title: Thymosin α1 reverses oncolytic adenovirus-induced M2 polarization of macrophages to improve antitumor immunity and therapeutic efficacy

status: Public on Jun 28 2024

city: Nanjing

first: kua

last: liu

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

summary: Although oncolytic adenoviruses have been widely studied for their direct oncolytic activity and immunomodulatory role in cancer immunotherapy, the immunosuppressive feedback loop induced by oncolytic adenoviruses remains poorly studied. Here, we showed that type V adenovirus (ADV) induces the polarization of tumor-associated macrophages (TAMs) to the M2 phenotype and increases the infiltration of regulatory T cells (Tregs) in the tumor microenvironment (TME). By selectively compensating for these deficiencies, Tα1 reprogrammed “M2-like” TAMs toward an antitumoral phenotype, thereby reprogramming the TME into a state more beneficial for antitumor immunity. Moreover, ADVTα1 was constructed by harnessing the merits of all the components for the aforementioned combinatorial therapy. Both in vitro and in vivo data showed that both exogenously supplied and adenovirus-produced Tα1 orchestrate TAM reprogramming and enhance the antitumor efficacy of ADV via CD8+ T cells, showing promising prospects for clinical translation. Our findings provide inspiration for improving oncolytic adenovirus combination therapy and designing new oncolytic engineered adenoviruses.

overall_design: To understand the mechanism of regulation of macrophages by ADV infection and additional Ta1 peptide,we performed RNA sequencing (RNA-seq) on 4T1 cells treated with PBS, ADV or ADV combined with Ta1.We then performed gene expression profling analysis using data obtained fo RNA-seq of 4T1 cells treated with different interventions.

first: Kua

first: Lingkai

last: Kong


title: EPDR1 promotes PD-L1 expression and antitumor immune evasion by inhibiting TRIM21-dependent ubiquitylation if IKBKB.

status: Public on Jun 29 2024

city: Guangzhou

first: Xiaoyu

last: Qian

state: Guangzhou

address: Guangzhou Panyu University City

country: China

institute: South China University of Technology

type: Expression profiling by high throughput sequencing

summary: While immune checkpoint blockade (ICB) has shown promise for clinical cancer therapy, its efficacy has only been observed in a limited subset of patients and the underlying mechanisms regulating innate and acquired resistance to ICB of tumor cells is poorly understood. Here, we identified EPDR1 as an important intrinsic tumor regulator of PD-L1 expression and the antitumor T-cell response that inhibits TRIM21-dependent ubiquitylation of IKBKB. Mechanistically, EPDR1 binds to TRIM21 and disrupts its interaction with IKBKB, which suppresses the ubiquitylation and autophagosome degradation of the IKBKB protein and thus enhances NF-κB-mediated transcriptional activation of PD-L1. We further confirmed through a mouse liver cancer model that EPDR1 mediates the exhaustion of CD8+ T cells and promotes tumor progression. In addition, we observed a positive correlation between EPDR1 and PD-L1 expression in both human and mouse liver cancer samples. Collectively, our study reveals an unappreciated role of EPDR1 in orchestrating tumor immune evasion and cancer progression, suggesting that targeting EPDR1-TRIM21 is a potential strategy for cancer immunotherapy.

overall_design: To investigate the pathway that involved in the EPDR1 mediated regulation of PD-L1,  we performed qRT‒PCR analyses on a series of immune-related molecules in HepG2 cells, HepG2 cells expressing NTC and shEPDR1 was collected and followed sequencing

first: Shengqi

last: Shen


title: Pre-clinical spheroid models identify BMX as a therapeutic target for metastatic MYCN non-amplified neuroblastoma

status: Public on Jun 30 2024

city: Illkirch

first: Anais

middle: Flore

last: Bardet

address: 1 rue Laurent Fries

country: France

institute: IGBMC

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Hypoxic Memory Mediates Prolonged Tumor Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression [RNA-Seq]

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

country: USA

institute: Weill Cornell

summary: Hypoxia is a common feature of many solid tumors due to aberrant proliferation and angiogenesis that is associated with tumor progression and metastasis. Most of the well-known hypoxia effects are mediated through hypoxia-inducible factors (HIFs). Identification of the long-lasting effects of hypoxia beyond the immediate HIF-induced alterations could provide a better understanding of hypoxia-driven metastasis and potential strategies to circumvent it. Here, we uncovered a hypoxia-induced mechanism that exerts a prolonged effect to promote metastasis. In breast cancer patient-derived circulating tumor cell (CTC) lines and common breast cancer cell lines, hypoxia downregulated tumor intrinsic type I interferon (IFN) signaling and its downstream antigen presentation (AP) machinery in luminal breast cancer cells, via both HIF-dependent and HIF-independent mechanisms. Hypoxia induced durable IFN/AP suppression in certain cell types that was sustained after returning to normoxic conditions, presenting a “hypoxic memory” phenotype. Hypoxic memory of IFN/AP downregulation was established by specific hypoxic priming, and cells with hypoxic memory had an enhanced ability for tumorigenesis and metastasis. Overexpression of IRF3 enhanced IFN signaling and reduced tumor growth in normoxic, but not hypoxic, conditions. The histone deacetylase inhibitor (HDACi) entinostat upregulated IFN targets and erased the hypoxic memory. These results point to a mechanism by which hypoxia facilitates tumor progression through a long-lasting memory that provides advantages for CTCs during the metastatic cascade.

overall_design: Gene expression profilling of Brx68 CTC lines in hypoxia and normoxia conditions.

first: Oihana

last: Iriondo

first: Min

last: Yu

first: Amal

last: Thomas


title: Effect of Irg1-Itaconate on Nrf2-transcripting genes in macrophages by using chromatin immunoprecipitation-sequencing (ChIP-seq) assays.

city: Beijing

first: Zhaoli

last: Luo

address: You An Men Wai, Feng Tai District

institute: Capital Medical University

summary: To investigate the role of Irg1-itacaonate on Nrf2-transcripting genes in macrophages, RAW264.7 cells were cultured and were treated 120 μM 4-octyl itaconate (4-OI) or Vehicle for 8 h. We then performed  ChIP-seq analysis from 4-OI or vehicle treated RAW264.7 cells using Nrf2 or IgG antibodies.

first: Qian

last: Li

first: Fei

last: Yang


title: Pre-clinical spheroid models identify BMX as a therapeutic target for metastatic MYCN non-amplified neuroblastoma (RNA-Seq)

summary: The development of targeted therapies has provided new hope for an increasing number of cancer patients affected by previously incurable diseases. The clinical success of this approach, however, is limited by numerous challenges, including a better control of cell plasticity, particularly in refractory and metastatic patients. Here we addressed this question in Neuroblastoma (NB), an aggressive pediatric malignancy, which remains a clinical challenge for high-risk patients. NB originates from neural crest-derived progenitors through defective differentiation programs combined with oncogenic activity due to genetic and epigenetic alterations. In order to identify critical genes responsible for tumor aggressiveness we performed combined chromatin and transcriptome analyses on matched primary xenografts, spheroids and differentiated adherent cultures, which we derived from metastatic non-MYCN amplified (nMNA) NB patients. Our approach identified the kinase BMX among the most differentially regulated genes between patient-derived xenografts and spheroids versus adherent models. We further found that BMX expression is associated with high tumor stage and poor patient survival in multiple NB transcriptomic datasets and critical to maintain the self-renewal and tumorigenic potential of NB spheroids. Moreover, we uncovered a positive correlation between BMX expression and the mesenchymal tumor cell phenotype, which was previously associated with increased chemo-resistance. Finally, we show that BMX inhibitors can readily reverse this cellular state, increase the sensitivity of NB spheroids toward standard of care chemotherapy, and reduce tumor growth in preclinical NB models. Altogether, our study identifies BMX as a novel promising therapeutic target for high-risk patients with relapsed or refractory nMNA NB tumors.

overall_design:
RNA-seq of matched neuroblastoma xenografts, spheroids and cells in adherent culture conditions
-------------------------------------------------
Raw patient data is deposited on zenodo https://doi.org/10.5281/zenodo.7431535 due to privacy restrictions

first: Santhoshkumar

last: Sundaramoorthy

first: Daniele

last: Colombo

first: Annick

last: Mühlethaler-Mottet

first: Anaïs

middle: F

first: Nicolò

last: Riggi


title: Effects of Irg1-itaconate or Hemin on gene expression in macrophages [RNA-seq]

summary: To investigate the role of Irg1-itaconate or Hemin in macrophages, bone marrow-derived macrophages (BMDMs) from WT mice and Irg1 KO mice were extracted and cultured. After 7 days of cells culture, the BMDMs from WT mice were treated 120 μM 4-octyl itaconate (4-OI) for 15 h, 15 μM Hemin for 12 h, and the BMDMs from Irg1 KO mice and WT mice were treated Vehicle for 12 h.   We then performed gene expression profiling analysis using data obtained from RNA-seq of  4-OI, Hemin or vehicle treated WT BMDMs and Irg1 KO BMDMs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4-OI-treated WT BMDMs, Hemin-treated WT BMDMs, vehicle-treated WT BMDMs, and vehicle-treated Irg1 KO BMDMs.


title: Hypoxic Memory Mediates Prolonged Tumor Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression [scRNA-seq]

overall_design: Single cell RNAseq profiling of tumors from 12 or 16-weeks old  FVB-MMTV-PyMT mice. N=2 for each timepoint.

first: Remi

last: Klotz


title: Atomic Vacancies of Molybdenum Disulfide Nanoparticles Stimulate Mitochondrial Biogenesis

status: Public on Jun 27 2024

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy, Medical Research and Education Building II Suite 4344

department: Department of Molecular and Cellular Medicine

institute: Texas A&M University

summary: Atomic vacancies rich MoS2 nanoflowers stimulate mitochondrial function by reducing cellualr ROS  generation and  upregulating the expression of genes required for mitochondrial biogenesis.

overall_design: Evaluating the effect of atomic vacancies  in MoS2 nanoparticles on hMSC fate. Untreated control hMSCs are compared to hMSCs treated with MoS2 nanoparticles containing low (1:1) or high (1:6) vacancies.

first: Kanwar

middle: A

first: Anna

middle: L

last: Kersey

first: John

last: Soukar

first: Vishal

middle: M

last: Gohil

first: Akhilesh

middle: K

last: Gaharwar


title: Gene expression profile at single cell level of HIV-1 and HIV-2 specific CD8 T cells

status: Public on Jun 26 2024

city: Bordeaux

first: Victor

last: Appay

address: 2 Rue Dr Hoffmann Martinot

institute: Immunoconcept

summary: CD8 T cells play a crucial role in controlling HIV infection. We employed single-cell RNA sequencing (scRNAseq) to analyze HIV-1 specific CD8 T cells after years of treated infection.  Additionally, HIV-2 specific CD8 T cells were studied to serve as a control for an effective anti-HIV response.

overall_design: HIV-specific CD8 T cells from all patients at each time point were  index-sorted by FACS into 96-well microtiter plates for scRNAseq analysis.

first: Eoghann

last: White


title: SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression [ChIP-seq]

city: Evanston

first: Carole

last: LaBonne

state: IL

address: 2220 Campus Drive

department: Molecular Biosciences

institute: Northwestern University

summary: Here we investigate a functional role for SoxB1 transcription factors, Sox2 and Sox3, on the transient embryonic cell population, the neural plate border. We find through gain/loss-of-function studies necessary for neural plate border cells to become neural crest cells.  and genomics experiments (ChIP-seq and RNA-seq) that SoxB1 transcription factors directly promote neural plate border formation. and that down-regulation of SoxB1 expression is

overall_design: We identify regions of Sox3 enrichment in blastula stem cells and neural plate border cells (St 11.5) through ChIP-seq studies. Furthermore, we assess changes in gene expression in soxb1 morphant (vs WT) blastula stem cells through RNA-seq.

first: Elizabeth

middle: N

last: Schock

first: Joshua

middle: R

last: York

first: Austin

middle: P

first: Ashlyn

middle: Y

last: Tu


title: SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression [RNA-seq]

last: Li


title: Activity-dependent Transcriptional Programs in Memory Regulate Motor Recovery after Stroke

status: Public on Jun 25 2024

city: Bar Harbor

first: Mary

middle: Teena

last: Joy

state: Maine

address: 600 Main St

institute: Jackson Laboratory

summary: Stroke causes death of brain tissue leading to long-term deficits. Behavioral evidence from neurorehabilitative therapies suggest learning-induced neuroplasticity can lead to beneficial outcomes. However, molecular and cellular mechanisms that link learning and stroke recovery are unknown. We show that in mouse models of stroke, with enhanced recovery of function from genetic perturbations of learning and memory genes, express activity-dependent transcriptional programs that are normally active during formation or storage of new memories. The expression of neuronal activity-dependent genes are predictive of recovery and occupy a molecular latent space unique to motor recovery. With motor recovery, networks of activity-dependent genes are co-expressed with their transcription factor targets forming gene regulatory networks that support activity-dependent transcription, that are normally diminished after stroke. Neuronal activity-dependent changes at the circuit level are influenced by interactions with microglia. At the molecular level, we show that enrichment of activity-dependent programs in neurons lead to transcriptional changes in microglia where they differentially interact to support intercellular signaling pathways for axon guidance, growth and synaptogenesis. Together, these studies identify activity-dependent transcriptional programs as a fundamental mechanism for neural repair post-stroke.

overall_design: Cortical neurons and microglia were FAC-sorted at different time points after stroke, where some cohorts of animals received treatments with either neuronal CREB over expression or neuronal CCR5 knockdown as a means to induce recovery of motor function. Each condition has replicates of 3-5 samples where each sample is produced from one animal per condition.

middle: T

first: S

last: Carmichael


title: Oncogenic KRAS-dependent stromal interleukin-33 directs the pancreatic microenvironment to promote tumor growth [bulk RNA-seq]

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

summary: This experiment was designed to investigate the intrinsic effect of interleukin-33 (IL-33) on pancreatic cancer associated fibroblasts. IL-33 wildtype (WT) or IL-33 knockout (KO) fibroblasts were grown with or without tumor conditioned media to stimulate cancer-associated fibroblast (CAF) polarization and harvested for bulk RNA sequencing.

overall_design: IL-33 WT or IL-33 KO fibroblasts were treated for 24h in 1% FBS DMEM or a 1:1 ratio of 1% FBS DMEM + 1% FBS 9805 tumor cell conditioned media. Doxycycline was provided to all groups as a control for 9805 culture conditions. RNA was harvested and submitted for bulk RNA sequencing.

first: Katelyn

last: Donahue


title: Oncogenic KRAS-dependent stromal interleukin-33 directs the pancreatic microenvironment to promote tumor growth [scRNA-seq]

summary: Here, we sought to understand the function of stromal interleukin-33 (IL-33) in PanIN and PDA. We collected pancreatic tissues from various mouse models of PanIN and PDA for single cell RNA sequencing to assess IL-33 expression across the microenviornment. We also implanted syngeneic orthotopic pancreatic tumors into mice harboring a conditional stromal IL-33 knockout and sequenced the resulting tumors.

overall_design: Pancreata from various mouse models of pancreatic tumorigenesis (spontaneous or orthotopic injection) collected and subjected to single cell RNA sequencing.

first: Yaqing

last: Zhang

first: Emily

last: Lasse-Opsahl


title: SoxB1 transcription factors are essential for intiating and maintaining neural plate border gene expression


title: Transcription of HIV-1 at sites of intact latent provirus integration

city: New York

first: Gabriela

middle: S

last: Silva Santos

address: 1230 York Avenue

institute: The Rockefeller University


title: Transcription of HIV-1 at sites of intact latent provirus integration [scRNA-seq]

summary: The study examined proviral and neighboring gene transcription at sites of intact latent HIV-1 integration in cultured T cells obtained directly from people living with HIV, as well as engineered primary T cells and cell lines and showed that the site of integration has a dominant effect on the transcriptional activity of intact HIV-1 proviruses in the latent reservoir

overall_design: CD4+ T cells harboring intact latent HIV-1 proviruses were enriched using their T cell receptors (Weymar et al., 2022). CD4+ T cells from participants 603 (Rockefeller University IRB-approved Protocols MCA-0866/TSC-0910) and 5104 (Protocols MCA-0965/TSC-0910) were isolated by magnetic separation using CD4+ T Cell Isolation Kit, human (Miltenyi Biotec, cat. 130-091-155) and CD45RA MicroBeads, human (Miltenyi Biotec, cat. 130-045-901) and prepared for cell sorting exactly as described (Weymar et al., 2022). Cells from 603 (CD4+TRBC1+TRBV19+) and 5104 (CD3+CD4+TRBC1+TRBV) were sorted into 96 well “U” bottom plates (5 cells per well) containing 200 µL of activation media (composition described above), plus feeder cells, supplemented with the following ARVs: 1µM Tenofovir, 1µM Emtricitabine, 1nM Nevirapine and 10 µM T-20. Cell sorting was performed on FACSymphony S6 using FACSDiva software (version 9.5.1, BD Biosciences) and data was analyzed using FlowJo (version 10.10.0, BD Biosciences). The culture media was replaced twice a week to replenish ARVs and avoid new infections. Three weeks after sorting, cells were screened for the presence of the HIV clone of interest by Env PCR and sequencing (Salazar-Gonzalez et al., 2008). Cell lines containing clones of interest were expanded in a T25 culture flask in 10 mL of activation medium. The frequency of latent cells in the cultures was determined three weeks after expansion by sorting single cells into 10 µL of RLT buffer (Qiagen, cat 79216) using Agencourt RNAClean XP and magnetic beads (Beckman Coulter, cat. A63987) for DNA preparation and Env PCR.

first: Ana

last: Teixeira

first: Cintia

last: Bittar

first: Thiago

last: Oliveira

first: Amy

last: Huang

first: Noemi

last: Linden

first: Isabella

last: Ferreira

first: Tetyana

last: Murdza

first: Frauke

last: Muecksch

first: R

middle: B

last: Jones

last: Caskey

first: Mila

last: Jankovic

first: Michel

middle: C

last: Nussenzweig


title: Vaginal Lactobacillus fatty acid response mechanisms reveal a metabolite-targeted strategy for bacterial vaginosis treatment

city: Cambridge

first: Douglas

last: Kwon

state: MA

address: 600 Main ST

institute: Ragon Institute

summary: Bacterial vaginosis (BV), a common syndrome characterized by Lactobacillus-deficient vaginal microbiota, is associated with adverse health outcomes. BV often recurs after standard antibiotic therapy in part because antibiotics promote microbiota dominance by Lactobacillus iners instead of Lactobacillus crispatus, which has more beneficial health associations. Strategies to promote L. crispatus and inhibit L. iners are thus needed. We show that oleic acid (OA) and similar long-chain fatty acids simultaneously inhibit L. iners and enhance L. crispatus growth. These phenotypes require OA-inducible genes conserved in L. crispatus and related lactobacilli, including an oleate hydratase (ohyA) and putative fatty acid efflux pump (farE). FarE mediates OA resistance, while OhyA is robustly active in the vaginal microbiota and enhances bacterial fitness by biochemically sequestering OA in a derivative form only ohyA-harboring organisms can exploit. OA promotes L. crispatus dominance more effectively than antibiotics in an in vitro BV model, suggesting a metabolite-based treatment approach.

sample_organism:
Lactobacillus gasseri
Lactobacillus crispatus
Lactobacillus jensenii

overall_design: We hypothesized that non-iners female genital tract (FGT) Lactobacillus species’ similar uLCFA growth responses reflected a shared response mechanism. We therefore assessed L. crispatus, L. gasseri, and L. jensenii transcriptional responses to oleic acid (OA), linoleic acid (LOA), and palmitoleic acid (POA).

first: Meilin

last: Zhu

first: Paul

last: Blainey

first: Seth

last: Bloom


title: Nitrogen signaling factor changes gene expression and binding of transcription factors [ChIP-seq]

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: High quality nitrogen sources such as NH4+ and glutamate inhibit the uptake of poor nitrogen sources including amino acids (leucine etc.), which is called “nitrogen catabolite repression (NCR)”. We found a cell-to-cell communication system in fission yeast that inactivates NCR and enables cells to take up leucine even on high NH4+ medium (referred to as adaptive growth). Furthermore, we identified novel oxylipins responsible for the adaptive growth, which are secreted from cells and are referred to as nitrogen signaling factors (NSF). RNA-seq analyses showed that mitochondrial respiratory-related genes are differentially expressed upon addition of synthetic NSF. These results suggest that the cell-to-cell communication via NSF reprograms the metabolic preference from glycolysis to mitochondrial respiration. Moreover, we also performed ChIP-seq of transcription factors  (TFs) and found that bindings of several TFs on DNA are regulated by NSF.

overall_design: To investigate global changes in transcription factor occupancy in response to 2h NSF exposure, we performed ChIP-seq of FLAG-tagged transcription factors Adn2, Atf1, Fil1, Hsr1, Php3, and Reb1  in triplicates (108 samples).

first: Shin

last: Ohsawa

first: Marc

last: Bühler


title: Transcription of HIV-1 at sites of intact latent provirus integration [ATAC-seq]

first: Gabriela

last: Silva Santos

overall_design: Cells were stimulated with 0.1 µg/mL of anti-CD3 and anti-CD28 monoclonal antibodies in above culture medium for 1 week (activated conditions) then cultured with 10 ng/mL of human IL-7 for an additional week (resting conditions).

first: Ana

last: Teixeira

first: Cintia

last: Bittar

last: Oliveira

first: Marina


title: Nitrogen signaling factor changes gene expression and binding of transcription factors


title: Hypoxic Memory Mediates Prolonged Tumor Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression

first: Christopher

last: Chin

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Pro-efferocytic nanotherapies reduce vascular inflammation without inducing anemia in a large animal model of atherosclerosis

status: Public on Jun 24 2024

city: SHANGHAI

first: Fudi

last: Wang

state: SHANGHAI

address: 320, YUEYANG ROAD

institute: Stanford University

summary: Atherosclerosis is an inflammatory disorder responsible for cardiovascular disease. Reactivation of efferocytosis, the phagocytic removal of cells by macrophages, has emerged as a translational target for atherosclerosis. Systemic blockade of the key ‘don’t-eat-me’ molecule, CD47, triggers the engulfment of apoptotic vascular tissue and potently reduces plaque burden.  However, it also induces red blood cell clearance, leading to anemia. To overcome this, we previously developed a macrophage-specific nanotherapy loaded with a chemical inhibitor that promotes efferocytosis. Because it was found to be safe and effective in murine studies, we aimed to advance our nanoparticle into a porcine model of atherosclerosis. Here, we demonstrate that production can be scaled without impairing nanoparticle function. At an early stage of disease, we find our nanotherapy reduces apoptotic cell accumulation and inflammation in the atherosclerotic lesion. Notably, this therapy does not induce anemia, highlighting the translational potential of targeted macrophage checkpoint inhibitors.

overall_design: To evaluate the efficacy and safety of a macrophage-specific nanotherapy loaded with a chemical inhibitor of SHP-1 in a porcine model of atherosclerosis, focusing on its ability to reduce apoptotic cell accumulation and inflammation without inducing anemia.

first: Sharika

last: Bamezai

first: Yapei

last: Zhang

first: Manisha

last: Kumari

first: Nicholas

middle: J

last: Leeper


title: Nitrogen signaling factor changes gene expression and binding of transcription factors [RNA-seq]

overall_design: To investigate global changes in gene expression in response to NSF exposure, we performed total RNA sequencing with cells that were grown in the presence of high ammonium concentrations and exposed to synthetic NSF for two, four, or six hours. Two - three replicates  per time-point were sequenced. Furthermore, to explore transcription factor occupancy with NSF treatment, ChIP-seq of FLAG-tagged transcription factors Adn2, Atf1, Fil1, Hsr1, Php3, and Reb1 was performed in triplicates on strains for input and FLAG-IP (108 samples).


title: Genome-wide interference of chromatin architecture and Mediator in transcriptional bursting and gene network regulation

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: Gene expression is a stochastic process that occurs in bursts of RNA synthesis. We applied a mathematical model to scRNA-Seq data to infer bursting dynamics transcriptome-wide under multiple perturbations in a wide range of cell types and identified possible molecular mechanisms. We find that mediator complex subunit MED26 primarily regulates frequency, MYC regulates burst size, while cohesin and super-enhancers can modulate both. Despite comparable effect sizes on RNA levels amongst these perturbations, we find that acute depletion of MED26 plays a larger role in perturbing gene regulatory networks. Furthermore, this perturbation acts downstream of both chromatin spatial architecture and preinitiation complex formation, indicating that later steps in the initiation of transcriptional bursts are primary nodes for integrating gene networks in single cells.

overall_design: scRNAseq, ChIPseq. mRNAseq, PROseq

first: Pawel

last: Trzaskoma

first: Aleksandra

last: Pekowska

first: Chrisopher

middle: H

last: Bohrer

first: Xiang

first: Faiza

last: Naz

first: Stefania

last: Dell'Orso

first: Wendy

last: Dubois

last: Olivera

first: Supriya

middle: V

last: Vartak

first: Yongbing

last: Zhao

first: Subhashree

last: Nayak

first: Andrew

last: overmiller

first: Maria

middle: I

last: Morasso

first: Vittorio

last: Sartorelli

first: Daniel

last: Larson

first: Carson

last: Chow

first: Rafael

last: Casellas

first: John

last: O'Shea


title: scRepli-seq analysis of aphidicolin treated embryos

city: Kobe

first: Hirohisa

last: Kyogoku

state: Hyogo

address: 1-1, Rokkodai-chou

department: Agricultural Science

country: Japan

institute: Kobe university

summary: To analyze chromosome abnormalities of 8-cell embryos with/without aphidicolin treatment, we performed single cell replication sequencing (scRepli-seq). This submission is similar to our submission GSE226309.

overall_design: Treatments for embryos, (1)  in vivo from the oviduct: [In vivo development zygotes were collected from the oviducts of pregnant mice that had been induced to superovulate and mated with male mice.] (2) Treatment: 4-cell embryos were treated with DMSO (without aphidicolin) or aphidicolin (75 ng/ml) during 4-cell stage. Each single-cell of 8-cell embryos was collected by mouth pipette under the microscopy. Metadata for each single-cell sample can be found in the supplementary file "BDF1_Aphidicolin_metadata.txt.gz"

first: Saori

last: Takahashi

first: Takuya

last: Hayakawa

first: Hisashi

last: Miura

first: Asami

last: Oji

first: Shin-ichiro

last: Takebayashi

first: Tomoya

last: Kitajima

first: Ichiro

last: Hiratani


title: scRepli-seq analysis of SCNT 4-cell and 8-cell embryos

summary: To analyze replication timing of SCNT 4-cell and 8-cell embryos, we performed single cell replication sequencing (scRepli-seq). This submission is similar to our submission GSE226309.

overall_design: We performed scRepli-seq experiments of SCNT 4-cell and 8-cell embryos. Metadata for each single-cell sample can be found in the supplementary file "SCNT_4C8C_metadata.txt.gz"


title: Macrophages preserve endothelial cell specialization in the adrenal gland to modulate aldosterone secretion and blood pressure (bulk RNA-Seq)

city: Zurich

first: Zheng

last: Fan

address: Winterthurerstrasse 190

department: Anatomy Institute

institute: University of Zurich

summary: The adrenal cortex is characterized by a distinct architecture as well as a high density of specialized sinusoidal blood vessels. The preservation of this particular endothelial cell phenotype is likely vital for proper adrenal gland function. The aldosterone-producing zona glomerulosa harbors macrophages in close association with sinusoidal capillaries. However, the function of this macrophage-endothelial cell-juxtaposition in steady-state conditions is unknown. We show that macrophages preserve capillary specialization in the adrenal gland and modulate aldosterone secretion. By combining macrophage-specific deletion of the angiogenic cytokine Vascular Endothelial Growth Factor A (VEGF-A), single-cell transcriptomics and functional phenotyping, we provide evidence that loss of VEGF-A in myeloid cells, including adrenal gland macrophages depletes a specialized subset of PLVAP+ fenestrated endothelial cells in the zona glomerulosa of mice, along with increased deposition of basement membrane collagen IV and induction of sub-endothelial fibrosis.

overall_design: To characterize the impact of macrophage VEGF-A on the whole adrenal gland, we conducted bulk RNAseq of adrenal gland from WT and VEGF/LysM mice.

first: Mara

last: Karakone

first: Christian

last: Stockmann


title: Spatial Transcriptome Assays Reveals Gliomas Heterogeneity

status: Public on Jun 23 2024

city: Chengdu

first: Yi

last: Wang

state: Please Select

address: 32 West Frist Ring Rd.,

institute: Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital

summary: Background: Glioma is a kind of highly heterogeneous central nervous system malignancy and controlled by various molecular processes such as neoplastic transformation, dysregulation of the cell cycle, and angiogenesis. Among these biomolecular events, the existence of inflammation and stress pathways in the development and driving factors of glioma heterogeneity has been reported. However, mechanisms of glioma heterogeneous under stress response remain unclear, especially from a spatial aspect. Methods: This study combined single-cell and spatially resolved transcriptomics and revealed that oxidative stress response genes play a vital role in oligodendrocyte precursor cells from two different types of gliomas: high- and low-grade (HG and LG). Results: In HG, stress triggers metabolic pattern changes from oxidative phosphorylation to glycolysis to avoid apoptosis, along with epithelial-to-mesenchymal transition and increased expression of genes of stress response. Scenic analysis indicated that oxidative stress induced the activation of AP1 in HG, thus enhancing the tumor survival and proliferation process. Conclusion: When all of these factors are considered together, we provide a unique perspective on how oxidative stress response occurs in different grades of gliomas, which would deepen our understanding of evolution and heterogeneity in gliomas.

overall_design: Our primary glioma samples were obtained from untreated patients and analyzed using single-cell spatial transcriptomics profiling

first: Zongze

last: He

first: Siyuan

last: Song


title: Macrophages preserve endothelial cell specialization in the adrenal gland to modulate aldosterone secretion and blood pressure

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

overall_design: Refer to individual Series


title: Open-ST: High-resolution spatial transcriptomics in 3D [xenium]

city: Berlin

first: Daniel

last: León-Perinán

address: Hannoversche Str. 28,

country: Germany

institute: Max Delbrück Center

summary: Spatial transcriptomics (ST) methods unlock molecular mechanisms underlying tissue development, homeostasis, or disease. However, there is a need for easy-to-use, high-resolution, cost-efficient, and 3D-scalable methods. Here, we report Open-ST, a sequencing-based, open-source experimental and computational resource to address these challenges and to study the molecular organization of tissues in 2D and 3D. In mouse brain, Open-ST captured transcripts at subcellular resolution and reconstructed cell types. In primary head-and-neck tumors and patient-matched healthy/metastatic lymph nodes, Open-ST captured the diversity of immune, stromal, and tumor populations in space, validated by imaging-based ST. Distinct cell states were organized around cell-cell communication hotspots in the tumor but not the metastasis. Strikingly, the 3D reconstruction and multimodal analysis of the metastatic lymph node revealed spatially contiguous structures not visible in 2D and potential biomarkers precisely at the 3D tumor/lymph node boundary. All protocols and software are available at https://rajewsky-lab.github.io/openst.

overall_design: The following fresh-frozen tissues were analyzed using the 10x Genomics Xenium platform: primary human grade-2 HPV-negative laryngeal head and neck squamous cell carcinoma (HNSCC), and one metastatic cervical level three lymph nodes from the same HNSCC patient.

first: Marie

last: Schott

last: León-Periñán

first: Elena

last: Splendiani

first: Giuseppe

last: Macino

first: Nikos

last: Karaiskos

first: Nikolaus

last: Rajewsky


title: The C-terminal 4CXXC-type zinc finger domain of CDCA7 recognizes hemimethylated DNA and modulates activities of chromatin remodeling enzyme HELLS

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

type: Methylation profiling by high throughput sequencing

summary: The chromatin-remodeling enzyme helicase lymphoid-specific (HELLS) interacts with cell division cycle-associated 7 (CDCA7) on nucleosomes and is involved in the regulation of DNA methylation in higher organisms. Mutations in these genes cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, which also results in DNA hypomethylation of satellite repeat regions. We investigated the functional domains of human CDCA7 in HELLS using several mutant CDCA7 proteins. The central region is critical for binding to HELLS, activation of ATPase, and nucleosome sliding activities of HELLS-CDCA7. The N-terminal region tends to inhibit ATPase activity. The C-terminal 4CXXC-type zinc finger domain contributes to CpG and hemimethylated CpG DNA preference for DNA-dependent HELLS-CDCA7 ATPase activity. Furthermore, CDCA7 showed a binding preference to DNA containing hemimethylated CpG, and replication-dependent pericentromeric heterochromatin foci formation of CDCA7 with HELLS was observed in mouse embryonic stem cells; however, all these phenotypes were lost in the case of an ICF syndrome mutant of CDCA7 mutated in the zinc finger domain. Thus, CDCA7 most likely plays a role in the recruitment of HELLS, activates its chromatin remodeling function, and efficiently induces DNA methylation, especially at hemimethylated replication sites.

overall_design: MethylC-seq analyisis in Cdca7 knockout mESCs

first: Yoichi

last: Shinkai


title: Open-ST: High-resolution spatial transcriptomics in 3D

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: The following fresh-frozen tissues were analyzed using our spatial transcriptomics method "Open-ST": E13 mouse head (sagittal section, C57BL/6N), p60 mouse brain hemisphere (coronal section, C57BL/6N), primary human grade-2 HPV-negative laryngeal head and neck squamous cell carcinoma (HNSCC), and two cervical level three lymph nodes from the same HNSCC patient (one healthy, one metastatic). From the HNSCC sample 19 serial sections were sequenced.

first: Schott

last: Marie

first: León-Periñán

last: Daniel

first: Splendiani

last: Elena

first: Macino

last: Giuseppe

first: Karaiskos

last: Nikos

first: Rajewsky

last: Nikolaus


title: Embryonic genome instability upon DNA replication timing program emergence

first: Hirohisa

last: Kyogoku


title: Synthetic essentiality of thymine DNA glycosylase in p53-deficient cancer [WGBS]

status: Public on Jun 21 2024

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Thymine DNA Glycosylase (TDG) is a versatile protein involved in DNA mismatch repair, DNA demethylation, and transcriptional regulation. Here, we identify TDG as a synthetic essential effector in p53-deficient tumours. We found that deletion of TDG inhibits cell proliferation specifically in p53-deficient cancer cells. Using a genetically engineered mouse model of lung adenocarcinoma (LUAD), we demonstrate that depletion of TDG suppresses tumour growth in the p53-deficient context. Notably, A novel and selective inhibitor developed to disrupt the DNA binding activity of TDG exhibits therapeutic efficacy against p53-deficient tumours in both cellular and xenograft models. Mechanistically, TDG coordinates with p53 to orchestrate the transcription of RNA helicase DHX9, which functions to eliminate dsRNA. Depletion of TDG in p53-deficient cells results in the downregulation of DHX9 and aberrant cytoplasmic double-strand (dsRNA) accumulation derived from Alu elements, subsequently activating the RIG-I/MDA5-MAVS mediated antiviral response. Moreover, single-cell RNA-sequencing analysis revealed the depletion of TDG in p53-deficient tumours facilitates the recruitment of tumour-infiltrating lymphocytes. We observed that TDG inhibition combined with immune checkpoint blockade (ICB) achieved a strong synergistic anti-tumour effect in p53-deficient tumours. This study highlights the function of TDG in maintaining p53-deficient tumour growth and provides an alternative therapeutic target for p53-deficient cancers.

overall_design: DNA methylation analysis of WGBS data for listed cells and tissues.

first: Jiaxin

last: Zhou


title: Atypical cellular responses mediated by intracellular constitutive active TrkB (NTRK2) kinase domains and a solely intracellular NTRK2-fusion oncogene

status: Public on Jun 20 2024

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

institute: University Hospital Würzburg

summary: We report the application of RNA-seq for molecular profiling of cultured, U87MG cells that stably express TrkB. Our data set is based on about 40 million unique reads per sample, in four independent mRNA preparations, for nine different testing conditions. U87MG is a standard human glioblastoma patient derived cell line. It serves as a cellular model for studying molecular characteristics of glioblastoma. We describe in our study the intracellular self-activation of TrkB via Y705 and its role in reducing actin dynamics and cell migraton. With this transcriptome dataset, we wished to highlight key players that are activated after TrkB self-activation. The dataset suggest a transcriptional level reprogramming and switching on of several genes that play a role in modulating immune responses and defense mechanisms, in the modified U87MG cells.

overall_design: We generated stable U87MG lines expressing TrkB, an inactive TrkB kinase mutant and a TrkB (NTRK2) gene fusion with SQSTM1 with the help of lentiviral vectors. We switched on the expression of these receptors by treating the cells with Doxycycline for 48 hours, followed by total RNA extraction. RNA seq was done to look at the upregulation and/or downregulation of genes, if any, after TrkB expression.

first: Rohini

last: Gupta

first: Thorsten

last: Bischler


title: Chronic pharmacologic manipulation of dopamine transmission ameliorates metabolic disturbance in trappc9-linked brain developmental syndrome

status: Public on Jun 17 2024

city: Shanghai

first: Yan

last: Li

state: Shanghai

address: 800 Dong Chuan Road

institute: Shanghai Jiao Tong University

summary: Loss-of-function mutations of the gene encoding the trafficking protein particle complex subunit 9 (trappc9) cause autosomal recessive intellectual disability and obesity by unknown mechanisms. Genome-wide analysis links trappc9 to non-alcoholic fatty liver disease (NAFLD). Trappc9-deficient mice have been shown to appear overweight shortly after weaning. Here, we analyzed serum biochemistry and histology of adipose and liver tissues to determine the incidence of obesity and NAFLD in trappc9-deficient mice and combined transcriptomic and proteomic analyses, pharmacological studies, and biochemical and histological examinations of postmortem mouse brains to unveil mechanisms involved. We found that trappc9-deficient mice presented with systemic glucose homeostatic disturbance, obesity and NAFLD, which were relieved upon chronic treatment combining dopamine receptor D2 (DRD2) agonist quinpirole and DRD1 antagonist SCH23390. Blood glucose homeostasis in trappc9-deficient mice was restored upon administrating quinpirole alone. RNA-sequencing analysis of DRD2- containing neurons and proteomic study of brain synaptosomes revealed signs of impaired neurotransmitter secretion in trappc9-deficient mice. Biochemical and histological studies of mouse brains showed that trappc9-deficient mice synthesized dopamine normally, but their dopamine-secreting neurons had a lower abundance of structures for releasing dopamine in the striatum. Our study suggests that trappc9 loss- of-function causes obesity and NAFLD by constraining dopamine synapse formation.

overall_design: DRD2-containing neurons were immunomagnetically isolated from both WT and trappc9 KO mice at age 3-4 weeks. In brief, brain tissue was minced into small pieces and treated with 30 U/mL papain at 37 °C for 20 minutes in neurobasal medium supplemented with 1% penicillin-streptomycin, 1% L-glutamine, 2% B27, and 2500 U DNase I. The digestion was terminated by adding 1 mL fetal bovine serum (FBS). The digested tissues were gently dissociated by pipetting through a blue tip and subsequently passed through 70-μm and 40-μm cell strainers (ThermoFisher). Cells in the flowthroughs were collected by a centrifugation at 200 x g for 10 minutes and washed once with neurobasal medium with 10% FBS and all supplements as above. Cells were resuspended in PBS (pH 7.2) containing 0.5% bovine serum albumin, 0.5 mM EDTA, 5 μg/mL insulin, and 1 g/L glucose and incubated with DRD2-specific antibodies precoupled on magnetic beads at 4 °C for 15 minutes. Cells on beads were washed once in above PBS buffers, separated on a magnetic grate, and resuspended in 1 mL TRIzol reagents for RNAseq analysis.

first: Muhammad

last: Usman

first: Ellen

last: Sapp

first: Yuting

last: Ke

first: Zejian

last: Wang

first: Adel

last: Boudi

first: Marian

last: DiFiglia

first: Xueyi


title: Comparative transcriptome reprogramming in oak galls containing sexual or asexual generations of parasitoid wasps

status: Public on Jun 18 2024

city: Sutton Bonington

first: Rupert

last: Fray

address: Sutton Bonington Campus

country: United Kingdom

institute: University of Nottingham

summary: Oak galls form when gall wasps lay their eggs into part of the tree; in some galls, this attachment point to the host consists of only a few cells. The gall itself comprises entirely of host tissue; however, the initiation, development, and physical appearance are controlled by the inducer. This raises the intriguing question of the molecular mechanisms underlying gall formation, by which one or a small number of cells are reprogrammed and commit to a novel developmental path. Gall wasps undergo two generations each year, and the galls formed by these two generations exhibit markedly different appearances. We sequenced the transcriptomes of both the sexual and asexual generations of Neuropterus quercusbaccarum and Neuroterus numismalis. The transcriptomes of the generations that occur at the same time of year are more similar to each other than they are to the opposite generation of their respective species.

overall_design: To understand the transcriptional differences between galls that appear in similar ecological niches and galls created by different generations of the same species were sequenced. The sexual generation galls are blister and currant and the asexual generation galls are button and spabgle from the two oak gall wasps Neuropterus quercusbaccarum and Neuroterus numismalis respectievly. The asexual generations and the sexual generations are found on Q. robur leaves together.

first: Eleanor

last: Bellows

first: Matthew

last: Heatley

first: Niraj

last: Shah

first: Nathan

last: Archer

first: Tom

last: Giles


title: Loss of LPAR6 and CAB39L Dysregulate Basal to Luminal Urothelial Differentiation Program Contributing to Bladder Carcinogenesis

status: Public on Jun 19 2024

city: Houston

first: Bogdan

middle: A

last: Czerniak

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

summary: In vitro and in vivo studies including single cell sequencing showed that LPAR6 and CAB39L play a major role in regulating basal to luminal urothelial differentiation. Their loss of function contributed to bladder carcinogenesis by dysregulating urothelial differentiation program and sensitizing the urothelium to N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) induced cancers, which recapitulated luminal and basal subtypes of human bladder cancer.

overall_design: Single cell sequencing of the bladder urothelium was performed on cells harvested from wild type, Lpar6 knockout and Cab39l knockout mice. For each group a pooled sample of single urothelial cell suspension harvested from 15 mice was prepared.

first: Sangkyou

last: Lee

first: Jolanta

last: Bondaruk

first: Yishan

first: Huiqin

last: Chen

first: June

middle: G

first: Tadeusz

last: Majewski

first: Rachel

middle: D

last: Mullen

first: David

last: Cogdell

first: Jiansong

first: Ziqiao

first: Hui

last: Yao

first: Pawel

last: Kus

first: Joon

last: Jeong

first: Ilkyun

first: Woonyoung

last: Choi

first: Neema

last: Navai

first: Charles

last: Guo

first: Colin

last: Dinney

first: Keith

last: Baggerly

first: Cathy

last: Mendelsohn

last: McConkey

first: Richard

last: Behringer

first: Marek

last: Kimmel

first: Peng

last: Wei


title: An in vitro model of acute horizontal basal cell activation reveals dynamic gene regulatory networks underlying the acute activation phase

city: Boston

first: Camila

last: Barrios-Camacho

address: 136 Harrison Avenue

institute: Tufts University

summary: Unlike most of the adult nervous system, the olfactory epithelium (OE) can regenerate neurons lost during normal homeostasis or after injury. This life-long regeneration is propagated by two populations of stem cells, the actively proliferating globose basal cells (GBCs) and the dormant horizontal basal cells (HBCs). HBCs only activate and contribute to epithelial regeneration in the context of severe injury, and this activation is mediated by the loss of the transcription factor Tp63. While the HBC differentiation trajectories that occur after activation have been described with lineage tracing and single-cell RNA seq experiments, the immediate consequences of injury on HBC gene expression and fate commitment have not been explored. We present an in vitro model of the acute activation process for HBCs in response to treatment with phorbol 12-myristate 13-acetate (PMA) to explore the molecular underpinnings of these early activation events. We find that treating HBCs with PMA induces the rapid degradation of TP63, and we find that this effect is partially reversed when cells are allowed to recover in maintenance media. Using bulk RNA sequencing we found that PMA-treated HBCs pass through various stages of acute activation identifiable by specific gene regulatory signatures. These transcriptomic phases are associated with varying degrees of plasticity with regards to activated HBCs ability to engraft in transplant models.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of three HBC populations at three stages of activation (0H, 6H, and 12H). Cells were activated with 50nM phorbol 12-myristate 13-acetate (PMA).

middle: M

first: Matthew

last: Zunitch

first: Jonathan

last: Louie

first: Woochan

last: Jang

first: James

middle: E

last: Schwob


title: Innate immune responses are increased in children with acute asthma exacerbation

city: Columbus

first: Rodney

last: Britt

state: Oh

address: 575 Childrens Crossroad

department: Center for Perinatal Research

institute: Nationwide Children's Hospital

summary: Our study aimed to better understand the immune responses during an acute asthma exacerbation in children. Gene expression profiles were examined by RNA-sequencing in blood samples. Samples were collected  on average 2.5 day after systemic corticosteroid treatment. Our findings show that pro-inflammatory genes and pathways related to innate responses and signaling remained increased in children hospitalized for acute asthma exacerbation. Genes and pathways involved in adaptive immune respones, particularly T lymphocyte activation, were decreased in children hospitalized for acute asthma exacerbation. These studies suggest that innate immune responses may remain activated following hospitalization for asthma exacerbation.

overall_design: Following informed consent, blood samples were collected from patients admitted to hospital for acute asthma exacerbation and healthy controls

last: Britt Jr

first: Shahid

last: Sheikh


first: Hirohisa

last: Kyogoku

summary: Faithful DNA replication is essential for genome integrity. Under-replicated DNA leads to chromosome segregation defects, which are reportedly common during embryogenesis. However, DNA replication regulation remains poorly understood in early mammalian embryos. Here, we constructed a single-cell genome-wide DNA replication atlas of pre-implantation mouse embryos and discovered an abrupt replication program switch accompanied by a transient period of genomic instability. In 1- and 2-cell embryos, we observed the complete absence of a replication timing (RT) program, and the entire genome replicated gradually and uniformly using extremely slow-moving forks. In 4-cell embryos, a somatic-cell-like RT program commenced abruptly. However, the fork speed was still slow, S-phase was extended, and SLX4 DNA repair foci increased during G2/M, which was followed by a transient increase in chromosome segregation errors. Importantly, live imaging captured longer S-phase of error cells, and the breakpoints identified by single-cell genome sequencing were enriched in late-replicating regions. By the 8-cell stage, forks gained speed, S-phase was no longer extended, and chromosome aberrations disappeared. Thus, a transient period of genomic instability exists during normal mouse development, which is preceded by a fragile S-phase lacking the coordination between replisome-level regulation and megabase-scale RT regulation, implicating the importance of their coordination for genome integrity.

overall_design: scRepli-seq experiments were performed using the embryos of the following mouse strains, conditions and the developmental stages (single cells were collected by the micromanipulation): (1) In-vitro developed embryos from the BDF1 strain including the developmental stages of 4-cell, 8-cell, 16-cell, ICM (inner cell mass), and TE (trophectoderm). Titles are: "BDF1_in-vitro_(developmental stage)_(project ID)" (2) In-vitro developed embryos by IVF (in-vitro fertilization) or ISCI (intracytoplasmic sperm injection) using the B6MSM strain (an F1-hybrid between B6 female and MSM male) by including the developmental stages of 1-cell, 2-cell, and 4-cell. Titles are: "B6MSM_(developmental stage)_(project ID)" (3) SCNT (somatic cell nuclear transfer, cumulus cells as donors) embryos using the BDF1 strain including the developmental stages of 1-cell, 2-cell. Titles are: "SCNT_(developmental stage)_(project ID)" (4) EdU labeled & stained embryos from the B6 strain including the developmental stages of 4-cell and 8-cell. Titles are: "B6_EdU_(developmental stage)_(project ID)" (5) In-vitro developed embryos from BDF1 strain collected mainly in the G1 phase, including the developmental stages of 4-cell and 8-cell. Titles are: "BDF1_in-vitro_G1_(developmental stage)_(project ID)" (6) In-vivo developed embryos from the oviduct of the mouse (BDF1 strain) including the developmental stages of 4-cell, 8-cell, and 16-cell. Titles are: "BDF1_in-vivo_(developmental stage)_(project ID)"  Project IDs are "DEP_01_XX", "P445_XX", or "LCS_01_XX"  Metadata for each single-cell sample can be found in the supplementary file "scRT_metadata.txt.gz"

first: Saori

last: Takahashi

first: Takuya

last: Hayakawa

first: Hisashi

last: Miura

first: Asami

last: Oji

first: Shin-ichiro

last: Takebayashi

first: Tomoya

last: Kitajima

first: Ichiro

last: Hiratani


title: ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma [RNA-seq siROR2 ]

city: Detroit

first: Simone

last: Benitz

address: 2799 W Grand Blvd

institute: Henry Ford Health System

summary: Cellular plasticity is a hallmark of pancreatic ductal adenocarcinoma (PDAC) starting from the conversion of normal cells to precancerous lesions to the progression of carcinoma subtypes associated with aggressiveness and therapeutic response. We found that normal acinar cell differentiation, maintained by the transcription factor Pdx1, suppresses a broad gastric cell identity that is maintained in metaplasia, neoplasia, and the classical subtype of PDAC in mouse and human. We have identified the receptor tyrosine kinase Ror2 as marker of a gastric metaplasia (SPEM)-like identity in the pancreas. Ablation of Ror2 in a mouse model of pancreatic tumorigenesis promoted a switch to a gastric pit cell identity that largely persisted through progression to carcinoma. In both human and mouse pancreatic cancer, ROR2 activity continued to antagonize the gastric pit cell identity, strongly promoting an epithelial to mesenchymal transition, conferring resistance to KRAS inhibition, and vulnerability to AKT inhibition.

overall_design: This dataset includes control and ROR2 siRNA-treated human pancreatic cancer cell lines PANC1 and UM5 (n=3).

first: Malak

last: Nasser

first: Howard

last: Crawford


title: Macrophages preserve endothelial cell specialization in the adrenal gland to modulate aldosterone secretion and blood pressure (scRNA-Seq)

first: Zheng

last: Fan

summary: The adrenal cortex is characterized by a distinct architecture as well as a high density of specialized sinusoidal blood vessels. The preservation of this particular endothelial cell phenotype is likely vital for proper adrenal gland function. The aldosterone-producing zona glomerulosa harbors macrophages in close association with sinusoidal capillaries. However, the function of this macrophage-endothelial cell-juxtaposition in steady-state conditions is unknown. We show that macrophages preserve capillary specialization in the adrenal gland and modulate aldosterone secretion. By combining macrophage-specific deletion of the angiogenic cytokine Vascular Endothelial Growth Factor A (VEGF-A), single-cell transcriptomics and functional phenotyping, we provide evidence that loss of VEGF-A in myeloid cells, including adrenal gland macrophages depletes a specialized subset of PLVAP+ fenestrated endothelial cells in the zona glomerulosa of mice, along with increased deposition of basement membrane collagen IV and in

overall_design: To characterize the impact of macrophage VEGF-A on the adrenal endothelial cell diversity, we isolated CD31+ CD45- endothelial cells from adrenal gland of WT as well as VEGF/LysM female mice at 12 weeks of age and performed single cell transcriptomics.

first: Mara

last: Karakone

first: Christian

last: Stockmann


title: ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma (snATAC-Seq)

overall_design: Nuclei were isolated from frozen tissue of Ptf1aERT, Ptf1aERT;K*, Ptf1aERT;Pdx1f/f and Ptf1aERT;K*;Pdx1f/f mice, 2 and 10 weeks after Tamoxifen-induced CreERT recombination (n=2). Nuclei were analyzed using snATACseq.

first: Alec

last: Steep

first: Ian

last: Loveless


title: ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma


title: Differential gene expression in triceps brachii muscle with and without unmodulated 40 Hz stimulation in SAMP-10 mice

status: Public on Jun 16 2024

city: Akita

first: Takako

last: Ohnuma

state: Akita

department: ARGG

institute: Akita University

summary: Unmodulated 40 Hz (u40Hz) stimulation, imperceptible to the human ear, which has been reported to improve cognitive function in human and mice. However, research on the effects of u40Hz stimulation is still limited. This study is the first to report the effects of u40Hz stimulation on glucose tolerance and muscle strength in SAMP-10 mice, an aging-accelerated model. SAMP-10 mice underwent five weeks of u40Hz stimulation, followed by glucose tolerance tests, cognitive and behavioral assessments, and frailty evaluations. Compared to the control group, the u40Hz-stimulated group exhibited mitigated age-related decline in glucose tolerance, a better Frailty Index (FI), and notably preserved muscle strength. Microarray analysis of stimulated muscle tissue revealed significant upregulation of peroxisome proliferator-activated receptor gamma (PPARγ) downstream and β-oxidation genes, and significant downregulation of clock genes.

overall_design: Triceps muscles from 3 SAMP-10 mice after 5 weeks of Unmodulated 40 Hz stimulation and 3 SAMP-10 mice as controls were subjected to microarray.

first: Tatsunori

last: Shimizu

first: Hidetaka

last: Ota


title: Expression data from cultured spermatogonia established from 10 day old mouse  testes

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

summary:
Spermatogonial stem cells (SSCs) undergo self-renewal division to sustain spermatogenesis. Although it is possible to derive germline stem (GS) cell cultures from most of the mouse strains by supplementing GDNF and FGF2, SSCs from a 129 background do not proliferate under the same culture conditions, which suggested that they have distinct self-renewal requirements. We modified previous culture conditions and established long-term culture of SSCs of 129 mice. 129 GS cells reinitiated spermatogenesis and produced offspring following transplantation into the seminiferous tubules of infertile mouse recipients. This dataset show the differences of gene expressions of GS cells between C57BL/6 and 129 mice, which have important implications in understanding requirements of self-renewal mechanisms.
In this dataset, we include the expression data obtained from cultured spermatogonia (GS cells) derived from C57BL/6, and 129 mice.  Each group contains 2 biological replicates.

overall_design: GS cells were established from testes of 10 day old  mice of C57BL/6 and 129 strains. Total RNA samples were extracted with TRIzol reagent (Invitrogen) and purified using the RNeasy cleanup system (QIAGEN, Valencia, CA). cDNA libraries were generated using a TruSeq stranded mRNA library preparation kit (Illumina, San Diego, CA). Sequencing was performed using NextSeq550 (Illumina) with a single-read sequencing length of 76 bp. 4 Total samples were analyzed.

first: Mito

last: Kanatsu-Shinohara


title: N6-methyladenosine profiling of differentiating human pancreatic β-cells in vitro

status: Public on Jun 13 2024

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: N6-methyladenosine (m6A) is the most abundant chemical modification in mRNA, and plays important roles in human embryonic stem cell pluripotency, maintenance, and differentiation. However, the role of m6A and the precise mechanisms involved during the development of β-cells are unexplored. Here, we differentiated human embryonic stem cells (hESCs) into pancreatic β-like cells and performed RNA-Seq and m6A-seq at different stages of in vitro β-like cell differentiation.

overall_design: H1 and MEL1 hESCs were differentiated to Stage 3 (S3), Stage 4 (S4) and Stage 6 (S6) as reported previously (Kahraman et al. Nat Metab. 2022). Total RNA was isolated by TRIzol reagent and mRNAs were purified by Dynabeads mRNA purification kit. Purified mRNA was fragmented by Bioruptor® Pico Sonication System and input was saved before m6A immunoprecipitation. m6A immunoprecipitation was performed with EpiMark®N6-Methyladenosine Enrichment Kit (NEB, E1610S) following the manufacturer protocol. Then, RNA libraries were prepared for both input and IP samples using TruSeq® Stranded mRNA Library Prep (Illumina, 20020594) following the manufacturer protocol. Sequencing was performed at the University of Chicago Genomics Facility on an Illumina NovaSeq 6000 machine.

first: Sevim

last: Kahraman

first: Dario

middle: F

last: DeJesus

first: Jiangbo

last: Wei

first: Chuan

last: He

first: Rohit

last: Kulkarni


title: Parkinson’s-linked LRRK2-G2019S derails AMPAR trafficking, mobility and composition in striatum with cell-type and subunit specificity

city: New York

first: Deanna

middle: L

last: Benson

address: 1470 Madison Avenue, 9-114

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Parkinson’s (PD) is a multi-factorial disease that affects multiple brain systems and circuits. While defined by motor symptoms caused by degeneration of brainstem dopamine neurons, debilitating non-motor abnormalities in fronto-striatal based cognitive function are common, appear early and are initially independent of dopamine. Young adult mice expressing the PD-associated G2019S missense mutation in Lrrk2 also exhibit deficits in fronto-striatal-based cognitive tasks. In mice and humans, cognitive functions require dynamic adjustments in glutamatergic synapse strength through cell-surface trafficking of AMPA-type glutamate receptors (AMPARs), but it is unknown how LRRK2 mutation impacts dynamic features of AMPAR trafficking in striatal projection neurons (SPNs). Here, we used Lrrk2G2019S knockin mice to show that surface AMPAR subunit stoichiometry is altered biochemically and functionally in mutant SPNs in dorsomedial striatum to favor incorporation of GluA1 over GluA2. GluA1-containing AMPARs were resistant to internalization from the cell surface, leaving an excessive accumulation of GluA1 on the surface within and outside synapses. This negatively impacted trafficking dynamics that normally support synapse strengthening, as GluA1-containing AMPARs failed to increase at synapses in response to a potentiating stimulus and showed significantly reduced surface mobility. Surface GluA2-containing AMPARs were expressed at normal levels in synapses, indicating subunit-selective impairment. Abnormal surface accumulation of GluA1 was independent of PKA activity and was limited to D1R SPNs. Since LRRK2 mutation is thought to be part of a common PD pathogenic pathway, our data suggest that sustained, striatal cell-type specific changes in AMPAR composition and trafficking contribute to cognitive or other impairments associated with PD.

overall_design: We used bulk RNAseq to compare expression in dorsal striatum of Lrrk2-G2019S knockin and wildtype control mice at postnatal day (P) 21.

first: Swati

last: Gupta

first: Bridget

last: Matikainen-Ankney

first: George

middle: W

last: Huntley


title: Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction

status: Public on Jun 14 2024

city: Salt Lake City

first: Nicholas

middle: Alonzo

last: Frost

state: UT

address: 383 Colorow Dr.

department: Neurology

institute: University of Utah

summary: Reliable representations of information regarding complex behaviors including social interactions  require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene. Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble

overall_design: Nuclei were isolated from the medial prefrontal cortex and cerebellum of male and female 4-5 month old WT mice following a social interaction paradigm and single nuclei RNA-seq was performed in order to determine the socially responsive ensemble via immediate early gene expression.

first: Hailee

last: Walker


title: Enhanced crosslinking and immunoprecipitation analysis of human fetal β-cells

summary: N6-methyladenosine (m6A) is the most abundant chemical modification in mRNA, and plays important roles in human embryonic stem cell pluripotency, maintenance, and differentiation. However, the role of m6A and the precise mechanisms involved during the development of β-cells are unexplored. Here, we performed enhanced crosslinking and immunoprecipitation (eCLIP) assays to identify m6A sites regulated by METTL14 in EndoC-βh1 human fetal β-cells.

overall_design: EndoC-βH1 cell lines were obtained from Univercell-Biosolutions (France). Culture plates were coated with DMEM (glucose 4.5 g L-1; Gibco) containing fibronectin (2 μg mL-1; Gibco), and extracellular matrix (1% vol vol-1; Sigma) for at least an hour in 5% CO2 at 37°C. EndoC-βH1 cells were grown on coated 6-well plates containing DMEM (glucose 1 g L-1), BSA fraction V (2% wt vol-1) (Roche), 2-mercaptoethanol (50 μM; Sigma), nicotinamide (10 mM; Sigma), transferrin (5.5 μg mL-1; Sigma), and sodium selenite (6.7 ng mL-1; Sigma). The eCLIP assays were performed by Eclipse Bioinnovations using UV-crosslinked EndoC-βH1 cells following the protocol detailed in (Van Nostrand et al. Nat Methods. 2016) using the anti-METTL14 antibody A305-847A (Bethyl Laboratories).


title: Expression profiling of METTL14 depleted human pancreatic β-like cells

summary: N6-methyladenosine (m6A) is the most abundant chemical modification in mRNA, and plays important roles in human embryonic stem cell pluripotency, maintenance, and differentiation. However, the role of m6A and the precise mechanisms involved during the development of β-cells are unexplored. Here, we explored the requirement of METTL14-mediated m6A RNA methylome in human pancreatic β-like cells by simultaneously inducing METTL14 knockdown in H1 human embryonic stem cells (hESCs) with doxycycline (Dox) treatment and differentiating hESCs towards pancreatic β-like cells in vitro.

overall_design: H1 hESCs were differentiated to Stage 6 (S6) β-like cells as reported previously (Kahraman et al. Nat Metab. 2022). Cells were harvested using TrypLE and neutralized in DMEM containing 10% FBS. The cell pellet was resuspended in DA-ZP1 containing cell media and incubated in 37°C for 30 min. Cells were washed with DPBS and the cell pellet was resuspended in fresh DA-ZP1–free media. Cells were sorted by Aria as described previously (Kahraman et al. Life Sci Alliance. 2021). Sorted cells were washed with DPBS and lysed in TRIzol for RNA isolation using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions. RNA libraries were prepared using SMARTer Stranded Total RNA-Seq kit v2 (Takara) and sequencing was performed on an Illumina NovaSeq 6000 according to the manufacturer instructions. Approximately 50 million paired-end 100-bp reads were generated for each sample.


title: Human Smc5/6 recognizes transcription-generated positive DNA supercoils

status: Public on Jun 10 2024

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

institute: University of Geneva, Faculty of Medicine / CMU

summary: Beyond its essential roles in ensuring faithful chromosome segregation and genomic stability, the human Smc5/6 complex acts as an antiviral factor. It binds to and impedes the transcription of extrachromosomal DNA templates; an ability which is lost upon chromosomal DNA integration. How the complex distinguishes among different DNA templates is unknown. Here we show that, in human cells, Smc5/6 preferentially binds to circular rather than linear extrachromosomal DNA. We further show that this binding is unlikely due to differences in the chromatin composition. Instead, the transcriptional process, per se, and more specifically the accumulation of DNA secondary structures known to be substrates for topoisomerases, is responsible for Smc5/6 recruitment. Those findings, in conjunction with our genome-wide Smc5/6 binding analysis showing that Smc5/6 localises at few but highly transcribe chromosome loci, reveal a previously unforeseen role of Smc5/6 in DNA topology management during transcription.

overall_design: Examination of HA-Smc6, RNAP II and GapR-HA whole genome binding/occupancy (ChIP-Seq) in immortalized human retina pigment epithelial cells (hTERT-RPE1).

first: Aurélie

last: Diman

first: Gaël

last: Panis

first: Cédric

last: Castrogiovanni

first: Julien

last: Prados

first: Bastien

last: Baechler

first: Michel

last: Strubin


title: ASCT2 is a major contributor to serine uptake in cancer cells

status: Public on Jun 11 2024

city: Chicago

first: Svetlana

last: Semina

address: 909 S Wolcott Avenue (MC 901), 2100 COMRB

department: physiology and Biophysics

institute: University of Illinois at Chicago

summary: The non-essential amino acid serine is a critical nutrient for cancer cells due to its diverse biosynthetic functions. While some tumors can synthesize serine de novo, others are auxotrophic and therefore reliant on serine uptake. Importantly, despite several transporters being known to be capable of transporting serine, the transporter(s) that mediate serine uptake in cancer cells are not known. Here, we characterize the amino acid transporter ASCT2 (SLC1A5) as a major contributor to serine uptake in cancer cells. ASCT2 is well-known as a glutamine transporter in cancer, and our work demonstrates that serine and glutamine compete for uptake through ASCT2. We further show that ASCT2-mediated serine uptake is essential for purine nucleotide biosynthesis and that ERα promotes serine uptake by directly activating SLC1A5 transcription. Together, our work defines an additional important role for ASCT2 as a serine transporter in cancer and evaluates ASCT2 as a potential therapeutic target.

overall_design:
To investigate changes in gene expression upon 48 hours of serine and glycine starvation in MCF7 breast cancer cells.
MCF7 cells growing in HPLM were starved of serine and glycine for 48 hours prior to harvesting of RNA.

first: Philippa

last: Burns

first: Kelly

last: Conger

first: Jonathan

last: Coloff


title: Analysis of early diagnostic markers for acute kidney injury after cardiac surgery

status: Public on Jun 08 2024

first: Pengtao

last: Liu

address: 1678th, Dongfang Road

department: Urology

institute: Shanghai Children's Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aimed to find diagnostic biomarkers for predicting cardiac surgery-associated acute kidney injury in children. We found that the change of exomiRs level in circulatory system occurred in the early stage after cardiac operation, and the changes of hsa-miR-184 and hsa-miR-6766-3p content in circulatory system could predict CSA-AKI well.

overall_design: At 4 hours after cardiac surgery, blood samples were collected for about 4ml. After standing at room temperature for 30 minutes，blood samples were centrifuged at 3,000 g at room temperature for 10 min. The upper liquid (serum) was frozen at −80°C until further analysis. After exosome extraction, we sequenced the miRNAs using  in each individual sample one by one. Sequencing libraries were constructed by QIAseq miRNA Library Kit for Illumina (Cat #331505, Qiagen) according to manufacturer's instructions. The sequencing was performed on an Illumina NovaSeq platform(Illumina, San Diego, CA, USA) and analyzed at Shanghai Biochip Co., Ltd., Shanghai, China.


title: Endothelial-to-mesenchymal transition contributes to accelerated atherosclerosis in Hutchinson–Gilford progeria syndrome

status: Public on Jun 05 2024

city: Oviedo

first: Magda

middle: Rita

last: Hamczyk

state: Asturias

address: C/ Fernando Bongera S/N, Edificio Santiago Gascon

department: Biochemistry and Molecular Biology

country: Spain

institute: Universidad de Oviedo

summary: The main goal of this study was to gain insight into the mechanisms underlying phenotypic changes in endothelial cells during atherosclerosis associated with Hutchinson-Gilford progeria syndrome, a premature aging syndrome. To this end, we performed an RNAseq experiment with aortic intima samples from atheroprone mice with ubiquitous and VSMC-specific progeria expression and their corresponding controls.

overall_design: Aortic intima samples were collected from: Apoe-/-LmnaG609G/G609G mice (with ubiquitous progerin expression), Apoe-/-Lmna+/+ mice (with wild-type lamin A/C expression; controls for mice with ubiquitous progerin expression), Apoe-/-LmnaLCS/LCSSM22αCre (with VSMC-specific expression) and Apoe-/-LmnaLCS/LCS mice (with lamin C only expression; controls for mice with VSMC-specific expression). For each genotype 3-4 samples were prepared, each consisting of a pool of 12-14 mice. Following RNA sequencing, 3 comparisons were performed: between Apoe-/-LmnaG609G/G609G mice and Apoe-/-Lmna+/+ control mice, between Apoe-/-LmnaLCS/LCSSM22αCre mice and Apoe-/-LmnaLCS/LCS control mice and between Apoe-/-LmnaLCS/LCS control mice and Apoe-/-Lmna+/+ control mice.


title: Mechanical stretching of keloid and normal skin fibroblasts

city: Changsha

first: Jingheng

last: Zhang

address: 87 Xiangya Rd

institute: Xiangya Hospital, Central South Uniiversity

summary: To study the effects of mechanical stretching on fibroblasts, two cell lines, HFF and KF, were subject to 50% uniaxial mechanical stretching for 6, 12, and 18 hours, followed by RNA-seq.

overall_design: with a custom-made cell stretching device, two cell lines, HFF and KF, as well as FACS-sorted CD74+ KF, were subject to 50% uniaxial mechanical stretching for 6, 12, and 18 hours, followed by RNA-seq.

first: Shuyao

last: Li

first: Min

last: Qi

first: Jianglin

first: Kai

last: Yuan


title: ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma [RNA-seq isoAC]

first: Simone

last: Benitz

overall_design: Acinar cells were isolated from pancreatic tissue of Ptf1aERT, Ptf1aERT;K*, Ptf1aERT;Pdx1f/f and Ptf1aERT;K*;Pdx1f/f mice, 2 weeks after CreERT-mediated recombination (n=3). RNA was isolated immediately after cell isolation and RNA was analyzed by bulk RNA-seq.

first: Alec

last: Steep

first: Howard

last: Crawford


title: Effect of BMP7 treatment overtime on H3.3K27M and H3.3 WT astrocytoma glioma cells (Res259)

status: Public on Jun 03 2024

city: Lyon

first: Marie

last: Castets

address: 28 Rue Laennec

institute: Cancer Research Center of Lyon

summary: Pediatric diffuse midline gliomas (pDMG) are an aggressive type of childhood cancer with a fatal outcome. Their major epigenetic determinism has become clear, notably with the identification of K27M mutations in histone H3. However, the synergistic oncogenic mechanisms that induce and maintain tumor cell phenotype have yet to be deciphered. In 20 to 30% of cases, these tumors have an altered BMP signaling pathway with an oncogenic mutation on the BMP type I receptor ALK2, encoded by ACVR1. However, the potential impact of the BMP pathway in tumors non-mutated for ACVR1 is less clear. By integrating bulk, single-cell and spatial transcriptomic data, we show here that the BMP signaling pathway is activated at similar levels between ACVR1 wild type and mutant tumors and identify BMP2 and BMP7 as putative activators of the pathway in a specific subpopulation of cells. By using both pediatric isogenic glioma lines genetically modified to overexpress H3.3K27M and patients-derived DIPG cell lines, we demonstrate that BMP2/7 synergizes with H3.3K27M to induce a transcriptomic rewiring associated with a quiescent but invasive cell state. These data suggest a generic oncogenic role for the BMP pathway in gliomagenesis of pDMG and pave the way for specific targeting of downstream effectors mediating the BMP/K27M crosstalk.

overall_design: To assess the potential synergy between K27M mutation and BMP7, Res259 cell lines were modified to either express H3.3K27M or wildtype histone H3.3. Cells were then harvested for RNA-sequencing at 0h, 3h and 24h after human recombinant BMP7 (50ng/mL) treatment.

first: Paul

last: Huchedé

first: Swann

last: Meyer

first: Samuel

last: Meignan


title: ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma (RNA-Seq)

overall_design: This dataset includes human pancreatic cancer cell lines HPAF-II and UM32 with either empty vector control or ROR2 expression construct (n=3).

first: Malak

last: Nasser


title: Spatial transcriptomics of 3 H3.3K27M pDMG samples

overall_design: Three FFPE pDMG tumors carrying the H3.3 K27M histone mutation were analysed using spatial transcriptomics.

first: Cyril

last: Degletagne

first: Alexandre

last: Vasiljevic


title: Molecular Cascade Reveals Sequential Milestones Underlying Hippocampal Neural Stem Cell Development into an Adult State

city: Philadelphia

first: Dennisse

last: Jimenez-Cyrus

state: PA

address: 415 Curie Blvd

institute: University of Pennsylvania

summary: Quiescent adult neural stem cells (NSCs) in the mammalian brain arise from proliferating NSCs during development. Beyond acquisition of quiescence, an adult NSC hallmark, little is known about the process, milestones and mechanisms underlying the transition of developmental NSCs to an adult NSC state. Here we performed targeted single-cell RNA-seq analysis to reveal the molecular cascade underlying NSC development in the early postnatal mouse dentate gyrus. We identified two sequential steps, first a transition to quiescence followed by further maturation, each of which involved distinct changes in metabolic gene expression. Direct metabolic analysis uncovered distinct milestones, including an autophagy burst before NSC quiescence acquisition and cellular ROS level elevation along NSC maturation. Functionally, autophagy is important for the NSC transition to quiescence during early postnatal development. Together, our study reveals a multi-step process with defined milestones underlying establishment of the adult NSC pool in the mammalian brain.

overall_design: Single-cell gene expression profiling of postnatal hippocampal quiescent neural stem cells (qNSCs) from P3, P7 and P14  Hopx-GFP reporter mice

first: Hongjun

last: Song


title: A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival [ChIP-seq]

status: Public on Jun 01 2024

city: Bern

first: Marco

last: Osterwalder

address: Murtenstrasse 24

department: DBMR

institute: Universiy of Bern

summary: Gene deserts spanning more than 500kb of non-protein coding genomic sequence are considered evolutionarily ancient and stable and are enriched in the vicinity of developmental regulator genes (Ovcharenko 2005). These extensive genomic regions typically harbor numerous conserved elements with predicted gene regulatory potential pointing to critical tissue-specific functions during development. Nevertheless, the biological necessity and underlying funtional enhancer landscapes of most gene deserts near developmental transcription factors (TFs) remain unknown, and it is unclear how precise pleiotropic expression patterns emerge from gene desert sequence. Here, we investigated the cis-regulatory architecture and function of a gene desert flanking the mouse Shox2 transcriptional regulator which itself is essential for embryonic limb, craniofacial, and cardiac pacemaker development. By combining epigenomic enhancer prediction, transgenic reporter validation and region-specific chromatin capture (C-HiC), we define the embryonic in vivo enhancer landscape and chromatin topology of the Shox2 gene desert. Targeted and context-specific genomic deletions uncover the gene desert not only as a regulator of embryonic survival through enhancer-mediated control of cardiac Shox2 expression, but also link distinct subsets of tissue-specific gene desert enhancers to the regulation of craniofacial patterning and proximal limb development. Our results hence identify the Shox2 gene desert as a fundamental genomic unit indispensable for pleiotropic patterning, robust organ morphogenesis and embryonic development progression by serving as a dynamic hub for tissue-specific developmental enhancers.

overall_design: H3K27ac ChIP-seq of human fetal atrial and ventricular tissues to determine genome-wide and chamber-specific cardiac enhancer signatures

first: Brandon

last: Mannion

first: Cailyn

last: Spurrell

first: Yoko

last: Yuzawa

first: Iros

last: Barozzi

first: Axel

last: Visel

first: Len

last: Pennacchio


title: A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival [ATAC-seq]

overall_design: ATAC-seq from whole-mount mouse embryonic hearts to determine genome-wide cardiac open chromatin regions

first: Matteo

last: Zoia


title: A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival [RNA-seq]

overall_design: Total RNA-seq of human fetal atrial and ventricular tissues to determine cardiac chamber-specific transcriptomes


title: A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

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

overall_design: Refer to individual Series


title: A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival [C-HiC]

overall_design: We used region capture Hi-C (C-HiC) in mouse embryos (mus musculus) with a probe set covering a 3,5Mb genomic interval containing the Shox2 gene. We performed CHi-C from embryonic forelimbs, mandibular processes, and hearts of wildtype embryos at E11.5 to define the tissue-specific 3D chromatin structure at the Shox2 locus.

first: Raquel

last: Rouco

first: Guillaume

last: Andrey


title: Regulation of Primary Cilia Disassembly Through HUWE1-Mediated TTBK2 Degradation Plays a Crucial Role in Cerebellar Development and Medulloblastoma Growth

city: Taipei

first: Won-Jing

last: Wang

address: 155, Sec.2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Development of the cerebellum requires precise regulation of granule neuron progenitor (GNP) proliferation. Although it is known that primary cilia are necessary to support GNP proliferation, the exact molecular mechanism governing primary cilia dynamics within GNPs remains elusive.  Here, we establish the pivotal roles for the centrosomal kinase TTBK2 (Tau tubulin kinase-2) and the E3 ubiquitin ligase HUWE1 in GNP proliferation. We show that TTBK2 is highly expressed in proliferating GNPs under Sonic Hedgehog (SHH) signaling, coinciding with active GNP proliferation and the presence of primary cilia. TTBK2 stabilizes primary cilia by inhibiting their disassembly, thereby promoting GNP proliferation in response to SHH. Mechanistically, we identify HUWE1 as a novel centrosomal E3 ligase that facilitates primary cilia disassembly by targeting TTBK2 degradation. Disassembly of primary cilia serves as a trigger for GNP differentiation, allowing their migration from the external granule layer (EGL) of the cerebellum to the internal granule layer (IGL) for subsequent maturation. Moreover, we have established a link between TTBK2 and SHH-type medulloblastoma (SHH-MB), a tumor characterized by uncontrolled GNP proliferation. TTBK2 depletion inhibits SHH-MB proliferation, indicating that TTBK2 may be a potential therapeutic target for this cancer type. In summary, our findings reveal the mechanism governing cerebellar development and highlight a potential anti-cancer strategy for SHH-MB.

overall_design: To investigate the therapeutic potential of targeting TTBK2 in SHH-MB, we generated TTBK2 knockout (TTBK2-/-) Daoy cells, a well-established SHH-MB cell line.

first: I-Hsuan

last: Lin

first: Yu-Wen

last: Cheng


title: Transcriptomic profile of monocytes/ macrophages from injured bone, muscle, skin or heart tissues of Treg-depleted mice

status: Public on May 31 2024

city: Clayton

first: Mikaël

last: Martino

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

summary: Mice were depleted of Tregs, and bone, muscle, skin or heart injuries were performed. On day 4 and 7 post-injury, the tissues were harvested and the endogenous monocytes/macrophages were sorted using FACS. These were then used for bulk RNA sequencing, to compare the transcriptomic profiles of injured tissue monocytes/ macrophages in Treg-depleted mice versus control mice post-injury.

overall_design: Ten-week-old Foxp3(DTR/GFP) (FDG) mice and wild-type (WT) C57BL/6J (control) mice received intraperitoneal injections of 20 ng/g diphtheria toxin (DT), starting two days prior to the induction of injury, and continuing daily until the day of injury, followed by every 2 days after injury, for 1 week.  Bone (cranial defect), muscle (volumetric muscle loss defect), skin (full-thickness biopsy punch) or heart (myocardial infarction) injuries were induced in 10 week old Foxp3(DTR/GFP) (FDG) mice and control C57BL6/J wild-type mice, that were treated with DT to deplete Tregs in the FDG mice. Only 1 injury per mouse was performed. On day 4 and 7 post-injury, endogenous monocytes/ macrophages were sorted from Foxp3(DTR/GFP) + DT mice (i.e FDG+DT, Treg-depleted), and wildtype C57BL/6J + DT mice (i.e. WT+DT, control), and used for bulk RNA sequencing.

first: Bhavana

last: Nayer

first: Yasmin

middle: K

last: Alshoubaki


title: Single-nuclei characterization of oxycodone's effects on dorsal peduncular nucleus

status: Public on Jun 07 2024

city: Charleston

first: Alexander

middle: CW

last: Smith

state: SC

address: 173 Ashley Ave, BS403

institute: Medical University of South Carolina

summary: In addition to their intrinsic rewarding properties. opioids can also evoke aversive reactions that protect against misuse. Cellular mechanisms that govern the interplay between opioid reward and aversion are poorly understood. We used whole-brain activity mapping to show that neurons in the dorsal peduncular nucleus (DPn) are highly responsive to the opioid oxycodone. Connectomic profiling revealed that DPn neurons innervate the parabrachial nucleus (PBn). Spatial and single-nuclei transcriptomics resolved a unique population of PBn-projecting pyramidal neurons restricted to the DPn that express μ-opioid receptors (μORs). Disrupting μOR signaling in these neurons switched oxycodone from rewarding to aversive and exacerbated the severity of opioid withdrawal. These findings identify DPn neurons as key substrates for the abuse liability of opioids.

overall_design: 2 saline-injected (IP) samples, 2 oxycodone-injected (5mg/kg) samples

middle: C

first: Paul

last: Kenny

first: Kristin

last: Beaumont

first: Robert

middle: P

last: Sebra


title: The tumor intrinsic role of the m6A reader YTHDF2 in regulating immune evasion [bulk RNA-seq]

city: Los Angeles

first: Sai

last: Xiao

state: California

address: 1500 E. Duarte Road

institute: City of Hope

summary: Tumors evade attacks from the immune system through various mechanisms. Here, we identify a component of tumor immune evasion mediated by YTH domain-containing family protein 2 (YTHDF2), a reader protein that usually destabilizes m6A-modified mRNA. Loss of tumoral YTHDF2 inhibits tumor growth and prolongs survival in immunocompetent tumor models. Mechanistically, tumoral YTHDF2 deficiency promotes the recruitment of macrophages via CX3CL1 and enhances mitochondrial respiration of CD8+ T cells by impairing tumor glycolysis metabolism. Tumoral YTHDF2 deficiency promotes inflammatory macrophage polarization and antigen presentation in the presence of IFN-γ. In addition, IFN-γ induces autophagic degradation of tumoral YTHDF2, thereby sensitizing tumor cells to CD8+ T cell-mediated cytotoxicity. Last, we identified a small molecule compound that preferentially induces YTHDF2 degradation, which shows a potent antitumor effect alone but a better effect when combined with anti-PD-L1 or anti-PD-1 antibodies. Collectively, YTHDF2 appears to be a tumor-intrinsic regulator that orchestrates immune evasion, representing a promising target for enhancing cancer immunotherapy.

overall_design: Total RNA was isolated by TRIzol reagent from fifty million WT and Ythdf2-KO B16-OVA tumor cells.

first: Jianhua

last: Yu


title: The tumor intrinsic role of the m6A reader YTHDF2 in regulating immune evasion [scRNA-seq]

overall_design: Tumors from WT or cKO mice were extracted and digested with collagenase type IV (1 mg/ml) and DNase type I (30 U/ml) for 30 min at 37 °C. The cells were filtered through the 70 μm cell strainers, washed with phosphate-buffered saline (PBS), lysed in red blood cell buffer, and resuspended in PBS. Tumor-infiltrating immune cells (CD45+ cells) were sorted by FACSAria Fusion Flow Cytometer (BD Biosciences). The cell suspension (300-600 living cells per microliter) was loaded onto the Chromium single cell controller (10 x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Libraries were subsequently prepared sing Single Cell 5’Library and Gel Bead Kit and sequenced on an Illumina NovaSeq 6000 instrument with pair-end 100 bp (PE100) reading strategy.


title: Suppression of the JAK/STAT Pathway Inhibits Neuroinflammation in the Line 61-PFF Mouse Model of Parkinson’s Disease

city: Birmingham

first: Yong

state: AL

address: 1918 University Blvd

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

summary: Parkinson’s disease (PD) is characterized by neuroinflammation, progressive loss of dopaminergic neurons, and accumulation of a-synuclein (a-Syn) into insoluble aggregates called Lewy pathology. The Line 61 a-Syn mouse is an established preclinical model of PD; Thy-1 is used to promote human a-Syn expression, and features of sporadic PD develop at 9-18 months of age. To accelerate the PD phenotypes, we injected sonicated human a-Syn preformed fibrils (PFFs) into the striatum, which produced phospho-Syn (p-a-Syn) inclusions in the substantia nigra pars compacta and significantly increased MHC Class II-positive immune cells. Additionally, there was enhanced infiltration and activation of innate and adaptive immune cells in the midbrain. We then used this new model, Line 61-PFF, to investigate the effect of inhibiting the JAK/STAT signaling pathway, which is critical for regulation of innate and adaptive immune responses. After administration of the JAK1/2 inhibitor AZD1480, immunofluorescence staining showed a significant decrease in p-a-Syn inclusions and MHC Class II expression. Flow cytometry showed reduced infiltration of CD4+ T-cells, CD8+ T-cells, CD19+ B-cells, dendritic cells, macrophages, and endogenous microglia into the midbrain. Importantly, single-cell RNA-Sequencing analysis of CD45+ cells from the midbrain identified 9 microglia clusters, 5 monocyte/macrophage (MM) clusters, and 5 T-cell (T) clusters, in which potentially pathogenic MM4 and T3 clusters were associated with neuroinflammatory responses in Line 61-PFF mice. AZD1480 treatment reduced cell numbers and cluster-specific expression of the antigen-presentation genes H2-Eb1, H2-Aa, H2-Ab1, and Cd74 in the MM4 cluster and proinflammatory genes such as Tnf, Il1b, C1qa, and C1qc in the T3 cluster. Together, these results indicate that inhibiting the JAK/STAT pathway suppresses the activation and infiltration of innate and adaptive cells, reducing neuroinflammation in the Line 61-PFF mouse model.

overall_design: We carried out single cell RNAseq on live immune cells (CD45+) from the midbrain of Line 61 mice treated with PBC (n=3), monomer (n=3), PFF + VH (n=4), and PFF + AZD1480 (n=5).

first: Huixian

last: Hong

first: Hongwei

last: Qin

first: Etty

middle: N

last: Benveniste


title: Acetaminophen overdose reveals protease activated receptor 4 as a low expressing but potent receptor on the hepatic endothelium in mice

city: Oklahoma City

first: Rahul

last: Rajala

state: Oklahoma

address: 825 NE 13th Street

department: Cardiovascular Biology

institute: Oklahoma Medical Research Foundation

summary: There is a paucity of data on how protease-activated receptors (PARs) regulate transcriptional reprogramming. We sought to determine how the expression of two members of the PAR family (PAR1 and PAR4) on hepatic endothelial cells (ECs) influence transcription in the liver after acetaminophen (APAP) overdose. We combined EC-specific translating ribosome affinity purification with next-generation sequencing (EC-TRAPseq) in endothelial-specific Par1 and Par4 knockout mice. This allowed us to gain an in vivo snapshot of how EC gene expression profiles change with APAP overdose and how the loss of endothelial PARs impacts transcriptional reprogramming in hepatic ECs. This approach also provided a high degree of sensitivity for detecting low-expressing transcripts. We found distinct transcriptional changes in APAP-overdosed ECs between endothelial Par1 and Par4 knockout mice.

overall_design: Total tissue lysate and EC-TRAP RNASeq data were collected from livers of 11-15 week-old male littermate control mice (RiboTag;Par1fl/+;iCdh5(PAC)-CreERT2) and experimental endothelial Par1 knockout mice (RiboTag;Par1fl/fl;iCdh5(PAC)-CreERT2) treated with saline or overdosed with 300 mg/kg APAP (n=3 for each genotype and treatment). Comparable samples were collected from control and endothelial Par4 knockout mice. This resulted in liver lysates and EC-TRAP samples from 24 mice (i.e., 48 distinct samples).

first: Audrey

last: Cleuren

first: Courtney

middle: T

last: Griffin