title: Deciphering PFAS Potency: Cracking the Code with Gene Expression Profiles of Liver Toxic and Non-Liver-Toxic Reference Compounds

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: Understanding the mechanisms by which environmental chemicals cause toxicity is necessary for effective human health risk assessment. High-Throughput Transcriptomics (HTTr) can be used to inform risk assessment on toxicological mechanisms, hazards, and potencies. We applied HTTr to elucidate the molecular mechanisms by which Per- and Polyfluoroalkyl Substances (PFAS) cause liver toxicity. We contrasted transcriptomic profiles of four prototype PFAS against transcriptomic profiles from liver-toxic and non-liver-toxic reference compounds, alongside chemicals that activate peroxisome proliferator-activated receptors (PPARs). Our analysis was conducted on metabolically competent 3-D human liver spheroids produced from primary cells of 10 donors. Pathway analysis showed that PFOS and PFDS perturb many of the same pathways as the liver-toxic compounds in the spheroids, and that the cholesterol biosynthesis pathways are significantly affected by exposure to these compounds. PFOA alters lipid metabolism-related pathways but its expression profile does not closely match reference compounds. PFBS upregulates many degradation-related pathways and targets many of the same pathways as the PPAR agonists and acetaminophen. Our transcriptional analysis does not support that these PFAS are DNA damaging in this model. A multidimensional scaling analysis revealed that PFOS, PFOA, and PFDS cluster together in the same 3-D space as liver-damaging compounds; whereas, PFBS clusters more closely with the non-liver-damaging compounds. Benchmark concentration-response modeling predicts that all the PFAS are sufficiently bioactive to be liver-toxic. Overall, our results show that these PFAS produce unique transcriptional changes as well as altering pathways associated with established liver-toxic chemicals in this liver spheroid model.

first: A

last: Rowan-Carroll

first: M

first: C

middle: L

last: Yauk

last: Williams

first: K

last: Leingartner

first: L

last: Lorusso

first: E

last: Atlas

middle: M

last: Bradford


title: Microbial metabolite drives ageing-related clonal haematopoiesis via ALPK1 [RNA-seq]

status: Public on Feb 10 2025

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Expression profiling by high throughput sequencing

summary: Despite the known associations between CHIP and increased all-cause mortality, our understanding of environmental and regulatory factors that underlie this process during aging remain rudimentary. Here we report that intestinal alterations, which can occur with age, lead to systemic dissemination of a microbial metabolite that promotes leukemic cell expansion. Specifically, we show that ADP-D-glycero-b-D-manno-heptose (ADP-heptose), a biosynthetic bi-product specific to gram-negative bacteria, is uniquely found in the circulation of older individuals and favors the expansion of pre-leukemic hematopoietic stem cells. Mechanistically, ADP-heptose binds its receptor, ALPK1, triggering transcriptional reprogramming that endows pre-leukemic cells with a competitive advantage. Thus, the accumulation of ADP-heptose represents a direct link between aging and expansion of rare pre-leukemic cells, suggesting that the ADP-heptose-ALPK1 axis is a promising therapeutic target to prevent progression of CHIP to overt leukemia and immune-related conditions.

overall_design: mRNA profile of Dnmt3aWT (Dnmt3a+/+;MxCre), Dnmt3aKO (Dnmt3aF/F;MxCre+) and Dnmt3aKO;Alpk1KO murine BM HSPC (LSK) treated with either water (H2O) or ADP-heptose for 90 min.

first: Puneet

last: Agarwal

first: Daniel

middle: T

last: Starczynowski


title: The volume-regulated anion channel LRRC8 is involved in initiation of epidermal differentiation and is deregulated in psoriasis

status: Public on Feb 09 2025

city: Frankfurt am Main

first: Magdalena

last: Jahn

address: Theodor-Stern-Kai 7

country: Germany

institute: University Hospital Frankfurt

summary: Recent studies have shown that LRRC8A, the essential subunit of the volume-regulated anion channel LRRC8, which is responsible for mediating cell volume regulation during hypotonic stress, is predominantly localized in the basal layer of the epidermis. This prompted us to investigate whether LRRC8A plays a role in maintaining epidermal homeostasis by regulating key processes initiated in this layer, such as cell proliferation and/or differentiation. LRRC8A was found to be strongly upregulated in transiently amplifying cells at the onset of differentiation. While LRRC8A mRNA remains high when keratinocytes mature further, the LRRC8A protein is drastically downregulated. Interference with LRRC8A expression at this step inhibits transition of keratinocyte stem cells into transiently amplifying cells and impairs terminal differentiation. As psoriasis is a common chronic inflammatory skin disease characterized by disturbed epidermal differentiation and aberrant function of transiently amplifying cells, we investigated the involvement of LRRC8A in this disease. Indeed, LRRC8A was strongly decreased in lesional psoriatic skin, which could also be mimicked in vitro using Th1/Th17 cytokine mixes. Thus, our data suggest that LRRC8 could serve as a therapeutic target for the topical treatment strategies of psoriatic lesions by restoring the capacity of keratinocytes to initiate differentiation.

overall_design: RNA-seq profiling of primary keratinocyte subpopulations. Populations were separated based on their adherence to collagen IV into keratinocyte stem cells (KSC), transiently amplifying cells (TAC) and post-mitotic cells (PMC).

first: Victoria

last: Lang

first: Oliver

last: Rauh

first: Torsten

last: Fauth

first: Claudia

last: Buerger


title: A systems-biology approach connects aging mechanisms  with Alzheimer’s disease pathogenesis

status: Public on Feb 07 2025

city: Cambridge

last: Leventhal

state: MA

address: 77 Massachusetts Avenue

department: Computational and Systems Biology

institute: Massachusetts Institute of Technology

summary: Age is the strongest risk factor for developing Alzheimer’s disease, the most common neurodegenerative disorder. However, the mechanisms connecting advancing age to neurodegeneration in Alzheimer’s disease are incompletely understood. We conducted an unbiased, genome-scale, forward genetic screen for age-associated neurodegeneration in Drosophila to identify the underlying biological processes required for maintenance of aging neurons. To connect genetic screen hits to Alzheimer’s disease pathways, we measured proteomics, phosphoproteomics, and metabolomics in Drosophila models of Alzheimer’s disease. We further identified Alzheimer’s disease human genetic variants that modify expression in disease-vulnerable neurons. Through multi-omic, multi-species network integration of these data, we identified relationships between screen hits and tau-mediated neurotoxicity. Furthermore, we computationally and experimentally identified relationships between screen hits and DNA damage in Drosophila and human iPSC-derived neural progenitor cells. Our work identifies candidate pathways that could be targeted to attenuate the effects of age on neurodegeneration and Alzheimer’s disease.

overall_design: RNA-seq was collected from NGN2 neural progenitor cells after knockdown of genes of interest: HNRNPA2B1, CSNK2A1 and NOTCH1


title: RNAseq in Acly wild-type or conditional KO mouse T-ALLs

status: Public on Feb 11 2025

city: New Brunswick

last: Herranz

state: New Jersey

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

summary: C57BL6 mice harboring Acly conditional knockout NOTCH1-ΔE-induced leukemias were treated with vehicle (control) or tamoxifen to induce isogenic deletion of Acly. Here we report the gene expression profile of leukemic blasts obtained from the spleen from control- or tamoxifen-treated leukemic mice, either in an acute setting (72h post-tamoxifen) or in long-term survival setting

overall_design: RNAseq analysis of leukemic spleens in two genotypes - 6 WT and 4 KO in acute, 5 WT and 5 KO in long-term survival

first: Amartya

last: Singh

last: da Silva-Diz


title: Chromatin Remodeling by the Histone Methyltransferase SETD2 Drives Cardiometabolic Heart Failure with Preserved Ejection Fraction

status: Public on Feb 12 2025

city: Zurich

first: shafeeq

middle: Ahmed

last: Mohammed

state: Zurich

address: wagistrasse 12

department: Centre for Translational and Experimental Cardiology

country: Switzerland

institute: University of Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cardiometabolic heart failure with preserved ejection fraction (cHFpEF) is highly prevalent and associated with a poor outcome. Pathological gene expressions in heart failure are accompanied by changes in active histone marks without major alterations in DNA methylation. Histone 3 trimethylation at lysine 36 (H3k36me3) - a chromatin signature induced by the histone methyltransferase SETD2 – has shown a strong correlation with changes in gene expression in the human failing heart; yet its role in cardiac disease is poorly understood. The present study investigates the role of SETD2/ H3k36me3 in cHFpEF.

overall_design: ChIP-seq of H3K27ac, H3K4me, H3K4me3 and H3k27ac in cardiomyocytes obtained from control and HFpEF were analyzed

first: Sarah

last: Costantino

first: Shafeeq

middle: A

first: Marialucia

last: Telesca

first: Francesco

last: Paneni


title: Anti-tumor CD4Th1 cells controls the migration and outgrowth of disseminated cancer cells

city: Tampa

first: Brian

middle: J

last: Czerniecki

state: FL

address: 12902 Magnolia Drive

department: Breast Oncology

institute: Moffitt Cancer Center

summary: Comparison of gene expression profiles of disseminated cancer cells with primary tumors and metastatic tumors

overall_design: To investigate the gene expression profiles of disseminated cancer cells compared to primary tumors and metastatic tumors in breast cancer and role of anti-tumor CD4Th1 immune response on the gene expression profiles, we performed RNA sequencing.

first: Ganesan

last: Ramamoorthi


title: A systems-biology approach connects aging mechanisms with Alzheimer’s disease pathogenesis [TCPY]

first: Matthew

overall_design: RNA-seq was collected from temporal cortex pyramidal neurons extracted from human post-mortem Alzheimer's disease brains by laser-capture microdissection


title: Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing

status: Public on Feb 08 2025

city: Durham

first: Madeline

last: Keenen

state: North Carolina

address: 308 Research Drive

department: Cell Biology

institute: Duke University

summary: The outer surface of chorionic villi in the human placenta consists of a single multinucleated cell called the syncytiotrophoblast (STB). The unique cellular ultrastructure of the STB presents challenges in deciphering its gene expression signature at the single-cell level, as the STB contains billions of nuclei in a single cell. There are many gaps in understanding the molecular mechanisms and developmental trajectories involved in STB formation and differentiation. To identify the underlying control of the STB, we performed comparative single nucleus (SN) and single cell (SC) RNA sequencing on placental tissue and tissue-derived trophoblast organoids (TOs). We found that SN was essential to capture the STB population from both tissue and TOs. Differential gene expression and pseudotime analysis of TO-derived STB identified three distinct nuclear subtypes reminiscent of those recently identified in vivo. These included a juvenile nuclear population that exhibited both CTB and STB marker expression, a population enriched in genes involved in oxygen sensing, and finally a subtype enriched in transport and GTPase signaling molecules. Notably, suspension culture conditions of TOs that restore the native orientation of the STB (STBout) showed elevated expression of canonical STB markers and pregnancy hormones, along with a greater proportion of the STB nucleus subtype specializing in transport and GTPase signaling, compared to those cultivated with an inverted STB polarity (STBin). Gene regulatory analysis identified novel markers of STB differentiation conserved in tissue and TOs, including the chromatin remodeler RYBP, that exhibited STB-specific RNA and protein expression. CRISPR/Cas9 knock out of RYBP in STBin TOs did not affect cell-cell fusion, but bulk sequencing demonstrates the downregulation of the pregnancy hormone CSH1 and upregulation of many genes that define the oxygen sensing STB nuclear subtype. Finally, we compared STB gene expression signatures amongst first trimester tissue, full-term tissue, and TOs, identifying many commonalities but also notable variability across each sample type. This indicates that STB gene expression is responsive to its environmental context. Our findings emphasize the utility of TOs to accurately model STB differentiation and the distinct nuclear subtypes observed in vivo, offering a versatile platform for unraveling the molecular mechanisms governing STB functions in placental biology and disease. The processed datasets can be visualized online at https://gladfelterlab.shinyapps.io/PlacentaRNAsequencing/.

overall_design: This study performed single cell (SC) or single nucleus (SN) RNA sequencing on either trophoblast organoids (TOs) or term placenta tissue with the 10x Genomics 3' RNA sequencing kit. TOs were grown in matrigel with the multinucleated syncytiotrophoblast facing inward (STBin), in suspension with the STB facing out towards the media (STBout), or in matrigel with a three step culture treatment to enrich for extravillous trophoblast cells (EVTenrich).

first: Amy

middle: S

last: Gladfelter

first: Carolyn

middle: B

last: Coyne


title: CHD3 regulates BMP signalling response during cranial neural crest cell specification

status: Public on Feb 05 2025

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

summary: CHD3 is a component of the NuRD chromatin remodeller. Mutations in CHD3 cause Snijders Blok-Campeau Syndrome, a neurodevelopmental disorder marked by intellectual disability and craniofacial abnormalities. To unveil the role of CHD3 in craniofacial development, we differentiated CHD3-null induced pluripotent stem cells (iPSCs) into cranial neural crest cells (CNCC). We found that CHD3 expression is low in iPSCs and neuroectoderm, but it is upregulated during CNCC specification, where CHD3-containing NuRD opens the chromatin at BMP-responsive enhancers, to allow binding of DLX5 and other factors. CHD3 loss leads to repression of BMP target genes and imbalance between BMP and Wnt signalling, which ultimately results in aberrant mesodermal fate. Consequently, cranial neural crest specification fails, replaced by mesodermal identity, which can be partially rescued by titrating Wnt levels. Our findings highlight a novel role for CHD3 as pivotal regulator of BMP signalling, essential for proper neural crest specification and craniofacial development.

overall_design:
RNA-seq of CHD3-WT, CHD3-HET-KO and CHD3-KO iPSC lines  (3 replicates per line)
RNA-seq of CHD3-WT and CHD3-KO cell lines at day 18 of in vitro cranial neural crest cell specification in late maintenance media (at least 2 replicates per line)
RNA-seq of CHD3-WT and CHD3-HET-KO cell lines at day 18 of in vitro cranial neural crest cell specification in early maintenance media (3 replicates per line)
RNA-seq of CHD3-WT and CHD3-KO cell lines at day 14 of in vitro cranial neural crest cell specification in early maintenance media (at least 2 replicates per line)
ChIP-seq of CHD3 in two CHD3-WT cell lines at day 14 of in vitro cranial neural crest cell specification
ChIP-seq of CHD3 in CHD3-WT cell line at day 18 of in vitro cranial neural crest cell specification
ChIP-seq of DLX5 in one CHD3-WT cell line and two CHD3-KO cell lines at day 14 of in vitro cranial neural crest cell specification
ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 18 of in vitro cranial neural crest cell specification (2 replicates per line)
ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 14 of in vitro cranial neural crest cell specification (2 replicates per line)
ATAC-seq of CHD3-WT and CHD3-KO iPSC lines (2 replicates per line)
ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 4 of in vitro cranial neural crest cell specification (2 replicates per line)
ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 10 of in vitro cranial neural crest cell specification (2 replicates per line)
ChIP-seq of MBD3 in two CHD3-WT cell lines at day 14 of in vitro cranial neural crest cell specification

first: Zoe

middle: H

last: Mitchell

first: Joery

last: den Hoed

first: Willemijn

last: Claassen

first: Martina

last: Demurtas

first: Laura

last: Deelen

first: Philippe

last: Campeau

first: Karen

last: Liu

first: Simon

last: Fisher


title: Sequencing of U18-treated yeast of different genetic background

status: Public on Feb 03 2025

city: Santiago

first: Benjamín

last: Szenfeld

state: Las Condes

address: Av Plaza 680

department: Genetics and Genomics

country: Chile

institute: Institute of Science and Innovation in Medicine

summary: This analysis correspond to the transcripts of four different yeast strains (NA, WA, WE, and SA) untreated and treated with the Ncr1p inhibitor U18666A

overall_design: RNA-seq profiling of four yeast strains (DBVPG6044 [West African, “WA”: Mat alpha ho::NatMX, ura3::KanMXY12], Y12 [Sake, “SA”: Mat alpha ho::NatMX, ura3::KanMX], YPS128 [North American, “NA”: Mat alpha ho::NatMX, ura3::KanMX], and DBVPG6765 [Wine/European, “WE”: Mat alpha ho::NatMX, ura3::KanMX]) was conducted under control and U18666A-treated conditions. Yeast cultures were grown in triplicates at 28°C to mid-log phase (OD600 ~0.8) in YNB medium (control) or YNB medium with U18666A (200 µg/mL). Cells were centrifuged and treated with zymolyase (2U) for 30 minutes at 37°C. Total RNA was extracted using the E.Z.N.A. Total RNA Kit I (OMEGA), followed by DNase I treatment (Promega) to remove genomic DNA. RNA integrity was verified using a Fragment Analyzer (Agilent). Library preparation and sequencing were performed by BGI using DNBseq™ technology.

first: Macarena

last: Las Heras

first: Valeria

last: Olguín

first: Juan Carlos

last: Rubilar

first: Juan Francisco

last: Calderón

first: Yanireth

last: Jimenez

first: Silvana

last: Zanlungo

first: Emanuele

last: Buratti

first: Andrea

last: Dardis

first: Francisco

last: Cubillos

first: Andrés

middle: D

last: Klein


title: SNP array analysis has facilitated the identification of novel chromosomal alterations associated with disease and SNPs related to Adverse Drug Reactions in neuroblastoma

status: Public on Feb 06 2025

city: Shanghai

first: Ying

last: Li

address: Lane 2555, Xiu-Pu Road, Pudong New District, Shanghai 200120, China

country: China

institute: Shanghai Cinopath Medical Laboratory Co., Ltd.

summary: Chromosome abnormalities are common characteristics of neuroblastoma and have been associated with treatment, relapse and survival risk factors. The processes governing the incidence or advancement of chromosomal copy number abnormalities remain unclear, despite progress in understanding their prognostic implications. Single nucleotide polymorphism (SNP) array analysis was performed on a set of 45 neuroblastoma samples in order to examine chromosomal CNAs and SNPs. The present study aimed to provide a comprehensive understanding of genetic alterations, clinical implications, and the association between copy number aberrations (CNAs) and clinical parameters.

overall_design: 45 neuroblastoma samples were analyzed with Infinium CytoSNP-850K v1.2 BeadChip SNP arrays.

first: Kailan

last: Chen

first: Hanpeng

first: Yujie

last: Luo

first: Jiaqi

first: Huichao

first: Yongli

last: Tian

first: Yifei

last: Yu

first: Yun

last: Xu

first: Li

first: Qiong


title: Mitochondrial metabolism sustains DNMT3A-R882-mutant clonal haematopoiesis

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: University of Cambridge

summary: Somatic DNMT3A R882 codon mutations drive the most common form of clonal haematopoiesis (CH) and are associated with increased acute myeloid leukaemia (AML) risk. Preventing expansion of DNMT3A-R882-mutant haematopoietic stem/progenitor cells (HSPCs) may therefore avert progression to AML. To identify DNMT3A-R882-mutant-specific vulnerabilities, we conducted a genome-wide CRISPR screen on primary mouse Dnmt3aR882H/+ HSPCs. Amongst the 640 vulnerability genes identified, many were involved in mitochondrial metabolism and metabolic flux analysis confirmed enhanced oxidative phosphorylation usage in Dnmt3aR882H/+ vs Dnmt3a+/+ (WT) HSPCs. We selected citrate/malate transporter Slc25a1 and complex I component Ndufb11, for which pharmacological inhibitors are available, for downstream studies. In vivo administration of SLC25A1 inhibitor CTPI2 and complex I inhibitors IACS-010759 and metformin, suppressed post-transplantation clonal expansion of Dnmt3aR882H/+, but not WT, LT-HSCs. The effect of metformin was recapitulated using a primary human DNMT3A-R882 CH sample. Notably, analysis of 412,234 UK Biobank participants revealed that individuals taking metformin had markedly lower prevalence of DNMT3A-R882-mutant CH, after controlling for potential confounders including glycated haemoglobin, diabetes and body mass index. Collectively, our data propose that modulation of mitochondrial metabolism as a therapeutic strategy for prevention of DNMT3A-R882-mutant AML.

overall_design: HSPCs were extracted from two primaryDnmt3R882H/+mice and used for the CRISPR screen.

first: Malgorzata

last: Gozdecka

first: Monika

last: Dudek

first: Sean

last: Wen

first: Margarete

last: Fabre

first: Justyna

last: Rak

first: Aristi

last: Damaskou

first: Brian

last: Huntly

first: George

last: Vassiliou


title: rbm24a is an organizer component of germ plasm to determine germ cell fate (202409 validation)

status: Public on Feb 01 2025

city: Tsingtao

first: li

middle: pan

last: feng

state: shandong

address: Ao Shan Wei Street

department: College of Life Sciences

institute: shandong university

summary: The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells (PGCs). They produce a set of localized maternal mRNAs and proteins to form phase-separated germ plasm that functions as the PGC determinants, but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs, which determines the specific grasp of germ plasm mRNAs into the phase-separated aggregates. Rbm24a-absent granules fail to undergo kinesin-dependent transport towards the cleavage furrows, where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs, resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm, highlighting an emerging common mechanism to read and recruit RNA component into phase-separated condensates.

overall_design: To comprehensively characterize the RNA-binding landscape of Rbm24a in zebrafish, we performed RIP-seq analysis using rbm24a-GFP knock-in samples, with IgG serving as the control.

last: Ang


title: Effects of SarsCov2 on small RNA transcriptome  in human lung cells

city: Innsbruck

first: Kai

last: Kummer

address: Schoepfstr. 41

department: Institute of Physiology

country: Austria

institute: Medical University of Innsbruck

type: Non-coding RNA profiling by high throughput sequencing

summary: SARS-CoV-2 infection initiates complex interactions at mucosal barriers. In primary human bronchial epithelial cells, we investigated changes in the small RNA transcriptome of a pathogenic SARS-CoV-2 variants. We uncovered differential expression of a specific set of miRNAs, piRNAs, snoRNAs, vault RNAs, Y RNAs, and lincRNAs such as MALAT1 and NEAT1, which inhibit apoptosis while promoting cell proliferation and viral infection. Conversely, differential expression of 7SL, U2, and RPPH1 RNAs, as well as miR-155-5p and miR-27a-5p, was involved in antiviral signaling. Expression of the protein-coding genes CXCL10, IFIT1, NCOA7, IFIT2, SIX3 and RPSA was increased during Delta infection.

overall_design: Expression profiling of small RNA by SarsCov2 at different time points (Uninf, 1h, 1d, 3d)

first: Glory

last: Ranches

first: Hubert

last: Hackl

first: Viktoria

last: Zaderer

first: Melanie

last: Ploner

first: Wilfried

last: Posch

first: Doris

last: Wilfingseder

first: Alexander

last: Huettenhofer


title: MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia [RNA-seq]

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

summary: The transcription factor MECOM, located at 3q26, is essential for hematopoietic stem cells (HSCs) in healthy individuals. Enhancer translocations, due to 3q26 rearrangements, drive out-of-context MECOM expression in an aggressive subtype of acute myeloid leukemia (AML). Aberrantly expressed MECOM is essential for the survival and immature phenotype of these leukemia cells. Direct depletion of MECOM using an endogenous auxin-inducible degron immediately upregulates expression of myeloid differentiation factor CEBPA. MECOM depletion is also accompanied by a severe loss of CD34 expression and gain of mature myeloid cell surface marker CD15. MECOM exerts its inhibitory effect on differentiation by binding to the +42kb CEBPA enhancer, which is required for neutrophil development. This is partially dependent on the interaction between MECOM and its essential co-repressor CTBP2, a potential target in this type of AML. We demonstrate that CEBPA overexpression can bypass the MECOM-mediated block of differentiation. In addition, AML patients with MECOM overexpression through enhancer hijacking show significantly reduced CEBPA. Our study provides insight into the mechanism by which MECOM maintains the stem cell state in AML. Furthermore, CEBPA levels are an important read-out for successful targeting of MECOM in 3q26-rearranged AML.

overall_design: We performed RNA sequencing (RNA-seq) experiments upon interference with MECOM function in the inv(3) MUTZ3 cell line using 2 different strategies: 1) we targeted the MECOM RNA for degradation with short hairpin RNA (shRNA); 2) we prevented interaction of MECOM with its partner CTBP using a PLDLS peptide.

first: Dorien

last: Pastoors

first: Marije

last: Havermans

first: Roger

last: Mulet-Lazaro

first: Leonie

last: Smeenk


title: RNA-binding proteins DND1 and NANOS3 coordinately suppress SOX4 in processing bodies for restricting the entry of germ cell lineage

city: Haining

first: zhaoyu

last: Gu

state: Zhejiang

address: 718 East Haizhou Road

department: ZJE

institute: Zhejiang University

summary: Specification of germ cell fate establishes the germline development during early embryogenesis, yet the underlying mechanisms remain largely unknown in humans. Here we focus on the functional roles of the RNA-binding protein (RBP) DND1 in human germline specification. We deleted the whole genomic region of DND1 in human embryonic stem cells (hESCs), based on which we generated human primordial germ cell-like cells (hPGCLCs). Interestingly, we discovered an increased percentage of hPGCLCs induced from DND1 deleted hESCs, suggesting that DND1 may restrict the specification of human germ cell lineage. Mechanistic investigation reveals that DND1 forms a complex with another RBP NANOS3, in which DND1 facilitates the binding of NANOS3 to their target mRNAs. Furthermore, by analyzing the mRNAs bound by DND1 and NANOS3, we identified SOX4 mRNAs as the key downstream factor for DND1 and NANOS3 complex to restrict the induction of hPGCLCs. Interestingly, DND1 and NANOS3 function in processing bodies (P-bodies) to repress the translation of SOX4 mRNAs, where NANOS3 bridges the interaction between DND1 and the translational repressor 4E-T. Altogether, these findings identify the RBPs DND1 and NANOS3 as “break system” to restrict the entry of germ cell fate in humans.

overall_design: RNAseq analysis of hESCs, mesoderm, endoderm, ectoderm and hPGCLCs in multiple knockout/overexpressed lines

first: Honglin

last: Yu

first: Ziqi

last: Wang

first: Qizhe

last: Shao

first: Zhaoyu

first: Yao

last: Yao

first: Di

last: Chen


title: RNA-seq profiles of various developmental stages and systematic nuclear hormone receptor (NHR) gene knockdowns in C. elegans

status: Public on Feb 02 2025

city: Worcester

first: Xuhang

last: Li

state: Massachusetts

address: 55 N Lake Ave

department: Department of Systems Biology

institute: University of Massachusetts Medical School

summary: The transcriptome is one of the most informative molecular phenotypes and is most frequently measured by RNA-sequencing (RNA-seq). Recently, Perturb-seq has been developed to measure the transcriptome in single cells upon perturbation of different genes by CRISPR-Cas9. While powerful, Perturb-seq has limited resolution and cannot easily be applied to intact animals. Here, we present ‘Worm Perturb-Seq (WPS)’, which combines whole-animal gene knockdown by RNAi in Caenorhabditis elegans with a large-scale, high-throughput bulk RNA-seq approach that produces high-resolution transcriptome profiles. WPS includes an analytical framework that identifies differentially expressed genes (DEGs) by using gene-specific models with empirical null distributions, rather than using control RNAi alone. Specifically, our approach identifies and corrects inflated P values obtained with standard methods, thus improving statistical rigor. We applied WPS to collect a detailed time course dataset for the animal at various developmental stages, from L2 larve to gravid adult stages. We also applied WPS to 103 C. elegans nuclear hormone receptors (NHRs) and revealed diverse functional modules featuring pairs of NHRs regulating shared target genes. WPS enables large-scale and high-quality transcriptomic analysis of genetic perturbations in an animal and can be implemented not only for RNAi but also for other perturbing conditions such as different bacterial diets, C. elegans strains, etc. WPS may also provide a platform for similar studies in other model organisms and human tissue culture cells.

overall_design: In this study, we applied Worm Perturb-seq (WPS), a massively parallel RNAi and RNA-seq technology, to perturb 103 nuclear hormone receptor (NHR) genes in nematode C. elegans, followed by a whole-animal, bulk RNA-seq readout. Samples were multiplexed to form pooled sequencing libraries with around 45 samples per library. The dataset includes eight libraries corresponding to 353 samples, covering the perturbations of 103 genes in biological triplicates. This record also contains the WPS library for time-course samples of C. elegans development that were used in the study. The developmental stage dataset includes  17 time points for animals at L2, L3, L4, Young Adult and Gravid Adult stages, ranging from 17 to 69 hours post L1 seeding, in biological triplicate. All RNA-seq libraries were constructed following WPS method, an adapted CEL-seq2 protocol, giving a multiplexed bulk RNA-seq library for 3'-end sequencing of C. elegans genes. The read 1 is used to encode barcode information and read 2 maps to the 3' end region of C. elegans transcripts. Barcode information can be found from the Supplementary Table "barcode_and_metadata_full_dataset.csv" ("barcode_and_metadata_dev_stages.csv" for developmental stages). These libraries can be directly processed by the WPS data processing pipeline (https://github.com/XuhangLi/WPS) providing the barcode information attached. A custom processing of the data is feasible following the typical demultiplexing methods for single-cell RNA-seq data that are able to process CEL-seq2 library. Please refer to our manuscript for decription of the design of read 1 and the pooling of samples.

first: Hefei

last: Zhang


title: Gene expression studies of barley low tillering mutants

city: SAINT PAUL

first: Gary

last: Muehlbauer

state: MN

address: 1991 Upper Buford Circle 411 Borlaug Hall

department: Agronomy and Plant Genetics

institute: University of Minnesota

summary:
Barley (Hordeum vulgare) uniculm2 (cul2) plants produce no tillers, while absent lower laterals (als), uniculm4 (cul4) and low number of tillers (lnt1) plants produce fewer tillers than wild-type barley plants. Gene expression was studied in comparison to wild-type cv. "Bowman" plants in embryo, crown, inflorescence and seedling tissue.
Gene expression studies for uniculm2 (Okagaki et al., Funct Integr Genomics (2013) 13:33–41), absent lower laterals (Dabbert et al., Theor Appl Genet (2009) 118:1351–1360) and low number of tillers (Dabbert et al., Theor Appl Genet (2010) 121:705–715) plants have been previously published.

overall_design: Barley embryo, crown, inflorescence and seedling tissue was collected from all genotypes for RNA extraction and hybridization on Affymetrix Barley1 GeneChip microarrays. For each genotype and tissue 3 biological replicates from at least 10 plants each were sampled.


title: MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia

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

overall_design: Refer to individual Series


title: rbm24a is an organizer component of germ plasm to determine germ cell fate

first: li

last: feng

overall_design: To elucidate the comprehensive RNA-binding landscape of Rbm24a in zebrafish, we employed RIP-seq analysis on both rbm24a-GFP knock-in and wild-type zebrafish.

first: Ang


title: Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations [PDX GBM22 orthotopic xenografts]

status: Public on Jan 31 2025

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

summary: Glioblastoma (GBM) remains the most common and lethal adult malignant primary brain cancer with few treatment options. One of the most significant issues hindering GBM therapeutic development is intratumor heterogeneity. GBM tumors consist of multiple neoplastic cell types with distinct transcriptional profiles. Identifying compounds that target these different cell types requires a platform that predicts differential sensitivity and resistance of cells within GBM tumors. To address this, we developed a novel framework to generate tumor cell-type-specific disease signatures and their predicted drug sensitivity. We performed single-cell RNA sequencing of newly diagnosed and recurrent GBM tumors and identified compounds from the LINCS L1000 database with transcriptional response signatures selectively discordant with distinct single-cell transcriptional states within GBM tumors. We then validated in silico predictions with in vivo findings in mice as the aurora kinase inhibitor alisertib induced a shift from NPC-like to MES-like transcriptional states upon treatment. To allow other investigators to predict selective tumor cell type drug sensitivity in silico we developed a platform termed ISOSCELES (Inferred cell Sensitivity Operating on the integration of Single-Cell Expression and L1000 Expression Signatures).  Our studies suggest that ISOSCELES is a novel platform to identify cell populations that are sensitive and resistant to targeted therapies in GBM, which can inform treatment decisions in future clinical trials.

overall_design: Single-cell RNA sequencing analysis of PDX GBM22 orthotopic xenografts treated with the aurora kinase inhibitor alisertib or a DMSO vehicle control.

middle: G

first: Robert

middle: K

last: Suter

first: Anna

last: Jermakowicz


title: Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitch

status: Public on Jan 30 2025

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

summary: Transcriptional regulation is a dynamic process that coordinates diverse cellular activities, and the use of small molecules to perturb gene expression has propelled our understanding of the fundamental regulatory mechanisms. However, small molecules typically lack the spatiotemporal precision required in highly non-invasive, controlled settings. Here, we present the development of a cell-permeable small-molecule DNA G-quadruplex (G4) binder, termed G4switch, that can be reversibly toggled on and off by visible light. We have biophysically characterised the light-mediated control of G4 binding in vitro, followed by cellular, genomic mapping of G4switch to G4 targets in chromatin to confirm G4-selective, light-dependent binding in a cellular context. By deploying G4switch in living cells, we show spatiotemporal control over the expression of a set of G4-containing genes and G4-associated cell proliferation. Our studies demonstrate a chemical tool and approach to interrogate the dynamics of key biological processes directly at the molecular level in cells.

overall_design: SLAM-seq , Chemmap , G4 CUT&Tag

first: Xiaoyun

first: Somdutta

last: Dhir

first: Yuqi

first: Zutao

first: Jochen

last: Spiegel

first: Angela

last: Simeone

first: Santosh

last: Adhikari

first: Shankar

last: Balasubramanian


title: Nicotinamide Riboside Kinase 1 protects against diet and age-induced pancreatic beta-cell failure

city: Lausanne

first: Carles

last: Canto

address: Ecole Polytechnique Fédérale de Lausanne

summary: Objective: Disturbances in NAD+ metabolism have been described as a hallmark for multiple metabolic and age-related diseases, including type 2 diabetes. While alterations in pancreatic -cell function are critical determinants of whole-body glucose homeostasis, the role of NAD+ metabolism in the endocrine pancreas remains poorly explored. Here, we aimed to evaluate the role of nicotinamide riboside (NR) metabolism in maintaining NAD+ levels and pancreatic -cell function in pathophysiological conditions.   Methods: Whole body and pancreatic -cell-specific NRK1 knockout (KO) mice were metabolically characterized in situations of high-fat feeding and aging. We also analyzed pancreatic -cell function and gene expression.   Results: We first demonstrate that NRK1, the essential enzyme for the utilization of NR, is substantially expressed in pancreatic -cells. While NR treatment did not alter glucose-stimulated insulin secretion in pancreatic islets from young healthy mice, NRK1 knockout mice displayed glucose intolerance and compromised -cells response to a glucose challenge upon high-fat feeding or aging. Interestingly, β cells dysfunction stemmed from the functional failure of other organs, such as liver and kidney, and the associated changes in circulating peptides and hormones, as mice lacking NRK1 exclusively in β-cells did not show altered glucose homeostasis.  Conclusions: This work unveils a new physiological role for NR metabolism in the maintenance of glucose tolerance and pancreatic -cell function in high-fat feeding or aging conditions.

overall_design: Both WT and NRK1 ins1Cre KO mice were submitted on HFD for 12 weeks and pancretic islets were collected at the sacrifice.

first: Angelique

last: Cercillieux

first: Joanna

last: Ratajczak

first: Magali

last: Joffraud

first: José

last: Sanchez-Garcia

first: Guillaume

last: Jacot

first: Alix

last: Zollinger

first: Sylviane

last: Métairon

first: Judith

last: Giroud-Gerbetant

first: Eleonora

last: Ciarlo

first: Miriam

last: Valera-Alberni

first: Audrey

last: Sambeat


title: Dissecting RNA Selectivity Mediated by Tandem RNA-Binding Domains

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason farm

department: Pharmacology

institute: UNC Chapel Hill

summary: RNA-protein interactions are pivotal to proper gene regulation. Many RNA-binding proteins possess multiple RNA-binding domains; however, how these domains interplay to specify and regulate RNA targets remains poorly understood. Here, we investigate three multi-domain proteins, Musashi-1, Musashi-2, and Unkempt, three factors which share a high degree of RNA specificity. We use a combination of massively parallel in vitro assays with random or naturally derived RNA sequences and find that individual domains within a protein can have differing affinities, specificities, and spacing preferences. Further, we emphasize that while all three proteins have overlapping motif specificities, non-overlapping sequences may allow for target discrimination. We carry out large scale competition assays between these proteins and determine how individual protein specificities and affinities influence competitive binding. Integration of in vivo binding and regulation with in vitro specificities shows that target selection involves a combination of the protein intrinsic specificities described here, but cellular context is critical to drive these proteins to motifs in specific transcript regions. Finally, evolutionarily conserved RNA regions display evidence of binding multiple RBPs in vivo, and these RNA regions recapitulate this trend with the highest affinity in vitro. We highlight the importance of understanding features of complex RNA-protein interactions and how protein-target discrimination can be established.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: RNA bind-n-seq (RBNS), positional RBNS (posRBNS), competition posRBNS (compPosRBNS), and natural sequence RBNS (nsRBNS) for unkempt (UNK), Musashi-1 (MSI1), and Musashi-2 (MSI2)

first: Sarah E.

last: Harris

first: Yue

last: Hu

first: Kaitlin

last: Bridges

first: Bryan B.

last: Guzmán

first: Francisco F.

last: Cavazos Jr.

first: Justin G.

last: Martyr

first: Maria M.

last: Aleman

first: Jernej

last: Murn


status: Public on Jan 24 2025

city: qingdao

first: yizhuang

last: zhang

address: No.72 Binhai Road  Jimo District

department: school of life sciences

overall_design: We performed single-cell RNA-seq (scRNA-seq) for shield-stage embryos to compare gene expression between Mrbm24a and sibling embryos. Another purpose of this omic analysis is to examine possible cell populations that can be affected by the loss of maternal Rbm24a.

first: Yizhuang

last: Zhang

first: Ming

last: Shao


title: Multidimensional Analysis of Twin Sets During an Intensive Week-Long Meditation Retreat: A Pilot Study

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: Meditation and other alternative practices have long been known to promote various health benefits, presumably by fostering a blood and tissue environment that enhances resilience to stress. Here, we used an integrated, multidisciplinary approach that couples quantitative electroencephalography (qEEG), biometrics, molecular, and biochemical data at multiple time points to investigate the impact of mind-based interventions on the body in a cohort of twins during an intensive week-long meditation retreat. We aim to show the feasibility of a novel design aimed to address individual changes controlling for intersubject trait variation (via twin control) and explore the role of genetic background on multi-omic factors during meditation. Interestingly, twin pairs showed significant spectral power correlations while in separate rooms and only one twin was meditating. These similarities were not observed in mismatched twin pairs. Heart rate dynamics assessments showed alignment among twin pairs that were absent between unmatched pairs. In addition, changes in gene expression, metabolites, and cytokines in blood plasma associated with specific meditative states showed patterns of change related to time points. Twin sets were similar in multiple domains before the start of the retreat, showed considerable divergence at the mid-point, and looked more similar by the end of the retreat. To our knowledge, this study is novel within the twin research paradigm and is a first step toward exploring the effects of meditation in twins.

overall_design: Whole blood samples were collected on days 0 (pre-meditation), 3, 5, and 7 of a 7 day from twin participants of intensive meditaiton retreat. Total RNAs was isolated from blood samples at each time point and analyzed by RNA-seq.

first: Hemal

last: Patel

middle: V

first: Juan

middle: P

last: Zuniga-Hertz

first: Sierra

last: Simpson

first: Ramamurthy

last: Chitetti

first: Chang

middle: F

last: Hsu

first: Han-Ping

last: Huang

first: Alex

last: Jinich-Diamant

first: Julie

last: Onton

first: Raphael

last: Cuomo

first: Joe

last: Dispenza

first: Dylan

last: Davis

first: Leonardo

last: Christov-Moore

first: Nicco

last: Reggente

first: Wanjun

last: Gu

first: Mitchell

last: Kong

first: Jacqueline

last: Bonds

last: Maree

first: Tatum

first: Andrew

last: Ahn

first: Michelle

last: Poirier

first: Tobias

last: Moeller-Bertram


title: Heterologous immunization combining vector- and mRNA-based vaccine elicits both robust innate and adaptive immune responses

status: Public on Jan 23 2025

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Heterologous vaccination regimens are increasingly recommended for their potential benefits, including reduced side effects and enhanced immunogenicity. In this study, we investigated the innate and adaptive immune responses elicited by heterologous prime-boost vaccination using adenoviral vector and mRNA vaccines against SARS-CoV-2 in a mouse model. Our findings show that heterologous vaccination induced superior serum neutralizing and binding antibody titers, as well as enhanced cellular immune responses against the Delta and Omicron (BA.5) variants, compared to homologous vaccination. Single-cell transcriptomic analysis at the injection site, conducted 16 hours post-vaccination, revealed that the lipid nanoparticle (LNP)-based mRNA vaccine—and even empty LNP injection—triggered significant immune cell infiltration, while adenoviral vector vaccination caused minimal changes in injection-site cell composition following the first dose. Notably, spike mRNA was predominantly expressed in fibroblasts and macrophages across both vaccine platforms, suggesting these cells’ role in local immune responses. Further analysis demonstrated that the adenoviral vector booster induced amplified immune responses, marked by increased transcriptional changes, particularly in stromal pro-inflammatory pathways. Heterologous vaccination (adenoviral prime, mRNA boost) further intensified these responses compared to homologous mRNA vaccination, indicating that adenoviral priming enhances inflammatory responses when followed by an mRNA boost. In summary, our results demonstrate that heterologous vaccination strategies elicit stronger innate and adaptive immune responses compared to homologous regimens, supporting their use as an effective approach for enhanced protection against variants.

overall_design: In this study, we evaluated the immunogenicity of SARS-CoV-2 spike adenoviral vector-based and LNP-mRNA vaccines, administered in both homologous and heterologous prime-boost regimens. Saline (phosphate-buffered saline; PBS) and empty lipid nanoparticle (LNP, formulated without the mRNA component) injections served as controls. To create a single-cell transcriptome atlas of injection-site responses, BALB/c mice were immunized intramuscularly with either mRNA or adenoviral vector vaccines, with a three-week interval between the prime and boost shots.

first: Ji Hyang

last: Jeon

first: Seongryong

last: Kim

first: Jinah

last: Yeo


title: A multi-omics integration approach relying on circulating factors does not discern subtypes in childhood type 1 diabetes.

status: Public on Jan 21 2025

city: Foligno

first: Nicola

last: Baldoni

state: PG

address: Via Maestà Formica, 12

country: Italy

institute: IRCCS Hospital San Raffaele

summary: Type 1 Diabetes (T1D) exhibits considerable heterogeneity, impacting prediction, prevention, diagnosis, and treatment. Precision medicine aims to tailor treatments using 'endotypes'—subtypes of disease with distinct pathophysiological mechanisms. However, proposed endotypes often lack mechanistic associations with clinical outcomes, remaining elusive in T1D. This study introduces an approach leveraging the multi-omics factor analysis (MOFA) strategy to explore endotypes through data integration. Analyzing data from 146 new-onset pediatric T1D patients, including circulating immunome, transcriptome, and serum metabolic hormones, we identify 12 factors explaining variability across the three data sets. Here we show that no clustering or direct association of these factors with clinical parameters, genetic predisposition and disease outcome are found, suggesting that a combination of clinical phenotypes is responsible for the differences across patients. These findings challenge the assumption that T1D heterogeneity reflects diverse developmental mechanisms, contributing substantially to the endotype discussion and impacting clinical trial design.

overall_design: RNA-seq profiling of blood samples from pediatric patients with new-onset type 1 diabetes; The analysis involved selecting the top 5000 most variable genes, which were then used in MOFA for multi-omics analysis.

first: Valentina

last: Codazzi

first: Giulia

last: Scotti

first: Anna

last: Giovenzana

first: Andrea

last: Rigamonti

first: Giulio

last: Frontino

first: Eugenia

last: Bezzecchi

first: Camillo

last: Bechi Genzano

first: Alessandra

last: Mandelli

first: Debora

last: Carnovale

first: Ilaria

last: Marzinotto

first: Vito

last: Lampasona

first: Paolo

last: Fiorina

last: Giustina

first: Lorenzo

last: Piemonti

first: Manuela

last: Battaglia

first: Marco

last: Morelli

first: Riccardo

last: Bonfanti

last: Petrelli


title: Orthopedia regulates Melanocortin 4 Receptor transcription and energy homeostasis

status: Public on Jan 15 2025

city: Dallas

first: Baijie

last: Xu

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Disruption of hypothalamic melanocortin 4 receptors (MC4Rs) causes obesity in mice and humans. Here, we investigate the transcriptional regulation of MC4R in the hypothalamus. In mice, we show that the homeodomain transcription factor Orthopedia (Otp) is enriched in Mc4r neurons in the paraventricular nucleus of the hypothalamus (PVN) and directly regulates Mc4r transcription. Deletion of Otp in PVN neurons during development or adulthood reduces Mc4r expression, causing increased food intake and obesity. In humans, four of five carriers of rare predicted functional OTP variants in UK Biobank had obesity. To explore a causal role for human OTP variants, we generated mice with a loss-of-function OTP mutation identified in a child with severe obesity. Heterozygous knock-in mice exhibit hyperphagia and obesity, reversed by treatment with an MC4R agonist. Our findings demonstrate that OTP regulates mammalian energy homeostasis and enable the diagnosis and treatment of people with obesity due to OTP deficiency.

overall_design: To determine whether Otp can directly bind to the Mc4r promoter, we performed a CUT&RUN (Cleavage Under Targets and Release Using Nuclease) assay in the adult PVN.

first: Chen

last: Liu


title: Identify transcriptional regulators of Mc4r in the hypothalamus [scRNA-Seq]

summary: Human MC4R mutations can increase or decrease obesity risk. Other than intracellular signaling, MC4R function is also influenced by its levels. However, the genetic programs that govern MC4R transcription in the brain remain largely unknown. Moreover, it is unclear whether human genetic variants exist that affect Mc4r expression and obesity risk. Here, we identify the homeodomain transcription factor Otp as one regulator of Mc4r expression in a specific subset of hypothalamic neurons. Selective loss of Otp in these neurons during development or adulthood results in reduced Mc4r expression and excessive body weight gain. Moreover, OTP interacts with upstream regulatory sequences of Mc4r to modulate its transcription.

overall_design: To investigate the changes of PVH neuron populations and mRNA expressions in OtpQ153R mice, we carried out single-nucleus RNA sequencing (snRNA-seq) in the PVH of Sim1-Cre; Sun1-GFP and Sim1-Cre; Sun-GFP; Otpfl/+ and Sim1-Cre; Sun1-GFP; OtpQ153R/+ mice. Following PVH collection at four weeks old, we used fluorescence-activated cell sorting (FACS) to enrich GFP-positive nuclei from seven Sim1-Cre; Sun1-GFP mice and four Sim1-Cre; Sun-GFP; Otpfl/+ mice and six Sim1-Cre; Sun1-GFP; OtpQ153R/+ mice.

first: Li

last: Li


title: Identify transcriptional regulators of Mc4r in the hypothalamus [RNA-Seq]

overall_design:
To identify transcriptional regulators of Mc4r in the mouse hypothalamus, we crossed Mc4r-Cre mice with Ai14 (R26RLSL-tdTomato) mice to generate double transgenic mice (Mc4r-Cre; Ai14) in which Mc4r-Cre-expressing neurons were labeled by the expression of a Cre-dependent tdTomato reporter. We then purified these neurons by fluorescence-activated cell sorting (FACS) and profiled their transcriptome using bulk RNA sequencing.
To elucidate the molecular basis of excessive weight gain, we isolated PVH neurons targeted with either AAV-GFP or AAV-Cre by FACS and compared their transcriptomes using RNAseq.


title: Eggerthella lenta Down Regulated Flavone and Flaconol Biosynthesis Promoted Kawasaki Disease

status: Public on Jan 10 2025

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: Kawasaki Disease (KD) is a multisystemic vasculitis of unknown etiology in children. The incidence of KD varies by geographic area and correlates with differences in gut microbiota patterns, with the highest incidence in Asian. This study aimed to investigate alterations in fecal microbiota and assess their relationship with systemic inflammation in KD patients.  A total of 59 patients and 55 matched controls were included. Fecal samples were collected at the onset of KD. The V3/V4 regions of 16S rDNA were sequenced using the MiSeq platform. PICRUSt 2 was used to analyze the potential functional pathways involved in gut dysbiosis. Alpha (p<0.042) and beta (p<0.001) diversity in KD were significantly decreased when compared to the control group. After multivariate regression, among the seven critical microbes, increased Bacteroides ovtaus (p=0.016) and decreased Eggerthella lenta (p=0.014) could also predict KD risk using receiver operating characteristic curve (ROC) analysis (Eggerthella lenta: area under the ROC curve, AUC=0.841, odds ratio=23.956; Bacteroides ovatus: AUC=0.816, odds ratio=31.365). Notably, Bacteroides ovatus was positively correlated with blood segment cells (p=0.006), but negatively correlated with blood lymphocytes (p=0.013). After multivariate regression, flavone and flavonol biosynthesis decreased in children with KD (p<0.001). Our results indicated that both Bacteroides ovatus and Eggerthella lenta may deregulate flavone and flavonol biosynthesis, consequently modulating immune cells and potentially triggering KD. This study suggests that alterations in the gut microbiota are closely associated with immune responses and provides a new perspective on the etiology, pathogenesis, and treatment of KD.

first: Yao-Tsung

last: Yeh

first: Cheng-Hsieh

last: Huang

first: Ho-Chang

last: Kuo


title: Identify transcriptional regulators of Mc4r in the hypothalamus


title: Identify transcriptional regulators of Mc4r in the hypothalamus [ATAC-Seq]

overall_design: To pinpoint the promoter region of Mc4r in PVH cells, we conducted an ATAC-Seq (transposase-accessible chromatin with sequencing) experiment in 12-week-old mice. To further validate the effect of Otp on Mc4r, we hypothesized that the absence of Otp could diminish transcriptional activity, resulting in less accessible chromatin near its transcriptional targets. To test this hypothesis, we analyzed ATAC peaks in the PVH of OtpPVH KO mice following the adult deletion of Otp.


title: mRNA stability fine tunes gene expression in the developing cortex to control neurogenesis [RNA-Seq]

city: Durham

first: Lucas

last: Serdar

address: 213 Research Dr

institute: Duke University

summary: RNA abundance is controlled by rates of synthesis and degradation. Although mis-regulation of RNA turnover is linked to neurodevelopmental disorders, how it contributes to cortical development is largely unknown. Here, we discover the landscape of RNA stability regulation in the cerebral cortex and demonstrate that intact RNA decay machinery is essential for corticogenesis in vivo. We use SLAM-seq to measure RNA half-lives transcriptome-wide across multiple stages of cortical development. Leveraging these data, we discover cis-acting features associated with RNA stability and probe the relationship between RNA half-life and developmental expression changes. Notably, RNAs that are upregulated across development tend to be more stable, while downregulated RNAs are less stable. Using compound mouse genetics, we discover CNOT3, a core component of the CCR4-NOT deadenylase complex linked to neurodevelopmental disease, is essential for cortical development. Conditional knockout of Cnot3 in neural progenitors and their progeny in the developing mouse cortex leads to severe microcephaly due to altered cell fate and p53-dependent apoptosis. Finally, we define the molecular targets of CNOT3, revealing it controls expression of poorly expressed, non-optimal mRNAs in the cortex. Collectively, our findings demonstrate that fine-tuned control of RNA turnover is crucial for brain development.

overall_design: We performed RNA-seq to investigate gene expression changes in Cnot3 conditional knockout (cKO) and Cnot3;Trp53 double conditional knockout (dcKO) mouse cortices verus control cortices.

first: Debra

last: Silver


title: mRNA stability fine tunes gene expression in the developing cortex to control neurogenesis [SLAM-seq]

overall_design: To investigate RNA stability in the developing cortex, we performed SLAM-seq using WT mouse primary cortical cells at three developmental stages - E11.5, E14.5, and E16.5.

first: Lucas D

first: Brad

last: Lackford

first: Brian D

last: Bennett

first: Guang

last: Hu

first: Debra L


title: Modeling retinal ganglion cell axonal pathology associated with glaucoma using human pluripotent stem cell-based microfluidic platforms

status: Public on Jan 13 2025

city: Portland

first: Chi

last: Zhang

state: Oregon

address: 3303 S.W. Bond Avenue

department: Biomedical Engineering

institute: Oregon Health & Science University

summary: Retinal ganglion cells (RGCs) are highly compartmentalized cells, and previous studies have demonstrated that RGC degeneration in glaucoma occurs in a compartmentalized manner, with distinct injury responses in axonal and somatodendritic compartments. Thus, the goal of this study was to establish a novel microfluidic-based platform for the analysis of RGC compartmentalization in health and disease states. Human pluripotent stem cell (hPSC)-derived RGCs were seeded into microfluidics, enabling the recruitment and isolation of axons apart from the somatodendritic compartment. Initial studies explored axonal outgrowth and compartmentalization of axons and dendrites. We then compared the differential response of RGCs differentiated from hPSCs carrying the OPTN(E50K) glaucoma mutation with isogenic control RGCs in their respective axonal and somatodendritic compartments, followed by analysis of axonal transport. Further, we explored the axonal transcriptome via RNA-seq, focusing on disease-related axonal differences. Finally, we established models to uniquely orient astrocytes along the axonal compartment combined with modulation of astrocyte reactivity as a pathological feature of neurodegeneration. Overall, RGC culture within microfluidic chips allowed enhanced cell growth and maturation, including long-distance axonal projections and proper compartmentalization. OPTN(E50K) RGCs exhibited axonal outgrowth deficits as well as decreased rate of axonal transport, compared to isogenic controls. Finally, upon introduction of astrocytes into the proximal axonal compartment, the induction of astrocyte reactivity led to the onset of neurodegenerative phenotypes in RGCs. These results represent the first study to effectively recapitulate the highly compartmentalized properties of hPSC-derived RGCs in healthy and disease states, providing a more physiologically relevant in vitro model for neuronal development and degeneration.

overall_design: RNA was extracted from the somatodendritic and axonal compartments of the microfluidic devices and RNA-sequencing was performed to assess transcriptional differences between (1) the somatodendritic and axonal compartments of RGCs, as well as (2) within the axonal compartment of OPTN(E50K) RGCs versus isogenic controls (axon-sequencing).

first: Catia

last: Gomes

first: Yue

last: Fang

first: Jason

last: Meyer


title: Distinct transcriptional changes distinguish efficient and poor remyelination in multiple sclerosis

status: Public on Jan 02 2025

city: Amsterdam

first: Alida

address: Meibergdreef 47, 1105 BA

institute: Netherlands Institute for Neuroscience

summary:
Multiple sclerosis (MS) is a highly heterogeneous disease with varying remyelination potential across individuals and between lesions. However, the molecular mechanisms underlying the potential to remyelinate remain poorly understood. In this study, we aimed to take advantage of the intrinsic heterogeneity in remyelinating capacity between MS donors and lesions to uncover known and novel pro-remyelinating molecules for MS therapies.
To elucidate distinct molecular signatures underlying the potential to remyelinate, we stratified MS donors from the Netherlands Brain Bank cohort (n=239) based on proportions of remyelinated lesions (RLs) into efficiently remyelinating donors (ERDs; n=21) and poorly remyelinating donors (PRDs; n=19). We performed bulk RNA sequencing of RLs, active lesions with ramified and amoeboid microglia/macrophage morphology (ALs non-foamy), active lesions with foamy microglia/macrophage morphology (ALs foamy), and normal-appearing white matter (NAWM) from ERDs and PRDs.
We found that ALs non-foamy were positively correlated with remyelination, whereas ALs foamy were not, indicating a role for microglia/macrophage state in influencing remyelination potential. Bioinformatics analyses were performed to identify key pathways and molecules implicated in the remyelination process. We found distinct differences between the donors with differing remyelination potential in comparable MS lesion types. RLs and ALs non-foamy of ERDs versus PRDs showed upregulation of epithelial–mesenchymal transition pathway, while in ALs foamy of PRDs, inflammation and damage-associated pathways (i.e. MTORC1 signaling, TNF signaling and oxidative phosphorylation) were upregulated compared to ALs foamy of ERDs, suggesting that these latter pathways may counteract remyelination. We found genes significantly upregulated in RLs and/or ALs non-foamy of ERDs that have previously been associated with remyelination, including CXCL12, EGF, HGF, IGF2, IL10, PDGFB, PPARG, and TREM2, illustrating the strength of our donor and lesion stratification. TGFB1, TGFB2, EGF, and IGF1 were determined as key upstream regulators of genes upregulated in RLs and ALs non-foamy of ERDs. We further identified potential novel pro-remyelinating molecules, such as BTC, GDF10, GDF15, CCN1, CCN4, FGF5, FGF10, and INHBB.
Our study identified both known and novel genes associated with efficient remyelination that may facilitate the development of therapeutic strategies to promote tissue repair and clinical recovery in MS.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of remyelinated lesions, active non-foamy (ramified-amoeboid) lesions and active foamy lesions from MS donors with different remyelinating capability.

first: Jiaqi

first: Niamh

last: McNamara

first: Hendrik

last: Engelenburg

first: Aldo

last: Jongejan

first: Dennis

last: Wever

first: Kaya

last: Hopman

first: Esmée

last: van Rixel

first: Paul

last: Nijhuis

first: Fred

last: de Winter

first: Perry

last: Moerland

first: Joost

last: Smolders

last: Verhaagen

first: Jörg

last: Hamann

first: Inge

last: Huitinga


title: Exon- and gene-Level transcriptional profiling in Lymphoblastoid Cell Lines (LCLs) from Williams syndrome patients and controls

status: Public on Jan 01 2025

city: Salt Lake City

first: Robert

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

summary:
Williams syndrome (WS), characterized by positive sociality, provides a unique model for studying transcriptional networks underlying social dysfunction, relevant to disorders like autism spectrum disorder (ASD) and schizophrenia (SCHZ). In a cohort lymphoblastoid cell lines derived from 52 individuals (34 WS patients, 18 parental controls), genome-wide exon-level arrays identified a core set of differentially expressed genes (DEGs), with WS-deleted genes ranking among the top transcripts. Findings were validated by PCR, RNA-seq, and western blots.
Network analyses revealed perturbed actin cytoskeletal signaling in excitatory dendritic spines, alongside interactions in MAPK, IGF1-PI3K-AKT-mTOR/insulin, and synaptic actin pathways. These transcriptional networks show parallels to ASD and SCHZ, highlighting shared mechanisms across social behavior disorders.

overall_design: Human lymphoblastoid cells immortailzed from WIlliams syndrome patients and non-affected parental controls were grown in RMPI 1640 with 10% FBS, 5% pen/strep, 5% L-glutamine and 0.5% gentamycin. Total RNA was extracted from each culture using the Qiagen RNeasy kit with DNase digestion. Prior to labeling, ribosomal RNA was removed from total RNA (1 μg per sample) using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen). Expression analysis was conducted using Affymetrix Human Exon 1.0 ST arrays following the Affymetrix hybridization protocols. Exon expression data were analyzed through Affymetrix Expression Console using exon- and gene-level PLIER (Affymetrix Power Tool with PM-GCBG background correction) summarization and sketch-quantile normalization methods.

first: Julie

middle: R

last: Korenberg


title: Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas

city: Los Angeles

first: David

last: Craig

address: 1450 Biggy St, 2nd Floor

department: Department of Translational Genomics

institute: University of Southern California

summary: We perform bulk RNA sequencing, tumor/normal DNA sequencing, and spatial transcriptomics on an initial discovery cohort of eleven glioma samples (comprising oligodendrogliomas, astrocytomas, one diffuse midline glioma, and glioblastomas) to identify both commonalities and distinct characteristics within the tumor microenvironment. Six additional high-grade IDH wild-type, EGFR positive glioblastomas are analyzed to validate subclonal somatic aneuploidy and copy number alterations associated with extrachromosomal DNA double-minutes. As part of the standard spatial transcriptomic analysis, we develop an integrated analysis framework combining germline/tumor exomes, bulk RNA-seq, and spatial transcriptomics to identify loss of heterozygosity by a hidden Markov model for segmenting consecutively expressed SNPs. In the discovery cohort, we identify focally amplified ecDNA in four of the eleven cases, with subclonal tumor heterogeneity present in two EGFR-amplified grade IV glioblastomas. In a TP53-mutated glioblastoma, we detect a subclone with EGFR amplification on ecDNA coupled to chromosome 17 LOH. To evaluate the impact of spatial subclonal chromosomal alterations on the p53/EGFR axis, we examine six additional EGFR positive gliomas, identifying MDM2/MDM4 ecDNA subclones in two samples. The spatial DNA heterogeneity of EGFR and p53 inactivation underscores the role of ecDNA in enabling rapid oncogene amplification and enhancing tumor adaptability under selective pressure.

overall_design:
Eleven surgically-derived gliomas of varied pathology and molecular phenotype were analyzed using the 10X Genomics Visium spatial transcriptomics protocol. Available data includes processed output files from the 10X Genomics spaceranger bioinformatic pipeline.

Six surgically-derived FFPE glioblastoma tissues were analyzed using the 10X Genomics Visium CytAssist Spatial Gene Expression for FFPE protocol. Available data includes processed output files from the 10X Genomics spaceranger bioinformatic pipeline.

-----------------------------
Authors state "Only processed data is included in this submission due to privacy concerns."

first: Michelle

last: Webb

first: Frances

last: Chow

first: Carmel

last: McCullough

first: Bohan

last: Zhang

first: John

last: Lee

first: Rania

last: Bassiouni

first: Norman

middle: E

last: Garrett III

first: Kyle

last: Hurth

last: Carpten

first: Gabriel

last: Zada

middle: W


title: Inhibition of epigenetic regulator UHRF1 attenuates renal fibrosis and retains transcription factor Krüppel-like factor 15 expression

city: Shanghai

first: Yulu

last: Gu

address: No.180 Fenglin Road,Xuhui District

institute: Zhongshan Hospital, Fudan University

type: Methylation profiling by high throughput sequencing

summary: Aberrant DNA methylation modification is well-known to be involved in renal fibrogenesis. As a critical cooperator in DNA methyltransferase 1 (DNMT)1-mediated maintenance of DNA methylation, the role of ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) in renal fibrosis remains unknown. In the present study, we observed the upregulation of UHRF1 in activated renal fibroblasts. Fibroblasts-specific depletion of UHRF1 reduced fibrotic lesions in both unilateral ureter obstruction- and unilateral renal ischemia-reperfusion injury-induced murine models of kidney fibrosis. Through Reduced Representation Bisulfite Sequencing, KLF15 was screened and further verified as the target methylated gene of UHRF1 and responsible for fibroblasts activation. Moreover, UHRF1 induced KLF15 methylation through interacting with DNMT1. Genetic depletion of UHRF1 or pharmacological inhibition the interaction decreased KLF15 methylation levels and restored its expression, resulting in reduced renal fibroblasts activation and kidney fibrosis. Collectively, our study suggests that UHRF1 might be a promising target for mitigating renal fibrosis.

overall_design: RRBS-seq profiling of renal fibroblasts from wildtype mice. Fibroblasts were sorted from Sham group and UUO group at 7 days after operation.

first: Xiaoyan


title: RNA-seq in murine LSKs after Cux1 and/or Ezh2 loss, in the presence or absence of the DNA damaging agent N-ethyl-N-nitrosourea

city: Chicago

first: Matthew

last: Jotte

address: 900 E 57th Street

institute: University of Chicago

summary: Loss of all or part of chromosome 7 [-7/del(7q)] is recurrent in myeloid neoplasms and associated with a poor response to chemotherapy. Chromosome 7-encoded genes that drive drug resistance and the consequences of combinatorial 7q tumor suppressor gene loss have remained unclear, the latter question being largely due to the challenges of modeling aneuploidy. Here, we use in silico datamining to uncover 7q genes involved in chemotherapy resistance. We establish murine models of del(7q) clonal hematopoiesis and drug resistance with multiplex CRISPR-Cas9-mediated inactivation of four genes, Cux1, Ezh2, Kmt2c, and Kmt2e. Post-genotoxic exposure, combined deficiency of Cux1 and Ezh2 preferentially promotes clonal myeloid expansion in vivo, with compounding defects in DNA damage response and repair. Transcriptome analysis reveals combined Cux1 and Ezh2 loss recapitulates -7 patient gene signatures and defective DNA damage response pathways, to a greater extent than single gene loss. This work reveals a genetic interaction between CUX1 and EZH2, and sheds light on how -7/del(7q) contributes to leukemogenesis and drug resistance characteristic of these adverse-risk neoplasms. These data support the concept of 7q as a contiguous gene syndrome region, in which combined loss of multiple gene drives pathogenesis.

overall_design: RNA-seq in control (shCtrl) and Cux1 knockdown (shCux1) murine hematopoietic progenitors transfected with CRISPR particles targeting Ezh2 (gEzh2), Kmt2c (gKmt2c), or an intron of Actin (gActin) as a control (4 replicates). A second RNA-seq experiment was performed in shCtrl and shCux1 murine hematopoietic progenitors treated with the Ezh2 inhibitor tazemetostat (Ezh2i) or vehicle, and the alkylating agent N-ethyl-N-nitrosurea (ENU).

first: Megan

last: McNerney


title: Single-cell dynamic RNA and glycosylation sequencing reveal the process of iPSC differentiation into HSCs in vitro

city: Haikou

first: wanyi

last: feng

state: Hainan

address: No.58 Renmin Avenue

institute: hainan university

summary: Understanding the differentiation process of human induced pluripotent stem cells (iPSCs) into hematopoietic stem/progenitor cells (HSPCs) is essential for advancing regenerative medicine and gaining insights into embryonic hematopoiesis. However, the connection between transcriptomic dynamics and glycation levels during this process remains unclear. In this study, we conducted a systematic analysis of the dynamic transcriptome and glycation changes of HSPCs derived from iPSCs during in vitro differentiation. Comprehensive analysis showed that there is a significant correlation between staged hematopoietic differentiation of iPSC-derived HSPCs and the degree of glycation, particularly during the endothelial differentiation stage. Additionally, there are similarities between in vivo embryonic hematopoiesis and in vitro differentiation models, which reinforces the utility of these models for studying human hematopoiesis. This study provides important insights into the link between the transcriptome and glycation of HSPCs derived from iPSCs.

overall_design: Cell samples from D0, D2, D4, D6, D8, and D10 in the in vitro model of iPSC-derived HSPC were collected and analyzed using single-cell RNA sequencing (scRNA-seq), single-cell Dynamic RNA-seq (DynaSCOPE), and single-cell Glycosylation-seq (ProMoSCOPE).


title: Smooth Muscle Cell Populations of Differing Embryonic Origins in the Ascending Aorta Exhibit Minor Differences in Angiotensin II-driven Transcriptional Alterations in Mice

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

summary: Ascending thoracic aortopathy is a life-threatening disease significantly influenced by angiotensin II (AngII). Thoracic aortopathy exhibits regional heterogeneity with the ascending region being susceptible. Smooth muscle cells (SMCs), a major component of the aortic wall, originate from two embryonic origins in the ascending aorta: second heart field (SHF) and cardiac neural crest (CNC). However, functional differences between the origins in AngII-induced thoracic aortopathy formation remain unknown. The present study determined transcriptomic differences between origins in response to AngII by single-cell RNA sequencing using the lineage tracing approach. Mef2c-Cre +/0 mT/mG mice were infused with AngII (1,000 ng/kg/day). To investigate causative mechanisms, ascending aortas were harvested after 3 days of AngII infusion, representing the prepathological phase of thoracic aortopathy. Aortic samples were also harvested from Mef2c-Cre +/0 mT/mG mice without AngII infusion as a control. Following single-cell suspension, cells were sorted based on their origin using mTotamto and mGFP signals. mGFP proteins were present on Mef2c-Cre-driven cells indicating the cells were derived from the SHF, while cells with mTomato signal were not derived from the SHF (nSHF). After sorting cells by origin, single-cell RNA sequencing was performed. Two-way ANOVA analysis identified 1718 differentially expressed genes (DEGs) in the interaction between origin and infusion. Among these DEGs, 1207 genes significantly differed between origins in response to AngII infusion. However, the magnitude of difference in most of these DEGs was modest, ranging between −0.05 and 0.05 Log2FC. Commonly studied molecules, such as TGF-β, SMC contraction, and extracellular matrix molecules, were undetectable or modestly different. In conclusion, transcriptomic differences in SMCs between origins in response to AngII were modest in the pre-pathological phase of AngII-induced thoracic aortopathy.

overall_design: Comparative gene expression analysis of scRNAseq data to determine transcriptomic differences in response to AngII infusion between cells derived from the second heart field and other origins in the ascending aorta of mice.


title: Multi-Omic Single-Cell Dissection of Leukemic T-Cell Lymphoma Following CAR T-Cell Therapy

status: Public on Jan 05 2025

city: Cologne

first: Till

last: Braun

address: Kerpener Strasse 62

department: Clinic I for Internal Medicine

institute: University Hospital of Cologne

summary: A 63-year-old male who received ciltacabtagene autoleucel (cilta-cel) CAR-T cells and the GPRC5DxCD3 bispecific talquetamab for early relapse of his multiple myeloma (MM) developed a leukemic peripheral T-cell lymphoma (PTCL) with cutaneous and intestinal involvement. Longitudinal single-cell RNA and T-cell receptor sequencing of peripheral blood and bone marrow revealed two hyperexpanded CAR-carrying, exhausted effector-memory T-cell clones with marked immunophenotypic as well as transcriptional alterations and different susceptibilities towards treatment with dexamethasone. Spatial transcriptomes of skin lesions confirmed the aberrant CAR-expressing T cells. Whole genome sequencing revealed three distinct integration sites, within the introns of ZGPAT, KPNA4, and polycomb-associated non-coding RNAs. Pre/post-CAR-T whole-genome analyses implicated clonal outgrowth of a TET2-mutated precursor propelled by additional sub-clone specific LOH and other secondary mechanisms

overall_design: (1) Peripheral blood (PB) stem cell apheresis products were collected three years prior to CAR-T infusion. (2) One PB and (3) one bone marrow (BM) sample were collected and cryopreserved 12 months after CAR T-cell infusion. (4) One PB sample was obtained one month later following dexamethasone treatment (month 13).

first: Michael

last: Rade

first: Maximilian

last: Merz

first: Hanna

last: Klepzig

first: Florian

last: Große

last: Fandrei

first: Nhu-Nguyen

last: Pham

first: Markus

last: Kreuz

first: Christina

last: Kuhn

last: Kuschel

first: Dennis

last: Löffler

first: Jörn

last: Meinel

first: Eva

last: Heger

first: Viola

last: Schweinsberg

first: Natali

last: Pflug

first: Uwe

last: Platzbecker

last: Hallek

first: Udo

last: Holtick

first: Ulrike

last: Köhl

first: Christof

last: Scheid

first: Kristin

last: Reiche

first: Marco

last: Herling

first: Tim

last: Richardson


title: Potentially Dysregulated Cholesterol, Cellular Interaction, Immune, and Extracellular Matrix in NTCU-Induced Lung Squamous Cell Carcinoma (LUSC) in Mice Model and LUSC Patients

status: Public on Dec 31 2024

city: Ipoh

first: Muhammad

middle: Asyaari

last: Zakaria

state: Perak

address: 3, Jalan Greentown

department: Faculty of Pharmacy and Health Sciences

country: Malaysia

institute: Universiti Kuala Lumpur-Royal College of Medicine Perak

summary: Lung squamous cell carcinoma (LUSC) is associated with poor survival owing to the lack of advanced targeted therapies, due to the incomplete characterization of complex genetic profiles. Therefore, it is essential to elucidate the molecular mechanisms of LUSC via the mice model and human database to understand the LUSC pathogenesis. A LUSC BALB/c mice model was established using N-nitroso-tris-chloroethylurea (NTCU). After termination of mice, the lung tissues were subjected to RNA sequencing. First, DESeq2 was used to normalize the read count, followed by gene set enrichment analysis (GSEA) to identify the affected pathways in LUSC. Subsequently, the pathogenic single nucleotide polymorphism (SNP) was determined using Protein Variation Effect Analyzer (PROVEAN) and Sorting Intolerant From Tolerant (SIFT), following scores of < 0.05 and < -2.5, respectively, which were then functionally enriched using g:Profiler. The transcriptomic profile of human LUSC patients was obtained from The International Cancer Genome Consortium (ICGC) and analyzed. The impact of pathogenic simple somatic mutation in human LUSC was determined using the Combined Annotation Dependent Depletion (CADD) score, which was functionally enriched using g:Profiler. Additionally, the enriched pathway of LUSC patients with complete remission (responsive) was compared with those with disease progression or deceased (non-responsive) post-GSEA treatment. All pathway analysis was possibly referred to the Reactome database, and an adjusted p-value < 0.05 was considered statistically significant. Based on the transcriptomic analysis of LUSC mice, the top pathway enriched from the animal study and human LUSC revealed similarity in four major themes: cholesterol, cellular interaction, immune, and extracellular matrix dysregulation. Furthermore, the overrepresented pathways identified in LUSC patients were consistent with the four major themes dysregulated in LUSC tumors. This study identified several biological pathways that may contribute to LUSC development and potential targets for future LUSC therapy.

overall_design: NTCU-induced LUSC in mice model was developed using N-nitroso-tris chloroethylurea for 30 weeks. We then isolate the lung tissues which were subjected to hematoxylin and eosin (H&E) and immunohistochemistry (IHC) staining. After confirmation of LUSC in the lung tissues, we randomly choose three lung tissues (n=3) from cancer group (LUSC) and three lung tissues (n=3) from normal group for RNA sequencing

first: Amnani

last: Aminuddin

first: Nor

last: Rajab

first: Siti

last: Masre

first: Eng

last: Chua


title: CMPD1 is a microtubule inhibitor with tumor-specific cytotoxicity

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

summary: Microtubule-targeting agents have been widely used for cancer treatment, yet their cancer specificity is a common challenge. In this study, we identified that CMPD1 as a promising cancer specific inhibitor. Both in vitro and in vivo experiments showed that CMPD1 efficiently inhibits tumor growth. Mechanistically, CMPD1 inhibits microtubule polymerization in mitosis. Collectively, CMPD1 has the high potential to serve as a cancer cell inhibitor.

overall_design: To investigate the impacts of CMPD1 treatment on global gene expression,RNA-seq was performed in non-transformed retinal pigment epithelial cells (RPE1) and MDA-MB-231 breast cancer cells 24 hours after treatment with 10 μM CMPD1.

first: Yu-Chia

last: Chen

first: Mamoru

last: Takada

first: Aerica

last: Nagornyuk

first: Wu

last: Muhan

first: Hideyuki

last: Yamada

first: Takeshi

last: Nagashima

first: Masayuki

last: Ohtsuka

first: Jennifer

last: DeLuca

first: Steven

last: Markus

first: Aussie

last: Suzuki


title: RNA-Seq of Chicken Embryo Liver Reveals Transcriptional Pathways Influenced by Egg Formaldehyde Treatment

status: Public on Jan 20 2025

city: Talas

first: Ghulam Asghar

last: Sajid

state: Kayseri

address: Yenidoğan, Turhan Baytop Sokak No:1

department: Animal Science Department

country: Turkey

institute: Erciyes University

summary: Hatchery fumigation is recognized as a crucial step to control the microbial bloom in the environment and formaldehyde is one of the most widely used disinfectants, to ensure successful hatchability and healthy production. Although in humans its usage is strictly regulated in many developed countries due to its carcinogenic properties, FA remains widely used in poultry hatcheries. Recent studies have shown it also poses significant risks to poultry health and performance. Yet, the impact of formaldehyde fumigation at molecular and cellular levels is not studied in poultry. The current study aimed to capture the in ovo transcriptional response of liver tissue to formaldehyde treatment. Chick embryos were subjected to formaldehyde fumigation treatment for 25 minutes at 24-25°C and 75% relative humidity, keeping a control group as untreated. On the 18th day of incubation at 37.8°C and 58-63% humidity, eggs were broken, and liver tissue were obtained for RNA isolation, cDNA library preparation and RNA sequencing. Bioinformatics analysis revealed 908 significant differentially expressed genes (DEGs), among which 814 were known genes and 94 were novel genes. Key DEGs and transcription factors were involved in oxidative stress, immuno-inflammatory responses, epigenetic modification and cellular adaptation related activities. These molecular and cellular findings might have a broader implication on early chick performance and health, especially in case of predisposition of disease conditions.

overall_design: Transcriptomic response of chicken embryo liver cells to formaledhye in stimulated, using control as non treated eggs.

first: M.

last: Özdemir

first: G. A.

first: S. B.

last: Beyzi

last: Kızılaslan

first: Y.

last: Arzık

first: S.

last: Yalçın

first: M. U.

last: Cinar


title: Effect of combined AURK and BCL2 inhibition on gene expression in double-hit lymphoma xenografted mice

city: Charlotte

middle: I.

last: Park

address: 1021 Morehead Medical Drive

department: Department of Hematologic Oncology and Blood Disorders

institute: Levine Cancer Institute

summary: To investigate the  mechanism behind drug synergism between MLN8237 and venetoclax we injected DoHH2 human tumor cells into SCID mice SQ, treated animals for 3 days, and harvested tumors for RNAseq.

overall_design: Comparative gene expression profile analysis of RNA-seq data for DoHH2 tumors harvested from mice, treated with either vehicle, MLN8237, venetoclax, or combination MLN8237 + venetoclax for 3 days


title: Genomic and Transcriptomic Insights into Chlorhexidine Adaptation in Oral Streptococcus spp.: Implications for Antimicrobial Resistance

city: Regensburg

first: Bernd

last: Daller

address: Franz-Josef-Strauß-Allee 11

institute: University Regensburg

summary: Chlorhexidine (CHX) is a widely used antiseptic agent in dental care due to its broad-spectrum antimicrobial properties. This study focuses on the transcriptomic changes associated with chlorhexidine adaptation in oral Streptococcus salivarius (73_wt, 73_a), Streptococcus vestibularis (78_wt, 78_e), and Streptococcus mitis (93_wt, 93_d) using RNA sequencing.

sample_organism:
Streptococcus salivarius
Streptococcus vestibularis
Streptococcus mitis

overall_design: Comparative gene expression profiling of wild-type streptococci and the corresponding strains adapted after prolonged exposure to CHX, with and without acute exposure to CHX.

first: Andreas

last: Hiergeist


title: Histone demethylation and c-MYC activation enhance translational capacity in response to amino acid restriction [RNA-seq]

first: Siavash

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

summary: Nutrient limitation may elicit adaptive epigenetic changes but the nature and mechanisms of the cellular response to specific nutrient deficiencies are incompletely understood. We report that depriving human cells of amino acids (AAs) induces specific loss of H4K20me1 from gene bodies and elevated binding of c-MYC at promoters genome-wide. These effects are most pronounced at ribosomal protein and translation initiation genes, which are upregulated, leading to enhanced protein synthetic capacity. Combination of H4K20 methyltransferase depletion and c-MYC over-expression in rich media is required and sufficient to recapitulate the effects of AA restriction. Our data reveal an unexpected and epigenetically implemented increase in translational capacity when AAs are limiting, likely to safeguard the proteome by making effective use of limited resources.

overall_design: Examine the expression of cells cultured in complete DMEM medium or in DMEM lacking amino acids by RNA-seq analysis.  Examine the expression of cells cultured in complete DMEM medium with Setd8 knockdown and/or c-Myc overexpression.

first: Chen

last: Cheng


title: Histone demethylation and MYC activation enhance translational capacity in response to amino acid restriction

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

overall_design: Refer to individual Series


title: A single-cell plume transcriptome atlas of the cold-seep tubeworm Paraescarpia echinospica [ONT]

status: Public on Dec 30 2024

city: shandong

first: Nannan

last: Zhang

address: Hengyun Mountain Road

institute: BGI Research, Qingdao, Shandong

summary: Vestimentiferan tubeworms are representative inhabitants of deep-sea chemosynthetic ecosystems. The plume serves as the primary organ in these invertebrates without mouths and guts, facilitating direct metabolic exchange with their surrounding environments. In this study, we present a single-cell transcriptome atlas of Paraescarpia echinospica plume and this study is the initial single-cell transcriptome sequencing for the plume of the deep-sea tubeworm. We annotated six cell clusters including hemocytes, proliferative cells, muscle cells, epithelial cells, nerve1 cells, nerve2 cells and profiled genes involved in immunity and transport. This work will provide a foundation for further studies of tubeworm at the single-cell level.

overall_design: bulk RNA-seq, Promethion, ONT

first: Xianghui

first: Yingying


title: Histone demethylation and c-MYC activation enhance translational capacity in response to amino acid restriction [ChIP-seq]

overall_design: Examine the enrichment of H4K20me1,H3K36me3, H4K20me3, cMYC, and RNA Pol II in HeLa cells cultured in complete DMEM medium or in DMEM lacking amino acids by ChIP-seq analysis.


title: A single-cell plume transcriptome atlas of the cold-seep tubeworm Paraescarpia echinospica

overall_design: The DNBelab C Series Single-Cell Library Prep Set (MGI) was utilized to produce libraries


title: CGH: Rag2_and_Rsv1-h_recombinant_haplotype_analysis

status: Public on Dec 27 2024

city: Saint Paul

first: Robert

middle: M

last: Stupar

address: 1991 Upper Buford Circle

institute: University of Minnesota

type: Genome variation profiling by genome tiling array

summary:
Soybean lines were compared to the reference genome Williams 82 (Wm82) by CGH to catalog feature polymorphisms in a Rag2 and Rsv1-h QTL region
The CGH comparisons reveal reveal feature polymorphisms among the parental and recombinant lines.

overall_design: Soybean parental and recombinant lines were compared to the reference genome Williams 82 (sub-line 'Wm82-ISU-01', PI 704477).  Each genotype was represented by a single individual plant.  The reported values show the log2 ratio of the normalized line hybridization signals (Cy3) over the normalized Williams 82 hybridization signal (Cy5).

first: Adrian

middle: O

last: Stec

first: George

middle: L

last: Graef

first: Luis

last: Posadas


title: Integrated computational analysis identifies therapeutic targets with dual action in cancer cells and T cells

status: Public on Dec 25 2024

city: Beijing

first: Zexian (Davis)

last: Zeng

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: Many cancer drugs that target cancer cell pathways have detrimental effects on the immune system. We developed a computational platform for the identification of therapeutic targets with beneficial effects in both cancer and immune cells. ICRAFT (https://icraft.pku-genomics.org/) enables integrated analysis of immune-related CRISPR screen datasets, scRNA-Seq data, and pre-treatment RNA-Seq data from clinical trials. This platform enabled the discovery of a substantial number of targets with dual action in cancer cells and T cells. Among these, TNFAIP3, a ubiquitin-editing enzyme also known as A20, emerged as a leading target. Inactivating TNFAIP3 in cancer cells sensitizes them to immune attacks by activating the NF-κB pathway, while targeting it in T cells significantly enhances their antitumor efficacy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To investigate the function of TNFAIP3 in the cancer cell immune response to T-cell-mediated cytotoxicity, we established A549 TNFAIP3-KO cell line by CRISPR-Cas9. To investigate the function of TNFAIP3 in CD8+ T cell immune function, we established OT-1 CD8+ T cells with Tnfaip3 knockout by CRISPR-Cas9.

first: Ce

last: Luo

first: Rui

last: Guo

first: Lijian

last: Wu

first: Teng

last: Xue

first: Yufeng

last: He

first: Yiteng

last: Jin

first: Yanping

last: Zhao

first: Zongxu

first: Peng

first: Sitong

last: Ye

first: Xiaohong

last: Li

first: Dian

first: Wubin

first: Chenfei

last: Wang

first: Luhua

last: Lai

first: Qiang

last: Pan-Hammarström

first: Kai

last: Wucherpfennig

first: Zhidong

last: Gao

first: Deng

last: Pan

first: Zexian


title: An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility

status: Public on Dec 26 2024

city: Gif-sur-Yvette

first: Katarzyna

last: Siudeja

address: 1, Avenue de la Terrasse

country: France

institute: Institute for Integrative Biology of the Cell (I2BC), INSERM U1280, CEA, CNRS, Université Paris-Saclay

summary: We characterize somatic retrotransposition in the Drosophila intestine using long-read DNA sequencing. We show that retroelement mobility does not change significantly upon aging and is limited to very few active sub-families of retrotransposons. Importantly, we identify a polymorphic donor locus of an endogenous LTR retroviral element rover, active in the intestinal tissue. We reveal that gut activity of the rover donor copy depends on its genomic environment. Without affecting local gene expression, the copy co-opts its upstream enhancer sequence, rich in transcription factor binding sites, for somatic expression. We further show that escargot, a snail-type transcription factor critical for gut progenitor cell function, can drive transcriptional activity of the active rover copy. These data provide new insights into how locus-specific features allow active retrotransposons to produce functional transcripts and mobilize in a somatic lineage.

overall_design: RNA-seq and direct ONT cDNA profiling of gut and head tissue in normal and Ago2 mutant conditions of the D. melanogaster strain with somatically active retrotransposon copies.

first: Natalia

last: Rubanova

first: Darshika

last: Singh

first: Louis

last: Barolle

first: Fabienne

last: Chalvet

first: Sophie

last: Netter

first: Mickaël

last: Poidevin

first: Nicolas

last: Servant

first: Allison

middle: J

last: Bardin


title: Comprehensive curation and validation of genomic datasets for chestnut

status: Public on Dec 24 2024

first: Yi

last: Zheng

address: No. 7, Beinong Road, Huilongguan Town, Changping District

institute: Beijing University of Agriculture

summary: The Chinese chestnut (Castanea mollissima) stands out as a plant with significant ecological and economic value, excellent nutritional quality and natural resistance to pests and diseases. Recent strides in high-throughput techniques have enabled the continuous accumulation of genomic data on chestnuts, presenting a promising future for genetic research and advancing traits in this species. To facilitate the accessibility and utility of this data, we have curated and validated a collection of genomic datasets for eight Castanea species, 213 RNA-Seq samples, and 348 resequencing samples. These datasets are publicly available on figshare, providing a robust resource for researchers studying Castanea genetics, functional genomics, and evolutionary biology. Additionally, the Castanea Genome Database (CGD, http://castaneadb.net) serves as a complementary platform, offering advanced data mining and analysis tools, including BLAST, Batch Query, GO/KEGG Enrichment Analysis, and Synteny Viewer, to enhance the usability of the curated datasets.

overall_design:
This study analyzes gene expression differences in embryos, somatic embryos, callus, roots, and mixed samples using RNA sequencing, in addition to the samples provided in the table, including 181 samples obtained from third-party sources. RNA-Seq reads were processed with FastQC (v0.11.9), trimmed with Trimmomatic, aligned using STAR (v2.7.10b), and normalized to FPKM values.
Mix dataset.
In addition, third-party reanalysis of RNA-Seq samples from SRA database (see TABLE below).