title: Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 4]

city: Freiburg

first: Thomas

last: Boehm

address: Stuebeweg 51

department: Developmental Immunology

institute: Max Planck Institute for Immunobiology and Epigenetics

summary: The generation of self-tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium, and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self-antigen expression have been extensively studied, the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover, the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here, we show that during mouse development, mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle, ionocyte, goblet and ciliated cells emerge before birth, whereas others, for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1, expression of a hypomorphic Foxn1 transcription factor, and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members, including the Foxn4 gene of the cephalochordate amphioxus, and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types, such as ciliated cells, develop in the thymus in the absence of Foxn1, mimetic cells appearing postnatally, such as enterohepatic cells, require the activity of the vertebrate-specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys, a representative of jawless vertebrates that exhibit an alternative adaptive immune system, also harbour cells expressing genes encoding peripheral tissue components, such as the liver-specific protein transthyretin. Our findings suggest an evolutionary model of successive changes of thymic epithelial genetic networks enabling the coordinated contribution of peripheral antigen expression and mimetic cell formation to achieve central tolerance for vertebrate-specific innovations of certain tissues, such as the liver.

overall_design: Nuclei of thymic cells were isolated and subjected to snRNAseq. Foxn1 heterozygous and knockout samples were processed.

first: Anja

last: Nusser

first: Oliver

last: Thomas

first: Gaoqun

last: Zhang

first: Daisuke

last: Nagakubo

first: Laura

last: Arrigoni

first: Brigitte

last: Krauth


title: ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution (human organoids subset)

status: Public on Apr 16 2025

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

type: Expression profiling by high throughput sequencing

summary: To investigate the celluar heterogeneity of ETMR and the role of pericytes in the tumor microenvironment, we performed single-cell RNA sequencing of about 140,000 cells from primary human and murine ETMR as well as from 2D ETMR cultures and 3D models of ETMR-harboring forebrain organoids. We also analysed 3 ETMR human samples by spatial transcriptomics.

overall_design: scRNA-seq (10xGenomics) of fresh frozen samples: n=12 forebrain organoids harboring human ETMR cell lines and control samples

first: Flavia

middle: W

last: de Faria

first: Nicole

middle: C

last: Riedel

first: Marta

last: Interlandi

last: Göbel

first: Viktoria

last: Melcher

first: Christian

first: Rajanya

last: Roy

first: Melanie

last: Schoof

first: Daniel

last: Münter

first: Ivan

last: Bedzhov

first: Natalia

last: Moreno

first: Monika

last: Graf

first: Marc

last: Hotfilder

first: Dörthe

last: Holdhof

first: Wolfgang

last: Hartmann

first: Martin

last: Hasselblatt

first: Ann-Katrin

last: Bruns

first: Angela

last: Brentrup

first: Friederike

last: Liesche-Starnecker

first: Bruno

last: Maerkl

first: Sarah

last: Sandmann

first: Julian

last: Varghese

last: Dugas

first: Sebastian

last: Balbach

first: Claudia

last: Rössig

last: Ebinger

last: Schuhmann

first: Aysegül

last: Canak

first: Jens

last: Schnittenhelm

first: Michael

middle: F

last: Frühwald

first: Ulrich

last: Schüller

middle: K

last: Alber

first: Jan

middle: M

last: Bruder

first: Kornelius

last: Kerl


title: ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution (human subset)

first: Carolin

last: Walter

overall_design: scRNA-seq (10xGenomics) of fresh frozen samples: primary human tumor (n=1)

first: Flavia

last: de Faria

first: Nicole

last: Riedel

first: Marta

last: Interlandi

last: Göbel

first: Viktoria

last: Melcher

first: Christian

last: Thomas

first: Rajanya

last: Roy

first: Melanie

last: Schoof

first: Daniel

last: Münter

first: Ivan

last: Bedzhov

first: Natalia

last: Moreno

first: Monika

last: Graf

first: Marc

last: Hotfilder

first: Dörthe

last: Holdhof

last: Hartmann

last: Hasselblatt

last: Bruns

last: Brentrup

first: Thomas


title: Ku suppresses RNA-mediated innate immune responses in human cells to accommodate primate-specific Alu expansion

city: New York

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

country: USA

institute: Columbia University

summary: Ku70 and Ku80 form Ku , a ring-shaped protein that initiates the non-homologous end-joining (NHEJ) DNA repair pathway. Specifically, Ku binds to double-stranded DNA (dsDNA) ends and recruits other NHEJ factors (e.g., DNA-PKcs and LIG4). While Ku binds to double-stranded RNA (dsRNA) and traps mutated-DNA-PKcs on ribosomal RNA in vivo, the physiological significance of Ku-dsRNA interactions in otherwise wild-type cells remains elusive. Intriguingly, while dispensable for murine development, Ku is essential in human cells. Despite similar genome sizes, human cells express ~100-fold more Ku than mouse cells, implying functions beyond NHEJ, possibly through a dose-sensitive interaction with dsRNA, which is 10~100 times weaker than with dsDNA. While investigating the essentiality of Ku in human cells, we found that depletion of Ku - unlike LIG4 - induces profound interferon (IFN) and NF-kB signaling via dsRNA-sensor MDA5/RIG-I and adaptor MAVS. Prolonged Ku-degradation also activates other dsRNA-sensors, e.g. PKR that suppresses protein translation, and OAS/RNaseL that cleaves rRNAs and eventually induces growth arrest and cell death. MAVS, RIG-I, or MDA5 knockouts suppressed IFN signaling and, like PKR knockouts, all partially rescued Ku-depleted human cells. Ku-irCLIP analyses revealed that Ku binds to diverse dsRNA, predominantly stem-loops in primate-specific Alu elements at anti-sense orientation in introns and 3’-UTRs. Ku expression rose sharply in higher primates tightly correlating with Alu-expansion (r = 0.94/0.95). Together, our study identified a vital role of Ku in accommodating Alu-expansion in primates by mitigating a dsRNA-induced innate immune response, explaining the rise of Ku levels and its essentiality in human cells.

overall_design: To investigate the function of Ku above NHEJ in human cells, we generated AID-tagged Ku80 HCT116 cell lines (3 independent clones, #1, #7, #9) and MAVS knockout clones (3 independent clones, #1, #13, #15) on the base of AID-Ku80. To confirm our results in different Ku80 depletion system or cell lines, we used the Ku86flox/- HCT116 cells with one deleted and one floxed Ku80 allele (sometimes referred to as Ku86 in human cells) to allow the 4-hydroxy tamoxifen (4OHT)-induced CreERT2 translocation to excise the remaining Ku80 allele (Ku86flox/-:CreERT2), and a recently published Ku70-KO HEK293 cells with Dox-inducible ectopic Ku70 (3 independent clones, Sa11, SB and TI). We treated the AID cells with IAA&Dox to degrade Ku80 with DMSO as the control, flox cells with 4OHT to deplete Ku80 with EtOH as the control, and HEK293 cells without Dox to deplete Ku70 with Dox as the control. We then performed gene expression profiling analysis using data obtained from RNA-seq of the independent clones (AID HCT116 cells and HEK293 cells) or samples from two independent experiments (Ku86flox/- and Ku86flox/-:CreERT2 cells).

first: Yimeng

last: Zhu

first: Brian

last: Lee


title: ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution

first: Carolin

last: Walter

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

first: Flavia

last: de Faria

last: Riedel

last: Interlandi

last: Göbel

first: Lea

last: Altendorf

first: Mathis

last: Richter

last: Melcher

first: Wolfgang

first: Ann-Katrin

first: Angela

first: Friederike

last: Liesche-Starnecker

first: Bruno

last: Maerkl

first: Sarah

last: Sandmann-Varghese

first: Julian

last: Varghese

first: Martin

last: Dugas

first: Pedro

middle: H

last: Pinto

first: Sebastian

middle: T

last: Balbach

first: I-Na

last: Lu

first: Claudia

last: Rossig

first: Oliver

last: Soehnlein

first: Aysegül

last: Canak

last: Ebinger

last: Schuhmann

first: Jens

last: Schittenhelm

first: Michael

last: Frühwald

first: Ulrich

last: Schüller

last: Albert

first: Jan

last: Bruder

first: Kornelius

last: Kerl


title: ETMR stem-like state and chemoresistance are supported by perivascular cells at single-cell resolution

status: Public on Apr 17 2025

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

summary: To investigate the cellular heterogeneity of ETMR and the role of pericytes in the tumor microenvironment, we performed sequencing at single-cell resolution of about 250,000 cells from primary human and murine ETMR as well as from 2D ETMR cultures and 3D models of ETMR-harboring forebrain organoids. We also analysed 3 ETMR human samples by spatial transcriptomics.

overall_design: Gene expression profiles of human ETMR (n=9) were generated of formalin-fixed, paraffin-embedded (FFPE) tissue samples using Chromium Fixed RNA Profiling for Multiplexed Samples technology (10X Genomics).

first: Flavia

last: de Faria

first: Nicole

last: Riedel

first: Daniel

last: Münter

first: Marta

last: Interlandi

first: Carolin

last: Göbel

first: Lea

last: Altendorf

first: Mathis

last: Richter

first: Viktoria

last: Melcher

first: Christian

last: Thomas

first: Rajanya

last: Roy

first: Melanie

last: Schoof

first: Ivan

last: Bedzhov

first: Natalia

last: Moreno

first: Monika

last: Graf

first: Marc

last: Hotfilder

first: Dörthe

last: Holdhof

first: Wolfgang

last: Hartmann

first: Ann-Katrin

last: Bruns

first: Angela

last: Brentrup

last: Liesche-Starnecker

last: Maerkl

last: Sandmann

first: Thomas

last: Walter


title: RNA sequencing of oocytes at different developmental stages in Astyanax mexicanus

status: Public on Apr 15 2025

city: Kansas City

first: Di

last: Wu

state: MO

institute: Stowers Institute for Medical Research

summary: We performed bulk RNA sequencing on different cell size categories to capture different oocyte developmental stages in surface fish, Pachón cavefish and Molino cavefish, allowing us to investigate the differences in reproductive abilities between surface fish and cavefish.

overall_design: Bulk RNA sequencing was performed on right-side ovaries at different cell size categories from age-matched adult surface fish, Pachón cavefish and Molino cavefish at approximately 520 days post fertilization.

first: Fanning

last: Xia

first: Ana

last: Santacruz

first: Nicolas

last: Rohner


title: Ovary transcriptomic profiles of Astyanax mexicanus


title: Effect of GSK3 inhibition on the transcriptional signature of human GM-CSF-dependent monocyte-derived macrophages

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

summary: The functional versatility of macrophages is intrincately tied to factors such as their ontogeny and the specific tissue and extracellular environment. Monocyte-derived macrophages are oppositely instructed by M-CSF or GM-CSF. GM-CSF drives monocyte-derived macrophages towards heightened pro-inflammatory activity and the acquisition of the lung alveolar macrophage phenotype and gene profile whereas M-CSF gives rise to anti-inflammatory, pro-resolving, and immunosuppressive monocyte-derived macrophages. We explored the molecular impact of blocking GSK3 on the gene expression profile in GM-CSF-primed human monocyte derived macrophages. GSK3 inhibition skewed the transcriptional profile of GM-MØ towards an anti-inflammatory phenotype.

overall_design: mRNA profiles of human macrophages differentiated with GM-CSF (GM-MØ) in presence or absence of 10 micromolar of GSK3  a/β inhibitor (CHIR99021) for 48 hours.

first: Israel

last: Ríos

first: Monica

last: Torres-Torresano

last: Puig-Kröger

first: Ángel

middle: L

last: Corbí


title: Single cell RNA sequencing reveals the functions of ovary in Astyanax mexicanus

summary: We performed single cell RNA sequencing to capture all somatic cell types and early germ cells in the ovary of surface fish, Pachón cavefish and Molino cavefish, allowing us to investigate the differences in reproductive abilities between surface fish and cavefish. This study represents the first transcriptomic characterization at the single cell level of the ovary in Astyanax mexicanus.

overall_design: Single cell RNA sequencing of left-side ovaries from approximately 520 days post fertilization adult surface fish, Pachón cavefish and Molino cavefish


title: Modeling heart failure by induced pluripotent stem cell-derived organoids.

city: Bologna

first: Silvia

last: Cetrullo

state: BO

address: Via Irnerio 48

department: DIBINEM

country: Italy

institute: University of Bologna

type: Non-coding RNA profiling by high throughput sequencing

summary: Cardiac organoids replicate tissue complexity better than 2D models, making them ideal for studying diseases like heart failure (HF). This study developed scaffold-free cardiac organoids from induced pluripotent stem cells (iPSCs) to model HF in vitro. Gene expression analysis confirmed a cardiac phenotype, and endothelin-1 (ET-1) treatment induced HF-like features. Key findings include upregulation of HF markers (ANP, BNP, ACTA1), altered miRNA profiles, reduced contractility, and protein aggregation. Nutraceutical co-treatment mitigated these effects, highlighting the model's utility in understanding HF mechanisms and testing therapies.

overall_design: small RNA-sequencing of scaffold-free cardiac organoids derived from induced pluripotent stem cells (iPSCs) treated or not with endothelin-1 (ET-1) as hypertrophic inducer.

first: Irene

last: Bissoli

first: Francesco

last: Alabiso

first: Cristina

last: Cosentino

first: Aleksandra

last: Seragnoli C.

first: Fabrizio

last: Ferré

last: Alviano

first: Pasquale

last: Marrazzo

first: Carla

last: Pignatti

first: Giulio

last: Agnetti

first: Romano

last: Regazzi

first: Flavio

last: Flamigni

first: Stefania

last: D'Adamo


title: RNA Sequencing of VeroE6 cells infected with SARS-CoV-2 in presence and absence of GYY4137

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary: Viruses modulate various aspects of host physiology, including carbon metabolism, redox balance, and mitochondrial bioenergetics, to acquire the building blocks for replication and regulate the immune response. Understanding newer ways of how SARS-CoV-2 alters host redox metabolism, carbon metabolism, and mitochondrial health may lead to potential treatments for COVID-19. Reports have shown direct corelation of H2S metabolism with SARS-CoV-2 disease severity. However, the molecular mechanism of how H2S controls virus replication remains unknown. In this study, we have attempted to delineate the pathways altered by SARS-CoV-2 infection, using multi-omics techniques, and effect of H2S donor GYY4137 in the same. We have infected VeroE6 cells with SARS-CoV-2 (HK variant) at an MOI of 0.01 for 48 hours in presence and absence of 5 mM GYY4137. The transcriptomic profiles of uninfected, infected and treated were compared, to understand the molecular pathways underlying and to understand how H2S can modulate host metabolism to control viral replication.

overall_design: The study involves RNA sequencing from RNA isolated from VeroE6 cells infected with SARS-CoV-2 in presence or absence of potent drug molecule GYY4137, a slow releasing H2S donor at 48 hours post-infection. The profiles of Infected samples were compared with untreated, while those of treated were compared with untreated(but infected) samples. Samples for all three conditions were prepared in triplicates. Upon SARS-CoV-2 infection, the major pathways upregulated were for cellular response towards viral infection. Signalling pathways like RIG-1 pathway, MAPK pathway, TLR signalling, Cytokine-chemokine signalling were highly enriched with infection. Viral infections have been shown to hijack host metabolism. In line with this, we have observed, deregulation of host central carbon metabolism pathways like glycolysis, PPP, OXPHOS, TCA cycle. We noticed that the treatment of GYY4137 moderately reversed the effect of SARS-CoV-2 infection on the expression of genes associated with the oxidoreductase complex and Nrf2- antioxidant pathway. Furthermore, pathways related to defence and cellular response to viruses, including TLR, TNF, Nod-like receptor, MAPK, RIG-1, and cytokine/chemokine signaling, were more induced in GYY4137 treated VeroE6 cells as compared to untreated cells.  We did not observe any effect of GYY4137 on the expression of central metabolism, respiration, and amino acid metabolism. We validated the expression changes of several Nrf2-specific antioxidant genes in response to GYY4137 by qRT-PCR. The qRT-PCR and RNA-seq results were highly consistent and indicated that antioxidant genes were downregulated by SARS-CoV-2 infection, whereas GYY4137 treatment reversed this effect. Altogether, H2S supplementation induces a major realignment of redox metabolism and immune pathways associated with SARS-CoV-2 infection.

first: Ragini

last: Agrawal

first: Inder

middle: R

first: Nitish

last: Malhotra

first: Aswin

middle: S

last: Seshasayee


title: Gene Expression profile of RORγt-lineage anitigen presenting cells collected from secondary lymphoid tissues in adult mice.

city: San Francisco

first: James

last: Gardner

state: CA

address: 505 Parnassus Ave

institute: UCSF

summary: A key feature of immune tolerance is the ability to distinguish pathogens from innocuous signals including dietary antigens, but the precise mechanisms of oral tolerance induction and the key cellular actors have remained unclear. Classical dendritic cells (cDCs) have previously been implicated in the generation of regulatory T cells (Tregs) and T-cell anergy in response to food antigens in gut-associated lymphoid tissue1, but here we demonstrate that RORγt-lineage antigen-presenting cells (APCs), specifically RORγt-lineage cells expressing the Autoimmune Regulator (Aire) gene – referred to as RORγt eTACs – are the critical APC population required for oral tolerance induction. We reconcile the identity of these rare RORγt-lineage APC populations across new and all known single-cell transcriptomic datasets to establish consensus identities and show that RORγt eTACs2 are a unique myeloid-derived lineage distinct from innate lymphoid cells (ILCs) which are both necessary and sufficient for oral tolerance induction.

overall_design: We obtained mLN, spleen and other LNs (cervical, inguinal, axillary, brachial, and para-aortic) from adult RORγt-lineage mice (RORγt-Cre×R26-lsl-tdTmt) and FACS-sorted tdTmt+ MHCII+ cells for subsequent scRNA-seq

first: Im

last: Sun

first: Jiaxi

last: Wang

first: Anita

last: Qualls

first: Han

last: Yin


title: Developmental trajectory and evolutionary origin of thymic mimetic cells  [dataset 2]

first: Thomas

last: Boehm

overall_design: Cells from whole thymic tissue from zebrafish were prepared  and subjected to bulk RNAseq. Foxn1+/+  samples and foxn1-/- samples were sequenced.

first: Anja

last: Nusser

first: Oliver

last: Thomas

first: Gaoqun

last: Zhang

first: Daisuke

last: Nagakubo

first: Laura

last: Arrigoni

first: Brigitte

last: Krauth


title: Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 1]

overall_design: Thymic epithelial cells (TECs) were purified via FACS and subjected to bulk RNAseq. Wild type samples of a variety of strains as well as samples of transgenic animals were sequenced.


title: G6PC3 promotes genome maintenance and is a candidate mammary tumor suppressor

city: Copenhagen

first: Claus

middle: Storgaard

last: Sørensen

state: København N

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: Mutations in genome maintenance factors drive sporadic and hereditary breast cancers. Here, we searched for potential drivers based on germline DNA analysis from a cohort consisting of early-onset breast cancer patients negative for BRCA1/BRCA2 mutations. This revealed candidate genes that subsequently were subjected to RNAi-based phenotype screens to reveal genome integrity impacts. We identified several genes with functional roles in genome maintenance, including Glucose-6-Phosphatase Catalytic Subunit 3 (G6PC3), SMC4, and CCDC108. Notably, G6PC3-deficient cells exhibited increased levels of γH2AX and micronuclei formation, along with defects in homologous recombination (HR) repair. Consistent with these observations, G6PC3 was required for the efficient recruitment of BRCA1 to sites of DNA double-strand breaks (DSBs). RNA sequencing analysis revealed that G6PC3 promotes the expression of multiple homologous recombination repair genes, including BRCA1. Through CRISPR-Select functional-genetic phenotype analysis of G6PC3 germline mutations, we identified two germline G6PC3 variants displaying partial loss-of-function. Furthermore, our study demonstrated that G6pc3 deficiency accelerates mammary tumor formation induced by TP53 loss in mice. In conclusion, our cohort-based functional analysis has unveiled genome maintenance factors and identified G6PC3 as a potential new tumor suppressor in breast cancer.

overall_design: For bulk RNA-seq, the samples were divided into control group (siUNC) and experimental group (siG6PC3) with three biological replicates in each group. U2OS cells were transfected with 30 nM siRNA using Lipofectamine RNAiMAX (Thermo Fisher Scientific, 13778500). Cells were collected 48 hours after transfection following RNA-seq.


title: Next Generation Sequencing of Retinal Pigment Epithelial (RPE) cells differentiated from induced pluripotent stem cells (iPSCs).

city: Bangalore

first: Rajarshi

last: Pal

address: CCAMP, NCBS

institute: Eyestem research

summary: We have previously reported on RPE differentiation protocol that mimic the morphological, molecular, and functional characteristics of RPEs (GSE140545). In the present study, we developed an improved protocol that generates clinical grade hiPSC-RPE cells with enhanced purity and maturity. NGS was performed on RPE cells generated using Research, GLP and GMP grade protocols to understand the differential gene expression of RPE maturity between the protocols. The genesets were grouped based on their spatiotemporal expression during retinogeneisis - Early RPE, committed RPE and late-stage mature RPE genes. When compared to the GLP and GMP protocols, the research protocol showed a significant up-regulation of genes related to early RPE development indicating the product comprised of a heteregnous propulation of committed, non-committed and mature RPE cells (predominantly differentiating RPE progenitor cells). Similarly, the GLP protocol showed increased expression of genes associated with both committed and mature RPEs, but the GMP protocol had significantly higher expression of late-stage and mature RPE genes than the other two protocols. Additionally, most genes related to cell cycle and proliferation were significantly down regulated in the GMP protocol compared to the research protocol which indicates that our GMP protocol generated a RPE product that is devoid of proliferating or tumor forming cells and is therefore completely safe for clinical applications. In this study, we have provided a detailed description of the modifications in our manufacturing protocol to eliminate immature cells in our final product and Chemistry, Manufacturing and Controls (CMC) studies performed during product development.

overall_design: RPE cells were generated using research grade protocol had a mixture of committed and mature cells. This protocol was modified by incorporating enrichment and scale up steps to generate mature RPE cells. RPE cells generated from 3 different protocols were analyzed for their molecular profile by NGS- Research grade RPE cells, Enriched RPE cells, Enriched and scaled up mature RPE cells


title: Ovary transciptomic profiles of starved surface fish and Tinaja females

first: Di

last: Wu

summary: We performed bulk RNA sequencing on the ovaries from control and starved females of surface fish and Tinaja cavefish, allowing us to study the effects of starvation on reproduction between surface fish and cavefish.

overall_design: Bulk RNA sequencing was performed on right-side ovaries from age-matched control and starved females of surface fish and Tinaja cavefish at approximately 660 days post fertilization.

first: Fanning

last: Xia

first: Ana

last: Santacruz

first: Nicolas

last: Rohner


title: Synthetic deconvolution reveals combinatorial properties in transcriptional regulation by auxin

city: Grenoble

first: Jérémy

last: LUCAS

address: 17 avenue des Martyrs

country: France

institute: CNRS

summary: Auxin orchestrates multiple transcriptional programs throughout plant development. In flowering plants, responses to auxin relies on a large multigenic family of transcription factors, the auxin response factors (ARF). While ARF combinations are thought to allow programming specific auxin target gene expression, this hypothesis has not been extensively tested. Here, we used a synthetic-driven reductionist approach to deconvolute the complexity of the ARF-dependent signaling. Synthetic promoters built from cis-elements identified as ARF preferential binding sites allowed us to demonstrate that ARF transcriptional properties are not intrinsic but depend on the cis-elements they bind to. Both in isolated cells and in planta, we show that specificity in transcription is encoded by both combinations of ARFs and of the cis-elements they target. Our results suggest that non-linear interactions between these two control layers constitute a unique regulatory system that can generate a wide diversity of gene expression patterns from the spatial auxin distribution.

overall_design: ampDAP-seq experiments with tagged ARF10 proteins were done on 2-weeks old Arabidopsis thaliana seedlings. Affinity purification was perfomed with ARF10 tagged proteins then mixed with DNA. Three replicates were done and only consensus peaks in all three were retained.

first: Emmanuel

last: Thevenon

last: Lucas

first: Renaud

last: Dumas

first: François

last: Parcy


title: ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution (murine subset)

first: Carolin

last: Walter

overall_design: scRNA-seq (10xGenomics) of fresh frozen samples: primary murine forebrain, harboring (n=8) and non-harboring (control) (n=2) ETMR; ETMR murine cell lines cultivated as neurospheres in mono-culture (n=2) and in co-culture with murine brain vascular pericytes (n=2)

first: Flavia

last: de Faria

first: Nicole

last: Riedel

first: Marta

last: Interlandi

last: Göbel

first: Viktoria

last: Melcher

first: Christian

first: Rajanya

last: Roy

first: Melanie

last: Schoof

first: Daniel

last: Münter

first: Ivan

last: Bedzhov

first: Natalia

last: Moreno

first: Monika

last: Graf

first: Marc

last: Hotfilder

first: Dörthe

last: Holdhof

first: Wolfgang

last: Hartmann

first: Martin

last: Hasselblatt

first: Ann-Katrin

last: Bruns

first: Angela

last: Brentrup

first: Friederike

last: Liesche-Starnecker

first: Bruno

last: Maerkl

first: Sarah

last: Sandmann

first: Julian

last: Varghese

last: Dugas

first: Sebastian

last: Balbach

first: Claudia

last: Rössig

last: Ebinger

last: Schuhmann

first: Aysegül

last: Canak

first: Jens

last: Schnittenhelm

first: Michael

last: Frühwald

first: Ulrich

last: Schüller

first: Thomas

last: Alber

first: Jan

last: Bruder

first: Kornelius

last: Kerl


title: FOXM1 acts sexually dimorphically to regulate functional B-cell mass (RNA-Seq)

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

institute: Johns Hopkins University

summary: FOXM1 increases beta cell proliferation and mass in aged male mice. Previous work also demonstates that reducing Foxm1 in the beta cell had a larger effect on male than female beta cell function. Here we investigate differences in FOXM1 action in the beta cell due to sex.

overall_design: FOXM1 was expressed in female mouse beta cells (b-FOXM1 mice) or human male and human islets, and glucose tolerance, beta cell mass, beta cell proliferation, and insulin secretion were examined. Samples were sequenced and the binding sites for FOXA2, FOXM1, and ER⍺ transcription factors were compared.

first: Guihong

last: Peng

first: Elham

last: Mosleh

first: Andrew

last: Yuhas

first: Kay

last: Katada

first: Maria

last: Golson


title: FOXM1 acts sexually dimorphically to regulate functional B-cell mass (ChIP-Seq)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Previous work demonstrated that reducing Foxm1 in the b-cell had a larger effect on male than female b-cell function. We access whether these differences result from estrogen receptor (ER)alpha action, since estrogen contributes to diabetes susceptibility differences between males and females and ERalpha is the primary mediator of B-cell estrogen signaling.


title: Inhibition of p53-MDM2 binding reduces senescent cell abundance and improves the adaptive responses of skeletal muscle from aged mice

status: Public on Apr 14 2025

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

summary: Skeletal muscle adaptation to external stimuli, such as regeneration following injury and hypertrophy in response to resistance exercise, are blunted with advanced age. The accumulation of senescent cells, along with defects in myogenic progenitor cell (MPC) proliferation, have been strongly linked as contributing factors to age-associated impairment in muscle adaptation. p53 plays an integral role in all these processes, as upregulation of p53 causes apoptosis in senescent cells and prevents mitotic catastrophe in MPCs from old mice. The goal of this study was to determine if a novel pharmaceutical agent (BI01), which functions by upregulating p53 through inhibition of binding to MDM2, the primary p53 regulatory protein, improves muscle regeneration and hypertrophy in old mice. BI01 effectively reduced the number of senescent cells in vitro but had no effect on MPC survival or proliferation at a comparable dose. Following repeated oral gavage with 2 mg/kg of BI01 (OS) or vehicle (OV), old mice (24 months) underwent unilateral BaCl2 injury in the tibialis anterior (TA) muscle, with PBS injections serving as controls. After 7 days, satellite cell number was higher in the TA of OS compared to OV mice, as was the expression of genes involved in ATP production. By 35 days, old mice treated with BI01 displayed reduced senescent cell burden, enhanced regeneration (higher muscle mass and fiber cross-sectional area) and restoration of muscle function relative to OV mice. To examine the impact of 2 mg/kg BI01 on muscle hypertrophy, the plantaris muscle was subjected to 28 days of mechanical overload (MOV) in OS and OV mice. In response to MOV, OS mice had larger plantaris muscles and muscle fibers than OV mice, particularly type 2b + x fibers, associated with reduced senescent cells. Together our data show that BI01 is an effective senolytic agent that may also augment muscle metabolism to enhance muscle regeneration and hypertrophy in old mice.

overall_design: RNA-seq profiling from tibialis anterior skeletal muscle tissue of young and old mice with and without BaCl-induced muscle injury. A cohort of old mice were treated with a senolytic compound, BI01.

first: Dungan

last: Cory

first: Wen

last: Yuan

first: Murach

last: Kevin


title: scRNA-seq of fasted or 1 hour refed mouse hypothalamus after 6 weeks of HFD

city: Vancouver

first: Francis

last: Lynn

state: BC

address: 950 28th Ave W

department: Surgery

country: Canada

institute: University of British Columbia

summary: Immediate Early Genes such as Npas4 are induced as part of the rapid response to environmental stimuli to regulate future transcription. The hypothalamus is made up of distinct neuronal populations and nuclei that regulate homeostatic processes such as POMC neurons that regulate feeding. To date, specific roles of Immediate Early Genes have not been studied in POMC neurons or any other hypothalamic population. Here, we have generated a single cell transcriptomic dataset from the hypothalami of adult male mice that were fed a 60% high fat diet for 6 weeks after Npas4 gene knockout specifically in POMC neurons, with or without a 1 hour refeed after an overnight fast. Our aim was to use this dataset to identify genes that are rapidly regulated by refeeding within 1 hour, as well as potential long-term transcriptomic differences as a result of the Npas4 knockout, in the general POMC neuron population.

overall_design: Adult male mice of either the POMC-CreER (CT) control genotype or POMC-NPAS4 KO (KO) genotype were used. Tamoxifen was administered to all mice at 6 weeks of age, and mice were fed a 60% high fat diet (HFD) from 7 weeks of age. 7 CT and 6 KO mice were used total to generate this dataset. All mice were fasted overnight before their hypothalamus was harvested. 4 CT mice and 3 KO mice were refed for 1 hour after the overnight fast, before harvest, resulting in 13 samples total with minimum n=3 per group (4 refed CT, 3 fasted CT, 3 refed KO, and 3 fasted KO).

first: Ji Soo

last: Yoon

first: Daniel

last: Gamu

first: William

last: Gibson


title: Ovary transciptomic profiles of starved surface fish and Pachón females

first: Di

last: Wu

summary: We performed bulk RNA sequencing on the ovaries from control and starved females of surface fish and Pachón cavefish, allowing us to study the effects of starvation on reproduction between surface fish and cavefish.

overall_design: Bulk RNA sequencing was performed on right-side ovaries from 2 batches of age-matched control and starved surface fish and Pachón cavefish at approximately 500 and 1200 days post fertilization.

first: Fanning

last: Xia

first: Ana

last: Santacruz

first: Nicolas

last: Rohner


title: Nerve-to-cancer transfers of mitochondria during cancer metastasis

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: The nervous system plays a pivotal role in cancer biology, and pathological investigations have linked intratumoural nerve density to metastasis. However, the precise impact of cancer-associated neurons and the communication channels at the nerve–cancer interface remain poorly understood. Previous cancer denervation models in rodents and humans have highlighted robust cancer dependency on nerves, but the underlying mechanisms driving nerve-mediated cancer aggressivity remain unknown. Here we show that cancer-associated neurons enhance cancer metabolic plasticity by transferring mitochondria to cancer cells. Breast cancer denervation and nerve–cancer coculture models confirmed that neurons significantly improve tumour energetics. Neurons cocultured with cancer cells undergo metabolic reprogramming, resulting in increased mitochondrial mass and subsequent transfer of mitochondria to adjacent cancer cells. To precisely track the fate of recipient cells, we developed MitoTRACER, a reporter of cell-to-cell mitochondrial transfer that permanently labels recipient cancer cells and their progeny. Lineage tracing and fate mapping of cancer cells acquiring neuronal mitochondria in primary tumours revealed their selective enrichment at metastatic sites following dissemination. Collectively, our data highlight the enhanced metastatic capabilities of cancer cells that receive mitochondria from neurons in primary tumours, shedding new light on how the nervous system supports cancer metabolism and metastatic dissemination.

overall_design: Breast xenograft tumors were grown with and without denervation with botox.  Cancer cells were extracted by laser-capture microdissection.  5 samples were collected from each group.

first: Gregory

last: Hoover

first: Shila

last: Gilbert

first: Olivia

last: Curley

first: Clémence

last: Obellianne

first: Mike

last: Lin

last: Hixson

first: Terry

last: Pierce

first: Joel

last: Andrews

first: Mikhail

last: Alexeyev

first: Yi

last: Ding

first: Ping

last: Bu

first: Fariba

last: Behbod

last: Medina

first: Gustavo

last: Ayala

first: Simon

last: Grelet


title: FOXM1 acts sexually dimorphically to regulate functional B-cell mass

first: Christopher

last: Cherry

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

overall_design: Refer to individual Series


title: Neocortical tau propagation is a mediator of clinical heterogeneity in Alzheimer’s disease

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Heterogeneity in progression of clinical dementia obstructs the general therapeutic potential of current treatments for Alzheimer’s disease (AD). Though the mechanisms of this heterogeneity remain unclear, the characterization of bioactive tau species and factors that regulate their seeding behavior might give valuable insight as pathological tau is well correlated with cognitive impairment. Here, we conducted an innovative investigation into the molecular basis of widespread, connectivity-based tau propagation that begins in the inferior temporal gyrus (ITG) and spreads to neocortical areas such as the prefrontal cortex (PFC). Biochemical analysis of human postmortem ITG and PFC tissues revealed individual variability in tau seeding, which correlated with cognitive decline, particularly in the ITG, a region known for promoting accelerated tau propagation. Notably, this study presents the first evidence that site-specific phosphorylation and isoform composition of both aggregation-prone high-molecular-weight (HMW) tau and the relatively unexplored, yet potentially crucial in AD progression low-molecular-weight (LMW) tau significantly contribute to tau propagation and cognitive decline. Our findings underscore the importance of comprehensively considering diverse tau forms including both HMW and LMW tau species in understanding AD progression. Additionally, these results are the first to identify distinct morphological strains within the AD brain associated with differing seeding propensity, potentially enabling patient stratification based on their tau profile. Furthermore, RNA-seq analyses of gene expression patterns in the ITG revealed molecular heterogeneity associated with tau seeding potential. Patients with higher levels of seed-competent tau displayed greater impairments in synaptic and neural plasticity, and increased neuroinflammation. This multidisciplinary study offers novel insights into various molecular mechanisms driving AD progression, suggesting potential molecular targets for early intervention and improved patient subtyping, which is critical for developing precision medicine approaches.

overall_design: RNA collected from eight control and twenty AD ITG brain tissue samples

first: Anjalika

last: Chongtham

first: Marissa

last: Farinas

first: Li

last: Shen

first: Ana

last: Pereira


title: Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 3]

first: Thomas

last: Boehm

summary: The generation of self-tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium, and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self-antigen expression have been extensively studied, the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover, the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here, we show that during mouse development, mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle, ionocyte, goblet and ciliated cells emerge before birth, whereas others, for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1, expression of a hypomorphic Foxn1 transcription factor, and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members, including the Foxn4 gene of the cephalochordate amphioxus, and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types, such as ciliated cells, develop in the thymus in the absence of Foxn1, mimetic cells appearing postnatally, such as enterohepatic cells, require the activity of the vertebrate-specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys, a representative of jawless vertebrates that exhibit an alternative adaptive immune system, also harbour cells expressing genes encoding peripheral tissue components, such as the liver-specific protein transthyretin. Our findings suggest an evolutionary model of successive changes of thymic epithelial genetic networks enabling the coordinated contribution of peripheral antigen expression and mimetic cell formation to achieve central tolerance for vertebrate-specific innovations of certain tissues, such as the liver.

overall_design: Thymic epithelial cells (TECs) were purified via FACS and subjected to bulk RNAseq. Samples from wild type and transgenic animals were sequenced.

first: Anja

last: Nusser

first: Oliver

last: Thomas

first: Gaoqun

last: Zhang

first: Daisuke

last: Nagakubo

first: Laura

last: Arrigoni

first: Brigitte

last: Krauth


title: Transcriptomic profile of the developing chicken lung

first: Kamryn

last: Gerner-Mauro

state: Texas

address: 1 Baylor Plz

institute: Baylor College of Medicine

summary: Alveolar development of the chicken lung has largely been studied by histology only. We conducted a study to uncover the transcriptomic profile of the lung alveolar cell types in the chicken by single-cell RNA-seq (scRNA-seq) and multiome.

overall_design: Cells dissociated from the chicken lung were isolated by Flourescence-activated cell sorting (FACs) according to  depletion of immune cells (CD45+) and/or enrichment of epithelial cells (ECAD+).

first: Lisandra

last: Vila-Ellis

first: Guolun

last: Wang

first: Richa

last: Nayak

first: Peter

last: Lwigale

first: Ross

last: Poche

first: Chen

last: Jichao


title: Cutaneous T cells promote distinct transcriptional programs in human skin structural cells associated with inflammatory disease

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: T cells coordinate with structural cells in the skin to promote appropriate inflammatory responses and subsequent restoration of barrier integrity following insult. Single cell studies of human skin have defined an assortment of transcriptionally distinct structural cell populations in healthy tissue and identified inflammatory disease-associated changes in epithelial keratinocytes and dermal fibroblasts. Cutaneous T lymphocyte activity is implicated in the development of inflammatory skin disease, but the mechanisms by which T cells promote disease-associated changes in the skin remain unclear. We show that distinct subsets of circulating and resident CD4+ cutaneous T cells promote a diverse array of transcriptional outcomes in human keratinocytes and fibroblasts. Using these in vitro generated transcriptional signatures, we identify T cell-dependent gene modules associated with inflammatory skin diseases in vivo, such as a set of Thelper17 cell-induced genes in keratinocytes that are enriched in the skin of patients with psoriasis and normalized in response to anti-IL-17 therapy. Thus, we present an approach to define the immune-dependent gene networks of skin structural cells, which we use to study the T cell contribution to inflammatory skin disease and response to anti-cytokine therapy.

overall_design: Cultured keratinocytes (N=65 total) or fibroblasts (N=70 total) were treated with T-cell supernatants from sorted populations of T cells for 24 hours or left untreated as a control prior to RNA isolation.

middle: A

last: Morawski

first: Hannah

last: DeBerg

first: Mitch

last: Fahning

first: James

last: Schlenker

first: William

last: Schmitt

first: Iris

last: Gratz

first: Jeffrey

last: Carlin

first: Daniel

middle: J

last: Campbell


title: Integrated analysis of transcriptional and metabolic responses to mitochondrial stress

city: Boston

first: Liam

last: Kelley

state: MA

address: 260 Longwood Ave

institute: Harvard Medical School

summary: Mitochondrial stress arises from a variety of sources, including accumulation of mutations in mitochondrial DNA, generation of reactive oxygen species, and insufficient supplies of oxygen or fuel. Cells utilize multiple pathways to respond to mitochondrial injury, including mitophagy, mitochondrial fusion, and the integrated stress response / mitochondrial unfolded protein response. However, the integration of transcriptional and metabolic signatures of distinct types of mitochondrial stress are still not well defined. We defined how primary human fibroblasts respond to a panel of well-characterized inhibitors that target key pathways in the mitochondria, using sub-lethal doses to trigger adaptive stress responses. By combining metabolomic and transcriptomic analyses, we established integrated signatures of mitochondrial stress. We developed a tool, SQUID, to infer molecular triggers of mitochondrial dysfunction in other datasets. Using SQUID, we globally investigated mitochondrial stress in the TCGA PanCancer Atlas and identified defects in pyruvate  import in IDH1 mutant glioma. Altogether, these studies provide a comprehensive resource detailing cellular stress responses that safeguard mitochondrial health.

overall_design: Comparative gene expression analysis of human fibroblasts treated with an array of mitochondrial inhibitors in order to study the transcriptional response to mitochondrial stress

middle: P

first: Song-Hua

last: Hu

first: Sarah

last: Boswell

last: Sorger

first: Alison

middle: E

last: Ringel

first: Marcia

last: Haigis


title: DNA methylation contributes to the site-specific regulation of HOXA cluster gene expression

status: Public on Apr 13 2025

city: Nagoya

first: Ryosuke

last: Okuno

state: Aichi

address: 2-7, Torimi-cho, Nishi-ku

country: Japan

institute: Nippon Menard Cosmetic Co., Ltd.

summary: The skin is the largest organ covering the entire body, composed of three layers: the epidermis, dermis, and subcutaneous tissue. While the thickness and elasticity of the skin are known to vary depending on the body site, the mechanisms underlying these differences remain unclear. Recent studies have reported that HOX genes, which determine positional identity during development, are also expressed and functional in adult tissues. We found that the expression of HOXA cluster genes in dermal fibroblasts derived from adult skin is regulated in a site-specific manner. Inhibition of HOXA9 expression in adult dermal fibroblasts resulted in decreased cell proliferation and downregulation of extracellular matrix-related genes. These results suggest that the HOX genes function as factors that produce site-specific differences in skin properties. To verify how site-specific expression of HOXA genes is regulated, methylation analysis was performed. The results showed that methylation level around the HOXA9 gene was higher in cells derived from the face than those from the abdomen and buttocks. This result suggests that region-specific expression during development is preserved in adult skin and is responsible for the regional differences in skin properties.

overall_design: To elucidate the regulatory mechanisms of site-specific HOXA gene expression, methylation arrays were performed using human dermal fibroblasts derived from the face, abdomen, and buttocks.

first: Seiji

last: Hasegawa

first: Mika

last: Kawagishi-Hotta

first: Yuichi

last: Hasebe


title: Generation of Hoxa11-3XFLAG and Hoxd11-3XFLAG alleles to investigate Hox11 genome-wide binding

city: Madison

first: Deneen

middle: Marie

last: Wellik

state: WI

address: 1111 Highland Avenue 4448 WIMR II

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary: Hox genes encode for evolutionary conserved transcription factors that direct the proper development of the body plan. Despite decades of research, little is known regarding their downstream target genes, especially in vertebrates. The strong evolutionary conservation of their DNA-binding homeodomain, their generic AT-rich binding sites, and the lack of specific antibodies has precluded rigorous examination. To circumvent these limitations, we have generated two mouse models in which a 3XFLAG epitope tag has been inserted into the 5’ end of the coding sequence of both Hoxa11 and Hoxd11 loci via Cas9/CRISPR. The alleles have been validated by sequencing, PCR genotyping, western blotting, and protein expression analyses, demonstrating proper targeting and expression. Breeding these alleles in combination produces viable and fertile Hoxa11FLAG/FLAG; Hoxd11FLAG/FLAG animals, with no overt patterning defects unlike Hoxa11/Hoxd11 mutants that are infertile and have severe kidney and limb defects. By performing CUT&RUN and CUT&Tag analyses, we have confirmed DNA binding to a known Six2 enhancer in the developing kidney. These novel alleles will allow characterization of the genome-wide binding profile of HoxPG11 proteins in vivo.

overall_design: CUT&Tag of IgG and FLAG from E13.5 Hoxa11FL/FL;Hoxd11FL/FL or Hoxa11FL/+;Hoxd11FL/FL pooled kidneys.

first: Martha

last: Echevarria-Andino

first: Jane

middle: Y

last: Song

first: Paul

last: van Ginkel

first: Shuyang

last: Chen

first: Corey

last: Flynn

first: Sunduz

last: Keles

first: Benjamin

last: Allen


title: Gene expression profile of the HOXA gene in adult dermal fibroblasts

summary: The skin is the largest organ covering the entire body, composed of three layers: the epidermis, dermis, and subcutaneous tissue. While the thickness and elasticity of the skin are known to vary depending on the body site, the mechanisms underlying these differences remain unclear. Recent studies have reported that HOX genes, which determine positional identity during development, are also expressed and functional in adult tissues. We found that the expression of HOXA cluster genes in dermal fibroblasts derived from adult skin is regulated in a site-specific manner. Inhibition of HOXA9 expression in adult dermal fibroblasts resulted in decreased cell proliferation and downregulation of extracellular matrix-related genes. These findings suggest that the positional memory established by HOX genes during development is maintained in adults, contributing to the homeostasis and regional differences observed in adult skin.

overall_design: To compare gene expression in various skin sites, gene expression profiling by RNA-seq was performed using dermal fibroblasts from the face, abdomen, and buttocks.


title: Impaired parvalbumin interneurons in the retrosplenial cortex as the cause of sex-dependent vulnerability in Alzheimer’s disease [GeoMx]

city: Calgary

first: Jonathan

last: Epp

state: Alberta

address: 2500 University Drive NW

institute: University of Calgary

summary: Alzheimer’s disease is a debilitating neurodegenerative disorder with no cure and few treatment options. In early stages of Alzheimer’s disease, impaired metabolism and functional connectivity of the retrosplenial cortex strongly predict future cognitive impairments. Therefore, understanding Alzheimer’s disease-related deficits in the retrosplenial cortex is critical for understanding the origins of cognitive impairment and identifying early treatment targets. Using the 5xFAD mouse model, we discovered early, sex-dependent alterations in parvalbumin-interneuron transcriptomic profiles. This corresponded with impaired parvalbumin-interneuron activity, which was sufficient to induce cognitive impairments and dysregulate retrosplenial functional connectivity. In fMRI scans from patients with mild cognitive impairment and Alzheimer’s disease, we observed a similar sex-dependent dysregulation of retrosplenial cortex functional connectivity and, in post-mortem tissue from subjects with Alzheimer’s disease, a loss of parvalbumin interneurons. Reversal of cognitive deficits by stimulation of parvalbumin interneurons in the retrosplenial cortex suggests that this may serve as a promising novel therapeutic strategy.

overall_design:
The retrosplenial cortices of four female wildtype mice, four male wildtype mice, four female 5xFAD mice, and four male 5xFAD mice were analyzed using NanoString GeoMX DSP
Alzheimer's Disease Neuroimaging Initiative (contributor)

first: Dylan

last: Terstege

first: Yi

last: Ren

first: Bo Young

last: Ahn

first: Heewon

last: Seo

first: Kabirat

last: Adigun

first: Liisa

last: Galea

first: Derya

last: Sargin


title: Imbalanced TGF-beta signalling and autophagy drive erythroid priming of hematopoietic stem cells in Beta-thalassemia

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

institute: Consiglio Nazionale delle Ricerche

summary: We evaluated how the disease impacts the  gene expression within hematopoietic stem cells and progenitors

overall_design: To profile transcriptional differences between Bthal and HD primitive hematopoietic cells, we performed RNAseq on different hematopoietic subpopulations isolated by Fluorecence-activated cell sorting (FACS) from Bthal and healthy donor (HD) bone marrow CD34+ cells .

first: Giuliana

last: Ferrari

first: Maria

last: Lidonnici

first: Giulia

last: Chianella

first: Matteo

last: Barcella


title: Targeting G9a Regulated m6A Modification Pathway to Hinder SARS-CoV-2 Replication

city: Chapel Hill

first: John

last: Wrobel

state: NC

address: 120 Mason Farm Rd

department: Department of Biochemistry and Biophysics

institute: University of North Carolina

summary: N6-methyladenosine (m6A) modification pathway is hijacked by several RNA viruses, including SARS-CoV-2, making it an attractive host-directed target for development of broad-spectrum antivirals. Here, we show that histone methyltransferase G9a, through its interaction with METTL3, regulates SARS-CoV-2 mediated rewiring of host m6A methylome to ultimately promote turnover, abundance, secretion and/or phosphorylation of various viral receptors and proteases, transcription factors, cytokines/chemokines, coagulation & angiogenesis associated proteins, and fibrosis markers. More importantly, drugs targeting G9a and its associated protein EZH2 are potent inhibitors of SARS-CoV-2 replication and reverse multi-omic effects of coronavirus infection in human alveolar epithelial cells (A549-hACE2) and COVID-19 patient PBMCs - with similar changes seen in multiorgan autopsy samples from COVID-19 patients. Altogether, we extend G9a function(s) beyond transcription to translational regulation during COVID-19 pathogenesis and show that targeting this master regulatory complex represents a new strategy (drug-class) that can be leveraged to combat emerging anti-viral resistance and infections.

overall_design: MeRIP-Seq/m6A-seq was performed using A549-hACE2 cells (mock or SARS-CoV-2 infected) and peripheral blood mononuclear cells (PBMCs) isolated from patient with COVID-19 under different treatment conditions (G9a inhibitor UNC0642, none) to identify transcripts showing differential m6A modification.

first: Adil

last: Muneer

first: Feng

last: Zhang

first: Xian

last: Chen


title: Methylomic profiling of melanoma tissues from patients prior to immune checkpoint blockade to identify predictors of response or resistance

city: Dunedin

first: Mike

last: Eccles

state: Otago

address: 56 Hanover Street

department: Pathology

country: New Zealand

institute: University of Otago

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of formalin-fixed paraffin-embedded (FFPE) melanoma tissue samples from patients prior to treatment with anti-PD1 immune checkpoint inhibitor therapy.
The MethylationEPIC v1.0 BeadChip array was used to obtain DNA methylation profiles across approximately 850,000 CpGs in bisulfite treated DNAs extracted from formalin-fixed paraffin embedded melanoma tissues prior to treatment with anti-PD1 immune checkpoint inhibitor therapy.

overall_design: Bisulphite converted DNA from the melanoma FFPE tissue samples were hybridized to the Illumina Infinium Human 850K MethylationEPIC v1.0 BeadChip array. Samples were collected prior to immune checkpoint blockade therapy.

first: Sultana

last: Hossain

first: Gregory

last: Gimenez

first: Peter

last: Stockwell

first: Robert

last: Weeks

first: Suzan

last: Almomani

last: Jones

first: Magda

last: Ratajska

first: Mathew

last: Shuen

first: Basharat

last: Bhat

first: Janusz

last: Ryś

first: Bozena

last: Cybulska-Stopa

first: Agnieszka

last: Harazin-Lechowska

first: Euan

last: Rodger

first: Christopher

last: Jackson

first: Aniruddha

last: Chatterjee

first: Michael


title: Single-nucleus profiling of the left ventricle of the mouse heart after chronic stress

city: Shijiazhuang

first: yaping

last: li

state: China

address: 河北医科大学

country: China

institute: 河北医科大学

summary: It is widely believed that stress and heart disease are related, but the exact mechanisms remain debatable. The Chronic Unpredictable Mild Stress (CUMS) paradigm can generally be regarded as an effective animal stress model, as it better simulates the stress frequently experienced by humans and prevents animals from adapting to a specific type of stress. To systematically understand the transcriptomic changes in cardiovascular stress-induced injury and lay the foundation for subsequent research on diagnostic and therapeutic targets, we further characterized the mRNA expression profiles of all cardiomyocytes in the left ventricle of mouse hearts using single-nucleus transcriptomics on the 10x Genomics platform.

overall_design: Eight C57BL/6N mice were randomly assigned to either a control group (CON, n = 4) or a stress group (CS, n = 4) for 28 days. Single nuclei were isolated from the left ventricles of both groups for transcriptomic sequencing and analysis.

first: Yaping

last: Li

first: Bin

last: Cong

first: Qian

last: Qi

first: Xia

last: Liu


title: GPM6B RNA-seq in PC9 cell line

city: Anhui

first: Xueyi

last: Feng

address: TangHe street

department: College of Life Science

institute: Anhui Medical University

summary: We aimed to detect the mRNA expression levels in stable-transfected PC9 cells after transfection with GPM6B over-expression or control virus.

overall_design: Extract total RNA from  PC-9 cell line after transfection with GPM6B over-expression or control virus, each sample use one well in 6 wells plate PC-9 cells.

first: Dai

last: Qian

first: Xufeng

last: Yao


title: The drug-elicitable alternative splicing module for tunable vector expression in the heart

city: Beijing

first: Zhan

last: Chen

address: 38 Xueyuan Rd, Haidian District, Beijing, China

institute: Peking University Health Science Center

summary:
RNA Seq datasets from WT or AAV-injected mice treated with 10 mg/kg risdiplam or solvent.
RNA Seq datasets from plasmid-transfection HEK293T cells  treated with 1uM risdiplam or DMSO.

overall_design:
Data from 5 risdiplam (10mg/kg) treated and 5 solvent treated WT mice heart  were obtained after sequencing on an Illumina NovaSeq 6000.
Data from 3 risdiplam (10mg/kg) treated and 3 solvent treated mice (tail vein AAV injection) heart (harvest at P10 or P20 or P30) were obtained after sequencing on an DNBSEQ-T7.
Data from 3 risdiplam (1uM) treated and 3 DMSO treated HEK293T cells  were obtained after sequencing on an DNBSEQ-T7.


title: Gene expression signatures in inflammatory and sclerotic morphea skin and blood distinguishes morphea from systemic sclerosis

city: Dallas

first: Henry

middle: W

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Morphea is an inflammatory disorder of the skin and soft tissue characterized by fibrosis that has been likened to systemic sclerosis (SSc). We sought to capture the molecular heterogeneity of morphea by examining lesional skin gene expression and blood biomarkers, and compare the gene expression profiles with those from SSc lesional and site matched non lesional skin, as well as sera obtained from adult patients with untreated morphea. We found the morphea transcriptome is dominated by IFNg-mediated Th1 immune dysregulation, with relative paucity of pathways associated with fibrosis. These results were mirrored when morphea gene expression profiles were compared with SSc. Interestingly, expression profiles of morphea skin samples clustered with the SSc inflammatory subset and distinct from the SSc fibro-proliferative subset. Unaffected morphea skin also differed from unaffected SSc skin in that it did not exhibit pathological gene expression signatures. Examination of downstream IFNg-mediated chemokines, CXCL9 and CXCL10, revealed increased transcription in the skin but not in sera. While elevated serum CXCL9 proteins quantified by ELISA were associated with active disease and widespread cutaneous disease. Taken together, these results indicate that inflammatory and sclerotic morphea is a skin directed process characterized by Th1 immune mediated dysregulation, which contrasts with fibrotic signatures and systemic transcriptional changes associated with SSc. The association of circulating CXCL9 concentration with clinical activity and burden of skin disease supports its potential as a readily accessible biomarker.

overall_design: We profiled the transcriptome of inflammatory (n=10) and sclerotic (n=15) lesional morphea versus site-matched unaffected skin (n=11) using microarray analysis.

first: Jane

last: Zhu

first: Viktor

last: Martyanov

last: Johnson

first: Lam

last: Tsoi

first: Grant

last: Barber

first: Jack

last: O'Brien

first: Jennifer

last: Coias

first: Nika

last: Cyrus

first: Neeta

last: Malviya

first: Stephanie

last: Florez-Pollack

first: Elaine

last: Kunzler

first: Gregory

last: Hosler

first: Johann

last: Gudjonsson

first: Dinesh

last: Khanna

last: Whitfield

first: Heidi

last: Jacobe


title: Molecular signatures define BAP1-altered meningioma as a distinct CNS tumor with deregulation of Polycomb repressive complex target genes

city: Seattle

first: Sonali

last: Arora

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Meningiomas are the most common primary intracranial neoplasms, exhibiting diverse patient outcomes. Despite most meningiomas being benign, a significant subset recurs postoperatively, posing substantial treatment challenges. Through an integrative analysis of DNA methylation data from over 10,000 meningioma samples, we identify BAP1-altered meningiomas as a molecularly distinct and biologically aggressive CNS tumor subtype, characterized by recurrent loss of chromosome 3p21 around the BAP1 locus and driven by diverse BAP1-inactivating alterations. While BAP1-altered meningiomas often exhibit rhabdoid morphology, this feature is not exclusive to them and should not serve as a definitive grading criterion. However, progression-free survival analysis indicates that patients with BAP1-driven meningiomas have a prognosis similar to WHO grade 3 meningiomas. Gene expression profiling reveals upregulation of PRC target genes and dysregulated Polycomb signaling, alongside elevated expression in various cellular and growth factor pathways. This molecular portrait of BAP1-altered meningiomas underscores potential pathway-specific therapeutic targets that should be prioritized for future investigation

overall_design: RNASeq of NF2, BAP1 AND h3k27me3 loss meningioma samples

first: Philipp

last: Sievers

first: Frank

last: Szulzewsky


title: Temperature-responsive transcriptome analysis in fkf1-t, gi-2 and fkf1-2gi-2 mutants

city: Seoul

first: Hong

middle: Gil

last: Lee

address: Gwanak-ro, Gwanak-gu

country: South Korea

institute: seoul national univesity

summary: FKF1–GI complex establishes a general scheme for temperature response in plants.

overall_design: Differentially expressed genes (DEGs) at 27°C relative to 22°C in each genotype and temperature-responsive genes that are dependent on FKF1 and GI.

middle: G

first: Jink

last: Wang

first: Kyung-Ho

last: Park

first: Hongwoo

first: Sol-Bi

last: Kim

first: Ji

last: Ahn

first: Jae-Hoon

last: Jung

first: Pil

last: Seo


title: REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA Polymerase IV transcription complexes.

status: Public on Apr 12 2025

city: Los Angeles

first: Steven

middle: E.

last: Jacobsen

state: CA

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: In plants, the maintenance of DNA methylation is controlled by several self-reinforcing loops involving histone methylation and non-coding RNAs. However, how methylation is initially patterned at specific genomic loci is largely unknown. Here, we describe four Arabidopsis REM transcription factors, VDD, VAL, REM12 and REM13, that recognize specific sequence regions, and together with the protein GENETICS DETERMINES EPIGENETICS1 (GDE1), recruit RNA polymerase IV transcription complexes. This targeted recruitment leads to the production of 24-nucleotide small interfering RNAs (24nt-siRNAs) that guide DNA methylation to specific genomic sites in plant female reproductive tissues. In the absence of GDE1, Pol IV transcription complexes are directed to loci bound by an alternative transcription factor, REM8, highlighting the role of REM transcription factors and GDE1 proteins as positional cues for epigenetic modulation. These findings establish a direct connection between sequence-specific transcription factors and the spatial regulation of siRNAs production and DNA methylation, offering new insights into the genetic control of epigenetic patterning.

overall_design: For ChIP-seq experiments, 1~2 g of unopen flower buds  from the T2 lines were collected. For sRNA-seq and WGBS, ovule or anther tissues (stage 9 or earlier) from 5- to 6-week-old plants were harvested.


title: The interactive effect of sustained sleep restriction and resistance exercise on skeletal muscle transcriptomics in young females

city: Burwood

first: Danielle

last: Hiam

state: Vic

address: 221 Burwood Hwy

department: IPAN

country: Australia

institute: Deakin University

summary: Both sleep loss and exercise regulate gene expression in skeletal muscle, yet little is known about how the interaction of these stressors affects the transcriptome. The aim of this study was to investigate the effect of nine nights of sleep restriction, with repeated resistance exercise (REx), on the skeletal muscle transcriptome of young, trained females.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in skeletal muscle of female who undertook nine nights of sleep restriction, with repeated resistance exercise.

first: Olivia

last: Knowles

first: Megan

last: Soria

first: Nicholas

last: Saner

first: Adam

last: Trewin

first: Sarah

last: Alexander

first: Spencer

last: Roberts

first: Andrew

last: Garnham

first: Eric

last: Drinkwater

first: Brad

last: Aisbett

first: Séverine

last: Lamon


title: A new model: radiation and cigarette smoke promote an aggressive cell phenotype and gene signature in head and neck cancer cells.  and gene signature in head and neck cancer cells.

city: Townsville

first: Lionel

last: Hebbard

state: QLD

address: 1 James Cook Dr, Douglas QLD 4811

institute: James Cook University

summary:
Background and purpose: Mucosal Head and Neck squamous cell cancers (HNSCCs) are aggressive invasive cancers. They arise in the oral cavity, oropharynx, nasopharynx, hypopharynx and larynx. To control local disease, radiation is used curatively and palliatively to destroy or reduce the tumour load. Smokers are at increased risk of developing these cancers, and smoking whilst receiving radiation worsens survival rates. However, the cellular and molecular mechanisms underlying this has not been well described. We developed a model to elucidate the effects of radiation and smoking and the pathways involved. This will enable the identification of novel pharmaceutical targets for patient trials.
Materials & Methods: FaDu hypopharyngeal cancer cells were subjected to a fractionated daily radiation procedure and cultured in smoke exposed media. Cells were examined for changes in tumoursphere number, proliferation, migration, invasion, CD44 and ALDH1 expression, and next generation sequencing was performed. Immunohistochemistry compared CD44 and ALDH1 expression in never-smokers and smokers.
Results: Radiation and smoking separately reduced FaDu Cancer Stem Cell (CSC) number and proliferation, and increased cell migration and invasion. Combined they further reduced CSC number and proliferation, and promoted migration. Through sequencing radiation and smoking produced a unique gene signature related to cell invasion, angiogenesis, and survival. CD44 expression and ALDH activity decreased after co-treatment and their expression did not associate with smoking status in a small patient cohort.

overall_design: FaDu cells were grown in control, smoke, radiation, or smoke+radiation conditions. RNA was isolated from treated cells with an Isolate II RNA Mini Kit (Bioline) and RNA integrity checked with an Agilent TapeStation. All RIN scorces exceeded 9.8. The Australian Genome Research Facility (AGRF) performed high-throughput Illumina sequencing.

first: Kylie

last: Lopes Floro

first: Rhys

last: Gillman

first: Miriam

last: Wankell

first: Brittany

last: Dewdney

first: Madhavi

last: Chilkuri

first: Ashley

last: Shackelford

first: Leslie

last: Kumar

first: Marcus

last: Powers


title: Habitual Exercise Modulates Neuro-Immune Interaction to Mitigate Aortic Stiffness

status: Public on Apr 11 2025

first: Tzung

last: Hsiai

state: California

address: 650 Charles E Young Dr S

institute: University of California Los Angeles

summary: Exercise augments hemodynamic shear to activate mechano-sensitive molecular transducers in the vascular endothelium. Recently, the central nervous system has been reported to mediate neuro-immune interaction in the aortic adventitia (AA). Whether exercise modulates the sympathetic nerve interaction with the immune cells to mitigate aortic stiffness remains unknown. Four weeks of Angiotensin II (Ang II) infusion to C57BL/6 mice increased neural activation to increase the expression of tyrosine hydroxylase (TH) for sympathetic nerve axons and norepinephrine levels along with the colocalization of synapsin and β2-adrenergic receptor (β2-AR) positive macrophages in the AA. This Ang II-mediated sympathetic nerve and macrophage interaction activated fibroblasts to increase vascular fibrosis and arterial pulse wave velocity (PWV). Sympathetic denervation with celiac ganglionectomy or 6-hydroxydopamine treatment abrogated Ang II-mediated TH+, AA thickness, and PWV. scRNAseq analyses of the AA revealed that Ang II increased the circulating monocyte-derived macrophages (Ccr2+CD80) but reduced the resident macrophages (Lyve1+CD163). Gene ontology analysis of differentially expressed genes unveiled that voluntary wheel running (VWR) mitigated Ang II-mediated increase in Ccr2+CD80 macrophages, cytokines-mediated signaling pathways in macrophages, and extracellular matrix deposition in fibroblasts. Macrophage depletion with Ki20227 (colony stimulating factor-1 receptor inhibitor) reduced Ang II-mediated synapsin+ macrophages. Using the Ccr2 knock-in (Ccr2GFP) / knock-out (Ccr2KO) mice, we observed that Ang II-mediated increases in Ccr2+ macrophages were expressed in Ccr2GFP mice but were absent in Ccr2KO mice. Also, Ang II-induced increases in synapsin expression, neighboring Ccr2+ cells, AA thickness, and PWV were reduced in Ccr2KO mice. Both Ki20227 and Ccr2KO reduced the Ang II-mediated increase in TH levels. Furthermore, VWR-mediated reduction in vascular fibrosis and aortic stiffness were mitigated by a β2-AR agonist, terbutaline, indicating β2-AR in neuro-immune modulation. Exercise mitigates Ang II-mediated sympathetic axon interaction with the circulating monocyte-derived macrophages in the AA to attenuate vascular fibrosis and aortic stiffness.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on aortic adventitial from 9 total mice (n = 3 for saline (Vehicle), n = 3 for angiotensin II (AngII), and n = 3 for AngII + voluntary wheel running (VWR))

first: Jae Min

last: Cho

first: Khoa

last: Vu


title: How infection impacts regulation of adipocyte metabolism and does IFNγ directly targets adipocytes and mediates lipid metabolism in vivo following infection

city: Amsterdam

first: Elena

last: Camerini

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

summary: Viral infection often causes us to lose fat, but how and why this happens is unclear. The immune system plays a major role in the regulation of adipose tissue biology during homeostasis and in context of metabolic disease. Here, we investigated whether immune cells also modulate adipocyte metabolism during viral infection. We find that visceral adipose tissue transiently decreases adiposity following viral infection. Upon pathogen encounter, adipose tissue upregulates surface expression of ligands for activating receptors on NK cells, which drives their secretion of IFNγ. This cytokine directly stimulates adipocytes to shift their balance from lipogenesis to lipolysis, which leads to their release of lipids in circulation, most notably of free fatty acids (FFAs). The FFA oleic acid stimulates early activated B cells by promoting oxidative phosphorylation. Oleic acid promoted expression of costimulatory B7 molecules on B cells and promoted their ability to prime CD8+ T cells. Inhibiting lipid uptake by activated B cells impaired CD8+ T cell responses, causing an increase of viral replication in vivo. Our findings uncover a new mechanism of metabolic adaptation to infection and provide better understanding of the interactions between immune cells and adipose tissue in response to inflammation.

overall_design: To analyze how infection impacts regulation of adipocyte metabolism and if IFNγ directly targets adipocytes and mediates lipid metabolism in vivo following infection we performed transcriptome analysis of adipose tissue from infected and non-infected IfngrFlox/Flox and AdipoqCreIfngrFlox/Flox mice. Adipocytes were isolated from VAT of these mice (4 mice for 4 diffrent conditions) and RNA was isolated.


title: Bacterial pneumonia induces senescence in resident alveolar macrophages that are outcompeted by monocytes

city: Hangzhou，Zhejiang

first: Yushi

last: Yao

address: Yuhangtang Rd, Zijingang Rd

institute: Zhejiang University

summary: This study show that embryonic-derived resident alveolar macrophages recovered from acute respiratory Streptococcal pneumoniae infection show features of cell senescence and reduced proliferation capacity. In the weeks after resolution of infection, these senescent resident alveolar macrophages are outcompeted by monocyte-derived alveolar macrophages with hyper-immunoreactivity and heterologous anti-infectious functions.

overall_design: After mice were infected with Streptococcus pneumoniae/PBS, AMs in the lungs were isolated at different time points and subjected to RNA-seq.

first: Jinjing

last: Zhang

first: Tao

last: Wang

first: Yanling

first: Ying

last: Li

first: Lu

first: Jiepu

first: Yuxuan

last: Miao

first: Feng

last: Xu


title: Single cell gene expression profile of WT and Opa1 knockout OT-I T cells

city: Aurora

first: Ross

middle: M

last: Kedl

state: CO

address: 12800 E. 19th Avenue

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: The goal of our study was to compare the gene expression of both naïve and activated T cells deficient in the mitochondrial protein Optic atrophy 1 (Opa1) using single cell RNA sequencing. A growing amount of evidence has begun to illustrate that the requirements driving effector- and memory-destined CD8 T cells during an infection are not shared with adjuvanted vaccine responses. Short-lived effector cells are characterized metabolically by a highly glycolytic state driving energy and biomass production whereas vaccine-elicited T cells can meet these requirements through mitochondrial metabolism. Here we show that the mitochondrial protein Optic atrophy 1 (Opa1) is critical for rapidly dividing CD8 T cells in vivo. This requirement, contrary to prior published data, is most pronounced in effector CD8 T cells. More specifically, Opa1 supports proper cell cycle initiation, progression, and supports the viability and survival of CD8 T cells during immune responses to both infections and vaccine challenges

overall_design: Opa1fl/fl mice were crossed to OT1 TCR transgenic mice (ovalbumin-specific) expressing Cre under the distal Lck (dLck) promoter to produce OT1 x Opa1fl/fl Cre+ (Opa1-/- OT1) mice.  Congenically distinct WT (CD45.1/2) and Opa1-/- (CD45.1/1) OT-I T cells were co-transferred into WT B6 recipients (CD45.2/2) and challenged with ActA-deficient LM (LM.Ova.ActA). On day 5, T cells were isolated and pooled from 4 mice prior to cell sorting of CD45.1+ CD8+ CD19- cells. Naïve OT-I T cells cells from unimmunized WT or Opa1-/-  were isolated using Biolegend CD8 isolation kit. Naïve and day 5 activated cells for each genotype were pooled at a 1:1 ratio prior to sequencing, resulting in two samples, one WT and one Opa1 -/-, which were then captured and processed for single cell squencing.

first: Scott

middle: B

last: Thompson


title: PLT012, a humanized CD36-blocking antibody, is effective for unleashing anti-tumor immunity against liver cancer and liver metastasis

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

institute: IDIBAPS

summary: Tumor cells develop various strategies to evade immune surveillance, one of which is the modulation of the metabolic state of the tumor microenvironment (TME). In response to metabolic stress in the TME, several tumor-infiltrating immune subsets upregulate CD36 to take up lipids. This leads to impaired anti-tumor immunity, as intratumoral regulatory T cells (Tregs) exhibit increased survival and suppressive activity, while CD8+ T cells become more susceptible to ferroptosis and exhaustion. Here, we develop a humanized anti-CD36 IgG4 antibody, PLT012, against the lipid-binding domain of CD36 with excellent safety and favorable pharmacokinetic features in mice and cynomolgus monkey. PLT012 alone or in combination with PD-L1 blockade or standard-of-care immunotherapy results in robust anti-tumor immunity in both immunotherapy-sensitive and -resistant hepatocellular carcinomas (HCCs). Notably, PLT012 also reprograms immune landscape of human HCC ex vivo. Our findings provide proof-of-concept evidence that PLT012 effectively reprograms anti-tumor immunity in HCC, positioning it as a first-in-class immunotherapy targeting CD36.

overall_design: To investigate the immune response to PLT012 treatment, we isolated CD45+ tumor-infiltrating cells from liver tumors and subjected them to single-cell RNA sequencing (scRNA-seq). Liver tissues were finely minced and enzymatically digested in RPMI medium containing 2% FBS, 1% penicillin-streptomycin, DNase I (1 µg/mL), and collagenase (0.5 mg/mL) at 37°C for 40 minutes. The digested suspension was filtered through a 70-μm strainer, treated with RBC Lysing Buffer, and washed with FACS buffer. Tumor-infiltrating leukocytes were enriched using Percoll density gradient centrifugation (800g, 20 minutes, room temperature). CD45+ cells were then isolated for scRNA-seq analysis, comparing transcriptional profiles between PLT012-treated and control groups.

first: Yi-Ru

last: Yu

first: Santiago

last: Carmona

first: Ping-Chih

last: Ho


title: Transcriptional factor Tj is the master regulator of the somatic piRNA pathway in the Drosophila ovarian follicle cells

city: Cambridge

first: Azad

last: Alizada

state: Cambridgeshire

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

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

overall_design: Refer to individual Series


title: Transcriptional factor Tj is the master regulator of the somatic piRNA pathway in the Drosophila ovarian follicle cells [RNA-seq]

summary: Transposable elements (TEs) pose a threat to genome integrity, and the piRNA pathway in animal gonads plays a crucial role in silencing TE activity. While the transcriptional regulation of piRNA pathway components in germline cells is well understood, the mechanisms orchestrating the transcriptional program of the somatic piRNA pathway in surrounding somatic cells remains poorly defined. Here, we demonstrate that Traffic Jam (Tj), an orthologue of a large Maf transcription factor in mammals, is a master regulator of the somatic piRNA pathway playing a crucial role in maintaining TE silencing and genomic integrity in somatic tissues . We show that Tj directly binds to the promoters of piRNA factors such as fs(1)Yb, nxf2, panx, and armi, as well as the flamenco piRNA cluster, a major locus for TE silencing in somatic cells. Knockdown of Tj in somatic follicle cells results in significant downregulation of these piRNA factors, a complete loss of flam expression, and derepression of TEs. We have identified an enhancer downstream of the flam promoter, including TJ binding sites, essential for high and specific flam expression in ovarian follicle cells in adult ovaries. This work uncovers a previously unappreciated layer of transcriptional regulation oc the piRNA pathway and we propose that Tj evolved to orchestrate the somatic piRNA pathway expression, ensuring efficient TE silencing in somatic cells that support germ cells, thereby preventing instability from being transmitted to the offspring.

overall_design: Differential RNA-seq analysis between tj-siRNA knockdowns and renilla-siRNA knockdowns in OSCs

first: Julia

last: Rodriguez-Suarez

first: Benjamin

last: Nicholson

first: Gregory

last: Hannon


title: Mitochondrial NNT promotes diastolic dysfunction in cardiometabolic Heart Failure with Reduced Ejection Fraction (HFpEF)

city: Stanford

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry road

department: Cardiovascular Medicine

institute: Stanford University

summary: Clinical management of heart failure with preserved ejection fraction (HFpEF) is hindered by a lack of disease-modifying therapies capable of altering its distinct pathophysiology. Despite the widespread implementation of a “two-hit” model of cardiometabolic HFpEF to inform precision therapy, which utilizes ad libitum high-fat and 0.5% N(ω)-nitro-L-arginine methyl ester (HFD+L-NAME) diet, we observe that C57BL6/J mice exhibit less cardiac diastolic dysfunction in response to HFD+L-NAME. Genetic strain-specific single-nucleus transcriptomic analysis identified disease-relevant genes that enrich oxidative metabolic pathways within cardiomyocytes. Because C57BL/6J mice are known to harbor a loss-of-function mutation affecting the inner mitochondrial membrane protein nicotinamide nucleotide transhydrogenase (Nnt), we used an isogenic model of Nnt loss-of-function to determine whether intact NNT is necessary for the pathological cardiac manifestations of HFD+L-NAME. Twelve-week-old mice cross-bred to isolate wild-type (Nnt+/+) or loss-of-function (Nnt-/-) Nnt in the C57BL/6N background, were challenged with HFD+L-NAME for 9 weeks (n = 6-10). Nnt+/+ mice exhibited impaired ventricular diastolic relaxation and pathological remodeling, as assessed via E/e’ (42.8 vs. 21.5, P = 1.2e-10), E/A (2.3 vs 1.4, P = 4.1e-2), diastolic stiffness (0.09 vs 0.04 mmHg/μL, P = 5.1e-3), and myocardial fibrosis (P = 2.3e-2). Liquid chromatography and mass spectroscopy exposed a 40.0% reduction in NAD+ (P = 8.4e-3) and a 38.8% reduction in GSH:GSSG (P = 2.6e-2) among Nnt+/+ mice after HFD+L-NAME feeding. Using single-nucleus ligand-receptor analysis, we implicate fibroblast growth factor 1 (Fgf1) as a putative NNT-dependent mediator of cardiomyocyte-to-fibroblast signaling of myocardial fibrosis. Together, these findings underscore the pivotal role of mitochondrial dysfunction in HFpEF pathogenesis and position both NNT and Fgf1 as novel therapeutic targets.

overall_design: Two cohorts of 12-week-old male and female mice possessing wild-type (NNT+/+) or deleted (NNT-/-) NNT were provided an ad libitum high-fat and 0.5% N(ω)-nitro-L-arginine methyl ester (HFD+LNAME) diet for 9 weeks (n = 6-10).

first: Philipp

last: Konrad

first: Sumra

last: Nazir

first: Matthias

last: Dewenter

first: Johannes

last: Backs


title: Targeting WEE1 in tumor-associated dendritic cells potentiates antitumor immunity [scRNA-Seq]

first: Haidong

last: Tang

address: Shuangqing Road

institute: Tsinghua University

summary: DNA damage is a prevalent event within the tumor microenvironment, significantly influencing cancer initiation, progression, metastasis, and immune cell functionality. Here, we observed that oxidative stress induces DNA damage in tumor-associated dendritic cells (TADCs), leading to the activation of the serine/threonine kinase WEE1, which facilitates DNA repair. Notably, this DNA damage also acts as a stimulus for DC activation. Pharmacological inhibition of WEE1 activates TADCs via the cGAS/STING pathway, resulting in an enhanced antitumor immune response and improved tumor control. Furthermore, WEE1 inhibition augments the efficacy of DC vaccines and work synergistically with immune checkpoint blockade therapy. These findings underscore the critical role of WEE1-mediated signaling in DNA damage repair in immune cells in the tumor microenvironment, which in turn dampens the antitumor immune response. Thus, targeting WEE1 in DCs presents a promising strategy to enhance DC-mediated T cell activation and improve the effectiveness of cancer immunotherapy strategies.

overall_design: Wild-type C57BL/6 mice were inoculated with MC38-EGFP tumor cells. After tumor establishment, cDC1 and cDC2 cells were sorted from tumor tissues and subjected to scRNA-seq analysis.


title: Single cell transcription profiles of hematopoietic stem and progenitor cells from Beta thalassemia transfusion dependent patients in steady state condition

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: We investigated the composition of the hematopoietic stem and progenitor pool in beta-thalassemia (BThal) patients by perfoming scRNA-seq on CD34+ hematopoietic stem progenitor cells (HSPCs) and on single phenotypic hematopoietic stem/multiputent cells (HSCs/MPPs). These single-cell approaches reveal molecular and functional heterogeneity within the HSPC compartment in the bone marrow from Bthal patients in steady state condition in comparison with aged matched pediatric patients.

overall_design: To better characterize the early steps of hematopoiesis in Bthal patients, we performed scRNA-seq on BM CD34+ cells and phenotypic HSC/MPP (CD34+ CD38- CD45RA-) cells isolated by Fluorecence-activated cell sorting (FACS) from 6 Bthal and 1 age-matched healthy donor (HD) bone marrow samples.

first: Giuliana

last: Ferrari

first: Maria

last: Lidonnici

first: Giulia

last: Chianella

first: Elisa

last: Laurenti


title: Type 4 resistant potato starch alters the microbiome, colon and cecal gene expression, and resistance to Citrobacter rodentium infection in mice fed a Total Western Diet

city: Beltsville

first: Allen

last: Smith

state: MD

address: 10300 Baltimore Ave, BARC-East, 307C

institute: USDA ARS

summary: Mice were fed a Total Western Diet based on the National Health and Nutrition Examination Survey (NHANES) 50th percentile intake for Americans supplemented with 0, 2, 5 or 10% type 4 resistant potato starch before being infected with Citrobacter rodentium to induce bacterial colitis. Changes in the cecal microbiome were investigated using 16S sequencing and changes in cecum and distal colon gene expression were evaluated using RNASeq analysis.

overall_design: Three week old C57BL/6 mice were fed the Total Western Diet (TWD) for 6 weeks and then subgroups of mice were fed either the TWD or TWD supplemented with 0, 2, 5 or 10% type 4 resistant potato starch for an additional 3 weeks. Mice were then euthanized and cecal contents and various tissues were collected for analyses.

middle: D

first: Harry

last: Dawson

first: Elizabeth

last: Pletsch

first: Jack

last: Ragonese

first: Lumei

last: Cheung

first: Celine

last: Chen


title: Transcriptional factor Tj is the master regulator of the somatic piRNA pathway in the Drosophila ovarian follicle cells [smallRNA-seq]

first: Azad

last: Alizada

overall_design: small RNA sequencing in ovaries

first: Nolween

last: Mouniee

first: Benjamin

last: Bertin

first: Aline

last: Martins

first: Emilie

last: Brasset


title: Single-cell protein-transcriptome atlas of haematopoiesis across the human lifespan

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

summary: Utilising advanced techniques like scRNA-seq and CITE-seq, we profiled over 250,000 cells across various human developmental stages, revealing significant age-related variations and tissue-specific characteristics in haematopoiesis.  This comprehensive atlas provides a valuable reference for understanding blood diseases and the intricate regulation of haematopoiesis.

overall_design: The experiments described herein were conducted in accordance with the protocols and methods outlined in a book chapter authored by Nicole Mende and Nicola K Wilson (Mende, N., Laurenti, E., Göttgens, B., & Wilson, N. K. 2022).

first: Mariana

last: Quiroga Londoño

first: Mende

last: Nicole

first: Emily

last: Stephenson

first: Deena

last: Iskander

first: Tomoya

last: Isobe

first: Simone

last: Webb

first: Issac

last: Goh

first: Vijay

last: Mahalingam Shanmugiah

first: Rebecca

last: Hannah

first: Anindita

last: Roy

first: Irene

last: Roberts

first: Nicola

last: Wilson

first: Muzlifah

last: Haniffa

first: Berthold

last: Göttgens


title: De novo variant in RING finger protein 213 causes systemic vasculopathy.

city: Bunkyo-ku

first: Ayako

last: Kashimada

state: Tokyo

address: Yushima 1-5-45

department: Pediatrics and Developmental Biology

institute: Institute of Science Tokyo

summary: Systemic arterial stenosis, including moyamoya disease (MMD) and middle aortic syndrome (MAS), is a rare condition of unclear etiology. MMD is a cerebral angiopathy, whereas MAS affects abdominal and thoracic aortas, leading to various complications. Although some genetic associations with MAS have been identified, the causes remain elusive. In this study, whole-exome sequencing was used to identify de novo heterozygous missense variants of RING finger protein 213 (RNF213) (p.His4058Pro and p.Thr4155Pro) in two unrelated families exhibiting both MAS and MMD. To understand the significance of these variants, we generated knockin mice carrying the Rnf213 p.His4058Pro variant. Notably, homozygous knockin mice exhibited perinatal lethality due to respiratory failure and lung dysplasia, suggesting that this variant is pathogenic. Lung dysplasia in homozygous knockin mice was associated with upregulated innate immunity and inflammatory responses and downregulated cell proliferation. The findings suggested that in mice, the RNF213 p.His4058Pro variant plays critical roles in lung development, innate immunity, and inflammation, revealing the complexity of RNF213 function in various tissues and species. In conclusion, this study provides insights into the genetic basis of MAS and MMD, highlights the potential involvement of RNF213 variants in systemic vasculopathy, and identifies unexpected associations with lung development and immune processes.

overall_design:
To investigate the effect of the de novo variant in RING finger protein 213, we generated the the Rnf213 knockin (KI) mouse model carrying a heterozygous variant by CRISPR-Cas9 genome editing.
We found that homozygote KI mice had perinatal lethality due to respiratory failure and had disorganized lung structure.whereas heterozygote KI mice grew normally.
We then performed gene expression profiling analysis of RNA-seq data of the lung from E18.5 KI mice.
Comparative gene expression profiling analysis of RNA-seq data between wildtype, heterozygote knock-in, and homozygote knock-in mice.

first: Tomoko

last: Mizuno

first: Eriko

last: Tanaka

first: Susumu

last: Hosokawa

first: Tomohiro

last: Udagawa

first: Yuichi

last: Hiraoka

first: Keisuke

last: Uchida

last: Morio

first: Kenjirou

last: Kosaki

first: Masatoshi

last: Takagi


title: A distinct priming phase regulates CD8 T cell immunity by orchestrating paracrine IL-2 signals

city: Würzburg

first: Milas

last: Ugur

state: Bayern

address: Versbacherstr. 9

department: Institute of Systems Immunology

institute: Universität Würzburg

summary: T cell priming is characterized by an initial activation phase that involves long-term interactions with dendritic cells (DC). How paracrine signals are spatiotemporally transmitted once activated T cells have disengaged from DC and resumed their migration is currently unclear. Here, we identified a separate phase that serves to expand high-affinity CD8 T cells in specific subfollicular niches in lymph nodes. CD8 T cells required stop signals mediated by CXCR3 and a high affinity TCR to re-engage with antigen-laden DC in restricted microdomains. There, CD4 T cells delivered paracrine IL-2 in a stop-and-go migration pattern and thereby played an essential role in scaling primary CD8 T cell responses. Our results revise the current paradigm of T cell priming and have direct implications for vaccinations and cellular immunotherapies.

overall_design: Foxp3-GFP-DTR mice were infected with Vaccinia virus subcutaneously in the foot hock and 28 hours later CD3+CD4+GFP+ regulatory T cells from the popliteal lymph node were sorted and analyzed by scRNAseq

first: Wolfgang

last: Kastenmüller

first: Lennart

last: Rüttger

first: Katarzyna

last: Jobin