title: Multisensory gamma stimulation mitigates the effects of demyelination induced by cuprizone in male mice

first: Daniela

middle: Rodrigues

last: Amorim

address: 43 Vassar Street, Bldg.46-1303 Cambridge

department: Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

summary: Demyelination is characterized by the loss of the myelin sheath that surrounds nerve fibers and myelin-supporting cells in the nervous system. This leads to increased vulnerability of axons to damage, resulting in significant atrophy and neuro-axonal degeneration. Demyelination is a common pathological feature in a wide range of diseases of the central nervous system (CNS). Multiple pathomolecular processes contribute to brain damage, including demyelination, neuroinflammation, oligodendrocyte (OLs) cell death, and progressive neuronal dysfunction. In this study, we used the cuprizone (CPZ) mouse model to investigate long-term non-invasive gamma entrainment using sensory stimulation (GENUS) as a potential therapeutic intervention for promoting myelination and reducing neuroinflammation. Our results demonstrate that GENUS effectively mitigated demyelination, stimulated oligodendrogenesis in the corpus callosum (CC), and preserved functional integrity and synaptic plasticity. Additionally, GENUS attenuated OLs ferroptosis-induced cell death. Furthermore, chronic GENUS exhibited a marked reduction in brain inflammation, decreasing both microgliosis and astrogliosis and proinflammatory molecules, such as high mobility group box 1 (HMGB1), complement component 1q (C1q) and complement C3 (C3). Considering the pro-remyelination and anti-neuroinflammatory effects observed with GENUS, these findings suggest its potential as a therapeutic approach for demyelinating disorders.

overall_design: A study was conducted to investigate the long-term non-invasive effects of GENUS in preventing demyelination and neuroinflammation in demyelinating conditions, utilizing the cuprizone (CPZ) mouse model and normal diet cohorts. The corpus callosum was collected from a total of 16 male C57BL/6J mice, consisting of 4 mice under the CPZ + GENUS group, 4 mice under the CPZ without stimulation, 4 mice under the normal diet + GENUS group, and 4 mice under the normal diet without stimulation. Subsequently, gene expression profiling analysis was performed.

last: Rodrigues-Amorim

first: Lorenzo

last: Bozzelli

first: TaeHyun

last: Kim

first: Liwang

last: Liu

first: Oliver

last: Gibson

first: Mitch

last: Murdock

first: Fabiola

last: Galiana

first: Md

last: RIslam

first: Dong

last: Park

first: Fatema

last: Abdurrob

first: Alissa

middle: J

last: Nelson

first: Jian

last: Ren

first: Vicky

last: Yang

first: Mathew

middle: P

last: Stokes

first: Li-Huei


title: Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation [GFP-L3mbt_CUT&RUN]

status: Public on Jun 07 2024

city: Chapel Hill

first: Robert

middle: J.

last: Duronio

state: NC

address: 250 Bell Tower Dr., Gen. Sci. Bldg. 3356, CB7100

country: USA

institute: UNC Chapel Hill

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mono-methylation of Lysine 20 of histone H4 (H4K20me1) is catalyzed by Set8 and thought to play important roles in many aspects of genome function that are mediated by H4K20me-binding proteins. We interrogated this model in a developing animal by comparing in parallel the transcriptomes of Set8null, H4K20R/A, and l(3)mbt mutant Drosophila melanogaster. We found that the gene expression profiles of H4K20A and H4K20R larvae are markedly different than Set8null larvae despite similar reductions in H4K20me1. Set8null mutant cells have a severely disrupted transcriptome and fail to proliferate in vivo, but these phenotypes are not recapitulated by mutation of H4K20 indicating that the developmental defects of Set8null animals are largely due to H4K20me1-independent effects on gene expression. Further, the H4K20me1 binding protein L(3)mbt is recruited to the transcription start sites of most genes independently of H4K20me even though genes bound by L(3)mbt have high levels of H4K20me1. Moreover, both Set8 and L(3)mbt bind to purified H4K20R nucleosomes in vitro. We conclude that gene expression changes in Set8null and H4K20 mutants cannot be explained by loss of H4K20me1 or L(3)mbt binding to chromatin, and therefore that H4K20me1 does not play a large role in gene expression.

overall_design: To assess L(3)mbt binding in Drosophila, we engineered an N-terminal GFP tagged l(3)mbt allele. To determine whether L(3)mbt recruitment to the genome required H4K20me we utilized this allele and performed CUT&RUN with a GFP-specific antibody in 3rd instar wandering imaginal wing discs in H4K20R, His4rnull, GFP-L(3)mbt, where all H4K20 is mutated, along with GFP-L(3)mbt and HWT, His4rnull, GFP-L(3)mbt control genotypes.

first: Aaron

middle: T

last: Crain

first: Megan

middle: B

last: Butler

first: Christina

middle: A

last: Hill

first: Mai

last: Huynh

middle: K

last: McGinty


title: Deciphering spatial domains from spatial multi-omics with SpatialGlue

city: Chicago

first: David

last: Gate

state: IL

address: 745 N Fairbanks Ct

department: Neurology

institute: Northwestern University

summary: Integration of multiple data modalities in a spatially informed manner remains an unmet need for exploiting spatial multi-omics data. Here, we introduce SpatialGlue, a novel graph neural network with dual-attention mechanism, to decipher spatial domains by intra-omics integration of spatial location and omics measurement followed by cross-omics integration. We demonstrate that SpatialGlue can more accurately resolve spatial domains at a higher resolution across different tissue types and technology platforms, to enable biological insights into cross-modality spatial correlations.

overall_design:
4 samples : 2 In-house human lymph node and 2 In-house tonsil datasets generated using 10x Genomics Visium RNA and protein co-profiling technology (section A1 and D1). Lymph node section A1 consists of 3,484 spots, 18,085 genes and 31 proteins; Lymph node section D1 consists of 3,359 spots, 18,085 genes and 31 proteins; Tonsil section A1 consists of 4337 spots, 18085 genes and 31 proteins; Tonsil section D1 consists of 4,519 spots, 18,085 genes and 31 proteins.
Please note that processed data generated from both transcriptomics and protein profiling is linked to the corresponding transcriptomics sample records.

first: Yahui

last: Long

first: Lynn

last: van Olst

first: Jinmiao

last: Chen


title: Effect of GRP75 deficiency on gene expression in DN3 thymocytes

status: Public on Jun 08 2024

city: hangzhou

first: wang

last: pengfei

address: yuhangtang road 866

country: China

institute: zhejiang university

type: Expression profiling by high throughput sequencing

summary: Mitochondria and endoplasmic reticulum contacts (MERCs) regulate multiple cellular processes including cell survival and differentiation. Based on the observations that MERCs were specifically enriched in the CD4-CD8- double negative (DN) stage, we studied their role in early thymocyte development. We found that T-cell-specific knockout of Hspa9, which encodes GRP75, a chaperone mediates MERC formation by assembling the IP3R-GRP75-VDAC complex, impaired DN3 thymocyte viability and resulted in thymocyte developmental arrest at the DN3-DN4 transition. Mechanistically, GRP75 deficiency induced mitochondrial stress, releasing mitochondrial DNA (mtDNA) into the cytosol and triggering the type I interferon (IFN-I) response. IFN-I pathway contributed to both the impairment of cell survival and DN3-DN4 transition blockage, while increased lipid peroxidation (LPO) played a major role downstream of IFN-I. Thus, our study reveals the essential role of GRP75-dependent MERCs in early thymocyte development and uncovers the governing facts of cellular survival and differentiation in the DN stage.

overall_design: To inveatigate the role of GRP75 in early thymocyte development, we isolated DN3 (Lin-, CD4-, CD8-, CD44-, CD25+) thymocytes from 5-week-old  WT and Hspa9 cKO mice. Then we performed gene expression profiling analysis using data obtained from RNA-seq of WT and Hspa9 cKO DN3 thymocytes.

first: Fan

last: Zhao

first: Zejin

last: Cui

first: Pengfei

last: Wang

first: Linrong

last: Lu


title: REXO5 Promotes Genomic Integrity Through Regulating R-loop Using Its Exonuclease Activity.

city: Ulsan

first: Hongtae

last: Kim

address: 50 UNIST-gil, Ulju-gun

department: Department of Biological Sciences

country: South Korea

institute: Ulsan National Institute of Science and Technology

summary: Chronic myeloid leukemia (CML), caused by BCR::ABL1 fusion gene, is known to regulate disease progression by altering the expression of genes. However, the molecular mechanisms underlying these changes are largely unknown. In this study, we identified RNA Exonuclease 5 (REXO5) as a novel gene with elevated mRNA expression levels in chronic myeloid leukemia (CML) patients. Additionally, using the REXO5 knockout (KO) K562 cell lines, we revealed a novel role for REXO5 in the DNA damage response (DDR). Compared to wild-type (WT) cells, REXO5 KO cells showed an accumulation of R-loops and increased DNA damage. We demonstrated that REXO5 translocates to sites of DNA damage through its RNA recognition motif (RRM) and selectively binds to R loops. Interestingly, we identified that REXO5 regulates R-loop levels by degrading mRNA within R-loop using its exonuclease domain. REXO5 KO showed ATR-CHK1 activation. Collectively, we demonstrated that REXO5 plays a key role in the physiological control of R-loops using its exonuclease domain. These findings may provide novel insights into how REXO5 expression contribute to CML pathogenesis.

overall_design: Peripheral blood mononuclear cells (PBMCs) were obtained from 6 chronic phase CML (CML-CP) patients after diagnosis and 6 healthy donors for microarray analysis.

first: Dong-Wook


title: Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation [H4K20me1_CUT&RUN]

overall_design: To determine how mutating Set8 or H4K20 impacted genome-wide levels of H4K20me1, we performed CUT&RUN with an H4K20me1-specific antibody in 3rd instar wandering imaginal wing discs in Set8null, Set8 catalytic (Set8rg), H4K20A, and H4K20R mutants along with wild-type controls.


title: Trafficking circuit of CD8+ T cells between the intestine and bone marrow governs antitumour immunity

city: Shanghai

first: duan

middle: cai

last: wen

address: 1678 dongfang road

institute: Shanghai Children's Medical Center

summary:
Purpose: The origin of CD8 in bone marrow after AML chemotherapy is still unclear. To solve this problem, we collected CD8 cells after the onset of disease and chemotherapy for RNA sequencing.
Methods:CD8 from bone marrow and tissue of mice after disease onset and chemotherapy were collected, sorted and sequenced.
Results:After chemotherapy, CD8 undergoes migration and phenotypic transformation home to the bone marrow.

overall_design: CD8 cells were stained with antibodies CD44 and CD62L and sorted by flow cytometry.

first: Rongyi

last: Shi

first: Neng

last: Zhou

first: Cai

middle: w

last: Duan


title: IFN𝛾-induced treatment of a Human Lung Adenocarcinoma Cell Line is Mediated by an Environmental Chemical Receptor (AhR) through PD-L1 and IDO Control (a549 bulk RNA)

city: Boston

middle: H

last: Sherr

state: MA

address: 72 East Concord St

department: Environmental Health

institute: Boston University

summary: While immunotherapy has shown efficacy in non-small cell lung cancer (NSCLC) patients, many respond only partially or not at all. One limitation in improving outcomes is the lack of a complete understanding of factors regulating immune checkpoint targets. Here, we sought to address a possible link between an environmental chemical receptor implicated in NSCLC and immune regulation, the aryl hydrocarbon receptor (AhR), and a known but counterintuitive mediator of immunosuppression, IFN𝛾, in regulation of two immune checkpoints, PD-L1 and the IDO1, in lung adenocarcinoma (LUAD). To this end we used AhR, PD-L1, and IFN𝛾R gene-edited LUAD cell lines, a syngeneic LUAD mouse model, bulk- and single cell-RNA sequencing of LUADs and tumor-infiltrating leukocytes, and existing human transcriptomic databases. The data demonstrate that: 1) the AhR regulates both PD-L1 and IDO1 in murine and human LUAD cells, 2) AhR-driven IDO1 results in production of Kyn which likely mediates an AhR→IDO1→Kyn→AhR amplification loop, 3) the previously characterized induction by IFN𝛾of PD-L1 and IDO is mediated by the AhR, 4) transplantation of LUAD cells in which the AhR is deleted results in long-term tumor immunity in approximately half of the mice; slow growing tumors in the other half exhibit significantly higher densities of CD4+ and CD8+ T cells expressing immunocompetence markers, and 5) deletion of either IFN𝛾R1 or PD-L1 does not provide the same level of immune protection as AhR deletion. The data definitively link IFN𝛾- mediated immunosuppression to the AhR and support the targeting of the AhR in the context of LUAD.

overall_design: The experiment is comprised of 6 samples, profiling RNA extracted from human A549 lung adenocarcinoma cells. The cells were either unmodified (naive, or "wild-type"), subjected to CRISPR with a non-targeting control sgRNA, or subjected to CRISPR with an sgRNA designed to knock out the aryl hydrocarbon receptor (AHR) gene. Each experimental group was represented in triplicate.

first: Megan

last: Snyder

first: Zhongyan

first: Brian

last: Lara

first: Jocelyn

last: Fimbres

first: Muzamil

last: Mohammed

first: Stefano

last: Monti


title: Bulk RNA sequencing of livers from Gubra-Amylin NASH diet fed Chrna2fl/fl and Chrna2fl/fl;Alb-Cre mice

city: Ann Arbor

first: Shanshan

last: Liu

state: Michigan

address: 210 Washtenaw Avenue

institute: University of Michigan

summary: Loss of Chrna2 in liver exacerbates development of Gubra-Amylin NASH diet induced non-alcoholic steatohepatitis.

overall_design: Liver mRNA profiles of Gubra-Amylin NASH diet fed Chrna2fl/fl (n=4) and Chrna2fl/fl;Alb-Cre (n=3) mice

first: Heejin

last: Jun

first: Jun

last: Wu


title: LINC00894 regulated cerebral ischemia/reperfusion injury by stabilizing EIF5 and facilitating ATF4-mediated induction of FGF21 and ACOD1

status: Public on Jun 06 2024

city: jiangsu yangzhou

first: chen

middle: yi

last: fei

address: No.368 hanjiang middle Road

institute: Yangzhou university

summary: Long intergenic non-coding RNA 894 (LINC00894) modulates cancer cell proliferation and drug resistance in several tissue types. However, its role in brain is still unclear. Using RNA-pull down combined with mass spectrometry and RNA binding protein immunoprecipitation, EIF5 was identified to physically interact with LINC00894. Furthermore, LINC00894 knockdown decreased EIF5 protein expression, whereas LINC00894 overexpression increased EIF5 protein expression in cultured cells. Additionally, LINC00894 affected the ubiquitination modification of EIF5. Adeno-associated virus (AAV) mediated LINC00894 overexpression in the brains of transient middle cerebral artery occlusion reperfusion (MCAO/R) mice and rats and inhibited the expression of activated caspase-3. Meanwhile, LINC00894 knockdown increased in the oxygen–glucose deprivation and reoxygenation (OGD/R) in vitro models, whereas its overexpression decreased apoptotic cells and expression of activated caspase-3. Further, LINC00894 overexpression was revealed to increase, whereas its knockdown shortened ATF4 protein half-life. LINC00894 knockdown also decreased the expression of glutamate-cysteine ligase catalytic subunit (GCLC) and ATF4, downregulated glutathione (GSH), and the ratio of GSH to oxidized GSH (GSH: GSSG) in vitro. RNA-seq analysis combined with qRT-PCR and immunoblot showed overexpression of LINC0084 upregulated ATF4, thereby potentially targeting fibroblast growth factor 21 (FGF21) and aconitate decarboxylase 1 (ACOD1) in the MCAO/R model. Finally, we revealed that ATF4 regulated FGF21 and ACOD1 expression by directly binding to promoters; and ectopic overexpression of FGF21 or ACOD1 in LINC00894 knockdown cells decreased activated caspase-3 expression in the OGD/R model. Our results indicated that LINC00894 regulated cerebral ischemia injury by stabilizing EIF5 and facilitating EIF5-ATF4-dependent induction of FGF21 and ACOD1

overall_design: Using RNA-pulldown combined with peptide mass spectrometry analysis identified the interaction between LINC00894 and EIF5, and validated the interaction between LINC00894 and EIF5. It was demonstrated that LINC00894 affects the ubiquitination modification of EIF5. Utilizing cell and animal models, it was shown that LINC00894 protects neuronal cells and brain tissues in oxygen-glucose deprivation and ischemia-reperfusion models. Through RNA-seq analysis, it was revealed that LINC00894 influences the expression of FGF21 and ACOD1 regulated by ATF4, thereby exerting a neuroprotective effect.


title: Act1 modulates mRNA metabolism upon IL-17 stimulation

city: cleveland

first: Lingzi

last: Hong

state: oh

address: 10900 Euclid Avenue

department: biochemistry

institute: Case western reserve university

summary: The IL-17 receptor adaptor molecule Act1, an RNA binding protein, plays a critical role in IL-17-mediated cancer progression. Here we report a novel mechanism for how IL-17/Act1 induces chemoresistance by modulating redox homeostasis through epitranscriptomic regulation of antioxidant RNA metabolism. Transcriptome-wide mapping of direct Act1-RNA interactions revealed that Act1 binds to the 5'UTR of antioxidant mRNAs and Wilms' tumor 1-associating protein (WTAP), a key regulator in m6A methyltransferase complex. Strikingly, Act1's binding sites are located in proximity to m6A modification sites, which allows Act1 to promote the recruitment of elF3G for cap-independent translation. Loss of Act1’s RNA binding activity or Wtap knockdown abolished IL-17-induced m6A modification and translation of Wtap and antioxidant mRNAs, indicating a feedforward mechanism of Act1-WTAP loop. We then developed antisense oligonucleotides (Wtap ASO) that specifically disrupts Act1’s binding to Wtap mRNA, abolishing IL-17/Act1-WTAP-mediated antioxidant protein production during chemotherapy. Wtap ASO substantially increased the antitumor efficacy of cisplatin, demonstrating a potential therapeutic strategy for chemoresistance.

overall_design: Cross-Linking and Immunoprecipitation in combination with next-generation sequencing (CLIP-seq) was performed to identify Act1-binding sites at high resolution in a transcriptome-wide manner.


title: Transcriptomic profiling of Neural Progenitors Cell and Neural Crest Cell Differentiation of Wild-Type and TSC2-Knockout Cultures from the Pluripotent State

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: TSC2 inactivating mutations elicit mTORC1 hyperactivation and underlie neurological dysfunction and the development of neural and mesenchymal tumors in the monogenic disease tuberous sclerosis complex (TSC). We present a multi-lineage model of TSC2-deficiency employing CRISPR-Cas9 engineering in human pluripotent stem cells (hPSCs) and differentiation into neural and neural crest lineages, cell types predicted to drive TSC manifestations. Temporal RNA-sequencing reveals a massive proteostatic stress response underlying early neuroepithelial induction of TSC2-deficient cells, which is resolved upon neural crest cell (NCC) specification but persists in neural precursor cells (NPCs). This culminates in long-term endosomal and metabolic reprogramming as cells age, and sensitivity of TSC2-/- NPCs, but not NCCs, to death via proteasome inhibition independent of mTORC1 activity. Thus, TSC2-deficiency induces lineage-specific stress adaptations which confer differential sensitivity to a commonly targeted pathway. These results exemplify the complexity of elucidating underlying biological mechanisms and therapeutic approaches for multisystem diseases, illustrating the power of utilizing hPSC disease models with tissue-specific relevance.

overall_design: 96 samples, 4 biological replicates of 6 time points of WT and TSC2 knockout for both NPC and NCC differentiation protocols

first: Sean

last: Delaney

first: Lisa

middle: M

last: Julian

first: William

middle: L

last: Stanford


title: Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation [RNA-Seq]

first: Robert

last: Duronio

overall_design: To investigate functions of Set8, L(3)mbt, and H4K20 in gene expression, we performed transcriptome analysis by rRNA-depleted total RNA sequencing in  Drosophila melanogaster whole female 3rd instar wandering larvae in Set8null, Set8 catalytic (Set8RG), L(3)mbtGM76, L(3)mbtPBac, H4K20A, and H4K20R mutants along with wild-type controls.

first: Aaron

last: Crain

last: Butler

first: Christina

last: Hill

first: Mai

last: Huynh

last: McGinty


title: Mast cells trap and cannibalize swarming neutrophils for metabolic independence

city: Freiburg

first: Michael

last: Mihlan

address: Stuebeweg 51

country: Germany

institute: MPI Immunobiology & Epigenetics

summary: Neutrophils are activated and attracted to sites of anaphylaxis by degranulating tissue resident mast cells. After they facilitate inflammation and an anti-microbial immune response. However, the dynamics of neutrophils and direct interactions with mast cells are poorly investigated yet. By approaching 2-photon intravital microscopy and live cell imaging, we show that degranulating mast cells induce neutrophil swarming by releasing leukotriene B4 (LTB4). Attracted neutrophils interact with mast cells and surprisingly penetrate inside mast cells where they are stably trapped inside mast cell granules. We call this novel form of cell-in-cell structure “Mast Cell Intracellular Trap” (MIT).  Trapped neutrophils and mast cells are both viable in the first 12 hours after MIT formation. However, neutrophils start to dye after 12hrs and translatome analysis of mast cells revealed improved mast cell metabolism and recovery. Therefore, neutrophils allow a faster and more efficient mast cell re-stimulation. Furthermore, mast cells get more resistant to extracellular nutrient limitations. Thus, beside their inflammatory role in anaphylaxis, neutrophils support mast cell recovery by forming a cell in cell structure. This might affect chronic inflammation and recurrent infections.

overall_design: Translatome comparisson of murine peritoneal mast cells (PMC) co-cultureed with or without neutrophils  12 and 24 hours after mast cell degranulation.

first: Stefanie

last: Wissmann

first: Alina

last: Gavrilov

first: Barbara

last: Hummel

first: Ryo

last: Suzuki

first: Markus

last: Frank

first: Axel

last: Roers

first: Ritwick

last: Sawarkar

first: Angelika

last: Rambold

first: Luise

last: Erpenbeck

first: Lukas

last: Kaltenbach

first: Magda

last: Babina

first: Manuel

last: Stecher

first: Marie

last: Britz

first: Katharina

last: Glaser

first: Marcus

last: Maurer

first: Ingo

last: Hilgendorf

first: Kristin

last: Franke

first: Tim

last: Lämmermann


title: A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set8.Bulk RNA-Seq P18 Cerebellum WT and Atoh7 remote Enhancer KO]

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: During retinogenesis, the proneural bHLH transcription factor Atoh7 is transiently expressed in retinal progenitor cells (RPCs) and is required for retinal ganglion cell (RGC) differentiation. In humans, a deletion in a distal non-coding regulatory region upstream of ATOH7 is associated with nonsyndromic congenital retinal nonattachment (NCRNA) disorder, characterized by optic nerve atrophy and complete blindness. Here we functionally interrogate the significance of the Atoh7 enhancer landscape to retinogenesis. We demonstrate that deletion of the enhancer structure upstream of Atoh7 in mice leads to RGC deficiency, optic nerve hypoplasia and blood vascular abnormalities, phenocopying inactivation of Atoh7 and recapitulating key features of NCRNA.  We further provide evidence that the loss of the Atoh7 remote enhancer impacts ipsilaterally-projecting RGCs and disrupts proper axonal projections to the brain targets.  Transcriptionally, deletion of the Atoh7 remote enhancer is associated with dysregulation of axonogenesis genes, including the derepression of the axon repulsive cue Robo3 which is normally epigenetically silenced in the developing retina. Our data provide novel insights into how Atoh7 enhancer elements function to promote RGC development and optic nerve formation and uncover a key role of Atoh7 in the transcriptional control of axon guidance molecules possibly via epigenetic mechanisms.

overall_design: Bulk RNA-Seq P18 Cerebellum WT and Atoh7 remote Enhancer KO: Three independent replicates of the developing cerebellum from WT or mouse Atoh7 remote enhancer knockout at P18 were processed for RNA extraction and submitted for RNA-Seq.

first: Kamakshi

last: Mehta

first: Marwa

last: Daghsni

first: Fuyun

last: Bian

first: Zhongli

last: Xu

first: Emily

last: Davis

first: Abigail

last: Naidich

first: Bingjie

last: Wang

first: Shaohua

last: Pi

first: Wei

last: Chen

first: Dennis

last: Kostka

first: Silvia

first: Jeffrey

last: Gross

first: Takaaki

last: Kuwajima

first: Issam

last: Aldiri


title: Bulk RNA sequencing of livers from high fat diet plus carbon tetrachloride challenged Chrna2 fl/fl and Chrna2 fl/fl;AlbCre mice.

first: Jun

last: Wu

address: 210 Washtenaw Ave.

summary: Loss of Chrna2 in the hepatocytes exacerbates the development of Metabolic dysfunction-associated steatohepatitis.

overall_design: Liver transcriptomic data of HFD CCL4 challenged Chrna2 fl/fl (n=3) and Chrna2 fl/fl;AlbCre (n=3) mice.

first: Heejin

last: Jun

first: Shanshan


title: A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set6.H3K27Ac and H3K4me2 ChIP-Seq cerebellum P18 WT]

first: Shuchang

overall_design: Mouse cerebellum from P18 pups were collected and subjected to chromatin prep and ChIP protocol ( Diagenode's iDeal ChIP-seq protocol) using H3K27AC antibody (Abcam ab4729) and H3K4me2  antibody (Abcam ab7766).

first: Kamakshi


title: Effect of Sin3a deletion on gene expression within FoxP3+ T-regulatory cells

city: Philadelphia

first: Lanette

last: Christensen

address: 3615 Civic Center Blvd.

department: Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia

summary: Foxp3 (forkhead box protein 3) functions as the master transcriptional regulator of Treg phenotype. Histone deacetylases 1 and 2 (HDAC1/2) contribute to the regulation of FoxP3 expression via interactions with a myriad of co-regulatory factors. While the nuclear scaffolding protein, Sin3a, has been well established as a co-factor of HDAC1/2, its role within FoxP3+ Tregs has not been. We analyzed the effects of conditional deletion of Sin3a in Foxp3+ Treg cells using three orthogonal approaches. Deletion of Sin3a from FoxP3+ Tregs resulted in the rapid onset of severe and fatal autoimmunity mirroring the phenotype of Scurfy mice. Numbers of Tregs were greatly reduced, residual Tregs had virtually complete loss of suppressive function, and inducible Treg production was blocked. Mice also showed activation of effector T cells, autoantibody production and widespread tissue injury. Mechanistically, Sin3a deletion resulted in decreased transcription of Foxp3 and other Treg signature genes. The reduction of Foxp3 expression was accompanied by the reduction of TET1 and 3 expression and a complete lack of CpG demethylation of the Foxp3 enhancer region CNS2. In addition, Foxp3 protein stability was impaired and fate mapping studies showed conversion of Tregs to ex-Tregs and  increased rates of programmed cell death. Thus, Sin3a plays a critical role in the maintenance of Treg identity and function and is essential for the expression and stability of Foxp3.

overall_design:
To study the role of Sin3a in T-regulatory cells, Sin3a conditional deletion within FoxP3+ cells was achieved by crossing Sin3a_fl/fl mice with Foxp3_YFPcre.
RNA isolated from FACS-sorted FoxP3+ Tregs collected from secondary lymphoid organs of Sin3a-/-FoxP3YFPcre or FoxP3YFPcre controls (equal number of samples from males and females) was used for RNAseq.
The differences in gene expression of FACS-sorted FoxP3+ Tregs with or without Sin3a were compared by RNAseq analysis.

first: Wayne

middle: W

last: Hancock


title: A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set5.H3K27me3 ChIP-Seq retina E14.5 WT and Atoh7 Remote enhancer KO]

last: Liu

overall_design: H3K27me3 ChIP-Seq retina E14.5 WT and Atoh7 Remote enhancer KO: E14.5 retinae from E14.5 WT or Atoh7 REN ko were collected and subjected to chromatin prep and ChIP protocol ( Diagenode's iDeal ChIP-seq protocol) using H3K27me3 antibody (Millipore 07-449).

last: Mehta

first: Marwa

first: Fuyun

first: Zhongli

first: Emily


title: Neutrophil trapping and nexocytosis are mast cell processes for inflammatory signal relay

first: Michael

last: Mihlan

summary: Neutrophils are sentinel immune cells with essential roles for our anti-microbial defense. Most of our knowledge on neutrophil trafficking and tissue navigation derived from models of sterile inflammation and infection. Here, we analyzed allergen-challenged mouse tissues and discovered that degranulating mast cells (MCs) trap living neutrophils inside them. MCs release the attractant leukotriene B4 to re-route neutrophils toward them, thus exploiting a chemotactic system which neutrophils normally use for intercellular communication. Neutrophils die as a consequence of mast cell intracellular trap (MIT) formation, but their undigested material remains stored inside MC vacuoles over days. MCs can use this debris to increase their functional and metabolic fitness. Additionally, they can also exocytose active neutrophilic compounds with a time delay (nexocytosis) and elicit a pro-inflammatory type 1 interferon response in surrounding macrophages. Together, our study highlights neutrophil trapping and nexocytosis as mast cell-dependent processes, which may relay neutrophilic features over the course of chronic allergic inflammation.

overall_design: bone marrow-derived mouse macrophages treated with mast cell or mast cell trap supernatant for 3.5 hours

first: Stefanie

last: Wissmann

first: Alina

last: Gavrilov

first: Angelika

middle: S

last: Rambold

first: Tim

last: Lämmermann


title: PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression [ChIP-seq]

city: Memphis

first: Jacquelyn

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

summary: Genes encoding subunits of SWI/SNF chromatin remodeling complexes are mutated in nearly 25% of cancers. The SWI/SNF subunit SMARCB1 is the driving mutation in nearly all cases of rhabdoid tumor (RT), highly malignant cancers of childhood. While loss of SMARCB1 drives cancer, its absence also creates unique dependencies, which can illuminate mechanism and reveal potential therapeutic vulnerabilities. To identify such dependencies we undertook a genome-scale CRISPR screen comparing RT cell lines to 800 other cancer lines. We identified PHF6 as specifically essential for RT cell survival. Germline mutations in both SMARCB1 and PHF6 cause Coffin-Siris syndrome, and somatic mutations in PHF6 or SWI/SNF occur in T-ALL, suggesting a mechanistic link. We establish that PHF6 co-localizes with residual SWI/SNF complexes at active promoters and enhancers. We find that PHF6 is specifically required for H3K14ac accumulation immediately downstream of active promoters and for release of paused Pol II. Collectively, our work identifies novel integrated roles for PHF6 in chromatin and Pol II regulation, establishes a mechanistic basis for dependence upon PHF6 in RT, and reveals a novel potential therapeutic vulnerability in RT.

overall_design: ChIP-Seq was performed on a minimum of duplicates or triplicates in either shPHF6 or non-targeting control for each mark.

first: Priya

last: Mittal

first: Charles

last: Roberts


title: PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression [RNA-seq]

summary: Genes encoding subunits of SWI/SNF(BAF) chromatin remodeling complexes are collectively mutated in nearly 25% of all cancers. Utilizing a genome-wide CRISPR-Cas9 screen, we identify PHF6 as a specific vulnerability in pediatric malignant rhabdoid tumors (RTs), which are driven by inactivation of the SMARCB1 subunit of SWI/SNF. We establish that PHF6 co-localizes with residual SWI/SNF subcomplexes at promoters and enhancers. Here, PHF6 facilitates transcriptional activation by regulating deposition of H3K14ac downstream of active promoters and contributes to the establishment of H3K27ac at active promoters and enhancers. We show that PHF6 is essential for the maintenance of these marks in part via the regulation of their writers, HB01 and CBP/p300, respectively. As it directly regulates the H3K14ac mark, PHF6 may regulate pausing and serve as a mediator between chromatin regulatory function and RNA POL II pause release. Together, our results establish a mechanistic basis for dependence upon PHF6 in SMARCB1-mutant RTs.

overall_design:
RNA-Seq was performed using 9 biological replicates of G401 shCTRL (control) and 11 biological replicates for shPHF6 (experimental).
RNA-Seq was performed using 3 biological replicates of MRT cell lines upon loss of PHF6 or BRD9 (via shRNAs) compared to controls


title: A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set4.Sc-RNA-Seq retina E14.5 WT and Atoh7 Remote Enhancer KO]

overall_design: Sc-RNA-Seq retina E14.5 WT and Atoh7 Remote Enhancer KO: Two replicates of E14.5 WT retina and Atoh7 REN ko were dissociated and processed for sc-RNA-Seq analysis according to 10X genomics protocol.

last: Daghsni

last: Bian

last: Xu

last: Davis

first: Abigail

last: Naidich

first: Bingjie

last: Wang

first: Shaohua

last: Pi

first: Wei

last: Chen

first: Dennis

last: Kostka

first: Silvia

first: Jeffrey

last: Gross

first: Takaaki

first: Issam


title: WTAP and m6A-dependent circRNAs modulation during stress response in acute myeloid leukemia progenitor cells

city: Rome

first: Francesco

last: Fazi

state: RM

address: Via Antonio Scarpa

department: Department of Anatomical, Histological, Forensic & Orthopaedic Sciences

country: Italy

institute: Sapienza University of Rome

type: Non-coding RNA profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is one of the most prevalent and conserved RNA modifications. It controls several biological processes, including the biogenesis and function of circular RNAs (circRNAs), which are a class of covalently closed-single stranded RNAs. Several studies have revealed that proteotoxic stress response induction could be a relevant anticancer therapy in Acute Myeloid Leukemia (AML). Furthermore, it has emerged a strong molecular interaction between the m6A mRNA modification factors and the suppression of the proteotoxic stress response. Since the proteasome inhibition leading to the imbalance in protein homeostasis is strictly linked to the stress response induction, we investigated the role of Bortezomib (Btz) on m6A regulation and in particular its impact on the modulation of m6A-dependent circRNAs expression. Here, we show that the treatment of AML cells with Btz downregulated the expression of the m6A regulator WTAP at translational level, mainly because of increased oxidative stress. Indeed, Btz treatment promoted oxidative stress, with ROS generation and HMOX-1 activation and administration of the reducing agent N-acetylcysteine restored WTAP expression. Additionally, we identified m6A-modified circRNAs modulated by Btz treatment, including circHIPK3, which is implicated in protein folding and oxidative stress regulation upon silencing. These results highlight the intricate molecular networks involved in oxidative and ER stress induction in AML cells following proteotoxic stress response, laying the groundwork for future therapeutic strategies targeting these pathways.

overall_design: MOLM13 cell treated with 5nM of Btz or with DMSO (CTR), were extracted for RNA, immunoprecipitated, treated with RNAse R and sequenced for circRNAs. Replicates are included.

first: Alessia

last: Iaiza

first: Gilla

last: Mazzanti

first: Frauke

last: Goeman

first: Bianca

last: Cesaro

first: Clelia

last: Cortile

first: Giacomo

last: Corleone

first: Claudia

last: Tito

first: Francesca

last: Liccardo

first: Luciana

last: De Angelis

first: Vincenzo

last: Petrozza

last: Masciarelli

first: Giovanni

last: Blandino

first: Maurizio

last: Fanciulli

first: Alessandro

last: Fatica

first: Giulia

last: Fontemaggi


first: Lingzi

last: Hong

overall_design: RNAseq of Mouse Embryonic Fibroblasts(MEFs) stimulated by IL-17 in vitro


title: A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set1.Sc-ATAC-Seq retina E14.5 WT retina]

first: Shuchang

last: Liu

overall_design: Sc-ATAC-Seq retina E14.5 WT retina: Two replicates of E14.5 WT retina were dissociated and processed for sc-ATAC-Seq analysis according to 10X genomics protocol.

first: Kamakshi

last: Mehta

first: Marwa

last: Daghsni

first: Fuyun

last: Bian

first: Zhongli

last: Xu

first: Emily

last: Davis

first: Abigail

last: Naidich

first: Bingjie

last: Wang

first: Shaohua

last: Pi

first: Wei

last: Chen

first: Dennis

last: Kostka

first: Silvia

first: Jeffrey

last: Gross

first: Takaaki

last: Kuwajima

first: Issam

last: Aldiri


title: Arachidonic acid mobilization and peroxidation promote microglial dysfunction in Aβ pathology

status: Public on Jun 05 2024

city: Columbus

first: Jie

last: Gao

state: OH

address: 460 W. 12th Ave

department: The Department of Neuroscience

institute: The Ohio State University

summary: Aberrant increase of arachidonic acid (ARA) has long been implicated in the pathology of Alzheimer's disease (AD), while the underlying causal mechanism remains unclear. In this study, we revealed a link between ARA mobilization and microglial dysfunction in Aβ pathology. Lipidomic analysis of primary microglia from AppNL-GF mice showed a marked increase in free ARA and lysophospholipids (LPLs) along with a decrease in ARA-containing phospholipids, suggesting increased ARA release from phospholipids (PLs). To manipulate ARA-containing PLs in microglia, we genetically deleted Lysophosphatidylcholine Acyltransferase 3 (Lpcat3), the main enzyme catalyzing the incorporation of ARA into PLs. Loss of microglial Lpcat3 reduced the levels of ARA-containing phospholipids, free ARA and LPLs, leading to a compensatory increase in monounsaturated fatty acid (MUFA)-containing PLs in the AppNL-GF mice. Notably, the reduction of ARA in microglia significantly ameliorated oxidative stress and inflammatory responses while enhancing the phagocytosis of Aβ plaques and promoting the compaction of Aβ deposits. Mechanistically, sc-RNA seq suggested that LPCAT3 deficiency facilitates phagocytosis by facilitating de novo lipid synthesis while protecting microglia from oxidative damage. Collectively, our study reveals a novel mechanistic link between ARA mobilization and microglial dysfunction in AD. Lowering brain ARA levels through pharmacological or dietary interventions may be a potential therapeutic strategy to slow down AD progression.

overall_design: To manipulate ARA-containing PLs in microglia, we genetically deleted Lysophosphatidylcholine Acyltransferase 3 (Lpcat3), the main enzyme catalyzing the incorporation of ARA into PLs.  We analyzed the impact of Lpcat3 deletion on microgllia response to Aβ pathology using immunostaining, bulk and single-cell RNA seq, and flow cytometry.

first: Da

last: Lin


title: PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression [ATAC-seq]

first: Jacquelyn

last: Myers

overall_design: Evaluating chromatin accessibility in G401 expressing GFP after 24hr.

first: Priya

last: Mittal

first: Charles

last: Roberts


title: Transport of perfluoroalkyl substances across human induced pluripotent stem cell-derived intestinal epithelial cells in comparison with primary human intestinal epithelial cells and Caco-2 cells

city: Wageningen

first: Benthe

last: van der Lugt

address: Akkermaalsbos 2

country: Netherlands

institute: Wageningen University & Research

summary: Humans can be exposed to per- and polyfluoroalkyl substances (PFASs) via many exposure routes, including diet, which may lead to several adverse health effects. So far, little is known about PFAS transport across the human intestinal barrier. In the current study, we aimed to assess the transport of 5 PFASs (PFOS, PFOA, PFNA, PFHxS and HFPO-DA) in a human induced pluripotent stem cell (hiPSC)-derived intestinal epithelial cell (IEC) model. This model was extensively characterized and compared with the widely applied human colonic adenocarcinoma cell line Caco-2 and a human primary IEC-based model, described to most closely resemble in vivo tissue. The hiPSC-derived IEC layers demonstrated polarized monolayers with tight junctions and a mucus layer. The monolayers consisted of enterocytes, stem cells, goblet cells, enteroendocrine cells, and Paneth cells that are also present in native tissue. Transcriptomics analysis revealed distinct differences in gene expression profiles where the hiPSC-derived IECs showed highest expression of intestinal tissue-specific genes relative to the primary IEC-based model, whereas the Caco-2 cells clustered closer to the primary IEC-based model than the hiPSC-derived IECs. The order of PFAS transport was largely similar between the models and the apparent permeability (Papp) values of PFAS in apical to basolateral direction in the hiPSC-derived IEC model were in the following order: PFHxS>PFOA>HFPO-DA>PFNA>PFOS. In conclusion, the hiPSC-derived IEC model highly resembles human intestinal physiology and is therefore a promising novel in vitro model to study transport of chemicals across the intestinal barrier for risk assessment of chemicals.

overall_design: Transcriptomics analysis was performed to assess the base level gene expression profiles of the following four intestinal models; hiPSC-derived IEC layers, Caco-2 cell layers, hiPSC-derived HIOs, and a human primary model for the intestine (EpiIntestinal).

first: Aafke

last: Janssen

first: Loes

last: Duivenvoorde

first: Karsten

last: Beekmann

first: Nicole

last: Pinckaers

first: Bart

last: van der Hee

first: Annelies

last: Noorlander

first: Liz

last: Leenders

first: Jochem

last: Louisse

first: Meike

last: van der Zande


title: Venetoclax resistance leads to broad resistance to standard-of-care anti-MM agents, but not to immunotherapies

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Venetoclax is the first example of personalized medicine for multiple myeloma (MM), with meaningful clinical activity as a monotherapy and in combination in myeloma patients harboring the t(11:14) translocation. However, despite the high response rates and prolonged PFS, a significant proportion of patients eventually relapse. Here, we aimed to study adaptive molecular responses after the acquisition of venetoclax resistance in sensitive t(11:14) MM cell models. We therefore generated single-cell venetoclax-resistant t(11:14) MM cell lines and investigated the mechanisms contributing to resistance as well as the cells’ sensitivity to other treatments. Our data suggests that acquired resistance to venetoclax is characterized by reduced mitochondrial priming and changes in BCL-2 family proteins’ expression in MM cells, conferring broad resistance to standard-of-care anti-myeloma drugs. However, our results show that the resistant cells are still sensitive to immunotherapeutic treatments, highlighting the need to consider appropriate sequencing of these treatments following venetoclax-based regimens.

overall_design: We modeled in vitro the development of an acquired venetoclax-tolerant/resistant phenotype in MM cells. We exposed t(11;14) venetoclax-sensitive myeloma cell lines (KMS12PE and KMS27) to high-dose venetoclax treatment and generated monoclonal DTEP clones from single cells (4-5 single cell clones for each cell line), To determine whether venetoclax resistance in DTEP clones is mediated by genomic or transcriptional adaptation, we conducted whole-genome sequencing (WGS) and RNA-seq analysis of the clones and compared them with the parental cell line.

first: Fong

middle: N

last: Jessica

first: Deng

last: Shuhui

first: Fulciniti

last: Mariateresa


title: Single-Cell and Spatially Resolved Interactomics of Tooth-Associated Keratinocytes in Periodontitis

city: Richmond

first: Kevin

last: Byrd

state: Virginia

address: 521 N 11th St

department: Oral and Craniofacial Molecular Biology

institute: Virginia Commonwealth University

summary: Periodontitis affects billions of people worldwide. To address relationships of periodontal niche cell types and microbes in periodontitis, we generated an integrated single-cell RNA sequencing (scRNAseq) atlas of human periodontium (34-sample, 105918-cell), including sulcular and junctional keratinocytes (SK/JKs). SK/JKs displayed altered differentiation states and were enriched for effector cytokines in periodontitis. Single-cell, metagenomics revealed 37 bacterial species with cell-specific tropism. Fluorescence in situ hybridization detected intracellular 16S and mRNA signals of multiple species and correlated with SK/JK proinflammatory phenotypes in situ. Cell-cell communication analysis predicted keratinocyte-specific innate and adaptive immune interactions. Highly multiplexed immunofluorescence (33-antibody) revealed peri-epithelial immune foci, with innate cells often spatially constrained around JKs. Spatial phenotyping revealed immunosuppressed JK-microniches and SK-localized tertiary lymphoid structures in periodontitis.  Here, we demonstrate impacts on and predicted interactomics of SK and JK cells in health and periodontitis, which requires further investigation to support precision periodontal interventions in states of chronic inflammation.

overall_design: Cells from human gingiva with induced gingivitis were dissociated, isolated using fluorescence-activated cell sorting (FACS), processed and sequenced using scRNAseq.

first: Quinn

last: Easter

first: Bruno

middle: F

last: Matuck

first: German

last: Stark

first: Catherine

last: Worth

first: Alexander

middle: V

last: Predeus

first: Brayon

last: Fremin

first: Khoa

last: Huynh

first: Vaishnavi

last: Ranganathan

first: Zhi

last: Ren

first: Diana

last: Pereira

first: Brittany

last: Rupp

first: Theresa

last: Weaver

first: Kathryn

last: Miller

first: Paola

last: Perez

first: Akira

last: Hasuike

first: Zhaoxu

last: Chen

first: Mandy

last: Bush

first: Xufeng

last: Qu

first: Janice

last: Lee

first: Scott

last: Randell

first: Shannon

last: Wallet

first: Ines

last: Sequeira

first: Hyun

last: Koo

first: Katarzyna

last: Tyc

first: Jinze

last: Liu

first: Kang

middle: I

last: Ko

first: Sarah

last: Teichmann


title: The chondrocyte “mechanome”: Activation of the mechanosensitive ion channels TRPV4 and PIEZO1 drives unique transcriptional signatures

city: Saint Louis

first: Farshid

last: Guilak

state: MO

address: 660 S Euclid Ave, Campus Box 8233

department: Dept of Orthopedics

institute: Washington University in St. Louis

summary: The mechanosensitive ion channels Transient Receptor Potential Vanilloid 4 (TRPV4) and PIEZO1 transduce physiologic and supraphysiologic magnitudes of mechanical signals in the chondrocyte, respectively. TRPV4 activation promotes chondrogenesis, while PIEZO1 activation by supraphysiologic deformations drives cell death. The mechanisms by which activation of these channels discretely drives changes in gene expression to alter cell behavior remains to be determined. To date, no studies have contrasted the transcriptomic response to activation of these channels, nor has any published data attempted to correlate these transcriptomes to alterations in cellular function. This study used RNA sequencing to comprehensively investigate the transcriptomes associated with activation of TRPV4 or PIEZO1, revealing that TRPV4 and PIEZO drive distinct transcriptomes, but also exhibit unique co-regulated clusters of genes. Notably, activation of PIEZO1 through supraphysiologic deformation induced a transient inflammatory profile that overlapped with the interleukin (IL)-1-responsive transcriptome and contained genes associated with cartilage degradation and osteoarthritis progression. However, both TRPV4 and PIEZO1 were also shown to elicit anabolic effects. PIEZO1 expression promoted a pro-chondrogenic transcriptome under unloaded conditions, and daily treatment with PIEZO1 agonist Yoda1 significantly increased sulfated glycosaminoglycan deposition in vitro. These findings emphasize the presence of a broad “mechanome” with distinct effects of TRPV4 and PIEZO1 activation in chondrocytes, suggesting complex roles for PIEZO1 in both the physiologic and pathologic responses of chondrocytes. The identification of transcriptomic profiles unique to or shared by PIEZO1 and TRPV4 (distinct from IL-1-induced inflammation) could inform future therapeutic designs targeting these channels for the management and treatment of osteoarthritis.

overall_design: To study the TRPV4-responsive transcriptome, primary chondrocytes were cast in 2% agarose to form tissue engineered cartilage constructs. Constructs were stimulated for 3 hours with cyclic, unconfined compressive loading (10% peak-to-peak deformation, 1 Hz) with or without TRPV4 antagonist GSK205 (10 uM) or treated with TRPV4 agonist GSK101 (1 nM) or 1 ng/mL of IL-1. Vehicle controls were exposed to DMSO (1:1000 in media) but left free swelling. For both TRPV4 and IL-1 stimulation groups, tissue constructs were taken down at 3 hours and 9 hours post stimulation onset, flash frozen, and stored at -80C (n=4 per group). To study the PIEZO1-responsive transcriptome, chondrocytes were plated at 500k cells per well in a 6 well plate and transfected (DharmaFECT Transfection Reagent, Dharmacon) with siRNA targeting PIEZO1 (siPIEZO1), a non-targeting control siRNA (siNTC), or left non-transfected (NT). All transfection groups were cast in 2% agarose to form tissue engineered cartilage constructs. Constructs were subjected to a single round of quasi-static unconfined compression to 80% deformation (supraphysiologic range) at 1.9% deformation/min (~0.73 um/sec), treated with PIEZO1 agonist Yoda1 (5 uM), or standard media with a DMSO vehicle control (1:1000) but left free swelling.  In response to stimulation, tissue constructs were taken down at 3 hours and 9 hours post stimulation onset, flash frozen, and stored at -80C (n=4 per group).

first: Robert

last: Nims

first: Daniel

last: Palmer

first: Jordan

last: Kassab

first: Bo

last: Zhang


title: Identification of factors that modulate Proliferative Arrest under the influence of seeds

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

summary: In monocarpic plants, after the production of a certain number of fruits/seeds, the activity of the Shoot Apical Meristem (SAM) and of the meristems of the secondary axes stop in a coordinated way, leading to the cessation of flower production. This phenomenon has been called Proliferative Arrest (PA). It can be assumed as a general phenomenon in monocarpic plants, as it has been described in different species of this economically important group of plants. Studies in the model species Arabidopsis thaliana and Pisum sativum have allowed the identification of factors that affect PA timing. One of them is the production of fruits and seeds. With this RNA-seq, we have identified factors that contribute to the modulation of PA in a seed-dependent manner in Pisum sativum.

overall_design: To better understand the influence of seeds in modulating Proliferative Arrest,  samples of Shoot Apical Meristem were collected at four  different stages of plant development (with/withouth seeds; active/arrested meristems)

first: Eduardo

last: Burillo-Richart

first: Vicente

last: Balanzá

first: Cristina

last: Ferrándiz


title: MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1

city: Nottingham

first: Angela

last: Downie Ruiz Velasco

address: School of Pharmacy, Science Road

department: School of Pharmacy

country: United Kingdom

institute: University of Nottingham

summary: In animals, microRNA (miRNA) biogenesis begins with cotranscriptional cleavage of the primary (pri-)miRNA by Microprocessor. Cotranscriptional splicing has been shown to influence Microprocessor cleavage for miRNAs hosted in introns of protein coding pri-miRNAs, but the impact of splicing on production of miRNAs hosted in long noncoding (lnc)RNAs is largely unknown. Here, we investigated the role of splicing in the biogenesis of miR-122, a lncRNA-hosted, highly expressed, medically important, liver-specific miRNA. We found that splicing inhibition by the SF3B1 inhibitor Pladienolide B (PlaB) led to strong and rapid reduction in transcription of endogenous, but not plasmid-encoded, pri-miR-122, resulting in reduced production of mature miR-122. To allow detection of rapid changes in miRNA biogenesis despite the high stability of mature miRNAs, we used SLAMseq to globally quantify the effects of short-term splicing inhibition on miRNA synthesis. We observed an overall decrease in biogenesis of mature miRNAs following PlaB treatment. Surprisingly, miRNAs derived from different genomic locations were similarly affected. Together, this study provides new insight into the emerging role for splicing in transcription, demonstrating novel biological importance in promotion of miR-122 biogenesis from a lncRNA, and shows that splicing is important for global miRNA biogenesis.

overall_design:
To understand the effects of splicing inhibition on miRNA biogenesis we treated Huh7 cells with SF3B1 inhibitor Pladienolide B (Pla B) or DMSO for 4h. To detect changes at this short time-point cells were metabolically labelled with 500 μM 4‑thiouridine (4SU). RNA isolated from the cells in each of the three treatment groups (Ctrl; no 4SU + DMSO, DMSO; 4SU + DMSO, Pla B; 4SU + Pla B) was alkylated using iodoacetamide. Libraries were generated from the alkylated RNA using the NEXTflex kit and were size selected after pooling. Following alkylation and library prep 4SU-modified positions were read as T>C conversions during sequencing. We analysed four biological repeats per treatment.
Two samples (DMSO A and DMSO B) produced a low number of reads on first sequencing. To address this, new libraries were prepared for these two samples (re-prep), and existing libraries were also re-amplified (re-amp). Both re-prepped and re-amplified libraries were sequenced, and reads from the three runs (original, re-prepped and re-amplified) were combined for analysis.

middle: D

last: Ruiz Velasco

first: Aimee

last: Parsons

first: Matthew

middle: C

last: Heatly

first: Athena

middle: R

last: Martin

first: Niraj

last: Shah

first: Alfredo

last: Smart

first: Catherine

last: Jopling


title: Inhibition of the Eukaryotic Initiation Factor-2-α Kinase PERK Decreases Risk of Autoimmune Diabetes in Mice

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

address: 900 E 57th street

department: Medicine

institute: University of Chicago

summary: Prevention or delay of autoimmune type 1 diabetes (T1D) onset is possible if molecular triggering events can be pharmacologically targeted. The integrated stress response (ISR) is activated during cellular stress to halt protein production and redirect energy towards cellular survival temporarily. We hypothesized that the activity of the ISR in the insulin-producing β cell during T1D becomes maladaptive and renders the cell prone to autoimmunity. We show that suppression of the ISR by using a novel inhibitor of the kinase PERK reverses the translation initiation block in stressed human islets and delays the onset of diabetes, reduces islet inflammation, and preserves β cell mass in T1D-susceptible mice. Single-cell RNA sequencing of islets from PERK-inhibited mice shows reductions in the unfolded protein response and PERK signaling pathways and alterations in antigen processing and presentation pathways in β cells. Spatial proteomics analysis of islets from these mice shows a post-transcriptional increase in the immune checkpoint protein PD-L1 in β cells. Golgi membrane protein 1, whose levels increase following ISR inhibition in human islets and EndoC-βH1 human β cells, interacts with and post-transcriptionally stabilizes PD-L1. Collectively, our studies show that the ISR, mediated by PERK, enhances β cell immunogenicity, and inhibition of PERK may offer a strategy to prevent or delay the development of T1D.

overall_design: Female NOD mice were oral-gavaged with vehicle or 6 mg/kg HC-5770 (PERK inhibitor) for 2 weeks (6-8 weeks of age). At the end of the treatment, mouse islets were isolated following Stull et al., 2012 and samples were submitted for scRNAseq (n=3 biological replicates per group).

first: Charanya

last: Muralidharan

first: Fei

last: Huang

first: Jacob

last: Enriquez

first: Jiayi

middle: E

last: Wang

first: Jennifer

middle: B

last: Nelson

first: Titli

last: Nargis

first: Sarah

last: May

first: Advaita

last: Chakraborty

first: Kayla

middle: T

last: Figatner

first: Svetlana

last: Navitskaya

first: Cara

last: Anderson

first: Veronica

last: Calvo

first: David

last: Surguladze

first: Mark

middle: J

last: Mulvihill

first: Xiaoyan

last: Yi

first: Soumyadeep

last: Sarkar

first: Scott

middle: A

last: Oakes

first: Bobbie-Jo

last: Webb-Robertson

first: Emily

middle: K

last: Sims

first: Kirk

last: Staschke

first: Decio

last: Eizirik

first: Ernesto

last: Nakayasu

first: Michael

last: Stokes

last: Tersey


title: A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set7.Bulk RNA-Seq P18 Cerebellum WT and Atoh7 Large Enhancer KO]

first: Shuchang

last: Liu

overall_design: Bulk RNA-Seq P18 Cerebellum WT and Atoh7 Large Enhancer KO: Three independent replicates of the developing cerebellum from WT or mouse Atoh7 large enhancer knockout at P18 were processed for RNA extraction and submitted for RNA-Seq.

first: Kamakshi

last: Mehta

first: Marwa

last: Daghsni

first: Fuyun

last: Bian

first: Zhongli

last: Xu

last: Davis

first: Abigail

last: Naidich

first: Bingjie

last: Wang

first: Shaohua

last: Pi

first: Wei

last: Chen

first: Dennis

last: Kostka

first: Silvia

first: Jeffrey

middle: M

last: Gross

first: Takaaki

last: Kuwajima

first: Issam

last: Aldiri


title: Efficient and reproducible generation of human iPSC-derived cardiomyocytes and cardiac organoids in stirred suspension systems

city: Boston

first: William

middle: T.

last: Pu

state: Ma

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

summary: Human iPSC-derived cardiomyocytes (hiPSC-CMs) have proven invaluable for cardiac disease modeling and cardiac regeneration. Challenges with quality, inter-batch consistency, cryopreservation and scale remain, reducing experimental reproducibility and clinical translation. Here, we report a robust stirred suspension cardiac differentiation protocol with careful functional characterization of the resulting hiPSC-CMs. In a bioreactor, the protocol produced 1.2E6/mL hiPSC-CMs with ～94% purity from 14 iPSC lines. Bioreactor-differentiated CMs (bCMs) showed high viability after cryo-recovery (>90%) and predominantly ventricular identity. Compared to standard monolayer-differentiated CMs (mCMs), bCMs had greater reproducibility and more mature functional properties, including pacing capture to 4 Hz and greater force production in 3D engineered heart tissues. In more readily available magnetically stirred spinner flasks, the protocol yielded 1.8E6/mL spinner-differentiated CMs (sCMs) with 94% purity. Differentiation scaled readily in spinner flasks, as a 3.8-fold increase in cultured volume yielded 3.4E6/ml sCMs. sCMs had intermediate functional properties between mCMs and bCMs. Minor protocol modifications generated the first bioreactor-derived cardiac organoids (bCOs) fully generated in suspension. These reproducible, scalable, and resource efficient approaches to generate cardiac cells and organoids with well-characterized properties will expand the applications of hiPSC-CMs.

overall_design: We performed scRNAseq of 15-day-old bioreactor-derived hiPSC-cardiomyocytes (bCMs; 2 biological replicates), monolayer-derived hiPSC-cardiomyocytes (mCMs; 2 biological replicates) and bioreactor-derived cardiac organoids (bCOs; 1 biological replicate).

first: Maksymilian

last: Prondzynski

first: Paul

last: Berkson

last: Trembley

first: Yashasvi

last: Tharani

first: Kevin

last: Shani

first: Raul

middle: H

last: Bortolin

first: Mason

last: Sweat

first: Joshua

last: Mayourian

first: Dogacan

last: Yucel

first: Albert

last: Cordoves

first: Beatrice

last: Gabbin

first: Cuilan

last: Hou

first: Nnaemeka

last: Anyanwu

first: Farina

last: Nawar

first: Justin

last: Cotton

first: Joseph

last: Milosh

first: David

last: Walker

first: Yan

last: Zhang

first: Fujian

first: Xujie

last: Parker

first: Vassilios

last: Bezzerides


title: SWI/SNF directed epigenetic and transcriptional response during macrophage inflammatory activation.

city: La Jolla

first: Jingwen

last: Liao

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute

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

overall_design: Refer to individual Series


title: A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set2.Bulk RNA-Seq retina E14.5 WT and Atoh7 Large Enhancer KO]

first: Shuchang

last: Liu

summary: During retinogenesis, the proneural bHLH transcription factor Atoh7 is transiently expressed in retinal progenitor cells (RPCs) and is required for retinal ganglion cell (RGC) differentiation. In humans, a deletion in a distal non-coding regulatory region upstream of ATOH7 is associated with nonsyndromic congenital retinal nonattachment (NCRNA) disorder, characterized by optic nerve atrophy and complete blindness. Here we functionally interrogate the significance of the Atoh7 enhancer landscape to retinogenesis. We demonstrate that deletion of the enhancer structure upstream of Atoh7 in mice leads to RGC deficiency, optic nerve hypoplasia and blood vascular abnormalities, phenocopying inactivation of Atoh7 and recapitulating key features of NCRNA.  We further provide evidence that the loss of the Atoh7 remote enhancer impacts ipsilaterally-projecting RGCs and disrupts proper axonal projections to the brain targets.  Transcriptionally, deletion of the Atoh7 remote enhancer is associated with dysregulation of axonogenesis genes, including the derepression of the axon repulsive cue Robo3 which is normally epigenetically silenced in the developing retina. Our data provide novel insights into how Atoh7 enhancer elements function to promote RGC development and optic nerve formation and uncover a key role of Atoh7 in the transcriptional control of axon guidance molecules possibly via epigenetic mechanisms.

overall_design: Bulk RNA-Seq retina E14.5 WT and Atoh7 Large Enhancer KO: four independent replicates from WT or Atoh7 TEN KO retinae at E14.5 were processed for RNA extraction and submitted for RNA-Seq

first: Kamakshi

last: Mehta

first: Marwa

last: Daghsni

first: Fuyun

last: Bian

first: Zhongli

last: Xu

first: Emily

last: Davis

first: Abigail

last: Naidich

first: Bingjie

last: Wang

first: Shaohua

last: Pi

first: Wei

last: Chen

first: Dennis

last: Kostka

first: Silvia

first: Jeffrey

last: Gross

first: Takaaki

last: Kuwajima

first: Issam

last: Aldiri


title: Sex-dependent APOE4 Neutrophil-microglia interactions drive cognitive impairment in Alzheimer's Disease

status: Public on Jun 04 2024

first: Neta

last: Rosenzweig

state: Massachusetts

address: 60 Fenwood Road, 10002K, Brigham and Women’s Hospital

institute: Brigham and Women's Hospital, Harvard Medical School

summary: APOE4 is the strongest genetic risk factor for Alzheimer's disease (AD) with increased odds ratios in females. Targeting amyloid plaques show modest improvement in male non-APOE4 carriers. Leveraging single cell transcriptomics across APOE variants in both sexes, multiplex flow cytometry and validation in two independent cohorts of APOE4 female AD patients, we identify a new subset of neutrophils, interacting with microglia associated with cognitive impairment. This phenotype is defined by increased IL-17 and IL-1 co-expressed gene modules in blood neutrophils and in microglia of cognitively impaired female APOE e4 carriers, showing increased infiltration to the AD brain. APOE4 female IL-17+ neutrophils upregulated the immunosuppressive cytokines IL-10 and TGFb, and immune checkpoints including LAG-3 and PD-1, associated with accelerated immune aging. Deletion of APOE4 in neutrophils reduced this immunosuppressive phenotype and restored microglial response to neurodegeneration (MGnD), limiting plaque pathology in AD mice. Mechanistically, IL-17F upregulated in APOE4 neutrophils interacts with microglial IL-17RA to suppress the induction of MGnD phenotype, and blocking this axis supported cognitive improvement in AD mice. These findings provide a translational basis to target IL-17F in APOE e4 female carriers with cognitive impairment.

overall_design: Splenic neutrophils were collected from 9-month-old APOE4 5xFAD mice treated with IL17F or IgG.Neutrophils were collected from the blood of 12-month-old female APOE3, APOE3NTKO, APOE4 and APOE4NTKO mice on an APP/PS1 background. Phagocytic and non-phagocytic microglia were collected from3-month-old Raggc mice treated with anti-IL17F or IgG.

first: Kilian

middle: L

last: Kleemann

first: Thomas

last: Rust

first: Madison

last: Carpenter

first: Madeline

last: Grucci

first: Michael

last: Aronchik

first: Nieske

last: Brouwer

first: Isabel

last: Valenbreder

first: Joya

last: Cooper-Hohn

first: Malvika

last: Iyer

first: Rajesh

last: Krishnan

first: Kisha

last: Sivanathan

first: Wesley

last: Brandão

first: Taha

last: Yahya

first: Ana

last: Durao

first: Jean

last: Chadarevian

first: Zhuoran

last: Yin

last: Properzi

first: Roni

last: Nowarski

first: Hayk

last: Davtyan

first: Mathew

last: Blurton-Jones

first: Hyun-Sik

last: Yang

first: Bart

last: Eggen

first: Reisa

last: Sperling

first: Oleg

last: Butovsky


title: Synthetic RIG-I agonist-mediated cancer immunotherapy synergizes with MAP-Kinase inhibition against BRAF mutated melanoma [YUMM1.7]

city: Bonn

first: Thais

middle: Marina

last: Schlee-Guimarães

address: Venusberg-Campus 1

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: University Hospital, University of Bonn

summary: The implementations of targeted molecular therapies and immunotherapy in melanoma vastly improved the therapeutic outcome in patients with limited efficacy of surgical intervention. Nevertheless, a large fraction of melanoma patients still remains refractory or acquires resistance to these new forms of treatment, illustrating a need for improvement. Here we report that the clinically relevant combination of MAP kinase inhibitors Dabrafenib and Trametinib synergizes with RIG-I agonist-induced immunotherapy to kill BRAF-mutated human and mouse melanoma cells. Kinase inhibition did not compromise the agonist-induced innate immune response of the RIG-I pathway in host immune cells. In a melanoma transplantation mouse model, the triple therapy outperformed the individual therapies. Our study suggests that targeted activation of RIG-I with its synthetic ligand 3pRNA could vastly improve tumor control in a substantial fraction of melanoma patients receiving MAP kinase inhibitors.

overall_design: YUMM1.7 cells were treated for 24 hours with DMSO, Dabrafenib, Trametinib or the combination of both. Additionally, each condition was left unstimulated, transfected with CA21 control RNA or the activating RIG-I ligand 3pRNA. Total RNA was isolated and subjected to poly-A based library preparation.

first: Christian

last: Grützner

last: Schlee-Guimaraes

first: Marius

last: Jentsch

first: Jonathan

last: Schmid-Burgk

first: Marcel

last: Renn

first: Rayk

last: Behrendt

first: Gunther

last: Hartmann


title: High recallability of memory B cells requires ZFP318-dependent transcriptional regulation of mitochondrial function

city: Beijing

first: Hai

last: Qi

address: Haidian District

institute: Tsinghua University

summary: Expression of the transcriptional regulator ZFP318 is induced in germinal center (GC)-exiting memory B cell precursors and memory B cells (MBCs). Using a conditional ZFP318 fluorescence reporter that also enables ablation of ZFP318-expressing cells, we found that ZFP318-expressing MBCs were highly enriched with GC-derived cells. Although ZFP318-expressing MBCs constituted only a minority of the antigen-specific MBC compartment, their ablation severely impaired recall responses. Deletion of the Zfp318 gene did not alter the magnitude of primary responses but markedly reduced MBC participation in recall. CD40 ligation promoted Zfp318 expression whereas BCR signaling was inhibitory. Enforced ZFP318 expression enhanced recall performance of MBCs that otherwise responded poorly. ZFP318-deficient MBCs expressed less mitochondrial genes, had structurally compromised mitochondria and were susceptible to reactivation-induced cell death. The abundance of ZFP318-expressing MBCs, instead of the number of antigen-specific MBCs, correlated with the potency of prime-boost vaccination. Therefore, ZFP318 controls the MBC recallability and represents a key checkpoint of humoral immune memory.

overall_design: RNA-seq analysis of tdTomato+ B1-8hi MBCs with induced or uninduced expression of Zfp318 at 7 post NP-OVA immunization.

first: Wen

last: Shao


title: Epigenetic therapy activates TE-chimeric transcripts to provide additional source of antigens in glioblastoma stem cells

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

department: Genetics

type: Methylation profiling by high throughput sequencing

summary: Epigenetic treatment induces TE-chimeric antigens in glioblastoma stem cells

first: H

last: Jang

first: Ju

last: Maeng

first: Xiaoyun

last: Xing

first: Ting

last: Wang


title: Epigenetic recording of stimulation history reveals BLIMP1-BACH2 balance in determining memory B cell fate upon recall challenge (ATAC-Seq 3)

summary: Long-term humoral immunity is partly maintained by memory B cells (MBCs). MBCs can be recalled to produce antibody-producing plasma cells (PCs) or form secondary germinal centers (GCs). The former process underlies markedly increased antigen-specific antibodies seen in the secondary response, while the latter process allows continuous somatic hypermutation and affinity maturation. MBC re-participation in the GC reaction is thought to be important for generating broadly neutralizing antibodies against highly mutating viruses such as influenza and HIV. However, how MBC recall is transcriptionally or epigenetically programmed to produce secondary PCs or GCs is not yet understood. Here we show that BACH2, a transcription factor required for GC formation and maintenance1,2, decreases across post-activation stages of B cells, from the naïve state to GC, memory, and the terminal PC state. In contrast, BLIMP-1, a transcription factor that promotes PC formation3,4 and is antagonistic to BACH2 (ref. 5), increases as B cells traverse the same course. The relative strength between BLIMP-1 and BACH2 progressively increases in favor of BLIMP-1 in GCs and MBCs through the primary response. MBCs of the isotype or subset identity that preferentially give rise to secondary GCs exhibit comparatively higher BACH2 but lower BLIMP-1 expression than those predisposed for PC formation. Using a tetracycline-controlled circuit implanted in MBCs, we show that skewing the BLIMP-1-BACH2 balance in favor of BACH2 markedly increases GC formation by otherwise PC-predisposed MBCs, whereas skewing the balance in favor of BLIMP-1 drives PC formation by GC-prone MBCs, indicating that the potential for GC re-participation or PC development rests in the relative strength of BLIMP-1 over BACH2 within individual MBCs. Underneath this relative BLIMP-1-over-BACH2 strength in naïve B cells, GCs, MBCs and PCs, we observe progressively increased accessibilities to chromatin loci that are specifically opened in PCs, particularly those that contain ISRE elements and are controlled by IRF-4. IRF-4 is universally upregulated in B cells when stimulated through the BCR, the CD40 receptor, or by innate stimuli. By analyzing time-stamped GC B cells, we demonstrate a progressive increase in chromatin accessibilities at PC-specific, IRF-4-controlled gene loci over time. Our results support a model of progressive IRF-4 imprinting in which the cumulative stimulation history of B cells is epigenetically recorded in an IRF-4-dependent manner, determines the relative strength between BLIMP-1 and BACH2 in individual MBCs, and thereby dictates their individual probabilities to develop into GCs or PCs upon re-stimulation.

overall_design: ATAC-seq analysis of pulse-labeled tdTomato- light zone GC B cells by tamoxifen adiministration from day6 to day8 and collected at day10 and day21 post NP-KLH immunization using mice of a S1pr2-creERT2;Rosa26-Ai14 genotype.


title: A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set3.Bulk RNA-Seq retina E14.5 WT and Atoh7 Remote Enhancer KO]

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

overall_design: Bulk RNA-Seq retina E14.5 WT and Atoh7 Remote Enhancer KO: three independent replicates from WT or Atoh7 REN KO retinae at E14.5 were processed for RNA extraction and submitted for RNA-Seq

first: Kamakshi

last: Mehta

first: Marwa

last: Daghsni

first: Fuyun

last: Bian

first: Zhongli

last: Xu

first: Emily

last: Davis

first: Abigail

last: Naidich

first: Bingjie

first: Shaohua

last: Pi

first: Wei

last: Chen

first: Dennis

last: Kostka

first: Silvia

first: Jeffrey

last: Gross

first: Takaaki

last: Kuwajima

first: Issam

last: Aldiri


title: Transcriptomic analysis of the downstream genes affected by LBD29 and MYB2

city: Qingdao

first: feng

last: zhang

state: Shandong

address: 72 Binhai Road

institute: shandong university

summary: The goal of this study is to clarify the function of LBD29 and MYB2 in the pathway of  lateral root development. We isolated total RNA from the roots of 8-day-old Col-0 and sevaral transgene seedlings. New genes act downstream of LBD29 and MYB2, during the lateral root formation, are discovered.

overall_design: We isolated total RNA from the roots of 8-day-old Col-0, Pro35S:LBD29-6Gly,Pro35S:MYB2 and Pro35S:MYB2-SRDX

first: Feng

last: Zhang

first: ZhaoJun

last: Ding


title: Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis

city: Umea

first: Peter

last: Kindgren

state: Vasterbotten

address: KB5C5, KBC building, Linnaeus väg 6

department: Department of Forest Genetics and Plant Physiology

country: Sweden

institute: Swedish University of Agricultural Sciences

summary: Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the Poly(A) signal (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing (RNA-seq) during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady state RNA techniques to identify biologically relevant players in stress responses.

overall_design: WT (Col-0) Arabidopsis seedlings (12 day old) were subjected to cold (4°C) for 12h after which RNA was isolated and sent for sequencing.

first: Susheel Sagar

last: Bhat


title: Microglia undergo sex-dimorphic transcriptional and metabolic rewiring during aging

city: Los Angeles

first: Helen

middle: S.

last: Goodridge

address: 8700 Beverly Blvd.

institute: Cedars-Sinai Medical Center

summary: Microglia, the brain’s resident macrophages, maintain brain homeostasis and respond to injury and infection. During aging they undergo functional changes, but the underlying mechanisms and their contributions to neuroprotection versus neurodegeneration are unclear. Previous studies suggested that microglia are sex dimorphic, so we compared microglial aging in mice of both sexes. RNA-sequencing of hippocampal microglia revealed more aging-associated changes in female microglia than male microglia, and more sex differences in old microglia than young microglia. Pathway analyses and subsequent validation assays revealed a stronger AKT-mTOR-HIF1α-driven shift to glycolysis among old female microglia and indicated that C3a production and detection was elevated in old microglia, especially in females. Recombinant C3a induced AKT-mTOR-HIF1α signaling and increased the glycolytic and phagocytic activity of young microglia. Single cell analyses attributed the aging-associated sex dimorphism to more abundant disease-associated microglia (DAM) in old female mice than old male mice, and evaluation of an Alzheimer’s Disease mouse model revealed that the metabolic and complement changes are also apparent in the context of neurodegenerative disease and are strongest in the neuroprotective DAM2 subset. Collectively, our data implicate autocrine C3a-C3aR signaling in metabolic reprogramming of microglia to neuroprotective DAM during aging, especially in females, and also in Alzheimer’s Disease.

overall_design: mRNA profiles (bulk RNAseq) of hippocampal microglia isolated from healthy young (4-month) and old (25-month) mice of both sexes (4 groups, 5 mice per group).

first: Kang

last: Seokjo

first: Goodridge

last: Helen S.


title: Epigenetic recording of stimulation history reveals BLIMP1-BACH2 balance in determining memory B cell fate upon recall challenge (ATAC-Seq II)

first: Hai

last: Qi

overall_design: ATAC-seq analysis of pulse-labeled tdTomato+ light zone GC B cells by tamoxifen adiministration from day6 to day8 and collected at day10 and day21 post NP-KLH immunization using mice of a S1pr2-creERT2;Rosa26-Ai14 genotype.

first: Wen

last: Shao


title: Myocardial infarction accelerates hepatic pathological progression of NASH by triggering immunoinflammatory response and induction of periostin

city: wenzhou

last: Xie

address: ouhai

institute: Wenzhou Medical University

summary: Patients with non-alcoholic fatty liver disease (NAFLD), especially advanced non-alcoholic steatohepatitis (NASH), have an increased risk of cardiovascular diseases (CVD) due to the production of pro-inflammatory factors, vasoactive and thrombogenic molecules, or insulin resistance and related disorders. While elevated risk and incidence of CVD events in NAFLD/NASH are well established, whether such events will, in turn, influence the pathogenesis of NAFLD remains unknown. Here, we show that myocardial infarction (MI) accelerates the linear hepatic pathological progression of NAFLD. In humans, NAFLD patients who experienced CVD events after their diagnosis of NAFLD show a rapid progression of hepatic fibrosis. In mouse models of NASH, MI promotes hepatic fibrosis, accompanied by elevated circulating Ly6Chi monocytes and their recruitment to the damaged liver tissues. Depleting these cells abrogate MI-induced hepatic pathological effects in mice with NASH. Meanwhile, MI substantially elevates circulating and cardiac periostin contents, which act on hepatocytes and stellate cells to promote hepatic lipid accumulation and fibrosis, finally exacerbating hepatic pathological progression of NASH. Additionally, specific silence of cardiac periostin markedly attenuates MI-induced hepatic pathological progression of mice with NASH. These preclinical and clinical results demonstrate that MI alternates systemic homeostasis and upregulates the production of pro-fibrotic factors, triggering cross-disease communication that accelerates hepatic pathological progression of NAFLD.

overall_design: To investigate the function of circulating monocytes, we sorted circulating Ly6Chi monocytes from CDAHFD-fed mice on the 7th day after MI or sham operation.

first: Jing

last: Gan

first: Huiying

last: Tian

first: Zhuofeng

last: Lin


title: FRA1 controls acinar cell plasticity during murine KrasG12D-induced pancreatic acinar to ductal metaplasia

city: New York

first: Anil

middle: K.

last: Rustgi

state: New York

address: 1130 St. Nicholas Avenue

institute: Columbia University


title: Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness

city: Winnipeg

first: Ute

last: Kothe

state: MB

address: 144 Dysart Road

department: Chemistry

institute: University of Manitoba

summary: All elongator tRNAs harbor 5-methyluridine at position 54 and pseudouridine at position 55 in the T arm, which are generated by the enzymes TrmA and TruB, respectively. Escherichia coli TrmA and TruB have both been shown to act as tRNA chaperones,  and strains lacking trmA or truB are outcompeted by wildtype. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion of trmA and truB in E. coli causes a global decrease in aminoacylation and alters other tRNA modification such as acp3U47 and 4-thiouridine. Whereas global protein synthesis is not significantly changed in ΔtrmA and ΔtruB, the expression of many specific proteins is altered at the translational level. In conclusion, we demonstrate that universal modifications of the tRNA T arm are critical for global tRNA function by enhancing other tRNA modifications, tRNA folding, tRNA aminoacylation, and translation of specific genes thereby improving cellular fitness and explaining their conservation.

overall_design: To examine how mRNA levels compare between Escherichia coli lacking trmA, truB,  or both trmA and truB genes and the parental E. coli BW25113 strain, we extracted  total RNA from each strain after growth in LB + 2% sodium formate to an OD600 between 0.3 and 0.4 using TRIzol. Three biological replicates were performed for each strain.

first: Sarah

last: Schultz

first: Christopher

middle: D

last: Katanski

first: Richard

last: Fahlman

first: Tao

last: Pan


title: Epigenetic recording of stimulation history reveals BLIMP1-BACH2 balance in determining memory B cell fate upon recall challenge (ATAC-Seq 4)

summary: Long-term humoral immunity is partly maintained by memory B cells (MBCs). MBCs can be recalled to produce antibody-producing plasma cells (PCs) or form secondary germinal centers (GCs). The former process underlies markedly increased antigen-specific antibodies seen in the secondary response, while the latter process allows continuous somatic hypermutation and affinity maturation. MBC re-participation in the GC reaction is thought to be important for generating broadly neutralizing antibodies against highly mutating viruses such as influenza and HIV. However, how MBC recall is transcriptionally or epigenetically programmed to produce secondary PCs or GCs is not yet understood. Here we show that BACH2, a transcription factor required for GC formation and maintenance1,2, decreases across post-activation stages of B cells, from the NAIVE state to GC, memory, and the terminal PC state. In contrast, BLIMP-1, a transcription factor that promotes PC formation3,4 and is antagonistic to BACH2 (ref. 5), increases as B cells traverse the same course. The relative strength between BLIMP-1 and BACH2 progressively increases in favor of BLIMP-1 in GCs and MBCs through the primary response. MBCs of the isotype or subset identity that preferentially give rise to secondary GCs exhibit comparatively higher BACH2 but lower BLIMP-1 expression than those predisposed for PC formation. Using a tetracycline-controlled circuit implanted in MBCs, we show that skewing the BLIMP-1-BACH2 balance in favor of BACH2 markedly increases GC formation by otherwise PC-predisposed MBCs, whereas skewing the balance in favor of BLIMP-1 drives PC formation by GC-prone MBCs, indicating that the potential for GC re-participation or PC development rests in the relative strength of BLIMP-1 over BACH2 within individual MBCs. Underneath this relative BLIMP-1-over-BACH2 strength in NAIVE B cells, GCs, MBCs and PCs, we observe progressively increased accessibilities to chromatin loci that are specifically opened in PCs, particularly those that contain ISRE elements and are controlled by IRF-4. IRF-4 is universally upregulated in B cells when stimulated through the BCR, the CD40 receptor, or by innate stimuli. By analyzing time-stamped GC B cells, we demonstrate a progressive increase in chromatin accessibilities at PC-specific, IRF-4-controlled gene loci over time. Our results support a model of progressive IRF-4 imprinting in which the cumulative stimulation history of B cells is epigenetically recorded in an IRF-4-dependent manner, determines the relative strength between BLIMP-1 and BACH2 in individual MBCs, and thereby dictates their individual probabilities to develop into GCs or PCs upon re-stimulation.

overall_design: ATAC-seq analysis of B cells stimulated with anti-IgM at different concentrations.


overall_design: RNA-seq analysis of wildtype or Zfp318 knockout Ai3+ MBCs at D30 post NP-KLH immunization.


title: RNA-seq analysis of intestinal epithelia of Ruminococcus torques treated mice

first: Chuan

last: Ye

address: 38 Xueyuan Road, Haidian District

institute: Peking University

summary: Purpose: To explore the influence of Ruminococcus torques treatment in mice intestinal epithelia. Method: Mice were pretreated with antibiotics for 3 days, then mice were fed with a high-fat diet and gavaged with PBS or R. torques (108 CFU/mouse) every 3 days for 2 weeks. mRNA profiles were generated by deep sequencing.Results: Several signaling pathways were changed after R. torques treatment, including response to hypoxia pathway. R. torques treatment significantly inhibits Epas1-mediated transcription effect.

overall_design: Expression profiling by RNA-seq, profiling of intestinal epithelia after R. torques treatment.

first: Yi

last: Zhang

first: Xuemei

last: Wang

first: Changtao

last: Jiang

first: Yanli

last: Pang


title: PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression

city: Memphis

first: Jacquelyn

last: Myers

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital


first: Hai

last: Qi

overall_design: RNA-seq analysis of wildtype or Zfp318 knockout naïve B cells.

last: Shao


title: SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE [Mouse_Neutro_Spleen_APOE3_4]

first: Neta

last: Rosenzweig

summary: APOE4 is the strongest genetic risk factor for Alzheimer's disease (AD) with increased odds ratios in females. Targeting amyloid plaques show modest improvement in male non-APOE4 carriers. Leveraging transcriptomics across APOE variants in both sexes, multiplex flow cytometry and validation in two independent cohorts of APOE4 female AD patients, we identify a new subset of neutrophils associated with cognitive impairment. This phenotype is defined by increased IL-17 and IL-1 co-expressed gene modules in blood neutrophils of cognitively impaired female APOE e4 carriers, showing increased infiltration to the AD brain. APOE4 female IL-17+ neutrophils upregulated the immunosuppressive cytokines IL-10 and TGFb, and immune checkpoints including LAG-3 and PD-1, associated with accelerated immune aging. Deletion of APOE4 in neutrophils reduced this immunosuppressive phenotype and restored microglial response to neurodegeneration (MGnD), limiting plaque pathology in AD mice. Mechanistically, IL-17Fupregulated in APOE4 neutrophils interacts with microglial IL-17RA to suppress the induction of MGnD phenotype, and blocking this axis supported cognitive improvement in AD mice. These findings provide a translational basis to target IL-17F in APOE e4 female carriers with cognitive impairment.

overall_design: Transcriptomic investigation of splenic neutrophils from transgenic APP/PS1 mice carrying the human APOE3 or APOE4 gene and having neutrophil specific deletion of APOE4.

first: Kilian

last: Kleemann

first: Thomas

last: Rust

first: Madeline

last: Grucci

first: Michael

last: Aronchik

first: Nieske

last: Brouwer

first: Madison

last: Carpenter

first: Isabel

last: Valenbreder

first: Joya

last: Cooper-Hohn

first: Malvika

last: Iyer

first: Rajesh

last: Krishnan

first: Kisha

last: Sivanathan

first: Wesley

last: Brandão

first: Taha

last: Yahya

first: Ana

last: Durao

first: Jean

middle: P

last: Chadarevian

first: Zhuoran

last: Yin

last: Properzi

first: Roni

last: Nowarski

first: Hayk

last: Davtyan

first: Mathew

last: Blurton-Jones

first: Hyun

middle: S

last: Yang

first: Reisa

last: Sperling

first: Bart

last: Eggen

first: Oleg

last: Butovsky


title: SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE [Microglia_IL17RA]

first: Neta

last: Rosenzweig

overall_design: Transcriptomic investigation of microglia from transgenic APP/PS1 mice with microglia specific deletion of IL17RA.

first: Kilian

last: Kleemann

first: Thomas

last: Rust

first: Madeline

last: Grucci

first: Michael

last: Aronchik

first: Nieske

last: Brouwer

first: Madison

last: Carpenter

first: Isabel

last: Valenbreder

last: Cooper-Hohn


title: Effects of an In Vivo Vaping Challenge on In Vitro IL-6 Biosynthesis Pathways in Arterial Endothelial Cells Derived from Human Embryonic Stem Cells

city: Madiaon

first: Stephane

last: Esnault

state: Wisconsin

address: 600 HIGHLAND AVE

institute: University of Wisconsin

summary: Electronic nicotine delivery system (ENDs) use among youth and young adults is increasing at a rapid pace and represents a growing public health threat.1 Newer generation devices heat e-liquids to higher temperatures and can achieve higher serum nicotine concentrations than older devices.1 Interleukin-6 (IL-6) is a cytokine that mediates atherogenesis and independently predicts future atherosclerotic cardiovascular disease events.2  Previous in vitro studies have demonstrated increased IL-6 production by human alveolar macrophages exposed to ENDs condensate.3 Although there has been considerable focus on the effects of ENDs use on airway inflammation, there are a paucity of data on the effects of ENDS on arterial inflammation.  Prior in vitro studies used venous endothelial cells (VECs) or human umbilical VECs as a proxy for arterial endothelial cells (AECs), limiting generalizability of their findings. Historically, use of AECs was limited by the invasive collection methods. We used a novel in vitro AEC model of human embryonic stem-cell-derived AECs to study differential expression (DE) of IL-6 pathway genes after exposure to serum from human participants taken before and after vaping using 3rd or 4th generation ENDs or no product use.

overall_design: We randomly selected serum from 10 chronic, exclusive ENDs users (exhaled carbon monoxide <5 ppm, positive urine nicotine) and 10 non-vaping, non-smoking controls from the Cardiac and LUng E-cigarette Smoking Study (CLUES, NCT03863509). ENDs users abstained from product use for >8 hours prior to the study visit. Participants completed a 15-minute ad libitum product use challenge in a dedicated room with external ventilation under remote supervision by a trained observer. ENDs users vaped with their ENDs product and controls rested. Post-challenge serum was collected in ENDs users 15-minutes after the product use challenge.

first: Matthew

middle: C

last: Tattersall

first: Ron

last: Stewart

first: David

last: Vereide

first: Scott

last: Swanson

first: Jue

last: Zhang

first: John

last: Steill

first: Nizar

last: Jarjour

first: Kristin

last: Hansen

first: Claudia

last: Korcarz

first: Timothy

last: Baker

first: James

last: Stein


title: SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE [Mouse_Microglia_APOE3_4]

first: Neta

last: Rosenzweig

overall_design: Microglia from 12-month-old female APP/PS1 mice expressing human APOE3 or APOE4 globally or either heterozygous APOE3 or APOE4 deletion in neutrophils via Ly6g Cre mediated deletion.

first: Kilian

last: Kleemann

first: Thomas

last: Rust

first: Madeline

last: Grucci

last: Aronchik

first: Joya

first: Malvika

last: Iyer

first: Rajesh

last: Krishnan

first: Kisha

last: Sivanathan

first: Wesley

last: Brandão

first: Taha

last: Yahya

first: Ana

last: Durao

first: Jean

last: Chadarevian

first: Zhuoran

last: Yin

last: Properzi

first: Roni

last: Nowarski

first: Hayk

last: Davtyan

first: Mathew

last: Blurton-Jones

first: Hyun

last: Yang

first: Reisa

last: Sperling

first: Bart

last: Eggen

first: Oleg

last: Butovsky


title: Epigenetic recording of stimulation history reveals BLIMP1-BACH2 balance in determining memory B cell fate upon recall challenge (ATAC-Seq I)

first: Hai

last: Qi

overall_design: ATAC-seq analysis of GC B cells, PCs, YFP+ and RFPhigh MBCs generated at day7 post NP-OVA immunization by B1-8hi PA-GFP+ donor B cells from a BARBE mouse and naïve B cells from unimmunized mouse with the same genotype.

first: Wen

last: Shao


title: Epigenetic recording of stimulation history reveals BLIMP1-BACH2 balance in determining memory B cell fate upon recall challenge (RNA-Seq)

overall_design: RNA-seq analysis of naïve B, GC B cells, MBCs and BMPCs generated at day14 post NP-KLH immunization.


title: SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE [Human_Female_HC_MCI_APOE23_33_34]

first: Neta

last: Rosenzweig

overall_design: Transcriptomic investigation of neutrophils from second validation cohort with females with APOE2/3 APOE3/3 or APOE3/4 genotype.

first: Kilian

last: Kleemann

first: Thomas

last: Rust

first: Madeline

last: Grucci

first: Michael

last: Aronchik

first: Nieske

last: Brouwer

first: Madison

last: Carpenter

first: Isabel

last: Valenbreder

first: Joya

last: Cooper-Hohn

first: Malvika

last: Iyer

last: Krishnan


title: High recallability of memory B cells requires ZFP318-dependent transcriptional regulation of mitochondrial function

overall_design: RNA-seq analysis of Zfp318 heterozygous or knockout tdTomato+ B1-8hi MBCs at 7 post NP-OVA immunization.


title: SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE [Human_F_M_HC_MCI_AD_E33_34]

overall_design: Transcriptomic investigation of neutrophils from cohort balanced for sex, age and APOE genotype.

first: Rajesh

first: Kisha

last: Sivanathan

first: Wesley

last: Brandão

first: Taha

last: Yahya

first: Ana

last: Durao

first: Jean

last: Chadarevian

first: Zhuoran

last: Yin

last: Properzi

first: Roni

last: Nowarski

first: Hayk

last: Davtyan

first: Mathew

last: Blurton-Jones

last: Yang


title: Effects of GOLIM4 knockdown on gene expression in H520 lung cancer cells

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

summary: The enhanced Golgi secretory pathway is increasingly recognized as a key driver of cancer progression. GOLIM4, a frequently amplified gene in human cancers, has been implicated in promoting tumor growth and metastasis by enhancing the secretion of oncogenic proteins. To gain further insights into the molecular mechanisms regulated by GOLIM4, we conducted transcriptomic profiling and identified the downstream pathways influenced by this gene.

overall_design: To explore the changes in gene expression, we depleted GOLIM4 in H520 cells using siRNAs and perform gene expression profiling analysis using the RNA-seq data.

first: Yuanxin

last: Xi

first: Xiaochao

last: Tan


title: Adrenal gland macrophages regulate glucocorticoid production through Trem2 and TGFβ [Bulk RNA-seq]

status: Public on Jun 03 2024

city: Minneapolis

first: Jesse

middle: W

last: Williams

state: MN

address: 2101 6th St. SE

department: Dept. Integrative Biology & Physiology

institute: University of Minnesota

summary: To elucidate how the influence of Trem2-deficiency on adrenal gland gene expression during a model of chronic atherosclerosis

overall_design: Whole adrenal gland transcript analysis from 12-week tamoxifen-high fat diet induced atherosclerosis in control or myeloid-specific conditional Trem2-deficient mice.

first: Yingzheng

last: Xu