEC)-specific knockout of HSPA8 upregulated the phosphorylation of INSIG1 and INSIG2, which disrupted the interaction between INSIG proteins and SCAP, leading to the translocation of the SCAP-SREBP complex to the Golgi apparatus, and the activation of SREBPs. TEC-specific overexpression of HSPA8 restrained these changes. INSIG1 and INSIG2 can be phosphorylated by protein kinase R (PKR), while HSPA8 can recognize PKR and recruit the E3 ubiquitin ligase (CHIP) to promote PKR ubiquitination and degradation. SREBP1 transcriptionally activated HSPA8 expression under temporary hyperglycemic stimulation. However, persistent hyperglycemia reduced HSPA8 levels by promoting nuclear factor (NF)-κB-mediated transcriptional inhibition and reducing USP43-mediated deubiquitination of HSPA8. Collectively, these findings indicate that the molecular chaperone HSPA8 serves as a negative feedback regulator of SREBPs, lipogenesis, and DKD development.

overall_design: 1. First, establish diabetic kidney disease (DKD) models in rodents and cell lines. For in vivo, use streptozotocin (STZ) injection. For in vitro, expose tubular epithelial cells (TECs) to high glucose. 2. Then, in TECs, knockdown HSPA8 using siRNA and overexpress it using plasmids. 3. Measure the phosphorylation levels of INSIG1 and INSIG2, the interaction between INSIG and SCAP, and the activation of SREBPs. 4. Examine the ubiquitination of PKR and HSPA8. 5. Analyze the transcriptional regulation of HSPA8 by SREBP1 and the effect of NF - κB and USP43 on HSPA8 levels. 6. Finally, assess lipid accumulation in TECs. Through these steps, we can clarify the role of HSPA8 as a negative feedback regulator in DKD.

first: Guangyan

first: Chuanrui

last: Ma

first: Yuanli

last: Chen

first: Jiaqing

last: Xiang

first: Lixing

last: Li

first: Yanchun

first: Lin

last: Kang

first: Zhen

last: Liang


title: RNA-Seq reveals heterogeneity in the submandibular glands and  submandibular gland draining lymph nodes of SS mice

first: Jin-Fen

summary: In this study, we analyzed the submandibular glands of  P40-/-CD25+/- (control mice) and P40-/-CD25-/- (SS mice) after PD-1-targeted CAR-T cells or control T cells treatment using RNA-Seq. We found that the transcription of inflammatory genes was down-regulated and the transcription of tissue repair genes was up-regulated in the submandibular glands of SS mice after PD-1-targeted CAR-T cells treatment.  In addition, PD-1+Tigit+CD8+ T cells in the submandibular gland draining lymph nodes of SS mice showed transcription characteristics of tissue resident memory precursors.

overall_design: The SS mice were treated with PD-1-targeted CAR-T cells or control T cells by tail vein injection. Treatment was started in mice around 8 weeks of age, injections were given on days 1 and 14, and mice were sacrificed 14 days after the last injection. Submandibular gland draining lymph nodes were harvested from SS mice at about 12 weeks.

first: Jinfen

first: Caiyue

last: Gao

first: Zhexiong

last: Lian


title: The essential clathrin adaptor protein complex-2 is tumor suppressive specifically in vivo

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

summary: The microenvironment is a rich source of new cancer targets.  While whole-genome CRISPR/Cas9 screens have identified vulnerabilities in cultured cells, it is a challenge to use this approach in tumors to interrogate the microenvironment.  To this end, we screened a panel of pancreatic cancer lines grown in culture versus as tumors with a phosphatidylinositol metabolism CRISPR/Cas9 library.  This revealed the Adaptor Protein complex-2 (AP2) of clathrin-mediated endocytosis behaves as common essential in culture but tumor suppressive in vivo.  These polar-opposite phenotypes were attributed to different microenvironments.  In culture, AP2 loss reduces endocytosis of transferrin and iron import.  In tumors, alternative iron transport pathways allow pro-tumor signaling to manifest.  In the most sensitive case, AP2 loss reprograms the plasma membrane proteome, retaining integrins on the surface leading to downregulation of the tumor-suppressor PTEN.  Analysis of human tumors suggests a similar tumor suppressive activity.  AP2 may foreshadow other proteins unique to the tumor-microenvironment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BXPC-3, PANC-1, CFPAC-1 cells and AP2S1 KO derivatives in cell culture and xenograft models.

middle: P

first: Christopher

last: Counter


title: Targeting the mevalonate pathway potentiates NUAK1 inhibition-induced immunogenic cell death and antitumor immunity

status: Public on Dec 11 2024

city: shanghai

first: Chen

last: kaiwen

state: Shanghai

address: shanghai jiaotong university

institute: shanghai jiaotong university

summary: The induction of immunogenic cell death (ICD) impedes tumor progression via both tumor cell-intrinsic and -extrinsic mechanisms, representing a robust therapeutic strategy. However, ICD-targeted therapy remains to be explored and optimized. Through kinome-wide CRISPR-Cas9 screen, NUAK1 is identified as a potential target. The ICD-provoking effect of NUAK1 inhibition depends on the production of reactive oxygen species (ROS), consequent to the downregulation of NRF2-mediated antioxidant gene expression. Moreover, the mevalonate pathway/cholesterol biosynthesis, activated by XBP1s downstream of ICD-induced endoplasmic reticulum stress, functions as a negative feedback mechanism. Targeting the mevalonate pathway with CRISPR knockout or HMGCR inhibitor simvastatin amplifies NUAK1 inhibition-mediated ICD and antitumor activity, while cholesterol dampers ROS, ICD and therefore tumor suppression. The combination of NUAK1 inhibitor and statin enhances the efficacy of anti-PD-1 therapy. Collectively, our study unveils the promise of blocking the mevalonate-cholesterol pathway in conjunction with ICD-targeted immunotherapy.

overall_design: Mouse tumors (each set containing three independent samples) were washed with ice-cold PBS and cut into small pieces, which were then subjected to enzymatic digestion with collagenase D and DNase I (Roche) using a gentleMACS Tissue Dissociator (Miltenyi Biotec). Cells were filtered through a 70-μm filter and washed with PBS. To extract immune cells, cells were stained with biotin anti-mouse CD45 antibody (Biolegend) and separated by anti-biotin MicroBeads (Miltenyi Biotec) according to the manufacturer’s protocol. Sorted immune cells with a purity greater than 95% and viability higher than 85% were subjected to 10x Genomics scRNA-seq. To control the final number of cells captured, approximately 30,000 cells per sample were loaded onto 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol. Finally, the library pool was prepared, and sequencing was performed on an Illumina NovaSeq 6000 platform.

first: Liming

last: Gui

first: Kaiwen

first: Jingjing

last: Yan

first: Pin

last: Cheng


title: Transcriptomic analysis of DEP (diesel exhaust particle) treated ACP-5 knock-out BEAS2B cells

city: Seoul

first: Aaron

last: Yu

address: Gwanak-ro 1

country: South Korea

institute: Seoul national university

summary: We have developed a ACP5 knock-out BEAS2B cell line. To understand the impact of DEP to ACP5 KO BEAS2B cell line, we treated DEP to ACP5 KO BEAS2B cell line and analyzed changes in transcriptome.

overall_design: To investigate the effect of ACP5 gene in the presence of DEP, we developed ACP5 KO BEAS2B cells which does not express ACP5, and treated DEP to ACP5 KO BEAS2B cells


title: Herpesviruses mimic zygotic genome activation to promote viral replication

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

institute: institute of Virology, University Medical Center Freiburg

summary: DUX4 is a germline transcription factor and a master regulator of zygotic genome activation. During early embryogenesis, DUX4 is crucial for maternal to zygotic transition at the 8-cell stage in order to overcome silencing of genes and enable transcription from the zygotic genome. In adult somatic cells, DUX4 expression is silenced and its activation in adult muscle cells causes the genetic disorder Facioscapulohumeral Muscular Dystrophy (FSHD). Here we show that herpesviruses actively induce DUX4 expression to promote viral transcription and replication. We demonstrate that HSV-1 immediate early proteins directly induce expression of DUX4 and its target genes including endogenous retroelements, which mimics zygotic genome activation. DUX4 directly binds to the viral genome, promotes viral transcription and genetic depletion of DUX4 by CRISPR/Cas9 abrogates viral replication. Our results show that viruses from alpha-, beta- and gamma-herpesvirus subfamilies induce DUX4 expression and downstream germline-specific genes and retroelements. Herpesviruses activate DUX4 expression in order to induce an early embryonic-like transcriptional program that prevents epigenetic silencing of the viral genome and facilitates herpesviral gene expression.

overall_design: CUT&RUN data of HSV1 infected HFF1 cells

first: Walter

last: Stephanie

first: Neugebauer

last: Eva

first: Tan

last: Jiang

first: Drayman

last: Nir

first: Franke

last: Vedran

first: Tay

last: Savas

first: Landthaler

last: Markus

first: Akalin

last: Altuna

first: Ensser

last: Armin

first: Wyler

last: Emanuel

first: Full

last: Florian


title: Canagliflozin treatment prevents follicular exhaustion and attenuates hallmarks of ovarian aging in genetically heterogenous mice

city: Oklahoma City

first: Michael

last: Stout

state: Oklahoma

address: 825 NE 13th St.

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Ovarian aging is characterized by declines in follicular reserve and the emergence of mitochondrial dysfunction, reactive oxygen species production, inflammation, and fibrosis, which eventually results in menopause. Menopause is associated with increased systemic aging and the development of numerous comorbidities; therefore, the attenuation of ovarian aging could also delay systemic aging processes in women. Recent work has established that the anti-diabetic drug Canagliflozin (Cana), a sodium-glucose transporter 2 inhibitor, elicits benefits on aging-related outcomes, likely through the modulation of nutrient-sensing pathways and metabolic homeostasis. Given that nutrient-sensing pathways play a critical role in controlling primordial follicle activation, we sought to determine if chronic Cana administration would delay ovarian aging and curtail the emergence of pathological hallmarks associated with reproductive senescence. We found that mice receiving Cana maintained their ovarian reserve through 12 months of age, which was associated with declines in primordial follicles FoxO3a phosphorylation, a marker of activation, when compared to the age-matched controls. Furthermore, Cana treatment led to decreased collagen, lipofuscin, and T cell accumulation at 12 months of age. Whole ovary transcriptomic and proteomic analyses revealed subtle improvements, predominantly in mitochondrial function and the regulation of cellular proliferation. Pathway analyses of the transcriptomic data revealed a downregulation in cell proliferation and mitochondrial dysfunction signatures, with an upregulation of oxidative phosphorylation. Pathway analyses of the proteomic data revealed declines in signatures associated with PI3K/AKT activity and lymphocyte accumulation. Collectively, we demonstrate that Cana treatment can delay ovarian aging in mice and could potentially have efficacy for delaying ovarian aging in women.

overall_design: RNAseq from ovaries of UM-HET3 12 months-old (mo) mice treated with Canagliflozin for 6 months, 6 mo control mice or 12 mo control mice.

first: José

middle: V

last: Vieira Isola

first: Subhasri

last: Biswas

first: Hashan

last: Jayarathne

first: Chase

last: Hubbart

first: Satoshi

last: Matsuzaki

last: Kinter

first: Kenneth

last: Humphries

first: Sarah

last: Ocañas

first: Marianna

last: Sadagurski


title: Gene expression profile of human bone marrow plasmacells

city: Erlangen

first: Ulrike

last: Steffen

address: Glueckstrasse 4a

department: Internal Medicine 3

institute: University Clinic Erlangen

summary: Immunoglobulin classes show differences in their glycosylation pattern. In this study, we aimed to find out if there are differences in the expression of glycosylation enzymes between IgA1 and IgA2 producing plasma cells.

overall_design: Human plasma cells were isolated from bone marrow via FACS and anaylzed via scRNAseq.

first: Maria

last: Sokolova

first: Arif

last: Ekici

first: Martin

last: Herrmann


title: Expression of foetal gene Pontin is essential in protecting heart against pathological remodelling and cardiomyopathy

city: Manchester

first: Delvac

last: Oceandy

address: Oxford Road

country: United Kingdom

institute: University of Manchester

summary: Cardiac remodelling is a key process in the development of heart failure. Reactivation of foetal cardiac genes is often associated with cardiac remodelling. Here we study the role of Pontin (Ruvbl1), which is highly expressed in embryonic hearts, in mediating adverse remodelling in adult mouse hearts. We observe that Pontin deficiency in cardiomyocytes leads to induced apoptosis, increased hypertrophy and fibrosis, whereas Pontin overexpression improves survival, increases proliferation and reduces the hypertrophic response. Moreover, RNAseq analysis show that genes involved in cell cycle regulation, cell proliferation and cell survival/apoptosis are differentially expressed in Pontin knockout and transgenic overexpression mice. Specifically, we detect changes in the expression of Hippo pathway components in the Pontin knockout and transgenic mice. Using a cellular model we show that Pontin induces YAP activity, YAP nuclear translocation, and transcriptional activity. Our findings identify Pontin as a modulator of adverse cardiac remodelling, possibly via regulation of the Hippo pathway. This study may lead to the development of a new approach to control cardiac remodelling by targeting Pontin.

overall_design: RNA-seq profiling of total RNA from the heart tissues of transgenic mice overexpressing Pontin specifically in cardiomyocytes (Pontin cTG) and wild type littermates after 2 weeks stimulation with angiotensin (1.5 mg/kg BW/day)

first: Ardiansah Bayu

last: Nugroho

first: Bayu

last: Lestari


title: Multi-tissue proteomics identifies a link between satellite DNA organization and heritable transposon repression in Drosophila

city: Zurich

first: Madhav

last: Jagannathan

address: Otto Stern-Weg 3

country: Switzerland

institute: ETH Zurich

type: Non-coding RNA profiling by high throughput sequencing

summary: Non-coding satellite DNA repeats are abundant at the pericentromeric heterochromatin of eukaryotic chromosomes. During interphase, sequence-specific DNA-binding proteins cluster these repeats from multiple chromosomes into nuclear foci known as chromocenters. Despite the pivotal role of chromocenters in cellular processes like genome encapsulation and gene repression, the associated proteins remain incompletely characterized. Here, we use two satellite DNA-binding proteins, D1 and Prod, as baits to characterize the chromocenter-associated proteome in Drosophila embryos, ovaries, and testes through quantitative mass spectrometry. We identify D1- and Prod-associated proteins, including known heterochromatin proteins as well as proteins previously unlinked to satellite DNA or chromocenters, thereby laying the foundation for a comprehensive understanding of cellular functions enabled by satellite DNA repeats and their associated proteins. Interestingly, we find that multiple components of the transposon-silencing piRNA pathway are associated with D1 and Prod in embryos. Using genetics, transcriptomics, and small RNA profiling, we show that flies lacking D1 during embryogenesis exhibit transposon expression and gonadal atrophy as adults. We further demonstrate that this gonadal atrophy can be rescued by mutating the checkpoint kinase, Chk2, which mediates germ cell arrest in response to transposon mobilization. Thus, we reveal that a satellite DNA-binding protein functions during embryogenesis to silence transposons, in a manner that is heritable across later stages of development.

overall_design: RNA-seq and small  RNA -seq profiling from D1 mutant (D1 Kyoto/ D1 Bsc666) and control (D1 Kyoto/TM6C) testes in a chk2 mutant background.

first: Ankita

last: Chavan

first: Lena

last: Skrutl

first: Federico

last: Uliana

first: Melanie

last: Pfister

first: Franziska

last: Brandle

first: Laszlo

last: Tirian

first: Delora

last: Baptista

first: Dominik

last: Handler

first: Anna

last: Sintsova

first: Pedro

last: Beltrao

first: Julius

last: Brennecke


title: Myeloid-biased HSC require Semaphorin 4A from the bone marrow niche for self-renewal under stress and life-long persistence

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: Tissue stem cells are hierarchically organized. Those that are most primitive serve as key drivers of regenerative response but the signals that selectively preserve their functional integrity are largely unknown. Here, we identify a secreted factor, Semaphorin 4A (Sema4A), as a specific regulator of myeloid-biased hematopoietic stem cells (myHSC), which are positioned at the top of the HSC hierarchy. Lack of Sema4A leads to exaggerated myHSC (but not downstream “balanced” HSC) proliferation after acute inflammatory stress, indicating that Sema4A enforces myHSC quiescence. Strikingly, aged Sema4A knock-out myHSC expand but almost completely lose reconstitution capacity. The effect of Sema4A is non cell-autonomous, since upon transplantation into Sema4A-deficient environment, wild-type myHSC excessively proliferate but fail to engraft long-term. Sema4A constrains inflammatory signaling in myHSC and acts via a surface receptor Plexin-D1. Our data support a model whereby the most primitive tissue stem cells critically rely on a dedicated signal from the niche for self-renewal and life-long persistence.

overall_design: ATAC sequencig were performed to compare the epigenome between Sema4aKO myHSCs and WT myHSCs.

first: Le

last: Zong

first: Isabel

last: Beerman

first: Lev

last: Silberstein


title: Intestinal mucosal barrier repair and immune regulation with an AI-developed gut-restricted PHD inhibitor

city: Shanghai

first: Chenxi

last: Xu

address: JinKe Road

institute: Insilico Medicine

summary: Hypoxia-inducible factor-prolyl hydroxylase (HIF-PHD) inhibitors have been approved for treating renal anemia, yet have failed clinical testing for inflammatory bowel disease (IBD) due to lack of efficacy. We use a multimodel multimodal generative AI platform to design an orally gut-restricted selective PHD1/2 inhibitor, which exhibits favorable safety and pharmacokinetic profiles in preclinical studies. ISM012-042 restores intestinal barrier function and alleviates gut inflammation in multiple experimental colitis models.

overall_design: Around 100 mg of colon tissues were collected from sham or TNBS-induced colitis mouse models treated with either vehicle or ISM012-042 on day 2 post-colitis induction.


title: Decreased SynMuv B gene activity in response to viral infection leads to activation of the antiviral RNAi pathway in C. elegans

city: Fort Collins

first: Taiowa

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

summary: Small RNA pathways regulate eukaryotic antiviral defense. Many of the Caenorhabditis elegans mutations that were identified based on their enhanced RNAi, the synMuv B genes, also emerged from unrelated genetic screens for increased growth factor signaling. The dozen synMuv B genes encode homologues of the mammalian dREAM complex found in nearly all animals and plants, which includes the lin- 35/retinoblastoma oncogene. In wild type animals, a combination of a synMuv A mutation and a synMuv B mutation are required for the Muv phenotype of increased growth factor signaling. But we showed that Orsay virus infection of a single synMuv A mutant can induce a Muv phenotype, unlike the uninfected single synMuv A mutant. This suggests that decreased synMuv B activity, which activates the antiviral RNAi pathway, is a defense response to viral infection. This study presents small RNA deep sequencing analysis of various dREAM complex mutants uncovering distinct siRNA profiles indicative of such an siRNA response.

overall_design: Small RNA high-throughput sequencing was done on wild-type, glp-4, and synmuv mutant strains of C. elegans. Total RNA was isolated from cell lysates from adult C. elegans cultured at 20˚C (glp-4+) or 25˚C (glp-4-). Small RNA data was processed using the tinyRNA pipeline.

first: Ashwin

last: Seetharaman


title: miRNA Nanostring Data on a Silk Scaffold model following CCI injury

city: Bethesda

first: Simone

last: Grant

state: MD

address: 4301 Jones Bridge Rd

department: PHA

institute: Uniformed Services University

summary: This study investigates the effects of controlled cortical impact (CCI), a form of traumatic brain injury (TBI), using a 3D silk scaffold cell culture model. Human induced neural stem cells (iNSCs), human induced astrocytes, and HMC3 microglial cells were seeded onto the silk scaffolds and allowed to grow under controlled conditions. A subset of these cell cultures was then subjected to CCI to simulate injury. The primary aim of the study was to assess the cellular and molecular response to CCI, particularly focusing on miRNA expression profiles. miRNA Nanostring technology was employed to quantify differential expression patterns associated with CCI exposure, providing insights into neuroinflammatory, regenerative, and apoptotic pathways impacted by the injury. These data contribute to a better understanding of miRNA's role as a biomarker for TBI and its potential involvement in cellular recovery and neuroprotection processes following traumatic injury.

overall_design: Each scaffold is one sample. Each independent experiment consisted of 36 samples. 6 sham (no CCI) and 6 CCI samples had media collected for miRNA analysis at the 3 timepoints assessed in this study (6, 24, and 72 hours). Thus, 12 samples were assessed at 6 hours, 12 at 24 hours, and 12 at 72 hours within Experiment #1. 2 independent experiments were used to generate this data. Both experiments together included 72 samples, 24 per timepoint.

first: Yang

last: Zhang

first: Maria

last: Savvidou

first: Volha

last: Liaudanskaya

first: Pramesh

last: Singh

first: Yuhang

last: Fu

first: Dustin

last: Snapper

first: Jessica

last: Gill

first: Amreen

last: Nasreen

first: Aviva

last: Symes

first: Abani

last: Patra

first: David

last: Kaplan

first: Afshin

last: Beheshti

first: Irene

last: Georgakoudi


title: A semidominant point mutation of Mediator tail subunit MED5b in Arabidopsis leads to altered enrichment of H3K27me3 and reduced expression of targets of MYC2 [RNA-seq]

city: West Lafayette

first: Joe

last: Ogas

state: Indiana

address: 175 S. University Street

department: Department of Biochemistry

institute: Purdue University

summary: The Mediator complex coordinates regulatory input for transcription driven by RNA Polymerase II in eukaryotes. reduced epidermal fluorescence4-3 (ref4-3) is a semidominant mutation that results in a single amino acid substitution in the Mediator tail subunit Med5b. Previous characterization of ref4-3 revealed altered expression of a variety of loci in Arabidopsis, including those contributing to phenylpropanoid biosynthesis.  Examination of existing RNA-seq data indicated that loci enriched for the transcriptionally repressive chromatin modification H3K27me3 are overrepresented among genes that are misregulated in ref4-3. We used ChIP-seq and RNA-seq to examine the possibility that perturbation of H3K27me3 homeostasis in ref4-3 plants contributed to altered transcript levels.  We observed that ref4-3 results in a modest global reduction of H3K27me3 at enriched loci and that this reduction is not dependent on gene expression; however, altered H3K27me3 was not strongly predictive of altered expression in ref4-3 plants. Instead, our analyses revealed a substantial enrichment of targets of the MYC2 transcriptional regulator among genes that exhibit decreased expression in ref4-3.  Consistent with previous characterization of ref4-3, we observed that ref4-3-dependent decreased expression of MYC2 targets can be suppressed by loss of another Mediator tail subunit, MED25. This observation is consistent with previous biochemical characterization of MYC2.  Our data highlight the diverse and distinct impacts that a single amino acid change in the tail subunit of Mediator can have on transcriptional circuits and raise the prospect that Mediator directly contributes to H3K27me3 homeostasis in plants.

overall_design: To investigate the possible contribution of perturbed H3K27me3 enrichment to altered transcript levels in ref4-3 plants

first: Jiaxin

last: Long

first: Shelby

last: Sliger

first: Zhi-Wei

last: Luo

first: Pete

middle: E

last: Pascuzzi

first: Clint

last: Chapple


title: A semidominant point mutation of Mediator tail subunit MED5b in Arabidopsis leads to altered enrichment of H3K27me3 and reduced expression of targets of MYC2 [ChIP-seq]

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for histone variant H2A.Z as well as the histone modification H3K27me3 in wild type (WT) and ref4-3 plants.


title: Mouse Skin Xenium In Situ Spatial Gene Expression

city: Charleston

first: Heehwa

last: Son

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

summary: To investigate the effecs of commensal papillomavirus immunity on the homeostasis of highly mutated normal skin, spatial transcriptomics (Xenium, 10x Genomics, Pleasanton, CA) was performed on SKH-1 mouse back skin. The mice were treated with mouse papillomavirus (MmuPV1) or virus-like particles (VLP), followed by UV exposure for 25 weeks.

overall_design: Formalin-fixed, paraffin-embedded (FFPE) mouse back skin samples, infected with MmuPV1 (n = 2, pooled onto one slide) or treated with virus-like particles (VLP; n = 2, pooled onto one slide) followed by UV exposure, were sectioned into 5 µm slices onto Xenium slides. Custom probe hybridization, ligation, amplification, cell segmentation staining, and autofluorescence quenching were then performed using the Xenium In Situ Analyzer.

first: Shadmehr

last: Demehri


title: Effects of Nova1 I197V substitution on Gene Expression in Brain Tissues [RNA-Seq]

city: NY

first: Yoko

last: Tajima

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: To elucidate the effect of human specific one amino acid substitution of Nova1 (I197V) in mice, gene expression profiling analysis was performed using humanized Nova1 mice (NOVA1hu/hu) and their littermate control mice (NOVA1wt/wt).

overall_design: To analyze changes in gene expression in NOVA1hu/hu mice, we performed RNA sequencing analysis of each brain region (cortex, midbrain, cerebellum).

first: Robert

middle: B

last: Darnell


title: Humanizing the RNA regulator NOVA1 in mice alters their vocal communication

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

overall_design: Refer to individual Series


title: Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of BRAF-mutant melanoma

city: Farmington

first: Jeffrey

middle: H

last: Chuang

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

summary: Over half of BRAF-mutant melanoma patients with initial response to targeted therapy will recur with resistant disease. It is thought that resistance can arise from the ability of cells to enter and exit a slow cycling persister state, evade treatment with relative dormancy, and repopulate the tumor when reactivated. However, the expression states of persister and resistant cells, their spatial relationships in the tumor environment, and the evolutionary progression among these populations are not well understood. Using patient derived xenograft (PDX) models, we track melanoma evolution longitudinally from pre-treatment through maximum treatment response and tumor regrowth. We perform spatial transcriptomics (ST) to 1. define expression signatures within treatment-sensitive, persister, and re-emergent populations, 2. uncover fluctuating metabolic priorities as a hallmark of tumor evolution both across treatment time and geographically across tissue sections, and 3. identify specific genes and pathways within persister and resistant lineages as candidate resistance mechanisms, suggesting potential therapeutic targets. Our novel computational pipeline integrates ST data with deep learning imaging features derived from accompanying histopathological slides. We identify phenotypic states that correlate with the persister cell state, exploiting the juxtaposition of transcriptomic and histological features toward the goal of identifying clonal populations using imaging data alone. In summary, we provide insight into the dynamics of shifting expression state and lineage selection in melanoma during multiple stages of treatment with novel spatiotemporal resolution, defining an evolutionary roadmap to acquired resistance.

overall_design: The two WISTAR PDX models, immunotherapy-treated WM4237-1 and treatment-naive WM4007, are BRAF V600E mutant metastatic melanomas of a subcutaneously implanted solid tumor on NSG mice. Twenty mice per model were used in the longitudinal experiment. When the tumors reached 300 mm3, measured biweekly, the continuous dose treatment of mice via chow with either a dual BRAF/MEK inhibitor or vehicle was initiated. One untreated mouse per model was sacrificed at time point T0, day 0. One vehicle-treated mouse per model was sacrificed at time point TC, days 42 and 38, WM4237-1 and WM4007, respectively. The tumors of therapy-treated sacrificed mice, one tumor tissue block per mouse per model per time point, were harvested at time points T1 (day 14), T2 (days 42 and 44), T3 (days 70 and 73), and T4 (days 94 and 133). We analyzed two near adjacent tissue sections from each tumor tissue block for each model and time point using 10x Visium Spatial Gene Expression.

first: Jill

middle: C

last: Rubinstein

first: Sergii

last: Domanskyi

first: Todd

last: Sheridan

first: Brian

last: Sanderson

first: SungHee

last: Park

first: Jessica

last: Kaster

first: Haiyin

last: Li

first: Olga

last: Anczukow

first: Meenhard

last: Herlyn


title: NOVA1-CLIP in cortex, midbrain and cerebellum of NOVA1hu/hu mice and NOVA1wt/wt mice [CLIP-Seq]

summary: Dissected brain regions (cortex, midbrain and cerebellum) from P21 NOVA1hu/hu mice and NOVA1wt/wt mice were subjected to CLIP to detect NOVA1 binding positions on transcripts

overall_design: Each dissected brain regions (cortex, midbrain and cerebellum) were UV-irradiated and subjected to NOVA1-CLIP


title: Nutrient-driven histone code determines exhausted CD8+ T cell fates [RNA-seq]

city: La Jolla

first: Shixin

last: Ma

state: CA

address: 10010 N Torrey Pines Rd

department: IMPL-K

institute: SALK Institute for biological studies

summary:
To investigate the role of ACSS2NLS in the regulation of  CD8+ T cell responses in B16-GP33 tumor model
Exhausted T cells (TEX) in cancer and chronic viral infections undergo metabolic and epigenetic remodeling, impairing protective capabilities. However, the impact of nutrient metabolism on epigenetic modifications that control TEX differentiation remains unclear. Our study reveals that TEX cells shift from acetate to citrate metabolism by downregulating acetyl-CoA synthetase 2 (ACSS2) while maintaining ATP-citrate lyase (ACLY) activity. This metabolic switch increases citrate-dependent histone acetylation, mediated by histone acetyltransferase KAT2A-ACLY interactions, at TEX signature-genes while reducing acetate-dependent histone acetylation, dependent on p300-ACSS2 complexes, at effector and memory T cell genes. Nuclear ACSS2 overexpression or ACLY inhibition prevents TEX differentiation and enhances tumor-specific T cell responses. These findings unveil a nutrient-driven histone code governing CD8+ T cell differentiation, with implications for metabolic- and epigenetic-based T cell therapies

overall_design: RNA-seq gene expression profiling analysis for EV and ACSS2NLS TILs in B16-GP33 tumor at day 21 post tumor implantation

first: Susan

last: Kaech


title: Nutrient-driven histone code determines exhausted CD8+ T cell fates [ChIP-seq]

summary:
To investigate the role of ACSS2 and ACLY  in the regulation of  epigenetic states of CD8+ T cells in cancer and chronic viral infections
Exhausted T cells (TEX) in cancer and chronic viral infections undergo metabolic and epigenetic remodeling, impairing protective capabilities. However, the impact of nutrient metabolism on epigenetic modifications that control TEX differentiation remains unclear. Our study reveals that TEX cells shift from acetate to citrate metabolism by downregulating acetyl-CoA synthetase 2 (ACSS2) while maintaining ATP-citrate lyase (ACLY) activity. This metabolic switch increases citrate-dependent histone acetylation, mediated by histone acetyltransferase KAT2A-ACLY interactions, at TEX signature-genes while reducing acetate-dependent histone acetylation, dependent on p300-ACSS2 complexes, at effector and memory T cell genes. Nuclear ACSS2 overexpression or ACLY inhibition prevents TEX differentiation and enhances tumor-specific T cell responses. These findings unveil a nutrient-driven histone code governing CD8+ T cell differentiation, with implications for metabolic- and epigenetic-based T cell therapies

overall_design: We then performed CnR analysis on H3K27ac, H3K9ac and H4ac on (i) TEXprog, TEXterm cells from LCMV-clone 13 infection; (ii) sgscramble and sgAcly TEX cells from in vitro exhaustion culture; (3) EV and ACSS2NLS TILs from B16-GP33 tumor.


title: TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architecture [CUT&Tag]

status: Public on Dec 10 2024

city: Beijing

first: Yuying

last: Shen

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: Mitotic bookmarking has been posited as an important strategy for cells to faithfully propagate their fate memory though cell generations. However, the physiological significance and regulatory mechanisms of mitotic bookmarking in neural development remain unexplored. Here, we identified TBP (TATA binding protein) as a crucial mitotic bookmarker for preserving fate memory of Drosophila neural stem cells (NSCs). Phosphorylation by the super elongation complex (SEC) is important for TBP to retain as discrete foci at mitotic chromosomes of NSCs to effectively transmit their fate memory. TBP depletion leads to drastic NSC loss, whereas TBP overexpression enhances the ability of SEC to induce neural progenitor dedifferentiation and tumorigenesis. Importantly, TBP achieves its mitotic retention through recruiting the chromatin remodeler EP400, which in turn increases local chromatin accessibility via depositing H2A.Z. Thus, local chromatin remodeling ensures mitotic bookmarking, which may represent a general principle underlying the preservation of cell fate memory.

overall_design: To compare DNA binding ability between TBP.ctrl and TBP.SA, we carried out in vivo CUT&Tag assay in Drosophila type II neural stem cells.

first: Kun

last: Liu

first: Jie

first: Jingwen

first: Tongtong

last: Ye

first: Runxiang

last: Zhao

first: Rulan

last: Zhang

first: Yan

last: Song


title: MICAL2 Is a Super Enhancer Associated Gene that Promotes Pancreatic Cancer Growth and Metastasis

first: Andrew

middle: M.

last: Lowy

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: UCSD Health

summary: Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest solid cancers and thus identifying more effective therapies is a major unmet need. In this study we characterized the super enhancer (SE) landscape of human PDAC to identify novel, potentially targetable, drivers of the disease. Our analysis revealed that MICAL2 is a super enhancer-associated gene in human PDAC. MICAL2 is a flavin monooxygenase that induces actin depolymerization and indirectly promotes SRF transcription by modulating the availability of serum response factor coactivators myocardin related transcription factors (MRTF-A and MRTF-B). We found that MICAL2 is overexpressed in PDAC and correlates with poor patient prognosis. Transcriptional analysis revealed that MICAL2 upregulates KRAS and EMT signaling pathways, contributing to tumor growth and metastasis. In loss and gain of function experiments in human and mouse PDAC cells, we observed that MICAL2 promotes both ERK1/2 and AKT activation. Consistent with its role in actin depolymerization and KRAS signaling, loss of MICAL2 expression also inhibited macropinocytosis. Through in vitro phenotypic analyses, we show that MICAL2, MRTF-A and MRTF-B influence PDAC cell proliferation, migration and promote cell cycle progression. Importantly, we demonstrate that MICAL2 is essential for in vivo tumor growth and metastasis. Interestingly, we find that MRTF-B, but not MRTF-A, phenocopies MICAL2-driven phenotypes in vivo. This study highlights the multiple ways in which MICAL2 impacts PDAC biology and suggests that its inhibition may impede PDAC progression. Our results provide a foundation for future investigations into the role of MICAL2 in PDAC and its potential as a target for therapeutic intervention.

overall_design: Chromatin Immunoprecipitation Sequencing (CHIP Seq) for H3K27AC from both normal pancreas and PDAC tumors.

first: Bharti

last: Garg

first: Sohini

last: Khan

first: Deepa

last: Babu

first: Evangeline

last: Mose

first: Kevin

last: Gulay

first: Shweta

last: Sharma

first: Divya

last: Sood

first: Alexander

last: T Wenzel

first: Alexei

last: Martsinkovskiy

first: Jay

last: Patel

first: Dawn

last: Jaquish

first: Guillem

last: Lambies

first: Anthony

last: D’Ippolito

first: Kathryn

last: Austgen

last: Johnston

first: David

last: Orlando

first: Gung

last: Ho Jang

first: Steven

last: Gallinger

first: Elliot

last: Goodfellow

first: Pnina

last: Brodt

first: Cosimo

last: Commisso

first: Pablo

last: Tamayo

first: Jill

last: P Mesirov

first: Herve

last: Tiriac

last: M Lowy


title: TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architecture [ATAC-seq]

first: Yuying

last: Shen

overall_design: To assess mitotic chromatin architecture of neural stem cells upon H2A.Z loss of function, we next performed in vivo ATAC-seq with mitotic neural stem cells.

first: Kun

last: Liu

first: Jie

first: Jingwen

first: Tongtong

last: Ye

first: Runxiang

last: Zhao

first: Rulan

last: Zhang

first: Yan

last: Song


title: Nutrient-driven histone code determines exhausted CD8+ T cell fates

first: Shixin

last: Ma


title: iPSC-derived mesenchymal stromal cells stimulate neovascularization less than their primary counterparts

city: Aachen

first: Julian

last: Gonzalez-Rubio

address: Forckenbeckstraße 55

department: BioTex

institute: RWTH University Aachen

summary: Aims Mesenchymal stromal cells (MSCs) are being tested and accepted as a source for cell therapy worldwide. However, the advanced age of the patients, together with the difficulties in achieving the required cell amounts, impede autologous treatments. Reprogramming of MSCs into induced pluripotent stem cells (iPSCs), followed by re-differentiation to MSCs has emerged as a promising and safe method to facilitate the cell expansion and the removal of aging-associated characteristics. However, the effect of reprogramming on the MSC’s pro-angiogenicity is poorly understood. Materials and Methods In this study, we use a microfluidic organ-on-a-chip platform designed for vascularization assays to study and compare the effects of bone marrow MSCs (BM-MSCs) and iPSC-derived MSCs (iMSCs) in stimulating the formation of vessels by endothelial cells. Cells were loaded in fibrin hydrogels, injected into the microfluidic channel, and grown for ten days. Key findings Fluorescence microscopy revealed that BM-MSCs promote the formation of long and interconnected endothelial vessels, while iMSCs barely stimulate neoangiogenesis. This was further confirmed and explained by bulk RNA sequencing, showing a decrease of pro-angiogenic agents in both of the iMSCs co-cultures. Furthermore, transmission electron microscopy revealed that BM-MSCs closely associate with the new vessels as perivascular cells, while iMSCs just remain in proximity. Significance These results highlight iMSCs as a promising substitute for BM-MSCs in the treatment of diseases with pernicious vascularization, such as osteoarthritis, ocular degeneration, and cancer.

overall_design: We prepared 3D co-cultures of endothelial cells and supporting cells in fibrin gels. The supporting cells were either bone marrow mesenchymal stromal cells (BMSC) or iPSC-derived mesenchymal stromal cells (iMSCs). The endothelial cells were human umbilical vein endothelial cells (HUVECs). The cells were in the gel in a 1:2 ratio (5x10^6 Supporting Cells and 10x10^6 HUVECs). The gels were cultured for 10 days with EGM MV2 media (PromoCell). The gels were minced and the RNA was isolated for a comparative RNA study.

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