title: Mid-Lobular Hepatocytes Exhibit Transient Proliferation Pause and Stress Response through Atf4-Ddit3 axis in Early Acute Liver Injury (CUT&Run)

city: Kunming

first: Yaying

last: Zhu

state: Yunnan

address: Chenggong district of yunnan university in kunming, yunnan province

institute: yunnan university

summary: Liver zonation remains a critical aspect of understanding its response to acute injury. This study investigates the impact of acetaminophen-induced acute liver injury on zonal heterogeneity during early phases of injury. Through Ki67 staining, we observed a transient pause in proliferation specifically among mid-lobular hepatocytes during the initiation phase. Using spatial transcriptomics, immunostaining, and in vivo assays, we elucidated that mid-lobular hepatocytes upregulate the Atf4-Ddit3 axis, offering temporary protection at the cost of reduced proliferation mediated by Btg2. Our findings underscore the unique zonal metabolism of acetaminophen as a determinant of differential tissue responses across lobular regions. This study highlights how distinct liver zones exhibit varied responses during the early stages of acute injury, with mid-lobular hepatocytes showing an integrated stress response characterized by protective mechanisms that temporarily suppress proliferation.

overall_design: We performed Cut&Run to identify the genomic regions where Ddit3 binds at 6 h post APAP.

first: Chengxiang

last: Deng

first: Bo

last: Chen

first: Jia

last: He


title: Bone marrow macrophage derived GPNMB protein binds to orphan receptor GPR39 and plays a critical role in cardiac repair

status: Public on Sep 17 2024

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: Levels of Glyco Protein Non-metastatic Melanoma protein B (GPNMB), a type I transmembrane protein, originally identified in non-metastatic melanomas has been shown to be strongly associated with human heart failure. However, the role of GPNMB in modulation of cardiac injury and cardiac function remains unclear. We analyzed human cardiac global gene expression data sets and observed increased GPNMB expression in failing hearts. In murine hearts after myocardial infarction (MI), we showed that GPNMB expression increased by an order of magnitude. Lineage tracing and bone marrow transplantation experiments demonstrated that bone marrow macrophages were the primary source of GPNMB in the injured heart. Using genetic loss of function approaches, we demonstrate that animals deficient in GPNMB exhibited significantly higher mortality, cardiac rupture and developed rapid post infarct LV dysfunction. Conversely gain of function approaches by increasing circulating GPNMB levels by viral delivery led to augmentation of post MI heart function. Single cell transcriptomics demonstrated pleiotropic effects of GPNMB on gene expression of myocytes and non-myocytes leading to enhanced myocyte contraction and decreased fibroblast activation. Using chemical cross-linking studies and immunoprecipitation studies, we identified the orphan receptor GPR39 as a receptor for circulating GPNMB. In animals deficient in GPR39, GPNMB failed to deliver beneficial effects on post infarct heart function. Taken together, these observations demonstrate that bone marrow macrophage derived GPNMB plays a pivotal role in cardiac repair following myocardial infarction, by mediating its pleiotropic effects in part via the orphan receptor GPR39

overall_design: GPNMB KO mice were infarcted by LAD ligation and on day 7 after injury the hearts were harvested, nuclei were isiolated for library construction and sequencing.

first: Sivakumar

last: Ramadoss

first: Arjun

last: Deb


title: Mid-Lobular Hepatocytes Exhibit Transient Proliferation Pause and Stress Response through Atf4-Ddit3 axis in Early Acute Liver Injury (10x Visium)

country: China

overall_design: To understand the temporal spatial response to acute APAP injury, liver sections from wild-type mice treated with APAP for 0 h to 72 h were subjected to spatial transcriptomics (ST) using the Visium (10 × Genomics) platform.


title: Effect of S127A mutation of ZBTB5 on gene expression in TNFα-treated murine B16F10 melanoma cells

city: Chongqing

first: Fanxuan

last: Tian

address: No. 10, Changjiang Zhi Road, Daping Street, Yuzhong District

institute: Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University

summary: Activation of mTORC1 is crutial for tumorigenesis. Here we identify ZBTB5 as an evolutionarily arisen regulator to translate inflammatory signals to activate mTORC1 pathway in the  tumor microenvironment. Mechanistically, inflammatory cytokine TNFα promotes phosphorylation of ZBTB5-S127 confering ZBTB5 as an adaptor to recruit the E3 ubiquitin ligase Cullin3 to activate mTORC1 signaling and promote tumorigenesis. Thus, disrupting inflammation-induced mTORC1 activity represents a promising therapeutic vulnerability of tumor.

overall_design:
To investigate the effect of the ZBTB5-S127 phosphorylation on the inflammtion-induced mTORC1 activation, we established the ZBTB5-S127A B16F10 cell line in which ZBTB5-S127 phosphorylation is silenced.
We then performed gene expression profiling analysis using data obtained from RNA-seq of TNFα-treated ZBTB5-S127A and wild-type control B16F10 cell.
Comparative gene expression profiling analysis of RNA-seq data for the ZBTB5-S127A cells and its wild-type control cells.

first: Bin

last: Wang

first: Junyu

last: Xiang


title: Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments [scRNA-seq]

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

summary: Long known as the site of ribosome biogenesis, the nucleolus is increasingly recognized for its role in shaping 3D genome organization. Still, the mechanisms governing the targeting of selected regions of the genome to nucleolus-associated domains (NADs) remain enigmatic. Here we reveal the essential role of ZNF274, a SCAN-bearing member of the Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFP) family, in sequestering lineage-specific gene clusters within NADs. Ablation of ZNF274 triggers transcriptional activation across entire genomic neighborhoods – encompassing, among others, protocadherin and KZFP-encoding genes – with loss of repressive chromatin marks, altered 3D genome architecture and de novo CTCF binding. Mechanistically, ZNF274 anchors target DNA sequences at the nucleolus and facilitates their compartmentalization via a previously uncharted function of the SCAN domain. Our findings illuminate the mechanisms underlying NADs organization and suggest that perinucleolar entrapment into repressive hubs constrains the activation of tandemly arrayed genes to enable selective expression and modulate cell differentiation programs during development.

overall_design: scRNAseq was performed in wild-type (wt) and ZNF274 knock-out (ZNF274KO) clones in NPC cell lines.

first: Martina

last: Begnis

first: Didier

last: Trono


title: Winter break? The effect of overwintering on immune gene expression in wood frogs

city: STORRS MANSFIELD

first: Grace

last: Vaziri

state: CT

address: 77 Forest Rd., Apt A

institute: University of Connecticut

summary: Among terrestrial ectotherms, hibernation is a common response to extreme cold temperatures and is associated with reduced physiological rates, including immunity. When winter wanes and temperatures increase, so too do vital rates of both ectothermic hosts and their parasites. Due to metabolic scaling, if parasite activity springs back faster than host immune functions then cold seasons and transitions between cold and warm seasons may represent periods of vulnerability for ectothermic hosts. Understanding host regulation of physiological rates at seasonal junctions is a first step toward identifying thermal mismatches between hosts and parasites. Here we show that immune gene expression is responsive to transitions into and out of the cold season in a winter-adapted amphibian, the wood frog (Lithobates sylvaticus), and that frogs experienced parasitism by at least two nematode species throughout the entirety of the cold season. In both splenic and skin tissues, we observed a decrease in immune gene expression going from fall to winter, observed no changes between winter and emergence from hibernation, and observed increases in immune gene expression after hibernation ended. At all timepoints, differentially expressed genes from spleens were more highly enriched for immune system processes than those from ventral skin, especially with respect to terms related to adaptive immune processes. Infection with nematode lungworms was also associated with upregulation of immune processes in the spleen. We suggest that rather than being a period of stagnation, during which physiological processes and infection potential cease, the cold season is immunologically dynamic, requiring coordinated regulation of many biological processes, and that the reemergence period may be an important time during which hosts invest in preparatory immunity.

overall_design: To describe seasonal changes in wood frog gene expression, we kept wild-caught adult frogs in outdoor enclosures through a winter. We periodically sampled frogs from these enclosures to obtain gene expression data. We collected samples from four timepoints before, during, and after frogs overwintered. We then collected a small section of ventral skin, and the spleen, and stored these samples separately in RNAlater buffer for 24h at 4°C before freezing them at -80°C until RNA extraction. We sequenced extraced RNA and peformed differential gene expression analysis.

middle: J

first: Noah

middle: M

last: Reid

first: Tracy

middle: A

last: Rittenhouse

first: Daniel

middle: I

last: Bolnick


title: Phosphodiesterase-4 inhibitors increase pigment cells proliferation and melanization in cultured melanocytes and within a 3D skin equivalent model

city: Aurora

first: Stanca

last: Birlea

state: CO

department: Dermatology

institute: University of Colorado, Anschutz Medical Campus

summary: Vitiligo is a common chronic autoimmune disease characterized by white macules and patches of the skin, having a negative impact on patients’ life, and without any definitive cure at present. Identification of new compounds to reverse depigmentation is therefore a pressing need for this disease. The pharmacologic compounds phosphodiesterase-4 inhibitors (PDE4i) are small molecules with immunomodulatory properties, used for treatment of inflammatory dermatoses. PDE4i have shown repigmentation effects in vitiligo patients, in some case reports. We characterized the proliferative and melanogenic potential of two known PDE4i, crisaborole and roflumilast, and of a more recently designed compound, PF-07038124. We used two in vitro model systems, the primary human melanocyte culture and a 3D co-cultured skin model (MelanoDermTM), with an exploratory testing platform composed of complementary assays (spectrophotometry, melanin and proliferation assays, immunostaining, Fontana-Masson staining, qRT-PCR, western blot and whole transcriptome RNA-Sequencing). We identified that the treatment with PDE4i was associated with increased melanocyte proliferation and melanization in both in vitro models, and with increase in the melanogenic genes and proteins expression in cultured melanocytes. These effects were found to be enhanced by addition of a-MSH. In the MelanodermTM tissue, numerous genes and canonical pathways modulated by PDE4i appear to control melanocytic cell function. Our findings support the use of PDE4i with or without a-MSH agonists in vitiligo trials.

overall_design: The MelanoDermTM 3D in vitro co-culture model (MatTek Corp., Ashland, MA) incorporates normal human epidermal MCs into well differentiated epidermis with normal human epidermal keratinocytes (Passeron et al., 2009). Tissues containing MCs from a Black donor (MEL-300-B) were cultured  in high and low Growth Factor media, and tissues were treated with crisaborole at 10 μM, PF-07038124 at 100 nM and DMSO vehicle control at the same v/v concentration as crisaborole. Tissues were collected 72hs after drug treatments for RNA extraction.

first: Nathaniel

middle: B

last: Goldstein


title: Expression profiling PDE4B inhibitor BI 1015550 treatment in a therapeutic Rat Lung Bleomycin Model

city: Biberach (Riss)

first: Katrin

last: Fundel-Clemens

address: Birkendorferstr. 65

department: gCBDS

country: Germany

institute: Boehringer Ingelheim Pharma GmbH&Co KG

summary: Idiopathic pulmonary fibrosis (IPF) is a progressing chronic and fibrotic lung response with poor prognosis. To study the underlying molecular mechanisms of IPF, the rat bleomycin model is commonly used. Intratracheal application of bleomycin is known to induce inflammatory and fibrotic processes in the lung, e.g. infiltratin of inflammatory cells and collagen deposition.  Recently, the PDE4B inhibitor BI 1015550 has been reported to prevent a decrease in lung function in patients with IPF.  Here we examined the effect of PDE4 inhibitor BI 1015550 in the rat bleomycin model on transcriptional level by RNASeq.

overall_design: Here we asses the effect of therapeutic PDE4B inhibition in the rat Bleomycin model of pulmonary fibrosis via RNASeq on the lung transcriptome.  The experiment consisted of control animals (n=6), Bleomycin treatment (1mg per kg in 0.9 percent NaCl aequeous solution) on day 0 (n=5), treatment with PDE4B inbibitor (BI 1015550) between day 10 and day 20 twice daily (n=6). The material collection took place on day 19 for the control group and on day 20 for treated animals.

first: Peter

last: Nickolaus

first: David

last: Lamb

first: Karsten

last: Quast


title: PANoptosis, a combination of inflammatory cell death mechanisms, induced by Ophiobolin A in breast cancer cell lines

city: Waco

first: Joe

last: Taube

state: Texas

address: One Bear Place #97388

institute: Baylor University

summary: An unmet challenge in managing breast cancer is treatment failure due to resistance to apoptosis-inducing chemotherapies. Thus, it is important to identify novel non-apoptotic therapeutic agents. Several non-apoptotic programmed cell death pathways utilize specific cellular signaling events to trigger lytic and pro-inflammatory cell death. PANoptosis, which encompasses pyroptosis, apoptosis and necroptosis, is of paramount importance in the regulation of cell death and immune responses. Our study illustrates that ophiobolin A (OpA) is an anti-cancer agent that triggers lytic cell death in breast cancer cells, including triple-negative breast cancer (TNBC), via a mechanism dependent on RIPK1. This study reveals that OpA induces typical pyroptosis-like characteristics, including cellular swelling, plasma membrane rupture, GSDMD cleavage and release of cytokines in breast cancer cells. The involvement of caspase 3, RIPK1, and GSDMD suggests that PANoptosis is activated upon OpA treatment in breast cancer. The induction of pro-inflammatory cell death suggests potential applications for OpA in cancer treatment.

overall_design: To investigate the impact of OpA on gene expression in MDA-MB-231 cells, we compared triplicate samples of vehicle-treated and OpA-treated cells.

first: Joseph

first: Santha

last: Ranganathan


title: Esketamine Enhances Post-Stroke Microglial Proliferation and Attenuates Neuroinflammation by Disrupting the Src-Pannexin1 Interaction

city: Hubei

first: zhang

middle: tian

last: tianhao

state: Hubei

address: sdggvsdv

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

summary: Previous research has suggested the potential of esketamine in alleviating post-stroke neuroinflammation, yet the underlying mechanism remained elusive. In our research, we have observed that esketamine increased the number of M2 anti-inflammatory phenotype microglia in the infarcted area after stroke, and this phenomenon is partly associated with the suppression of Panx1. Further research revealed that esketamine suppresses the phosphorylation of sarcoma kinase (Src) at the tyrosine 416 (Y416) site and inhibits the interaction between Src and Panx1, ultimately suppressing the function of Panx1. However, we found esketamine's inhibitory effect on post-stroke Panx1 activation is the underlying mechanism driving the increase in unactivated microglia, yet esketamine's influence on microglial polarization is mediated through a mechanism independent of Panx1.Our research suggests that esketamine, as a drug already used in clinical anesthesia, could potentially provide a solution during the periprocedural period to mitigate the damage caused by aseptic inflammation post-stroke.

overall_design: To further explore the reasons behind the increase in Src following Panx1 inhibition, we subjected the BV2 microglial cell line to glucose-oxygen deprivation and inhibited Panx1 using 10panx1.By comparing the RNA-seq results of the group subjected solely to glucose-oxygen deprivation with those of the 10panx1+ glucose-oxygen deprivation group, we were able to identify pathways related to changes in Src.

first: Tianhao

last: Zhang

first: Shiqian

last: Huang

first: Linlin

last: Han

first: Xiangdong

last: Chen


title: Regulation of developmentally controlled enhancer activity by extrinsic signals in normal and malignant cells: AP-1 at the center [ChIP-Seq]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The ability of cells to respond to external stimuli is one of the characteristics of life as we know it. Multicellular organisms have developed a huge machinery that interprets the cellular environment and instigates an appropriate cellular response by changing gene expression, metabolism, proliferation state and motility. Decades of research have studied the pathways transmitting the various signals within the cell. However, whilst we know most of the players, we know surprisingly little about how extrinsic signals are interpreted and integrated within the genome and lead to systems level responses within a chromatin environment. In this article we touch upon this question by summarizing our work and that of others to explain what is known about signaling responsive cis-regulatory elements and by highlighting the features of AP-1 as one of the most important signaling-responsive transcription factor family. We propose that cytokines and other signals are the main driver of cell differentiation, acting via inducible transcription factors such as AP-1 that transmit signaling processes to the genome and are essential for changing gene expression within a given gene regulatory network. Importantly, inducible transcription factors interact with cell type specific factors within a pre-existing chromatin landscape and integrate multiple signaling pathways at specific enhancer elements, to both maintain and alter cellular identities. We also propose that signaling processes and signaling responsive transcription factors are at the heart of tumor development.

overall_design: RUNX1 and H3K27me3 ChIP-Seq in in-vitro derived floating haematopoietic progenitors

first: Alexander

last: Maytum

first: Nadine

last: Obier

first: Constanze

last: Bonifer


title: Transcriptomic profiling of antibiotic-resistant Salmonella Heidelberg in the presence of commensal Escherichia coli of poultry origin

city: Gainesville

first: Yasir Razzaq

last: khan

state: Florida

address: 2015 SW 16th Ave

department: Large Animals Clinical Sciences

institute: university of Florida

summary: The non-typhoidal Salmonella enterica serotype Heidelberg is a major foodborne pathogen primarily transmitted to humans through contaminated poultry products. Current control measures emphasize novel approaches to mitigate Salmonella Heidelberg colonization in poultry and the contamination of poultry products, thereby reducing its transmission to humans. This study highlight that commensal E. coli 47-1826 can potentially be used to control of S. Heidelberg 18-9079 in poultry

sample_organism: Salmonella enterica subsp. enterica serovar Heidelberg

overall_design: To investigate the differential gene expression in S. Heidelberg 18-9079,  we  co-cultured the S. Heidelberg 18-9079 with E. coli 47-1826 in anaerobic environment

first: Yasir

middle: R

last: Khan

first: Lekshmi

middle: K

last: Edison

first: Thomas

last: Denagamage

first: Subhashinie

last: Kariyawasam


title: Impacts on Atlantic killifish from neurotoxicants: genes, behavior, and population relevant outcomes

city: Mississippi State,

first: Adam

last: Thrash

state: MS

address: 2 Research Blvd., Box 9627

department: Institute for Genomics, Biocomputing & Biotechnology

institute: Mississippi State University

summary: Molecular, cellular, and organismal alterations are important descriptors of toxic effects, but our ability to extrapolate and predict ecological risks is limited by the availability of studies that link measurable endpoints to adverse population relevant outcomes such as cohort survival and growth. In this study, we used laboratory gene expression and behavior data from two populations of Atlantic killifish Fundulus heteroclitus (one reference site (SCOKF) and one PCB-contaminated site (NBHKF) to inform individual-based models simulating cohort growth and survival from embryonic exposures to environmentally relevant concentrations of neurotoxicants. Methylmercury exposed SCOKF exhibited brain gene expression changes in the si:ch211-186j3.6, si:dkey-21c1.4, scamp1, and klhl6 genes, which coincided with changes in feeding and swimming behaviors, but our models simulated no growth or survival effects of exposures.  PCB126 exposed SCOKF had lower physical activity levels coinciding with a general upregulation in nucleic and cellular brain gene sets (BGS) and down regulation in signaling, nucleic and cellular BGS. The NBHKF, known to be tolerant to PCBs, had altered swimming behaviors that coincided with 98% fewer altered BGS. Our models simulated PCB126 decreased growth in SCOKF and survival in SCOKF and NBHKF. Overall, our study provides a unique demonstration linking molecular and behavioral data to develop quantitative, testable predictions of ecological risk.

overall_design: Two populations of Atlantic killifish (KF) were tested, Scorton Creek, Barnstable, MA (SCOKF) and New Bedford Harbor, MA (NBHKF).  Embyros were exposed to methylmercury (MeHg) via a parental tuna-based diet resulting in high MeHg KF breeding stock and a salmon-based diet was used to produce low MeHg or reference (control) KF breeding stock [Hg; 186.10 ± 23.30 ng tHg/g dw KF, standard deviation (SD), n=5, sampled April 27, 2017).  The low MeHg KF breeding stock received a daily estimated dose of ~ 300 ng tHg/g dw KF/day through their salmon-based diet resulting in a lower MeHg body concentration [162.46 ± 20.21 ng tHg/g dw KF (SD, n=8)]. Subsamples of the embryos from SCOKF Low MeHg diet and NBHKF Low MeHg diet KF were exposed directly during development, 1 to 7 days post fertilization, with 40 or 400 ng/L PCB126.

first: Janice

middle: L

last: Albers

first: Lori

middle: N

last: Ivan

first: Bryan

middle: W

last: Clark

first: Diane

middle: E

last: Nacci

first: Rebekah

middle: H

last: Klingler

first: Juan

middle: P

last: Steibel

first: Natalia

last: Garcia-Reyero Vinas

first: Michael

last: Carvan

first: Cheryl

last: Murphy


title: Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments [RNA-seq]

first: Julien

last: Duc

summary: Epigenetic mechanisms influencing chromatin architecture are key to the spatio-temporal control of transcription. Here we identify ZNF274 as a new regulator of chromosome compartmentalization that silences lineage-specific gene clusters. ZNF274 is a SCAN-bearing member of the Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs). Ablation of ZNF274 results in the transcriptional activation of genomic neighbourhoods encompassing, among others, zinc finger and protocadherin-encoding genes, with loss of H3K9me3 repressive mark, altered 3D genome conformation and de novo CTCF binding. In contrast to other factors that have been implicated in chromatin anchoring, ZNF274 is necessary both for transcriptional silencing and nucleolar tethering. While the establishment of silencing depends on the KRAB domain, we demonstrate that the SCAN domain is required to gather ZNF274 complexes at the nucleolus and efficiently spread heterochromatin. Thus, ZNF274 orchestrates the segregation of developmentally regulated gene clusters at nucleoli to allow timely and selective activation of cell-restricted alleles.

overall_design: RNAseq was performed in biological replicates on independent wild-type (wt) and ZNF274 knock-out (ZNF274KO) clones in hEK293T cell line and H1 hES cell line differentiated into NPC.

first: Martina

last: Begnis

first: Didier

last: Trono


title: Mid-Lobular Hepatocytes Exhibit Transient Proliferation Pause and Stress Response through Atf4-Ddit3 axis in Early Acute Liver Injury

first: Yaying

last: Zhu

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

overall_design: Refer to individual Series


title: Bank1 modulates the differentiation and molecular profile of key B cell populations in autoimmunity

city: GRANADA

first: Daniel

last: Toro

state: Spain

address: Avenida de la Ilustracion

department: Bioinformatics

country: Spain

institute: GENYO

summary: This study aimed at defining the role of the B-cell adaptor protein BANK1 in the appearance of age-associated B cells (ABCs) in two SLE mouse models (TLR7.tg6 and Imiquimod-induced mice), crossed with Bank1-/- mice. The absence of Bank1 led to a significant reduction in ABC levels, also affecting other B cell populations. To gain deeper insights into their differentiation pathway and the impact of Bank1 on B cell populations, a single-cell transcriptome assay was performed. In the TLR7.tg6 model, we identified 10 clusters within B cells, including an ABC-specific cluster which was decreased in Bank1-deficient mice. In its absence, ABCs exhibited an anti-inflammatory gene expression profile, while being pro-inflammatory in Bank1-sufficient lupus mice. Trajectory analyses revealed that ABCs originated from marginal zone and memory-like B cells, ultimately acquiring transcriptional characteristics associated with atypical memory cells and long-lived plasma cells. Also, Bank1 deficiency normalized the presence of naïve B cells, which were nearly absent in lupus mice. Interestingly, Bank1 deficiency significantly reduced a distinct cluster containing IFN-responsive genes. These findings underscore the critical role of Bank1 in ABC development, impacting early B cell stages towards ABC differentiation, and the presence of IFN-stimulated gene-containing B cells, both populations determinant for autoimmunity.

overall_design: Transcriptomic data were obtained from single cells sorted from total splenocytes of three mice per group: healthy control wild-type, TLR7.tg6 and TLR7.tg6.Bank1-/- mice

first: Gonzalo

last: Gómez Hernández

last: Toro Domínguez

first: Georgina

last: Galicia

first: Maria

last: Morell

first: Marta

last: Alarcón Riquelme


title: Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection

city: Irapuato

first: Obed

middle: Ramirez

last: Sanchez

state: Guanajuato

address: Km. 9.6 Libramiento NorteCarr. Irapuato-León

department: langebio

country: Mexico

institute: cinvestav

summary: By using RNA-seq analysis on purified extracellular vesicles from the infected tissue, we found that host plant Arabidopsis thaliana secretes a panel of messenger RNAs (mRNAs) in extracellular vesicles. These mobile plant mRNAs were delivered into cells of the interacting fungal pathogen Botrytis cinerea. While using Translating Ribosome Affinity Purification (TRAP) profiling and polysome analysis, we observed that the delivered host mRNAs were associated with active fungal polysomes isolated from the infected tissue, suggesting that they are translated in the fungal cells.

sample_organism:
Arabidopsis thaliana
Botrytis cinerea

platform_organism:
Arabidopsis thaliana
Botrytis cinerea

overall_design: Detection of cross-kingdom mRNA trafficking between the plant host and the fungal pathogen.

first: Shumei

last: Wang

first: Baoye

last: He

first: Huaitong

last: Wu

last: Ramírez-Sánchez

first: Qiang

last: Cai

first: Cei

last: Abreu-Goodger

first: Hailing

last: Jin


title: Dysregulation of global mRNA splicing in a Huntington’s disease neuronal differentiation cell line model

city: Singapore

first: Vincent

last: Tano

address: 14 Medical Dr

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

summary:
To study cell type- and HTT CAG length-dependent transcriptional and alternative splicing changes associated with HD, we conducted deep RNA-sequencing analysis on human embryonic stem cells (hESC), NPC and neuron cell lines (ESC and NPC, NEU) expressing wild-type (27/ and 30 CAG repeats), 45 CAG (45Q; representing 45 polyQ mutant HTT protein) and 81 CAG (81Q) repeat expansion HTT gene (n=3).
The cell lines were derived from an isogenic HTT CAG repeat expansion allelic cell line panel (IsoHD) where hESC H9 cells were genetically modified with monoallelic knockin of expanded CAG tract in exon 1 of HTT representing early onset (45Q) and late onset (81Q) HD, with the 27Q/30Q genotype as healthy control phenotype (Ooi et al., 2019).
The sequencing experiment generated 2.9 billion pairs of 150 bp paired-end reads from 27 samples (3 clones, 3 genotypes, 3 cell lines), with 80 to 110 million read pairs per sample. Transcriptome alignment yielded 75 to 100 million uniquely mapped read pairs across all samples.

overall_design: Whole transcriptome profiling analysis of RNA-seq data for hESC, NPC, and neurons expressing either wild-type HTT, 45 CAG repeat HTT, or 81 CAG repeat HTT

first: Sarah

last: Langley


title: Transcriptome profiling of circadian day and night gene expression in the suprachiasmatic nucleus of wild-type and Gpr176-deficient mice

city: Kyoto

first: Masao

last: Doi

department: Department of Systems Biology

country: Japan

institute: Kyoto University, Graduate School of Pharmaceutical Sciences

summary: This array set was used to identify gene expressions that are affected by the absence of the orphan G-protein-coupled receptor Gpr176 in the mouse suprachiasmatic nuclei (SCN).

overall_design: C57BL/6J WT or Gpr176−/− mice were entrained on a 12-h light:12-h dark cycle for > 2 weeks and released into constant darkness. The SCN were isolated by laser microdissection from 10 individual animals and pooled for a single DNA microarray analysis, at either circadian time (CT) 6 or CT18 (n = 2 biological replicates at each time point per genotype). CT6 and CT18 correspond, respectively, to 6 and 18 hours after presumptive onset of daytime under constant darkness.


title: AOS10-FMT could rescue the adverse effects of myocardial damage

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of Busulfan on the heart, and foud that the AOS could rescue the side-effect of Busulfan in many factors, such as fight inflammanation, lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged heart induced by Busulfan

first: Xiangping

last: Ma


title: A forward genetic screen identifies potassium channel essentiality in SHH medulloblastoma maintenance [DNA-seq]

status: Public on Sep 16 2024

city: Toronto

first: Michael

middle: D

last: Taylor

address: 686 Bay St

country: Canada

institute: The Hospital for Sick Children

summary: Sequencing cancer genomes is predicted to uncover therapeutic tumor vulnerabilities. This has been complicated by the abundance of genetic alterations which are either non-functional, or only important in tumor initiation or progression. Distinguishing tumor maintenance genes from initiation, progression, and passenger genes is critical for developing effective cancer therapy. We employed a functional genomic approach using the Lazy Piggy transposon to identify tumor maintenance genes in vivo, and apply this to SHH medulloblastoma (MB). Combining Lazy Piggy screening in mice and transcriptomic profiling of human MB, we discovered candidate maintenance genes including the voltage-gated potassium channel Kcnb2. Genetic knockout of Kcnb2 impairs MB growth. Kcnb2 mediates potassium efflux in MB-propagating cells to govern cell volume. Loss of Kcnb2 leads to chronic osmotic swelling and decreased plasma membrane tension, which elevates endocytosis to dampen Egfr signaling, thereby mitigating proliferation of MB-propagating cells. Kcnb2 is largely dispensable for mouse development and synergizes with anti-SHH therapy in treating MB. These results demonstrate the utility of the Lazy Piggy functional genomic approach in identifying cancer maintenance genes, and elucidate a mechanism by which a potassium channel integrates biomechanical and biochemical signaling to promote MB aggression.

overall_design: To identify Shh medulloblastoma maintenance driver genes, we sequenced restriction SPLINK gDNA libraries from Lazy Piggy mouse tumours from mice treated or untreated with tamoxifen.


title: A forward genetic screen identifies potassium channel essentiality in SHH medulloblastoma maintenance [RNA-seq]

overall_design: To identify transcriptional changes following tamoxifen-induced remobilization of Lazy Piggy transposons, we sequenced cDNA libraries reverse transcribed from bulk RNA from mouse Lazy Piggy-induced Shh tumours. Additionally, to identify transcriptional changes following Kcnb2 knockout in an established model for Shh medulloblastoma, we sequenced cDNA libraries reverse transcribed from bulk RNA from mouse Math1-Cre; SmoM2 tumours that were Kcnb2 wild-type or knockout.


title: Induction of a distinct macrophage population and protection from lung injury and fibrosis by Notch2 blockade [Ipt]

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

summary: Macrophages are pleiotropic and diverse cells that populate all tissues of the body. Besides tissue-specific resident macrophages such as alveolar macrophages, Kupffer cells and microglia, multiple organs harbor at least two subtypes of other resident macrophages at steady state. During certain circumstances, like tissue insult, additional subtypes of macrophages are recruited to the tissue from the monocyte pool. Recently, a recruited macrophage population marked by expression of Spp1, Cd9, Gpnmb, Fabp5, and Trem2 has been described in several models of organ injury and cancer, and linked to fibrosis in mice and humans. Here, we show that Notch2 blockade, given systemically or locally, leads to an increase in this putative pro-fibrotic macrophage in the lung and that this macrophage state can only be adopted by monocytically derived cells and not resident alveolar macrophages.  Unexpectedly, using a bleomycin and COVID19 model of lung injury and fibrosis, we find that the expansion of these macrophages before lung injury does not promote fibrosis but rather appears to ameliorate it. This suggests that these damage-associated macrophages are not by themselves drivers of fibrosis in the lung.

overall_design: CD45.1 Csf2raKO mice were transplanted with CD45.2 WT alveolar macrophages. aNotch2 or control antibody was applied IT to the mice. Lung intersitital macrophages, monocytes, and alveolar machrophages were isolated, labeled with CD45.1 and CD45.2 CITE-Seq antibodies and analyzed using the 10x system (5').

first: Mayra

last: Cruz Tleugabulova

first: Sandra P

first: Antonie

last: Lechner

first: Basak

last: Corak

first: Christoph

last: Schneider

first: Maximilian

last: Nitschke

first: Andrey

last: Shaw


title: Effect of depletion of CDK4 on gene expression of MCF-7 breast cance cells

city: shanghai

first: Fan

last: Wei

address: 501 haike road

department: Divison of Anti-Tumor Pharmacology

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary: CDK4/6 inhibitors act as a cytostatic by targeting CDK4/6-cyclin D, and have achieved great success in hormone receptor-positive breast cancer treatment. Beyond cell cycle signaling pathway, recent research on non-cell cycle related functions of CDK4/6 has been blooming. Insights in this field may expand the therapeutic benefits of CDK4/6 inhibitors. Here, we attempt to explore the effects of CDK4/6 inhibitors on breast cancer from the perspective of epigenetic modifications, especially histone modifications, through high-throughput proteomic and genomics approaches. We reveal that inhibition of CDK4 directly suppresses phosphorylation of p300, an acetyltransferase, stimulates its ubiquitin degradation, and down-regulates the histone H3K27ac. Then, p300-mediated transcriptionally inhibition of BRCA1 and enrichment of breast cancer stem cells (BCSC) gene signatures lead to the increase of the proportion of ALDH1+ breast CSCs in ER+ breast cancer after long treatment with CDK4/6 inhibitors in vitro and in vivo. our results reveal a novel phosphorylation substrate of CDK4/cyclin D complex, and offer an unrecognized side effect of CDK4/6 inhibitors, inducing stem cell properties in ER+ breast cancer.

overall_design: We established MCF-7 cell line in which target gene has been knocked down by siRNA.


title: AtMAN6 coordinates cell growth and secondary cell wall formation in xylem development

city: 上海市

first: bo

last: li

state: 上海

address: 上海市徐汇区枫林路300号植物生理生态研究所

institute: SIPPE

summary: We observed that the Arabidopsis endo-1,4-mannanase gene AtMAN6 is involved in the formation of cell walls in vascular tissues. In the inflorescence stem, the man6 mutant had smaller vessel cells with thicker secondary cell walls and shorter fiber cells. Elongation growth was reduced in the root, and secondary cell wall deposition in vessel cells occurred early. Overexpression of AtMAN6 resulted in the inverse phenotypes of the man6 mutant. AtMAN6 was discovered on the plasma membrane and was specifically expressed in vessel cells during its early development. The AtMAN6 protein degraded galactoglucomannan to produce oligosaccharides, which caused secondary cell wall deposition in vessel and fiber cells to be delayed. Transcriptome analysis revealed that the expression of genes involved in the secondary cell wall synthesis pathway was changed in both man6 mutant and AtMAN6 overexpression plants. AtMAN6's carboxyl-terminal cysteine repeats motif (CCRM) was found to facilitate homodimerization and is required for its activity. According to the findings, the oligosaccharides produced by AtMAN6 hydrolysis may act as a signal to mediate this coordination between cell expansion and SCW deposition.

overall_design: In order to examine the MAN6 genetic function in regulation of cell wall formation, the T-DNA insertion mutant man6 (SALK_129977) and the transgenic Arabidopsis (MAN6 overexpression, OE-1 and OE-4, two separate lines with strong transgene expression) were collected and generated for characterization of their inflorescence stem growth


title: Restoring hippocampal glucose metabolism rescues cognition across Alzheimer disease pathologies

city: Stanford

first: Katrin

last: Andreasson

address: 1201 Welch Road MSLS P250

department: 1Dept of Neurology & Neurological Sciences

institute: Stanford University

summary: Impaired cerebral glucose metabolism is a pathologic feature of Alzheimer Disease (AD), and recent proteomic studies highlight a disruption of glial carbohydrate metabolism with disease progression. Here, we report that inhibition of indoleamine-2,3-dioxygenase 1 (IDO1), which metabolizes tryptophan to kynurenine (KYN) in the first step of the kynurenine pathway, rescues hippocampal memory function and plasticity in preclinical models of amyloid and tau pathology by restoring astrocytic metabolic support of neurons. Activation of IDO1 in astrocytes by amyloid-beta42 and tau oligomers, two major pathological effectors in AD, increases KYN and suppresses glycolysis in an AhR-dependent manner. Conversely, pharmacological IDO1 inhibition restores glycolysis and lactate production. In amyloid-producing APPSwe-PS1∆E9 and 5XFAD mice and in tau-producing P301S mice, IDO1 inhibition restores spatial memory and improves hippocampal glucose metabolism by metabolomic and MALDI-MS analyses. IDO1 blockade also rescues hippocampal long-term potentiation (LTP) in a monocarboxylate transporter (MCT)-dependent manner, suggesting that IDO1 activity disrupts astrocytic metabolic support of neurons. Indeed, in vitro mass-labeling of human astrocytes demonstrates that IDO1 regulates astrocyte generation of lactate that is then taken up by human neurons. In co-cultures of astrocytes and neurons derived from AD subjects, deficient astrocyte lactate transfer to neurons was corrected by IDO1 inhibition, resulting in improved neuronal glucose metabolism. Thus, IDO1 activity disrupts astrocytic metabolic support of neurons across both amyloid and tau pathologies and in a model of AD iPSC-derived neurons. These findings also suggest that IDO1 inhibitors developed for adjunctive therapy in cancer could be repurposed for treatment of amyloid- and tau-mediated neurodegenerative diseases.

overall_design: The goal of this project was to investigate the impacts of IDO1 inhibition in Alzheimer's disease and cognitively normal astrocytes via the small molecule PF-068. To achieve this, isogenic astrocytes and neurons were co-cultured in a transwell system for 2 days. The cell types were then separated overnight and astrocytes were treated with PF-068 or vehicle. Following a PBS wash, neurons and astrocytes were reunited and fed fresh medium for 4 hours.

first: Paras

last: Minhas

first: Jeffrey

last: Jones

first: Amira

last: Latif-Hernandez


title: Transcriptome of type 2 alveolar epithelial cells (AT2 cells) with DNMT1 inihibition in vivo

city: New York

first: Xueqian

last: Zhuang

address: 417 E 68th Street

institute: Memorial Sloan Kettering Cancer Center

summary: DNA methylation patterns alter with age. However, it remains largely unknown how suppression of DNA methyltransferase changes the DNA methylation in AT2 cells. Here we looked into the transcriptome of AT2 with in vivo treatment of DNMT1 inhibitor in young mice and inverstigated how that alters the transcriptome.

overall_design: Young (12-16 weeks old) wildtype C57BL6/J mice were treated with 10mg/kg DNMT1 inhibitor (GSK 3685032) or vehicle twice per day. AT2 cells were harvested by FACS after 8 dyas treatment from young and aged vehicle-treated and young DNMT1i-treated mice.

first: Qing

last: Wang

first: Tuomas

last: Tammela

first: Emily

middle: S

last: Wong


title: Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments  [Hi-C and UMI4C]

city: Lausanne

first: Julien

last: Duc

address: Station 19 CH-1015 Lausanne

institute: EPFL

overall_design: HiC and UMI4C in HEK293T in WT, ZNF274KO conditions

first: Martina

last: Begnis

first: Didier

last: Trono


title: Tumor-intrinsic P2RY6 signaling promotes prostaglandin E2 production to suppress anti-tumor immunity [ATAC]

city: Beijing

first: Xilong

last: Xu

address: 7 Science Park Road ZGC Life Science Park, Beijing

institute: National Institute of Biological Sciences, Beijing

summary: Our RNAseq results showed that P2RY6 induced the expression of Ptgs1 and Ptgs2 in MC38 cells. To confirm whether P2RY6 increases the opening of cis-regulatory elements to promote Ptgs1/2 transcription, we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to determain the chromatin accessibility across the genome in MC38 cells with or without P2RY6 expression.

overall_design: Comparative profiling analysis of ATAC-seq data from control cells and P2ry6-expressing MC38 cells treated with UDP 12 hours (n=2).

first: Ting

last: Han


title: Dual Impacts of Serine/Glycine Free Diet in Enhancing Antitumor Immunity and Promoting Evasion via PD-L1 Lactylation [scTCR]

city: Chengdu

first: Zedong

last: Jiang

state: Sichuan

address: Guoxue road

institute: Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.

summary: The effect of Serine/glycine free diet (-SG diet) on colorectal cancer (CRC) remains unclear, meanwhile PD-1 inhibitors are less effective for most CRC patients with proficient mismatch repair/microsatellite stable (pMMR/MSS) characteristics. Here, we demonstrate that -SG diet inhibits CRC growth and promotes the accumulation of cytotoxic T cells to enhance anti-tumor immunity. Additionally, we also identified the lactylation of PD-L1 in tumor cells as a mechanism of immune evasion during cytotocix-T-cell-mediated anti-tumor responses, and blocking PD-1/PD-L1 signaling pathway is able to rejuvenate the function of CD8+ T cells recruited by -SG diet, indicating the clinical potential of combining -SG diet with immunotherapy. Finally, we conducted a single-arm, phase I study, which suggested -SG diet could be a feasible and safe strategy to regulate systemic immunology. Collectively, our findings highlight the promising therapeutic future of -SG diet for treating solid tumors.

overall_design: We collected subcutaneous tumors from mice treated with control diet and -SG diet respectively.

first: Huan

last: Tong

first: Linlin

last: Song

first: Keqin

last: Tan

first: Xiaomeng

last: Yin

first: Xuelei

last: Ma


title: Dual Impacts of Serine/Glycine Free Diet in Enhancing Antitumor Immunity and Promoting Evasion via PD-L1 Lactylation [scRNA-Seq]


title: Heritable states influence stem cell fates upon acquisition of cancer mutations

city: Barcelona

first: Daniel

last: Fernandez-Perez

state: Choose State

address: Carrer Baldiri Reixac 12

department: Aging and Metabolism

institute: IRB Barcelona

summary: Tumors with the same driver mutations can display a striking variation in their progression and treatment response, but the origins of this variation are still unclear. In this study, we use state-fate analysis to unveil that heritable stem cell states can influence how individual cells respond to the acquisition of the same cancer mutation. We develop a new methodological pipeline, single-cell Tracking of Recombinase Activation And Clonal Kinetics, and apply it to hematopoietic stem cells carrying Cre/Flp-conditional leukemia alleles. Tracking the gene expression changes and expansion kinetics of a common set of stem cell clones, with and without the same myeloid leukemia mutations, we unveil a striking heterogeneity in the malignant fates of diverse stem cells. First, we define that heritable clonal states persist in expansion cultures and cause the selection of a small group of clones with a specific fitness signature. Then, using mouse models of the most frequent initiating mutations, we define that these pre-existent stem cell states influence the mutation-induced changes in expansion, fate, and malignant gene expression programs. Initiating driver mutations increase the survival probability of clones with low fitness through enhancing their stemness programs. Surprisingly, the fate of high-fitness stem-cell clones is sometimes reversed, producing more mature leukemias, yet still carrying markers of their cell of origin. We further validate these HSC-of-origin signatures in bulk and single-cell RNAseq datasets from cancer patients. Our findings suggest that aggressive premalignant clonal expansions arise from low-fitness stem cells more frequently than previously expected.

overall_design: LARRY single-cell RNA-seq tracing experiment. 3 different timepoints (D7, D14, D27) and 3 different conditions (WT, Dnmt3a-mut, Npm1-mut), 2 biological replicates per timepoint and condition (replicate 1 is a male donor, replicate 2 is a female dolor).

first: Indranil

last: Singh

first: Alejo

last: Rodriguez-Fraticelli


title: Human enteroids as a tool to study conventional and ultra-high dose rate radiation

first: Katarina

last: Klett

address: 466 Lomita Mall

summary: Radiation therapy, one of the most effective therapies to treat cancer, is highly toxic to healthy tissue. The delivery of radiation at ultra-high dose rates, FLASH radiation therapy (FLASH), has been shown to maintain therapeutic anti-tumor efficacy while sparing normal tissues compared to conventional dose rate irradiation (CONV). Though promising, these studies have been limited mainly to murine models. Here, we leveraged enteroids, three-dimensional cell clusters that mimic the intestine, to study human-specific tissue response to radiation. We observed enteroids have a greater colony growth potential following FLASH compared with CONV. In addition, the enteroids that reformed following FLASH more frequently exhibited proper intestinal polarity. While we did not observe differences in enteroid damage across groups, we did see distinct transcriptomic changes. Specifically, the FLASH enteroids upregulated the expression of genes associated with the WNT-family, cell-cell adhesion, and hypoxia response. These studies validate human enteroids as a model to investigate FLASH and provide further evidence supporting clinical study of this therapy. Insight Box Promising work has been done to demonstrate the potential of ultra-high dose rate radiation (FLASH) to ablate cancerous tissue, while preserving healthy tissue. While encouraging, these findings have been primarily observed using pre-clinical murine and traditional two-dimensional cell culture. This study validates the use of human enteroids as a tool to investigate human-specific tissue response to FLASH. Specifically, the work described demonstrates the ability of enteroids to recapitulate previous in vivo findings, while also providing a lens through which to probe cellular and molecular-level responses to FLASH. The human enteroids described herein offer a powerful model that can be used to probe the underlying mechanisms of FLASH in future studies.

overall_design: To determine transcriptional differences between FLASH- and CONV-irradiated human small intestine enteroids, enteroids were irradiated using 5 Gy doses of either FLASH or CONV and compared to an unirradiated control. Enteroids were pulled at 1 hr and 96 hrs for bulk RNA-sequencing. Three independent replicates were included per sample.

first: Briana

last: Martin-Villa

first: Victoria

last: Villarreal

first: Stavros

last: Melemenidis

first: Vignesh

last: Viswanathan

first: Rakesh

last: Manjappa

first: Ramish

last: Ashraf

first: Luis

last: Soto

first: Brianna

last: Lau

first: Suparna

last: Dutt

first: Erinn

last: Rankin

first: Billy

last: Loo

first: Sarah

last: Heilshorn


title: Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments

first: Julien

last: Duc

overall_design: Refer to individual Series


title: A single cell RNA-Seq 5’ study of splenic marginal zone lymphomas (SMZL) and spleen healthy donors

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

country: France

institute: IUCT-ONCOPOLE

summary:
Purpose: Single cell RNA-Seq was used to characterize in depth splenic samples obtained from splenic marginal zone lymphomas
Methods: 3 frozen samples of spleen and blood from SMZL patients, and healthy donors were selected and thawed for performing a 10X genomics single cell RNA-Sequencing 5' assay.
Results: Tumor cells formed mainly patient specific-B cell clusters, while  T-cells from the 3 patients and healthy donors clustered together.
Conclusion: Single RNA-Seq unveils inter- and intra-patient heterogeneity.

overall_design: Frozen cell suspensions obtained from diagnosed splenic marginal zone lymphomas and healthy donors were selected for injection in the 10X chromium device for droplet-based RNA extraction, reverse transcription and cDNA amplification. Libraries were made with the Chromium i7 sample index plate (GENO55823). Sequencing was performed on a NextSeq 550 (Illumina).

first: Juan

last: Cerapio Arroyo

first: Camille

last: Laurent

first: Jean-Jacques

last: Fournié


title: Nuclear IMPDH2 controls the DNA damage response by modulating PARP1 activity

first: Sdelci

last: Lab

address: Dr. Aiguader 88

department: Genome Biology

institute: Centre for Genomic Regulation (CRG)

summary:
Nuclear metabolism and DNA damage response are intertwined processes, but the precise molecular connections remain elusive. Here, we delve into this crosstalk using as a model triple-negative breast cancer (TNBC), a subtype often prone to DNA damage accumulation. We reveal that the de novo purine synthesis enzyme Inosine monophosphate dehydrogenase 2 (IMPDH2) is enriched on chromatin in TNBC when compared to other subtypes. IMPDH2 chromatin localization is DNA damage dependent and IMPDH2 repression leads to DNA damage accumulation. On chromatin, IMPDH2 interacts and modulates Poly [ADP-ribose] polymerase 1 (PARP1) activity by controlling nuclear availability of nicotinamide adenine dinucleotide (NAD+) -a shared metabolic cofactor- to fine-tune the DNA damage response. However, when IMPDH2 is restricted to the nucleus, it depletes nuclear NAD+, leading to PARP1 cleavage and cell death. Our study identifies a non-canonical nuclear role for IMPDH2 that act as convergence point of nuclear metabolism and DNA damage response.
# Contributed equally
*Corresponding authors: sara.sdelci@crg.eu; marta.garciacao@crg.eu

overall_design: To investigate the role of IMPDH2 in MDA-MB-231 triple-negative breast cancer (TNBC) cell line, IMPDH2 gene was knocked-out and reconstituted in different forms and under different growth conditions.

first: Lorena

last: #Espinar

first: Marta

last: #*Garcia-Cao

first: Alisa

last: Schmidt

first: Savvas

last: Kourtis

first: Antoni

middle: G

last: Zapater

first: Carla

last: Aranda-Vallejo

first: Ritobrata

last: Ghose

first: Laura

last: Garcia-Lopez

first: Ilir

last: Sheraj

first: Natalia

last: Pardo-Lorente

first: Marina

last: Bantulà

last: Pascual-Reguant

first: Evangelia

last: Darai

first: Maria

last: Guirola

first: Joan

last: Montero

first: Sara

last: *Sdelci


title: Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments [ChIP-seq]

first: Julien

last: Duc

summary: Epigenetic mechanisms influencing chromatin architecture are key to the spatio-temporal control of transcription. Here we identify ZNF274 as a new regulator of chromosome compartmentalization that silences lineage-specific gene clusters. ZNF274 is a SCAN-bearing member of the Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs). Ablation of ZNF274 results in the transcriptional activation of genomic neighbourhoods encompassing, among others, zinc finger and protocadherin-encoding genes, with loss of H3K9me3 repressive mark, altered 3D genome conformation and de novo CTCF binding. In contrast to other factors that have been implicated in chromatin anchoring, ZNF274 is necessary both for transcriptional silencing and nucleolar tethering. While the establishment of silencing depends on the KRAB domain, we demonstrate that the SCAN domain is required to gather ZNF274 complexes at the nucleolus and efficiently spread heterochromatin. Thus, ZNF274 orchestrates the segregation of developmentally regulated gene clusters at nucleoli to allow timely and selective activation of cell-restricted alleles.

overall_design: ChIP-seqs of H3K9me3 and ZNF274 mutants in ZNF274KO HEK293T cells. Cut&Tag of H3K9me3 in WT and ZNF274 KO HEK293T cells.

first: Martina

last: Begnis

first: Didier

last: Trono


title: Protective variant in PLCγ2 mitigates Alzheimer’s disease associated pathology via enhancing beneficial microglia functions

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: PLCγ2-P522R (phospholipase C gamma 2, proline 522 to arginine) is a protective variant that reduces the risk for late onset Alzheimer’s disease (LOAD). Recently, it was shown to decrease β-amyloid pathology in 5XFAD mouse model of AD. In this study, our goal was to investigate the protective functions of PLCγ2-P522R variant in less aggressive mouse model of AD as well as to assess underlying mechanisms at the molecular and cellular level using mouse and human microglia models. The effects of the protective PLCγ2-P522R variant on microglia activation, AD-related β-amyloid and neuronal pathologies, as well as behavioral changes were investigated in PLCγ2-P522R knock-in mice crossbred with an APP/PS1 mouse model of AD. Transcriptomic, proteomic, and functional studies were carried out in cultured and acutely isolated adult PLCγ2-P522R mouse microglia to study molecular mechanisms. Finally, microglia-like cell models generated from blood and skin biopsy samples of the PLCγ2-P522R variant carriers were employed to translate the key findings in human cells. Our results demonstrate that the PLCγ2-P522R variant reduces brain β-amyloid plaque burden of APP/PS1 mice. Simultaneously, PLCγ2-P522R variant increased non-proinflammatory microglia activation and microglia clustering around β-amyloid plaques, leading to reduced β-amyloid plaque-associated neuronal dystrophy. In cultured mouse primary microglia, PLCγ2-P522R variant decreased accumulation of large lipid droplets, reduced cell stress, and increased acute response to strong inflammatory stimuli. Transcriptomic and proteomic analyses in acutely isolated adult mouse microglia as well as in human monocyte-derived microglial cells showed that PLCγ2-P522R upregulates mitochondrial fatty acid oxidation and downregulates inflammatory/interferon signaling pathways. Accordingly, PLCγ2-P522R increased mitochondrial respiration in iPSC -derived microglial cells. Together, these findings suggest that PLCγ2-P522R variant exerts protection against AD-associated β-amyloid and neuronal pathologies via enhancing microglial barrier formation around β-amyloid plaques, but suppressing pro-inflammatory activation. Observed changes in fatty acid metabolism and mitochondrial flexibility as well as the downregulation of genes involved in inflammatory signaling pathways suggest that these protective effects of the PLCγ2-P522R variant are mediated through an anti-ageing mechanism.

overall_design: APP/PS1xPLCG2-P522R knock in mice (n=4) and respective APP/PS1 control animals (n=4) were sacrificed and transcardially perfused with saline at the age 13-months. Half of the brain was dissected into regional blocks and snap frozed in liquid nitrogen. Temporo-occipital cortex was then homogenized on DPBS and an aliquot was subjected to RNA sequencing (see protocol section). The whole brain of subset of above-described mice was used for acute CD11b+ microglia isolation utilizing magnetic bead-based isolation and subjected to RNA sequencing. Wildtype animals without the AD background were included as controls in the above mentioned analyses. Similarly, CD11b+ microglia isolated from 13-month-old PLCG2-P522R knock in (n=4) and wildtype (n=3) mice without the AD background were used for RNA sequencing studies.

first: Mari

last: Takalo

first: Mikko

last: Hiltunen

first: Heli

last: Jeskanen

first: Inka

last: Kervinen


title: Gene Expression Data for the study of the Interaction of Uteroplacental Insufficiency and Postnatal Western Diet on the Hepatic Transcriptome in Young Adult Female and Male Guinea Pigs

city: London

first: Ousseynou

last: Sarr

state: United States

address: 1811 Creekside Street

department: Physiology & Pharmacology

institute: Western universitry

summary:
We explored the hypothesis that gene expression will be dysregulated in the liver of low birth weight (LBW) offspring, distinct from normal birth weight (NBW) offspring, in young adulthood when both birth weight outcomes are challenged with a lifelong postnatal Western diet (WD).
Independent of diet, in LBW vs. NBW males, 7 differentially expressed genes (DEGs) were identified, most of which downregulated (5 vs. 2) in LBW males. A similar trend was observed in LBW vs. NBW females, where 12 DEGs were identified, predominantly downregulated in the LBW group (9 vs. 3), irrespective of diet. Lifelong WD consumption exerted a marked influence on liver transcription profiles. Notably, 553 (444 upregulated and 109 downregulated) and 639 (533 upregulated and 106 downregulated) DEGs were identified in males and females, independent of birth weight, respectively. Additionally, in females, birth weight and WD both impacted six genes. Further, transcriptomic analysis revealed 22 (9 upregulated and 13 downregulated) and 55 (12 upregulated and 43 downregulated) DEGs between LBW/WD and NBW/WD groups in males and females, respectively.

overall_design: A whole-Transcript Expression Analysis Gene Titan was conducted (Genome Québec Innovation Centre, QU, Canada) on guinea pig livers of 5 NBW/CD males, 5 LBW/CD males, 5 NBW/WD males, 5 LBW/WD males, 5 NBW/CD females, 5 LBW/CD females, 3 NBW/WD males, and 5 LBW/WD females. The microarray .CEL files were imported into the Transcriptome Analysis Console (TAC) (version 4.0) (Life Technologies, Carlsbad, CA) and the raw data  normalized using the Robust Multiple-Array Averaging (RMA) method. Differentially expressed genes (DEGs) were identified using the TAC Expression (Gene) analysis method, following the TAC user guide. Two-way ANOVA and customized comparisons in TAC software were performed to determine the main effect of birth weight and diet, and to compare LBW and NBW within each diet, respectively. To determine the significance of DEGs, a cut-off for the fold change value ± 2 and p-value < 0.05 was applied.

first: Jennifer

middle: A

last: Thompson

first: Patti

last: Kiser

first: Timothy

last: Regnault


title: Transcriptome of primary KP lung adenocarcinoma cells with Nupr1 knockout

first: ZHUXUAN

last: LI

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

summary: The aim for this bulk mRNA sequencing project is to understand the age-specific impact of Nupr1 suppression in lung adenocarcinoma by CRISPR-Cas9 mediated gene knockout in vivo.

overall_design: Lung adenocarcinomas were induced in aged (> 2 years old) vs young (12-16 weeks old) Kras LSL-G12D/+; Trp53 fl/fl; Rosa26-LSL-EGFP-Cas9 (KPCas9) mice. Mice were intubated with lentivirally delivered Cre recombinase, together with a control or two sgRNAs targeting murine Nupr1. Ten weeks after tumor induction, GFP positive tumor cells were sorted by FACS from both aged and young tumor-bearing mice and subjected to mRNA sequencing.

first: Xueqian

last: Zhuang

first: Simon

last: Joost

first: Tuomas

last: Tammela


title: Age-related Increase of CD38 Directs Osteoclastogenic Potential of Monocytic Myeloid-Derived Suppressor Cells through Mitochondrial Dysfunction

city: Buffalo

first: Jonathan

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

summary: An aged immune system undergoes substantial changes where myelopoiesis dominates within the bone marrow. Monocytic-MDSCs (M-MDSCs) have been found to play an important role in osteoclastogenesis and bone resorption. In this study, we sought to provide a more comprehensive understanding of the osteoclastogenic potential of bone marrow M-MDSCs during normal aging through transcriptomic and metabolic changes. Using young mature and aged mice, detailed immunophenotypic analyses of myeloid cells revealed that the M-MDSCs were not increased in bone marrow, however M-MDSCS were significantly expanded in peripheral tissues. Although aged mice exhibited a similar number of M-MDSCs in bone marrow, these M-MDSCs had significantly higher osteoclastogenic potential and greater bone resorption capacity. Intriguingly, osteoclast progenitors from aged bone marrow M-MDSCs exhibited greater mitochondrial respiration rate and glucose metabolism. Further, transcriptomic analyses revealed the upregulation of mitochondrial oxidative phosphorylation and glucose metabolism genes. Interestingly, there was a 3-fold increase in Cd38 mRNA gene expression, consistent with the Mouse Aging Cell Atlas transcriptomic database. CD38 regulates NAD+ availability, and 78c, a small molecule inhibitor of CD38, reduced the mitochondrial oxygen consumption rate and glucose metabolism and inhibited the osteoclastogenic potential of aged mice bone marrow-derived M-MDSCs. These results indicate that the age-related increase in Cd38 expression in M-MDSCs bias the transcriptome of M-MDSCs towards osteoclastogenesis. This enhanced understanding of the mechanistic underpinnings of M-MDSCs and their osteoclastogenesis during aging could lead to new therapeutic approaches for age-related bone loss and promote healthy aging.

overall_design: Total RNA was obtained from sorted CD11b+Ly6G-Ly6Chi M-MDSCs from young and old mice using RNeasy Mini Kit (Qiagen, USA). The whole-genome sequencing was performed using NovaSeq 6000 System (Illumina Inc, San Diego, CA). The FastQC and FastQ were used to review the sequencing quality and detect potential contamination, respectively. Bioconductor package DESeq2 version 1.32.0. was used to detect the differentially expressed genes.

first: Ramkumar

last: Thiyagarajan

first: Lixia

last: Zhang

first: Omar

last: Glover

first: Hyu

last: Kwack

first: Sara

last: Ahmed

first: Emma

last: Murray

first: Nanda

last: Yellapu

first: Kenneth

last: Seldeen

first: Bruce

last: Troen

first: Keith

last: Kirkwood


title: HNRNPU is essential for proper murine skin development

city: Wonju

first: Seung-Phil

last: Hong

address: 20 Ilsan-ro

department: Department of Dermatology

country: South Korea

institute: Yonsei University Wonju College of Medicine

summary: Loss of Hnrnu in epidermis of mouse resulted in developmental failure of the epidermis and hair follicle.

overall_design: Comparing the transcriptome analysis (bulk RNA seq) between Hnrnpu-KO epidermis and control epidermis

first: George

last: Sen


title: Rice amino acid transporter OsMP1 is involved in amino acid homeostasis and mediates broad-spectrum resistance to blast fungus and bacterial blight through upregulating JA signaling pathway

city: Nanjing

first: Tingting

last: Jiang

address: NO.1 Weigang

institute: NANJING AGRICULTURAL UNIVERSITY

summary: To investigate the molecular mechanisms about how OsMP1 regulates rice blast resistance, we established the CR4 line in which target gene has been knocked down by CRISPR-Cas9 gene editing. We then performed gene expression profiling analysis using data obtained from RNA-seq of CR4 and wild-type Hei.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type Hei and OsMP1 knockdown expression transgenic line CR4.

first: Ning

last: Huang

first: Zhixue

last: Wang

first: Lu

last: Ma

first: Xinying

first: Lingtong

last: Shen

first: Ying

first: Yao

last: Yu

first: Wei

first: Yunxin

last: Fan

first: Kunquan

last: Liu

first: Zhi

last: Zhao

first: Ziwei

last: Xiong

first: Qisheng

last: Song

first: Haijuan

last: Tang

first: Hongsheng

first: Yongmei

last: Bao


title: STUB1-mediated K63-linked ubiquitination of UHRF1 promotes the progression of cholangiocarcinoma by maintaining DNA hypermethylation of PLA2G2A

city: Wuhan

first: Junsheng

last: Chen

state: Wuhan

address: Bao Feng Street

department: Department of Biliary-Pancreatic Surgery

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

summary: Cholangiocarcinoma (CCA) is a highly malignant tumor characterized by a lack of effective targeted therapeutic strategies. The protein UHRF1 plays a pivotal role in the preservation of DNA methylation and works synergistically with DNMT1.      Posttranscriptional modifications (PTMs), such as ubiquitination, play indispensable roles in facilitating this process. Nevertheless, the specific PTMs that regulate UHRF1 in CCA remain unidentified. We confirmed the interaction between STUB1 and UHRF1 through mass spectrometry analysis. Furthermore, we investigated the underlying mechanisms of the STUB1-UHRF1/DNMT1 axis via co-IP experiments, denaturing IP ubiquitination experiments, nuclear‒cytoplasmic separation and immunofluorescence experiments. STUB1-UHRF1/DNMT1-mediated DNA methylation plays a crucial role in promoting the epigenetic silencing of tumor suppressor genes (TSGs) and facilitating tumor progression. To investigate the specific TSGs regulated by the STUB1-UHRF1/DNMT1 axis in CCA cells, RNA-seq analysis of overexpressed STUB1 and negative control TFK1 cells was performed.

overall_design: To investigate the specific tumor suppressor genes (TSGs) regulated by the STUB1-UHRF1/DNMT1 axis in CCA cells, RNA-seq analysis of overexpressed STUB1 and negative control TFK1 cells (with 3 replicates in each group) was performed.

first: Da

first: Guanhua

last: Wu

first: Fei

first: Wenzheng

first: Qi

first: Yiyang

last: Kuai

first: Wenhua

first: Yongqiang

last: Qi

first: Bing

first: Yongjun


title: ThymoSpheres culture: a model to study human polyclonal unconventional T cells

city: Ghent

first: Laurenz

last: De Cock

address: Corneel Heymanslaan 10

department: Department of Diagnostic Sciences

country: Belgium

institute: Ghent University

summary: In vitro cultures remain crucial for studying the fundamental mechanisms of human T cell development. Here, we introduce a novel in vitro cultivation system based on ThymoSpheres (TS): dense spheroids of DLL4 expressing stromal cells and human hematopoietic precursor cells (HPCs), in the absence of thymic epithelial cells. These spheroids are subsequently cultured at the air-liquid interphase. TS generate large numbers of mature T cells, are easy to manipulate, scalable, and can be repeatably sampled to monitor T cell differentiation. The mature T cells generated from primary human HPCs were extensively characterized using single-cell RNA and combinedT cell receptor (TCR) sequencing. These predominantly CD8α T cells exhibit transcriptional and CDR3 characteristics recently described in a human polyclonal αβ unconventional T cell (UTC) lineage. This includes the expression of hallmark genes associated with agonist selection, such as IKZF2(Helios), and expression of various Natural Killer (NK) receptors. The TCR repertoire of these UTCs is polyclonal and enriched for CDR3-associated autoreactive features and early rearrangements of the TCRα chain. In conclusion, TS cultures offer an intriguing platform to study the development of this human polyclonal UTC lineage and its inducing selection mechanisms.

overall_design: Multiple TS-containing inserts were harvested and pooled after 9 weeks of culture. The CD3+ TCRγδ- fraction was sorted for single-cell analysis.

first: Lore

last: Billiet

first: Niels

last: Vandamme

first: Bart

last: Vandekerckhove


title: Decoding Reciprocal Regulation of ASPM and FoxM1 Amplifies the Oncogenic Progression in Human Hepatocellular Carcinoma Protein Composition of Whole Nucleosomes with Nuc-MS

city: Xi'an Shaanxi

first: Xiang

last: Zhang

address: Changle West Road 169

institute: The Fourth Military Medical University

summary: Fork-head box protein M1 (FoxM1) is a transcription factor which plays critical roles in development and progression of multiple cancers, including human hepatocellular carcinoma (HCC). However, the regulatory mechanism of FoxM1 itself remains largely unclear. Here, we discovered a novel role of abnormal spindle-like microcephaly associated (ASPM) in HCC, which binds to FoxM1 protein and enhances its stability by preventing proteasome-mediated degradation. ChIP-sequencing data showed that ASPM and FoxM1 co-occupies on the promoter region of multiple genes to promote their transcriptions, leading to the enhancement of a FoxM1-driven oncogenic progression. Intriguingly, FoxM1 binds to the promoter region of ASPM and transcriptionally activates the ASPM expression. Furthermore, data from clinical samples showed that a higher co-expression of ASPM and FoxM1 significantly correlates with poor prognosis in HCC, indicating that a positive feedforward loop between ASPM and FoxM1 coordinately promotes the aggressive progression in HCC. Collectively, our study reveals that reciprocal regulation of ASPM and FoxM1 amplifies the oncogenic progression and emphasizes an ASPM-FoxM1 feedforward loop could be a potential biomarker and therapeutic target in HCC.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ASPM and FoxM1 in HepG2 cells.

first: Rui

first: Xunliang

last: Jiang

first: Ke

last: Wang


title: ERK5 suppression overcomes FAK inhibitor resistance in mutant KRAS-driven non-small cell lung cancer [p697_ERK5]

city: Bern

first: Georgia

last: Konstantinidou

address: Inselspital, INO-F

institute: Institute of Pharmacology, University of Bern

summary: Mutated KRAS serves as the oncogenic driver in 30% of non-small cell lung cancers (NSCLCs) and is associated with metastatic and therapy-resistant tumors. Focal Adhesion Kinase (FAK) acts as a mediator in sustaining KRAS-driven lung tumors, and although FAK inhibitors are currently undergoing clinical development, clinical data indicated that their efficacy in producing long-term anti-tumor responses is limited. Here we revealed two FAK interactors, extracellular-signal-regulated kinase 5 (ERK5) and cyclin-dependent kinase 5 (CDK5) as key players underlying FAK-mediated maintenance of KRAS mutant NSCLC. Inhibition of ERK5 and CDK5 synergistically suppressed FAK function, decreased proliferation and induced apoptosis owing to exacerbated ROS-induced DNA damage. Accordingly, concomitant pharmacological inhibition of ERK5 and CDK5 in a mouse model of KrasG12D-driven lung adenocarcinoma suppressed tumor progression and promoted cancer cell death. Cancer cells resistant to FAK inhibitors showed enhanced ERK5-FAK signaling dampening DNA damage. Notably, ERK5 inhibition prevents resistance to FAK inhibitors, significantly enhancing the efficacy of antitumor responses. Therefore, we propose ERK5 inhibition as a potential co-targeting strategy to counteract FAK inhibitor resistance in NSCLC.

overall_design: A549 cells were treated either with ERK5 inhibitor (XMD8-92) or a CDK5 inhibitor (Seliciclib, also named roscovitine "ROSCO") or in combination (combo) and RNA was extracted for RNA seq.

first: Chiara

last: Pozzato

first: Gonçalo

last: Outeiro-Pinho

first: Mirco

last: Galiè

first: Giorgio

last: Ramadori


title: ERK5 suppression overcomes FAK inhibitor resistance in mutant KRAS-driven non-small cell lung cancer [p826_PND_A549]

overall_design: RNA seq from A549 parental cells, or VS-4718 (FAK inhibitor) resistant cells (VS4718-T) or parental cells treated acutely with VS-4718 (for 12h)


title: Lung cancer bone metastasis

city: Shanghai

first: Xiaoshen

state: Shanghai

address: 1239 siping road

institute: Tongji University

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


title: Single-cell transcriptome profiling of lung cancer bone metastasis

summary: Single nuclei transcriptome profiling of metastatic lesions for lung cancer bone metastasis.

overall_design: To investigate gene and cell signatures in osteolytic bone metastatic niche.

first: Zhiyu

first: Yifeng

last: Gu

first: Fengying

first: Guanghui

last: Gao

first: Wei

last: Li

first: Hui

last: Zhao

first: Xuefei

first: Anwen

last: Xiong

first: Lei

first: Chunxia

last: Su

first: Shengxiang

last: Ren

first: Caicun

last: Zhou


title: ELONGATED HYPOCOTYL5-mediated light signaling promotes shoot regeneration in Arabidopsis thaliana

city: Yokohama

first: Yu

last: Chen

address: 1-7-22 Suehirocho, Tsurumi-ku

institute: RIKEN

summary: Injured plant somatic tissues regenerate themselves by establishing the shoot or root meristems. In Arabidopsis (Arabidopsis thaliana) a two-step culture system ensures regeneration by first promoting the acquisition of pluripotency and subsequently specifying the fate of new meristems. Although previous studies have reported the importance of phytohormones auxin and cytokinin in determining the fate of new meristems, it remains elusive whether and how the environmental factors influence this process. In this study, we investigated the impact of light signals on shoot regeneration using Arabidopsis hypocotyl as explants. We found that light signals promote shoot regeneration while inhibiting root formation. ELONGATED HYPOCOTYL 5 (HY5), the pivotal transcriptional factor in light signaling, plays a central role in this process by mediating the expression of key genes controlling the fate of new meristems. Specifically, HY5 directly represses root development genes and activates shoot meristem genes, leading to the establishment of shoot progenitor from pluripotent callus. We further demonstrated that the early activation of photosynthesis is critical for shoot initiation, and this is transcriptionally regulated downstream of the HY5-dependent pathways. In conclusion, we uncovered the intricate molecular mechanisms by which light signals control the establishment of new meristem through the regulatory network governed by HY5, thus, highlighting the influence of light signals on plant developmental plasticity.

overall_design: To investigate the impact of HY5-mediated light signals in organ regeneration, we performed gene expression profilling analysis using Arabidopsis hypocotyl explants. The RNA-seq data with three biological replicates are obtained from the explants incubated on callus-inducing medium (CIM) and shoot-inducing medium (SIM) under different conditions for wild-type Col-0 and hy5-2 mutant at four time points.

first: Ayako

last: Kawamura

first: Takamasa

last: Suziki

first: Keiko

last: Sugimoto


title: Prostate cancer cancer-associated fibroblasts with stable markers post-androgen deprivation therapy associated with tumor progression and castration resistant prostate cancer

city: Shenyang

first: Bitian

last: Liu

state: Liaoning

address: No.36 Sanhao Street

institute: China Medical University

summary: The specificity and clinical relevance of cancer-associated fibroblasts (CAFs) in prostate cancer (PCa), as well as the impact of androgen deprivation therapy (ADT) on CAFs, remain to be fully elucidated. Employing cell lineage diversity and weighted gene co-expression network analysis (WGCNA), we pinpointed a unique CAF signature exclusive to PCa. The specificity of this CAF signature was validated through single-cell RNA sequencing (scRNA-seq), cell line RNA sequencing, and immunohistochemistry. This signature associates CAFs with tumor progression, elevated Gleason scores, and the emergence of castration resistant prostate cancer (CRPC). Utilizing scRNA-seq on collected samples, we demonstrated that the CAF-specific signature is not altered by ADT, maintaining its peak signal output. Identifying a PCa-specific CAF signature and observing signaling changes in CAFs after ADT lay an essential groundwork for further PCa studies.

overall_design: One month after androgen deprivation therapy, single-cell suspensions were obtained from 2 cases of prostate cancer, and samples were loaded for 10xGenomics scRNA-seq

first: Shen

last: Pan

first: Zhenhua


title: Conditional deletion of HIF-2α in mouse nucleus pulposus reduces fibrosis and provides mild and transient protection from age-dependent structural changes in intervertebral disc

city: Philadelphia

first: Shira

last: Johnston

state: PA

address: 1025 Walnut St., Suite 511 College Bldg.

institute: Thomas Jefferson University

summary:
Hypoxia inducible factors (HIFs) are critical to the development and homeostasis of the intervertebral disc. While HIF-2α, one of the main HIF-α isoforms is expressed in nucleus pulposus (NP) cells, its functions remain unknown.
We used microarrays to explore the transcriptomics of differentially expressed genes between control and HIF-2α cKO NP cells in 6M and 14M mice.

overall_design: NP tissue were dissected from discs from control (n=4) and HIF-2α cKO mice (n=4). Mice were aged until they became 6-months-old or 14-months-old. RNA extraction was prefomed and hybridization on Affymetrix microarrays.

first: Makarand

middle: V

last: Risbud


title: Integrative single-cell and spatial transcriptomic analyses identify a pathogenic cholangiocyte niche and TNFRSF12A as therapeutic target for biliary atresia

city: Guangzhou

last: Luo

state: Guangzhou

address: Number 58, zhongshan er road, Yuexiu,

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: We performed single cell 5' RNA sequencing, and B cell receptor and T cell receptor V(D)J sequencing analyses on liver biopsies of nine patients with biliary atresia and three patients with choledochal cyst at diagnosis to generate the liver cell atlas.

overall_design:
Single cell 5' RNA sequencing and V(D)J sequencing analyses of liver biopsies from nine patients with biliary atresia and three patients with choledochal cyst were collected at the time of diagnosis.
10x Genomics Chromium Next GEM Single Cell 5' RNA-seq and single cell V(D)J sequencing.

**Submitter declares that the raw data have not been provided due to patient privacy concerns**


title: TSC/mTORC1 mediates mTORC2/AKT1 signaling in c-MYC-induced murine hepatocarcinogenesis via centromere protein M

status: Public on Sep 15 2024

city: Honolulu

first: Xue

last: Wang

state: Hawaii

address: 701 Ilalo Street

institute: University of Hawaii Cancer Center

summary: Activated mTORC2/AKT signaling plays a role in hepatocellular carcinoma (HCC). Research has shown that TSC/mTORC1 and FOXO1 are distinct downstream effectors of AKT signaling in liver regeneration and metabolism. However, the mechanisms by which these pathways mediate mTORC2/AKT activation in HCC are not yet fully understood. Amplification and activation of c-MYC is a key molecular event in HCC. In this study, we explored the roles of TSC/mTORC1 and FOXO1 as downstream effectors of mTORC2/AKT1 in c-MYC-induced hepatocarcinogenesis. Using various genetic approaches in mice, we found that manipulating the FOXO pathway had minimal impact on c-MYC-induced HCC. In contrast, loss of mTORC2 inhibited c-MYC-induced HCC, an effect that was completely reversed by ablating TSC2, which activated mTORC1. Additionally, we discovered that p70/RPS6 and 4EBP1/eIF4E act downstream of mTORC1, regulating distinct molecular pathways. Notably, the 4EBP1/eIF4E cascade is crucial for cell proliferation and glycolysis in c-MYC-induced HCC. We also identified centromere protein M (CENPM) as a downstream target of the TSC2/mTORC1 pathway in c-MYC-driven hepatocarcinogenesis, and its ablation entirely inhibited c-MYC-dependent HCC formation. Our findings demonstrate that the TSC/mTORC1/CENPM pathway, rather than the FOXO cascade, is the primary signaling pathway regulating c-MYC-driven hepatocarcinogenesis. Targeting CENPM holds therapeutic potential for treating c-MYC-driven HCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the mouse c-MYC/MCL1 HCCs treated with MLN0128, everolimus, vehicle as well as C57BL/6 wild-type normal livers

first: Yi

first: Shu

last: Zhang

first: Guoteng

last: Qiu

first: Andrew

last: Yonemura

first: Hongwei

last: Xu

first: Guofei

last: Cui

first: Shanshan

last: Deng

first: Joanne

last: Chun

first: Nianyong

first: Meng

first: Xinhua

last: Song

first: Jingwen

first: Zijing

first: Youping

first: Matthias

last: Evert

first: Diego

middle: F

last: Calvisi

first: Shumei

last: Lin

first: Haichuan

first: Xin


title: Histone deacetylation primes chromatin to preserve epigenetic memory for self-propagation of heterochromatin domains [H3K9me3 ChIP]

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array

summary:
ChIP-chip analyses of lysine-9 trimethylated histone H3 in clr3-CDx2 and wild type cells.
Chromodomain-mediated HDAC loading sustains self-templated propagation of extended heterochromatin domain.

overall_design: DNA co-purified with H3K9 trimethylated chromatin was random-prime PCR amplified and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals.

first: Martin

last: Zofall

first: Sahana

last: Holla

middle: I


title: Histone deacetylation primes chromatin to preserve epigenetic memory for self-propagation of heterochromatin domains [H3-T7 ChIP]

summary:
ChIP-chip analyses of pulse-expressed H3-T7 in clr3-CDx2 and wild type cells
Chromodomain-mediated HDAC loading suppresses histone turnover at self-templated heterochromatin domain.
Chromodomain-mediated  loading targets  Clr3-CDx2  to heterochromatin domains.

overall_design: DNA co-purified with H3-T7 immunoprecipitated chromatin was random-prime PCR amplified and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals.


city: Xi'an

first: Yi

last: Zhou

state: Shaanxi

address: 277# Yanta West Road

institute: The First Affiliated Hospital of Xi'an Jiaotong university

first: Shu

first: Guoteng

first: Xue

first: Andrew

first: Hongwei

first: Guofei

last: Chen


title: Visium Spatial Transcriptomics of IPMN model mice with Kras;Gnas mutation

city: New York

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

summary: Pancreata were collected from two Kras;Gnas mice and analyzed by Visium Spatial Gene Expression to evaluate the transcriptional profile.

overall_design: Samples were collected from mice at 14 weeks post doxycycline treatment (22 weeks of age) and were fixed with paraformaldehyde. The FFPE samples were then H&E stained and analyzed with the Visium Spatial Gene Expression platform from 10x genomics.

first: Benson

last: Chellakkan Selvanesan

first: Kimal

last: Rajapakshe

first: Yuki

last: Makino

first: Fredrik

last: Thege


title: Effect of mutant GNAS expression in doxycycline-inducible murine pancreatic cancer cell lines

summary: We investigated the transcriptomic effect of GNAS(R201C) expression in murine cell lines derived from the Kras;Gnas model of pancreatic intraductal papillary mucinous neoplasms where transgenic mutant GNAS is doxycycline inducible (LGKC; p48(Cre), Kras(LSL-G12D), Rosa26(LSL-rtTA)), Tg(TetO-GNAS(R201C)) using bulk RNA-seq.

overall_design: Four Kras;Gnas (LGKC) cell lines were incubated with or without 1000 ng/ml doxycycline for 24 hours prior to RNA isolation (two replicates per cell line and condition).


title: IPMN model mice with Kras;Gnas mutation

overall_design: Refer to individual Series


title: Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells.

city: Baltimore

first: Annukka

last: Antar

address: 733 North Broadway Room 869

department: Medicine - Infectious Diseases

institute: Johns Hopkins School of Medicine

summary: The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field’s understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.

overall_design:
To test whether the natural physiology of memory CD4+ T cells (e.g., HIV as inert “passenger” hypothesis) is sufficient to explain reservoir clonality and dynamics or whether selective factors related to HIV infection itself are required to explain these observations, we generated longitudinal clonality data from memory CD4+ T cells in HIV seronegative individuals and from HIV proviruses and CD4s simultaneously from PWH on ART. We compared the longitudinal (~10 year) clonality of HIV proviruses (intact and defective) from resting CD4+ T cells with the longitudinal clonality of their putative carrier cells, resting memory CD4+ (rmCD4) T cells from the same blood samples from PWH on ART. We also compared proviral clonality of the replication competent reservoir at single time points from PWH on long-term ART with the clonality of rmCD4s from the same blood samples. To determine whether suppressed HIV infection itself is associated with significantly different mCD4 clonality, we compared the longitudinal cohort of PWH on ART to HIV-seronegative people matched on age, race, and sex. We identified antigen specific (CMV and HIV) mCD4 cells in a subset of people and compared their clonality and decay rates with that of HIV-infected cells and all mCD4s. To make these comparisons, we modeled clonotype abundance distributions and calculated clonality and diversity metrics.
***Adaptive Biotechnologies does not release raw data.***

first: Daniel

middle: B

last: Reeves


title: Bulk RNA seq of hPSCs-derived inducible GBA knockout astrocytes with and without inflammation

city: Houston

first: Robert

last: Krencik

state: Texas

address: 6670 Bertner Ave

department: Department of Neurosurgery, Center of Neuroregeneration

institute: Houston Methodist

summary: RNA sequencing analysis was conducted to compare human-derived astrocytes with GBA knockout in two conditions, sham and inflammatory environment.

overall_design: All cells are from the same parental human pluripotent stem cell line (WT-C11) and all samples were extracted from cell cultured on matrigel in neuronal media with and without Interleukin 1, TNFα, Complement C1q (ITC) treatment

first: Aboud

last: Tahanis


title: Identifying modulators of inflammation in an in vitro airway epithelial inflammation model using an arrayed CRISPRi screen

first: Jasper

last: Anckaert

institute: OncoRNAlab

summary: To study modulators of inflammatory airway disease, we developed an in vitro bronchial epithelial cell model system based on the BEAS-2B cell line exposed to lipopolysaccharide (LPS) and diesel exhaust particles (DEP). Combined LPS and DEP exposure triggered a molecular inflammatory phenotype, including elevated TSLP and IL-8 mRNA expression, similar to that observed in airway epithelial cells from asthma patients. In this model, we performed high-throughput perturbation of 24 mRNA and long non-coding (lncRNA) target genes through an arrayed CRISPR-interference screen, followed by shallow RNA-sequencing to identify modulators of inflammation. Perturbation of individual targets had a significant impact on the BEAS-2B DEP/LPS transcriptome. Some mRNA targets reversed the DEP/LPS gene expression signature upon knockdown and could serve as candidate therapeutic targets. Perturbation of other target genes however further amplified the pro-inflammatory signature and thus may have an anti-inflammatory role in these cells. In conclusion, we present a novel in vitro model system for airway inflammation that exhibited an inflammatory profile relevant for asthmatic patients, and demonstrate the feasibility to perform high-throughput target perturbation and molecular phenotyping by integrating CRISPR-interference and shallow RNA-sequencing.

overall_design: High throughput perturbation of 24 mRNA and long non-coding (lncRNA) target genes through an arrayed CRISPR-interference screen, followed by shallow RNA-sequencing to identify modulators of inflammation

first: Fien

last: Gysens

first: Ramiro

last: Martinez

first: Nurten

last: Yigit

first: Wim

last: Trypsteen

first: Willem

last: van Snippenberg

first: Louis

last: Delhaye

first: Annelies

last: Bontinck

first: Tationa

last: Karp

first: Joyceline

last: De Volder

first: Maaren

last: van den Berge

first: Guy

last: Brusselle

first: Aurélie

last: Crabbé

first: Ken

last: Bracke

first: Tania

last: Maes

first: Eric

last: de Bony de Lavergne

first: Pieter

last: Mestdagh


title: Saccharomyces Cerevisiae Modulates Cell Growth via Alternative Polyadenylation

first: LiuTao

last: Chen

address: Waihuan West Road 132, University TownHigher Education Mega Center

institute: The Sun YAT-SEN UNIVERSITY

summary: Dynamic 3' UTRs variation mediated by APA is one of the major determinants of post-transcriptional regulation. Though some progress has been made in understanding its function in mammalian cells, the role of APA in the model organism S. cerevisiae, which lack of miRNAs, is a matter of debate. Unlike mammalian cells, most of S. cerevisiae genes tend to express mRNAs with longer 3′ UTRs in proliferating cells. Further analysis demonstrated that 3' UTRs length and mRNA expression were negatively correlated in different growth conditions. By combining APA sequencing and polysome profiling, we observed that mRNA isoforms with shorter 3' UTRs with a higher translational efficiency in proliferating cells but not quiescent. Further analysis demonstrated that different function genes translational efficiency control by APA are differential modulated and closely related with growth conditions. Furthermore, we observed the correlation between asRNAs and translational efficiency of different length 3′ UTR transcripts, suggests asRNAs may involve in the regulation of translational efficiency mediated by APA. Thus, this study indicates conservation of molecular function of APA in different Eukaryotes, highlighting the importance of APA in regulating gene function.

overall_design:
S. cerevisiae S288C cells (ATCC, 204508) were cultured at 30°C in rich YPD media (1% Yeast Extract, 2% Peptone, 2% Dextrose) with shaking at 220 rpm. The exponential phase cells were harvested at mid-log phase with the OD600 values being 0.6-0.8. For stationary cells, the same cells were then grown to an OD600 of 2.1–2.3. Then exponential and stationary phase cells were sequenced to identify dynamic 3’UTR change by IVT-SAPAS as previous (Fu et al., 2015). Furthermore, exponential and stationary phase cells were performed polysome profiling to analysis relationship of 3’UTR length and translational efficiency according to DAVID Bartel lab’s protocol (http://bartellab.wi.mit.edu/protocols.html.) with some modification.
To identify the genes with significant poly(A) sites switching, we performed the test of linear trend alternative to independence (Agresti, 2003). Briefly, a 2XC table was constructed with the number of reads of APA sites for each gene, with APA sites as columns (from the site with shortest 3' UTR to that with longest) and the two compared samples as rows; then, Pearson correlation r and statistic   were calculated to obtain a p values. A threshold of FDR<=0.01 & | r |>0.1 was used to identify significant poly(A) sites switching.

first: Liutao


title: BACH1 as a master regulator gene in vascular cells during aging

first: Jieyu

last: Guo

address: 138 Yixueyuan Rd,

institute: fudan university

summary: We identify transcription factor BACH1 as a master regulator in vascular cells during aging. BACH1 is upregulated in the aorta of old mice. We find BACH1 is located on open chromatin and BACH1 binds to CDKN1A gene enhancer and activates its transcription in endothelial cells. Finally, BACH1 aggravates endothelial cell senescence under oxidative stress. Thus, these findings demonstrate a crucial regulatory role of BACH1 in vascular aging.

overall_design: HUVEC cells were treated with consiRNA or Bach1 siRNA

first: Dan

last: meng


title: Transcriptome profiling of lung cancer bone metastasis

first: Xiaoshen

last: Zhang

summary: Transcriptome profiling of primary and metastatic lesions for lung cancer bone metastasis.

overall_design: To investigate distinctive gene features in both lung lesions with bone metastasis and metastatic lesions of bone, and discover potential signatures acting as biomarker or key element during metastasis.

first: Zhiyu

last: Wang

first: Yifeng

last: Gu

first: Fengying

last: Wu

first: Guanghui

last: Gao

first: Wei

last: Li

first: Hui

last: Zhao

first: Anwen

last: Xiong

first: Lei

first: Caicun

last: Zhou


title: Pseudouridylation is coupled with polyadenylation ot promote mRNA stability

city: wuhan

first: linjian

last: xia

address: wuhan

institute: wuhan University

summary: Here, we developed a Ψ RNA immunoprecipitation sequencing method (Ψ-RIP-seq) combined with direct RNA sequencing by Oxford Nanopore Technologies to detect mRNA Ψ transcriptome-wide. We identified a large number of novel Ψs in mRNA, revealing a conserved enrichment of Ψ in mRNA 3′ UTR. We further showed that a genome-wide association of Ψ with mRNA polyadenylation, and uncovered that cleavage factor complex I (CFI)  regulated Ψ generation in mRNA 3′ UTR. We finally demonstrated that Ψ in mRNA 3′ UTR promoted mRNA stability in a CFI-dependent manner.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Examination of  mRNA pseudouridylation and polyadenylation. In total, we analyzed 40 RNA samples,  28 for  Ψ-RIP seq or RIP-seq, 12 for RNA-seq to examine RNA half lifetime. Each type contains at least two replicates.

first: Laixin

last: Xia