title: Transcriptome analysis of spinal tuberculosis associated long non coding RNAs in human clinical bone tissues

city: Lanzhou City

first: Yapeng

last: Wang

address: 82 Cuiyingmen, Chengguan District

department: Department of Orthopaedics

summary: Objective: The purpose of this study is to investigate the differential expression of genes in spinal tuberculosis using transcriptomics, with the aim of identifying novel therapeutic targets and prognostic indicators for the clinical management of spinal tuberculosis. Methods: Patients who visited the Department of Orthopedics at the Second Hospital & Clinical Medical School, Lanzhou Univeristy from January 2021 to May 2023 were enrolled. Based on the inclusion and exclusion criteria, there were 5 patients in the experimental group (test group) and 5 in the control group. Total RNA was extracted and paired-end sequencing was conducted using the KAPA Stranded mRNA-Seq Kit on the Illumina Novaseq 6000 sequencing platform. After processing the sequencing data with clean reads and annotating the reference genome, FPKM normalization and differential expression analysis were performed. The differentially expressed genes (DEGs) and long non-coding RNAs (LncRNAs) were analyzed for KEGG and GO enrichment. The cis-regulation of differentially expressed mRNAs by LncRNAs was predicted and analyzed to establish a co-expression network between the two. Finally, WGCNA analysis was conducted. Results: High-throughput sequencing analysis identified 2366 differentially expressed genes, with 974 genes significantly upregulated and 1392 genes significantly downregulated. KEGG enrichment revealed that the upregulated genes are associated with cytokine-cytokine receptor interactions, tuberculosis, and TNF-α signaling pathways, primarily enriched in biological processes such as immunity and inflammation. Downregulated genes are related to muscle development, contraction, fungal defense response, and collagen metabolism processes. Analysis of lncRNAs from bone tuberculosis RNA-seq data using an RPKM threshold of >0.5 detected a total of 3652 lncRNAs, with 356 significantly upregulated and 184 significantly downregulated. Further analysis identified 311 significantly different lncRNAs that could cis-regulate 777 target genes, enriched in pathways such as muscle contraction, inflammatory response, and immune response, closely related to bone tuberculosis. There are 51 genes enriched in the immune response pathway regulated by cis-acting lncRNAs. LncRNAs that regulate immune response-related genes, such as upregulated RP11-451G4.2, RP11-701P16.5, AC079767.4, AC017002.1, LINC01094, CTA-384D8.35, and AC092484.1, as well as downregulated RP11-2C24.7, may serve as potential prognostic and therapeutic targets. Multiple molecules related to immune regulation identified through WGCNA analysis can serve as markers for early diagnosis and molecular targets for the treatment of bone tuberculosis. Conclusion: The differentially expressed mRNAs and LncRNAs in spinal tuberculosis are both associated with immune regulatory pathways. These pathways not only promote or inhibit the binding infection and development at the mechanistic level but may also serve as important markers for the earliest detection of tuberculosis metastasis to bone tissue at the clinical level.

overall_design: To investigate the differential expression of genes in spinal tuberculosis using transcriptomics, with the aim of identifying novel therapeutic targets and prognostic indicators for the clinical management of spinal tuberculosis, We selected 5 patients with BJTB as the test group and 5 patients with lumbar disc degeneration as the control group, and compared the differential expression profiles between the two groups, performed KEGG and GO enrichment on differentially expressed genes (DEGs) and long non-coding RNAs (LncRNAs), and predicted the differential mRNAs regulated in cis by the differentially expressed LncRNAs. We established a co-expression network between them and finally conducted a WGCNA analysis

first: Tian'en

last: Xu

first: Wenjuan

last: Fan

first: Cong

last: Chen

first: Kai

last: Feng

first: Xiaoyun

last: Sheng

first: Hong

last: Yang

first: Bao

first: Xu


title: The RNA content of plasma-derived extracellular vesicles in cerebral malaria

status: Public on Aug 02 2024

city: Kilifi

first: Abdirahman

last: Abdi

state: Not US or Canada

address: Mombasa-Malindi Road

department: Bioscience

country: Kenya

institute: KEMRI-Wellcome Trust Research Programme

type: Expression profiling by high throughput sequencing

summary: We sequenced the RNA content of circulating extracellular vesicles obtained from retinopathy- positive (CM-R⁺) and negative cerebral malaria (CM-R⁻) patients and community controls (CC) without Plasmodium falciparum infection. We found that some of the transcripts enriched in circulating extracellular vesicles are highly expressed in the brain compared to other tissues and could have a diagnostic potential in the cerebral malaria context.

overall_design: To investigate the biological content of extracellular vesicles obtained from the plasma of cerebral malaria patients and community healthy controls without Plasmodium falciparum infection.

first: Kioko

last: Mwikali


title: Essential functions of RNA helicase Vasa in Drosophila spermatogenesis, from maintenance of germline stem cells to passage through meiosis between Drosophila melanogaster and Drosophila simulans [RNA-seq]

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

summary: DEAD-box RNA helicase Vasa is required for gonad development and fertility in multiple animals. In Drosophila, Vasa performs essential functions in oogenesis, including the maintenance of germline stem cells (GSCs), piRNA silencing of mobile elements, translation regulation, and primordial germ cell specification. Despite its evident significance, the mechanistic basis of Vasa action and its precise role in spermatogenesis become incomprehensible. Several papers affirm the fertility of males carrying vasa mutations. However, it is also shown that Vasa is essential for piRNA-mediated repression of Stellate genes needed for the maintenance of male fertility.Here we found that loss-of-function vasa mutations led to a rapid decline in GSC maintenance in the testes, a severe loss of total germ cell content, and a strong decrease in male fertility over time. With the aid of analysis of small RNA libraries, we revealed that collapse of piRNA biogenesis in the absence of vasa expression. Despite that, we did not reveal increasing cell death events in the early germ cells of vasa mutant testes. The introduction of the transgene rhino copy, encoding a nuclear component of the piRNA pathway, in vasa mutant background allowed us to rescue premeiotic stages of spermatogenesis, including GSC maintenance and the development of spermatogonia and spermatocytes. However, the progression of spermatocytes through meiosis and the fertility of the rhino transgene-rescued males were disrupted by strong Stellate gene derepression owing to the absence of corresponding piRNAs. We have shown that Vasa functions in spermatogenesis are essential at two separate developmental stages: in GSCs for their maintenance and in spermatocytes for the repression of Stellate genes.

overall_design: To study the contribution of Vasa in Stellate silencing in more detail, we prepared and sequenced on the Illumina platform whole-transcriptome libraries and 18–29 nt small RNAs isolated from the testes of vasa mutants, control heterozygous males, and males with the transgenic construct rhi-GFP in the background of vasa mutations.

middle: A


title: Specific 3-O-sulfated heparan sulfate domains regulate salivary gland basement membrane metabolism and epithelial differentiation [female]

city: Bethesda

first: Vaishali

middle: N

last: Patel

state: Maryland

address: 9000 Rockville Pike

department: NIDCR

country: USA

institute: National Institutes of Health

summary: FGF signaling is essential for salivary gland (SG) development and heparan sulfate (HS) regulation of FGFR function is determined by immense structural diversity of sulfated HS domains. The basement membrane (BM), containing HS proteoglycans, collagens and laminins, separates epithelia from stroma and controls growth factor-matrix cross-talk. 3-O-sulfotransferases generate highly 3-O-sulfated HS domains (3-O-HS) and Hs3st3a1 and Hs3st3b1 are enriched in myoepithelial cells (MECs), which produce BM and are a growth factor signaling hub. To investigate 3-O-HS regulation of MEC function and growth factor signaling, we generated Hs3st3a1;Hs3st3b1 double knockout (DKO) mice. The DKO HS loses specific highly 3-O-sulfated tetrasaccharides, which increases FGF/FGFR-complex binding to HS. During development this leads to increased FGFR-, BM- and MEC-related gene expression. However, in adult DKO SGs the secretory units containing acinar and MECs, have reduced MECs, increased BM and disrupted acinar polarity, resulting in salivary hypofunction. We used defined 3-O-sulfated-HS in FGFR pulldown assays and primary organ cultures to investigate 3-O-HS-dependent mechanisms regulating MEC development. We find that 3-O-HS modulates FGFR signaling to regulate MEC BM synthesis which is critical for secretory unit homeostasis and acinar function. Understanding how sulfated HS regulates development will inform the use of HS mimetics in organ regeneration.

overall_design: Three submandibular glands from WT and DKO female mice were used to isolate RNA and perform RNA-sequencing to determine the differentially expressed genes.

first: Marit

middle: H

last: Aure

first: Sophie

last: Choi

first: James

last: Ball

first: Ethan

middle: D

last: Lane

first: Zhangjie

first: Yongmei

first: Changyu

last: Zheng

first: Xibao

last: Liu

first: Daniel

last: Martin

first: Jillian

last: Pailin

first: Michaela

last: Prochazkova

first: Ashok

last: Kulkarni

first: Toin

last: van Kuppevelt

first: Indu

middle: S

last: Ambudkar

first: Jian

first: Matthew

middle: P

last: Hoffman


title: The human liver circadian transcriptome and its carcinogenic perturbation by hepatitis C virus infection (ChIP-Seq)

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chronic liver disease and cancer are global health challenges. The role of the circadian clock (CC) as a regulator of physiology and disease is well established in animal models. However, in human liver the identity of circadian genes and their epigenetic regulation is unknown. Here, we unraveled the circadian transcriptome and epigenome of human hepatocytes using a human liver chimeric mouse model. We identified genes coding for transcription factors, chromatin modifiers, and critical enzymes which are expressed rhythmically in human hepatocytes, and which differ from the mouse liver circadian transcriptome. Moreover, we show that hepatitis C virus (HCV) infection, a major cause of liver disease and cancer world-wide, perturbs the human hepatocellular clock leading to an activation of pathways mediating steatosis, fibrosis and cancer. The HCV-disrupted rhythmic hepatic pathways remained deregulated in patients cured of HCV suggesting a major role in liver cancer development, and in the identification of therapeutic targets.

overall_design: Messenger RNA from three biological replicates per mice group (control, HCV-infected) for each Zeitgeber time (ZT0, ZT4, ZT8,  ZT12,  ZT16,  ZT20) was isolated and sequenced.

first: Atish

last: Mukherji

first: Michio

last: Imamura

first: Hiromi

last: Abe-Chayama

first: Alexandre

last: Haller

first: Philippe

last: Baltzinger

first: Kazuaki

last: Chayama

first: Irwin

last: Davidson

first: Thomas

middle: F

last: Baumert


title: The human liver circadian transcriptome and its carcinogenic perturbation by hepatitis C virus infection (RNA-Seq II)


title: The human liver circadian transcriptome and its carcinogenic perturbation by hepatitis C virus infection (RNA-Seq I)

overall_design: Messenger RNA of paired biopsies from HCV-infected patients and the same patients after DAA-treatment was sequenced and analyzed.


title: An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Hyaluronan mediates cold-induced adipose tissue beiging

status: Public on Aug 01 2024

city: Houston

first: Yi

last: Zhu

state: TX

department: Pediatrics

institute: BAYLOR COLLEGE OF MEDICINE

summary: Adipose tissue beiging refers to a process through which beige adipocytes emerge in classical white adipose tissue depots. Beige adipocytes dissipate chemical energy and secrete adipokines like classical brown adipocytes to improve systemic metabolism, which offers benefits for people with obesity and metabolic diseases. Cold exposure and β3-adrenergic receptor (AR) agonist treatment are two commonly used stimuli for increasing beige adipocytes in mice, but their underlying biological processes are different. Transcriptional analysis of inguinal white adipose tissue (iWAT) has revealed that changes in extracellular matrix (ECM) pathway genes are specific to cold exposure. Hyaluronic acid (HA), a non-sulfated linear polysaccharide produced by nearly all cells, is one of the most common components of ECM. We found that cold exposure significantly increases iWAT HA levels while β3-AR agonist CL316,243 fails to do so. Increasing HA level in iWAT by Has2 overexpression significantly increases cold-induced adipose tissue beiging; in contrast, decreasing HA by Spam1 overexpression, which encodes a hyaluronidase that digests HA, significantly decreases cold-induced iWAT beiging. All of these data implicate a role of HA in promoting adipose tissue beiging that is unique to cold exposure. Given the failure of β3-AR agonists in clinical trials for obesity and metabolic diseases, increasing HA could serve as a new approach to recruiting more beige adipocytes to combat metabolic diseases.

overall_design: To understand how HA may mediate cold-induced adipose tissue beiging, we performed RNA-sequence analysis on iWAT harvested from Apn-Has2 (overexpressed Has2 in adipose tissue) or Apn-PH20 (overexpressed Spam1 in adipose tissue) compared to their respective littermate Apn-rtTA controls. Transgene expressions were induced by supplementing 200 mg/kg doxycycline in the chow diet for five days for all mice, which resulted in no divergence of body weight or other metabolic phenotypes, allowing us to understand the primary effect of changes in HA levels on gene expression.

first: Xi

last: Chen

first: Yifan

last: Wang

first: Huiqiao

last: Li

first: Yanru

last: Deng

first: Charlise

last: Jiang

first: Anying

last: Song

first: Qiong


title: β-diketone accumulation in modern bread wheat varieties

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Cuticular waxes coating leaf surfaces can help tolerate drought events by reducing non-stomatal water loss. Despite their role in drought tolerance, little is known about the cuticular wax responses of Canadian bread wheat varieties. To fill in this gap, RNAseq was performed on the flag leaf of four modern varieties to identify potential markers that could be used for selection of higher accumulation of cuticular waxes. This analysis revealed that the W1 locus is a good candidate for higher accumulation of β-diketones.

overall_design: We investigate the transcriptome of the flag leaf of four Canadian bread wheat modern varieties, with three replicates for each line.

first: Raju

last: Soolanayakanahally

first: Aswini

last: Kuruparan

first: Eliana

last: Gonzales-Vigil


title: CA19-9-positive extracellular vesicles are the risk for cancer-associated thrombosis in pancreatic cancer

city: Hongo, Bunkyo-ku

first: Chikako

last: Shibata

state: Tokyo

country: Japan

institute: The University of Tokyo

summary: To investigate the effect of pancreatic cancer cell-derived EVs on HUVEC, we performed gene expression analysis of HUVEC treated with or without EVs for 5h.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVEC-SELE cells treated with or without pancreatic cancer cell-derived EVs.

first: Motoyuki

last: Otsuka

first: Kazunaga

last: Ishigaki

first: Mitsuhiro

last: Fujishiro


title: Specific 3-O-sulfated heparan sulfate domains regulate salivary gland basement membrane metabolism and epithelial differentiation [male]

first: Vaishali

last: Patel

overall_design: 4 WT and 5 DKO submandibular glands from male mice to was used to isolate RNA and compare differentially expressed genes using RNA-sequencing analysis.

first: Marit

last: Aure

first: Sophie

last: Choi

first: James

last: Ball

first: Ethan

last: Lane

first: Zhangjie

first: Yongmei

last: Xu

first: Changyu

last: Zheng

first: Xibao

last: Liu

first: Daniel

last: Martin

first: Jillian

last: Pailin

first: Michaela

last: Prochazkova

first: Ashok

last: Kulkarni

first: Toin

last: van Kuppevelt

first: Indu

last: Ambudkar

first: Jian

first: Matthew

last: Hoffman


title: RNA sequencing of extracellular vesicles, secreted by young and adult mouse adipocytes [miRNA-Seq]

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

country: Germany

institute: University of Ulm

type: Non-coding RNA profiling by high throughput sequencing

summary:
We used male C57BL/6 mice (Charles River Laboratories, Wilmington, MA), housed under SPF conditions. Primary adipocytes from the inguinal fat depot at postnatal day (P6, young mice) and postnatal day 56 (P56, adult mice) were isolated by collagenase digestion and separation of cell fractions and subsequently  cultured in EV-free media (FBS was EV-depleted).
Article: Röszer T., MicroRNA Profile of Mouse Adipocyte-Derived Extracellular Vesicles

overall_design: We compared the RNA profile of extracellular vesicles (EVs) secreted by adipocytes of P6 and P56 mice. We compared P6 (N=3) to P56 samples (N=3).


title: Specific 3-O-sulfated heparan sulfate domains regulate salivary gland basement membrane metabolism and epithelial differentiation

first: Vaishali


title: Loss of Sphingosine-1-Phosphate Receptor 4 weakens innate mechanisms leading to defective lymph node hypertrophy and germinal center formation

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

summary: The successful development of germinal centers (GC) relies heavily on innate mechanisms to amplify the initial inflammatory cascade.  In addition to their role in antigen presentation, innate cells are essential for redirection of circulating lymphocytes toward the draining lymph node (dLN) to maximize antigen-surveillance and identification of cognate lymphocytes.  Sphingosine-1-phosphate (S1P) and its receptors (S1PR1-5) regulate various aspects of immunity, however, the role of S1PR4 in adaptive responses is not well understood. Here we use a localized TH1 footpad immunization model to carefully monitor changes in immune populations within circulation, the immunization site, and the dLN.  We found that mice lacking S1PR4 ultimately developed attenuated GC and activation pathways due in part to upstream defects in neutrophil activity.  Within hours of immunization, failed neutrophil mobilization and infiltration into the tissue of S1PR4-/- mice resulted in reduced local inflammation and vascular changes.  Using depletion antibodies, we show that neutrophils were necessary to facilitate the early edema as well as the redirection of circulating lymphocytes into the dLN, thereby contributing to reduced dLN hypertrophy in S1PR4-/-.  Using in vivo adoptive transfer, we demonstrated that these homing deficiencies were not lymphocyte-intrinsic but instead due to microenvironment failures within the S1PR4-/- host.  Consistent with the known role of lymphocyte entry promoting DC emigration, the dLN of these mice exhibited defects in the prolonged but not early accumulation of DC.  This was accompanied by inadequate growth of the vascular network, and reduced expression of the leukocyte tethering ligand, PNAd, within high endothelial venule (HEV) regions, all of which can contribute to LN expansion.  Overall, our study reveals that S1PR4 plays an important amplifying role during the early innate response that affects the magnitude of a downstream GC reaction.

overall_design: Differential expression of wild type and S1PR4 knockout in Tfh cells, non-Tfh CD4 T-cells, germinal center B-cells, and non-germinal center B-cells.

first: Andrea

middle: J

last: Luker

first: Abigail

last: Wukitch

first: Joseph

middle: M

last: Kulinski

first: Sundar

last: Ganesan

first: Juraj

last: Kabat

first: Justin

last: Lack

first: Pamela

last: Frischmeyer-Guerrerio

first: Dean

last: Metcalf

first: Ana

last: Olivera


title: RNA sequencing of extracellular vesicles, secreted by young and adult mouse adipocytes

summary:
This SuperSeries is composed of the SubSeries listed below.
Article: Röszer T., MicroRNA Profile of Mouse Adipocyte-Derived Extracellular Vesicles


title: TetR-like regulator BP1026B_II1561 controls aromatic amino acid biosynthesis and intracellular pathogenesis in Burkholderia pseudomallei [RNA-seq]

status: Public on Jul 31 2024

city: Honolulu

first: Ian

last: McMillan

state: HI

address: 1800 East-west road

institute: University of Hawaii

summary: We identified BP1026b_II1561 to be an important transcriptional regulator controling late stages of intracellular infection. RNA-seq analysis was performed to further investigate the regulatory network of II1561 regulation. ChIP-seq was also performed under the same conditions.

overall_design: Differential gene expression and ChIP seq was performed comparing a strain expressing II1561 to an empty vector control.

first: Michael

last: Norris

first: Tung

middle: T

last: Hoang


title: RNA sequencing of extracellular vesicles, secreted by young and adult mouse adipocytes [RNA-Seq]


title: In vivo CRISPR screens identify a dual function of MEN1 in regulating tumor-microenvironment interactions [CT26 IMC RNA-seq]

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

country: China

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

summary: In this study, we used a targeted CRISPR/Cas9 screen to identify genes that determine growth of A549 cells in vivo and in vitro.

overall_design: mRNA profiling of wild-type(WT) and Men1 knockout CT26 cells

first: Peiran

last: Su

first: Housheng

last: He

first: Ming-Sound

last: Tsao

first: Tianyi

last: Chen


title: TetR-like regulator BP1026B_II1561 controls aromatic amino acid biosynthesis and intracellular pathogenesis in Burkholderia pseudomallei [ChIP-seq]


title: Evaluation of the Mammalian Aquaporin Inhibitors Auphen and Z433927330 in Treating Breast Cancer

city: South Bend

first: Verodia

last: Charlestin

state: IN

address: 1234 N. Notre Dame Ave

department: Chemistry and Biochemistry

institute: University of Notre Dame

summary: AQPs contribute to breast cancer progression and metastasis. We previously found that genetic inhibition of Aqp7 reduces primary tumor burden and metastasis in breast cancer. In this study, we utilized two AQP inhibitors, Auphen and Z433927330, to evaluate the efficacy of therapeutic inhibition of AQPs in breast cancer treatment. The inhibitors were evaluated in breast cancer for both cytotoxicity and in metabolic stability assays across both murine and human breast cancer cell lines. Both AQP inhibitors also affected expression of other AQP transcripts and proteins, which demonstrates compensatory regulation between AQP family members. As a single agent, Auphen treatment in vivo extended overall survival but did not impact primary or metastatic tumor burden. However, Auphen treatment made cells more responsive to chemotherapy (doxorubicin) or endocrine treatment (tamoxifen, fulvestrant). In fact, treatment with Tamoxifen reduced the overall AQP7 protein expression. RNA-Seq of breast cancer cells treated with Auphen identified mitochondrial metabolism genes as impacted by Auphen and may contribute to reducing mammary tumor progression, lung metastasis, and increased therapeutic efficacy of endocrine therapy in breast cancer. Interestingly, we found that Auphen and tamoxifen cooperate to reduce breast cancer cell viability, which suggests that Auphen treatment makes the cells more susceptible to Tamoxifen. Together, this study highlights AQPs as therapeutic vulnerabilities of breast cancer metastasis that are promising and should be exploited. However, the pharmacologic results suggest additional chemical refinements and optimization of AQP inhibition are needed to make these AQP inhibitors appropriate to use for therapeutic benefit in overcoming endocrine therapy resistance.

overall_design: To understand how Auphen contributes to the cooperative effects of combination treatment and cell viability, we analyzed gene expression by conducting RNA-sequencing (RNA-Seq) analysis of vehicle or Auphen treated PyMT and MCF-7 cells.

first: Elijah

last: Tan

first: Carlos

middle: E

last: Arias-Matus

first: Junmin

last: Wu

first: Maria

middle: C

last: Miranda-Vergara

first: Mijoon

last: Lee

first: Man

last: Wang

first: Dharma

last: Nannapaneni

first: Parinda

last: Tennakoon

first: Brian

last: Blagg

first: Brandon

middle: L

last: Ashfeld

first: William

last: Kaliney

first: Jun

last: Li

first: Laurie

last: Littlepage


title: Transcriptomic changes in oligodendrocytes and precursor cells predicts clinical outcomes of Parkinson's disease

city: Tuebingen

first: Mo

last: Dehestani

address: Otfried-Müller-Straße 23

institute: DZNE

summary: Several prior studies have proposed the involvement of various brain regions and cell types in Parkinson's disease (PD) pathology. Here, we performed snRNA-seq on the prefrontal cortex and anterior cingulate regions from post-mortem control and PD brain tissue. We found a significant association of oligodendrocytes (ODCs) and oligodendrocyte precursor cells (OPCs) with PD-linked risk loci and report several dysregulated genes and pathways, including regulation of tau-protein kinase activity, regulation of inclusion body assembly and protein processing involved in protein targeting to mitochondria. In an independent PD cohort with clinical measures (681 cases and 549 controls), polygenic risk scores derived from the dysregulated genes significantly predicted Montreal Cognitive Assessment (MoCA)-, and Beck Depression Inventory-II (BDI-II)-scores but not motor impairment (UPDRS-III). We extended our analysis of clinical outcome prediction by incorporating three separate datasets that were previously published by different laboratories. In the first dataset from the anterior cingulate cortex, we identified a correlation between ODCs and BDI-II. In the second dataset obtained from the substantia nigra (SN), OPCs displayed notable predictive ability for UPDRS-III. In the third dataset from the SN region, a distinct subtype of OPCs, labeled OPC_ADM, exhibited predictive ability for UPDRS-III. Intriguingly, the OPC_ADM cluster also demonstrated a significant increase in PD samples. These results suggest that by expanding our focus to glial cells, we can uncover region-specific molecular pathways associated with PD symptoms.

overall_design: The study investigated postmortem brain tissues from four male Parkinson's disease (PD) patients and two healthy controls, aged between 65 and 80. The PD patients had either the LRRK2 G2019S or the GBA1 mutations (samples 1 and2 with L444P and samples 5 and 6 with E326K), while the controls were healthy. Brain regions, specifically the prefrontal cortex and anterior cingulate cortex, were analyzed. The tissues were sourced from the Netherlands Brain Bank and UCL Queen Square Brain Bank, adhering to institutional ethical guidelines. Single nuclei were isolated from the tissues using a detergent lysis technique, followed by RNA sequencing using 10x Genomics technology to generate single-cell gene expression libraries. Quality control and differential gene expression analyses were performed to identify disease-relevant cell types. The study also incorporated cell-type-specific gene expression association with genetic risk of PD using MAGMA and polygenic risk scores, highlighting differences in gene expression profiles between PD patients and controls.

first: Mohammad

first: Velina

last: Kozareva

first: Cornelis

last: Blauwendraat

first: Ernest

last: Fraenkel

first: Thomas

last: Gasser

first: Vikas

last: Bansal


title: Spatial Transcriptomic Analysis Of Primary And Metastatic Pancreatic Cancers Highlights Tumor Microenvironmental Heterogeneity

city: Indianapolis

first: Ashiq

last: Masood

address: Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine

department: Hematology & Oncology

institute: IU School Of Medicine

summary: Although the spatial, cellular, and molecular landscapes of resected pancreatic ductal adenocarcinoma (PDAC) are well documented, the characteristics of its metastatic ecology remain elusive. By applying spatially resolved transcriptomics to matched primary and metastatic PDAC samples, we discovered a conserved continuum of fibrotic, metabolic, and immunosuppressive spatial ecotypes across anatomical regions. We observed spatial tumor microenvironment heterogeneity spanning beyond previously appreciated in PDAC. Through comparative analysis, we show the  spatial ecotypes exhibit distinct enrichment between primary and metastatic sites, implying adaptability to the local environment for survival and progression. The invasive border ecotype exhibits both protumorigenic and antitumorigenic cell-type enrichment, suggesting a potential immunotherapy target. The ecotype heterogeneity across patients emphasizes the rationale to map individual patient landscapes to develop personalized treatment strategies. Collectively, our findings provide critical insights into metastatic PDAC biology and serve a valuable resource for future therapeutic exploration and molecular investigations.

overall_design: An atlas of Spatial Transcriptomics from a unique cohort of 30 specimens: 10 primary PDAC tumors (PTs), 3 normal pancreata (NPs), 12 matched hepatic metastases (HMs), 5 matched lymph node metastases (LNMs), along with adjacent normal liver and lymph node tissues, totaling 91,496 spot transcriptomes.

first: Ateeq

last: Khaliq

first: Meenakshi

last: Rajamohan

first: Omer

last: Saeed


title: Chronic stress deficits in reward behaviour co-occur with low nucleus accumbens dopamine activity during reward anticipation specifically

city: Biberach an der Riss

first: Gregorio

last: Alanis-Lobato

address: Birkendorfer Str 65

department: Global Computational Biology and Digital Sciences

institute: Boehringer Ingelheim Pharma

summary: Whilst reward pathologies e.g., anhedonia and apathy, are major and common in stress-related neuropsychiatric disorders, their neurobiological bases and therefore treatment are poorly understood. Functional imaging studies in humans with reward pathology indicate that attenuated BOLD activity in nucleus accumbens (NAc) occurs during reward anticipation/expectancy but not reinforcement; potentially, this is dopamine (DA) related. In mice, chronic social stress (CSS) leads to reduced reward learning and effortful motivation and, here, DA-sensor fibre photometry was used to investigate whether these behavioural deficits co-occur with altered NAc DA activity during reward anticipation and/or reinforcement. In CSS mice relative to controls: (1) Reduced discriminative learning of the sequence, tone-on + appetitive behaviour = tone-on + sucrose reinforcement, co-occurred with attenuated NAc DA activity throughout tone-on and sucrose reinforcement. (2) Reduced effortful motivation during the sequence, operant behaviour = tone-on + sucrose delivery + tone-off / appetitive behaviour = sucrose reinforcement, co-occurred with attenuated NAc DA activity at tone-on and typical activity at sucrose reinforcement. (3) Reduced effortful motivation during the sequence, operant behaviour = appetitive behaviour + sociosexual reinforcement co-occurred with typical NAc DA activity at female reinforcement. Therefore, in CSS mice attenuated NAc DA activity is specific to reward anticipation and as such potentially causal to deficits in learning and motivation. CSS did not impact on the transcriptome of ventral tegmentum DA neurons, suggesting that its stimulus-specific effects on NAc DA activity originate elsewhere in the neural circuitry of reward processing.

overall_design: Mice were injected in VTA with two viral vectors, each of which expressed a fluorescent protein, one under the control of the promoter for tyrosine hydroxylase (Th) to label DA neurons (EGFP+), and the other under the control of the promoter for glutamic acid decarboxylase 67 (Gad1) to label GABA interneurons (mScarlet-I+). After recovery, mice underwent CSS (n=5) or CON (n=6)  and, after an interval of 3 days, were then euthanized and perfused with PBS for blood-free brain collection. From the frozen brains, coronal sections including the VTA were cut at 10 µm, mounted onto PET membrane slides and dehydrated-fixed. Using laser capture microdissection, samples (Ø=35 µm) of EGFP+ tissue i.e., the putative cell bodies of DA neurons, were collected, whilst simultaneously avoiding any tissue samples that were also m-Scarlet-I+, i.e., overlapping putative cell bodies of GABA interneurons. Per mouse, n = ~500 neurons were collected, pooled, lysed, and RNA extraction and library preparation were followed by RNA sequencing.

first: Chengeng

last: Zhang

first: Alec

last: Dick

first: Christopher

middle: R

last: Pryce


title: Identification of potential genomic targets of CDCA7

first: Bin

last: Liu

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: CDCA7, encoding a protein with a C-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a disease related to hypomethylation of peri/centromeric satellite DNA. Previous work suggests that the CDCA7 CRD is implicated in DNA binding, which plays a key role in directing the DNA methylation mechinery to peri/centromeric regions. To identify potential genomic targets of CDCA7, we performed ChIP-Seq using CDCA7 knockout (KO) mouse embryonic stem cells (mESCs) stably expressing HA-tagged wild-type (WT) or ICF mutant (R285H) mCDCA7.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-Seq) to identify CDCA7 genomic targets in mouse embryonic stem cells (mESCs).

first: Chen

last: Taiping

first: Hardikar

last: Swanand

first: Ying

last: Zhengzhou

first: Liu

last: Bin


title: Cut and run profiling of RELA binding sites in primary human proximal tubular cells

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

overall_design: We performed cut and run assay to identify RELA binding sites in human primary proximal tubular cells (Lonza) with or without TNFa treatment

first: Benjamin

last: Humphreys


title: Guselkumab reduces disease- and mechanism-related biomarkers more than adalimumab in patients with psoriasis: a VOYAGE 1 substudy

city: San Diego

first: Yanqing

last: Chen

address: 3210 Merryfield Row

institute: Johnson and Johnson

summary: In the phase 3 VOYAGE-1 trial (ClinicalTrials.gov identifier: NCT02207231), guselkumab demonstrated superior efficacy versus placebo and the tumor necrosis factor (TNF)-α antagonist, adalimumab, in patients with moderate-to-severe plaque psoriasis (Blauvelt et al., 2017). Here, skin samples were collected from patients in VOYAGE-1 and pharmacodynamic (PD) responses to guselkumab (vs adalimumab) treatment were assessed over 48 weeks.

overall_design: Psoriasis lesional skin (LS) and nonlesional skin (NL) samples were collected from 39 VOYAGE-1 trial patients who provided consent to participate in an optional skin biopsy substudy to evaluate PD effects on psoriasis transcriptomics, and were profiled using GeneChip HT HG-U133+ PM 96-Array Plate (Affymetrix, Santa Clara, CA, USA)

first: Andrew

last: Blauvelt

first: Richard

middle: G

last: Langley

first: Patrick

last: Branigan

first: Xuejun

first: Samuel

last: DePrimo

first: Keying

last: Ma

first: Brittney

last: Scott

first: Kim

last: Campbell

first: Ernesto

last: Muñoz-Elías

last: Papp


title: Single Cell Chromatin Accessibility Profiling on the human kidneys with acute kidney injury

summary: We performed paired single nucleus RNA-seq (snRNA-seq) and ATAC-seq (snATAC-seq) to generate multimodal single nucleus atlas of the human kidneys with acute kidney injury (AKI).

overall_design: We performed snRNA-seq/ snATAC-seq to n=4 postmortem cortex samples of human subjects with AKI


title: MYBL2 drives prostate cancer plasticity and identifies CDK2 as a therapeutic vulnerability in RB1-loss and neuroendocrine prostate cancer

status: Public on Jul 30 2024

city: Rockville

first: Kun-Lin

last: Ho

address: 10322 Strathmore Hall St Apt 405

institute: HJF

summary: Phenotypic plasticity is a recognized mechanism driving therapeutic resistance in prostate cancer (PCa) patients. While underlying molecular causations driving phenotypic plasticity have been identified, therapeutic success is yet to be achieved. To identify putative master regulator transcription factors (MR-TF) driving phenotypic plasticity in PCa, this work utilized a multiomic approach using genetically engineered mouse models of prostate cancer combined with patient data to identify MYBL2 as a significantly enriched transcription factor in PCa exhibiting phenotypic plasticity. Genetic inhibition of Mybl2 using independent murine PCa cell lines representing phenotypic plasticity demonstrated Mybl2 loss significantly decreased in vivo growth as well as cell fitness and repressed gene expression signatures involved in pluripotency and stemness. Because MYBL2 is currently not druggable, a MYBL2 gene signature was employed to identify cyclin-dependent kinase-2 (CDK2) as a potential therapeutic target. CDK2 inhibition phenocopied genetic loss of Mybl2 and significantly decreased in vivo tumor growth associated with enrichment of DNA damage. Together, this work demonstrates MYBL2 as an important MR-TF driving phenotypic plasticity in PCa. Further, high MYBL2 activity identifies PCa that would be responsive to CDK2 inhibition.

overall_design: To investigate the function of Mybl2 in the development of phenotypic plasticity in neuroendocrine like prostate cancer models, we established two Mybl2 KO cell lines using a CRISPR/Cas9

first: Leigh

last: Ellis


title: MYBL2 drives prostate cancer plasticity and identifies CDK2 as a therapeutic vulnerability in RB1-loss and neuroendocrine prostate cancer [ChIP-seq]

overall_design: To investigate the change in the regulatory landscape in phenotypic plasticity in prostate cancer we performed H3K27ac ChIPseq in Pten KO (SKO) and Pten:Rb1 KO (DKO) GEMMs.


title: Single-cell RNA sequencing of mouse forebrain cells 5 weeks after injections of a control AAV9 or a VEGF-C/D trap AAV9

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: In this work we have induced meningeal lymphatic ablation by decreasing the circulating levels of VEGF-C and -D (VEGF-C/D trap), via injection of an AAV9 expressing domains 1 to 3 of murine VEGFR3 coupled to an Ig domain (VEGF-C/D trap). Control mice were injected with an AAV9 expressing domains 4 to 7 of  murine VEGFR3 coupled to an Ig domain (controls). 5 weeks upon the initial injections, animals were perfused, and the forebrain tissue was collected and processed for single-cell RNA sequencing (10x Genomics).

overall_design: Young adult mice mice were injected intraperitoneally with AAV9 encoding a control vector (mVEGFR34–7-Ig, control) or soluble VEGFR3 (mVEGFR31–3-Ig, VEGF-C/D trap), at weeks 0 and 3. Hemi-forebrain samples were collected at week 5. Each individual sample results from brain cells pooled from 2 mice.

first: Sofia

last: das Neves

first: Nickoleta

last: Delivanoglou

first: Chiara

last: Starvaggi Cucuzza

first: Mateusz

last: Makuch

first: Francisco

last: Almeida

first: Megan

last: Barber

first: Guadalupe

last: Sanchez

first: Shanon

last: Rego

first: Racquelle

last: Schrader

first: Ayman

last: Faroqui

first: Jean-Leon

last: Thomas

first: Pamela

last: McLean

first: Tiago

last: Oliveira

first: Sarosh

last: Irani

first: Fredrik

last: Piehl

first: Sandro

last: Da Mesquita


title: RNA-seq comparison of YT-Indy based reconsituted cytotoxic T cells and primary activated CD8+ T cells

city: Vancouver

first: Govinda

last: Sharma

address: 7th floor, 675 W 10th Ave

department: Michael Smith Genome Sciences Centre

institute: British Columbia Cancer Research Institute

summary: Current tools for functionally profiling T cell receptors with respect to cytotoxic potency and cross-reactivity are hampered by difficulties in establishing model systems to test these proteins in the contexts of different HLA alleles and against broad arrays of potential antigens. We have implemented a granzyme-activatable sensor of T cell cytotoxicity in a universal prototyping platform which enables facile recombinant expression of any combination of TCR-, peptide-, and class I MHC-coding sequences and direct assessment of resultant responses. This system consists of an engineered cell platform based on the immortalized natural killer cell line, YT-Indy, and the MHC-null antigen-presenting cell line, K562. These cells were engineered to furnish the YT-Indy/K562 pair with appropriate protein domains required for recombinant TCR expression and function in a non-T cell chassis, integrate a fluorescence-based target-centric early detection reporter of cytotoxic function, and deploy a set of protective genetic interventions designed to preserve antigen-presenting cells for subsequent capture and downstream characterization. As part of the development of the system, we conducted an RNA-seq study to characterize transcript expression in the base YT-Indy cell line, the genome engineered YT-rCTL version in the presence or absence of cognate antigen-presenting cells, and primary tissue derived TCR-T comparator cells in the presence or absence of cognate antigen-presenting cells. These data represent a supplement to the bioRxiv pre-print (DOI 10.1101/2023.11.20.567960) and the final published version in npj Precision Oncology (2024). An identical dataset corresponding to this entry has also been previously deposited in the Zenodo repository (DOI 10.5281/zenodo.8428843).

overall_design: Files named YT-Indy denote unmodified, non-co-cultured samples of the YT-Indy base cell line. Files named with a3a-rCTL nomenclature denote YT-rCTL cell lines (YT-Indy cells transduced with all human CD3 and CD8 genes) harboring the a3a T cell receptor. Files named with a3a-TCRT nomenclature denote host effector cells are primary healthy donor cytotoxic T cells, isolated from cryopreserved healthy donor PBMC by sorting on CD8+ CD4- CD56- population, and activated by anti-CD3/28 stimulation. The additional modifier "AgExp" indicates that the corresponding effector cell format was co-cultured with antigen-bearing target cells for 12 hours prior to FACS re-isolation and immediate cryopreservation. Included here are raw paired-end 150bp Illumina reads in fastq format. Data is compressed as .gz files. These data are derived from RNA-seq conducted on polyA selected mRNA from flash-frozen cell pellets performed off-site using a commercial NGS service provider.

first: Robert

last: Holt


title: Effects of TrkB-ICD overexpression on the morphology, activity and transcriptome of cultured primary cortical neurons

city: Basel

last: Rodrigues

address: Mittlere Strasse 91

country: Switzerland

institute: Institute of Molecular and Clinical Ophthalmology Basel

summary: In Alzheimer’s disease (AD), amyloid β (Aβ)-triggered cleavage of TrkB-FL impairs brain-derived neurotrophic factor (BDNF) signaling, thereby compromising neuronal survival, differentiation, as well as synaptic transmission and plasticity. In addition to compromising canonical BDNF signalling pathways, TrkB-FL cleavage produces an intracellular fragment (TrkB-ICD), which was shown to accumulate in the nucleus and to display tyrosine kinase activity. To dissect the role of TrkB-ICD overexpression from the loss of endogenous signaling throught TrkB-FL, we used lentiviruses to overexpress the TrkB-ICD sequence in cultured primary cortical neurons and performed morphological, electrophysiological and transcriptomics studies. While TrkB-ICD overexpression did not affect cell survival, it caused a significant decrease in the number of dendritic spines, both compared to untransduced and GFP-transduced neurons. Furthermore, TrkB-ICD overexpressing neurons presented a hyperpolarized resting membrane potential and increased frequency of miniature excitatory postsynaptic currents (mEPSCs). Finally, TrkB-ICD overexpression was associated with the upregulation of genes involved in (i) neuronal survival, growth and differentiation; (ii) neuronal cytoarchitecture and spine morphology; (iii) neurodegenerative processes, including AD; and (iv) synaptic transmission and plasticity. Overall, these results show that TrkB-ICD overexpression causes dendritic spine loss, alters excitatory synaptic transmission and causes transcriptome-wide changes, namely in genes coding for proteins involved in synaptic processes.

overall_design:
To investigate the effects of TrkB-ICD overexpression, we transduced cultured primary cortical neurons at DIV3 with lentiviruses (LVs) expressing TrkB-ICD or enhanced green fluorescent protein [EGFP] (as a control), under the regulation of the neuron-specific CaMKIIa promoter. We also sequenced untransduced neurons from the same cell culture batches, as an additional control. For each condition, 3 biological replicates (i.e., from 3 independent cultures) were prepared.
We performed gene expression profiling analysis using data obtained from RNA-seq of the 3 experimental conditions mentioned above, using 3 biological replicates for each.
Using the gene expression profiles, we performed comparative analyses, namely differential gene expression and pathway enrichment using Gene Ontology (GO) terms.

first: Maria

last: Diógenes


title: Next Generation Sequencing Facilitates Quantitative Analysis of db/m and db/db bone marrow derived LSK (Lineage negative Sca1-ckit positive cells) Transcriptomes I

first: Neha

last: Mahajan

state: Indiana

address: 1160 W Michigan St

department: Ophthalmology

institute: Indiana University

summary: The Lin-Sca1+c-Kit+ (LSK) fraction of the bone marrow (BM) comprises multipotent hematopoietic stem cells (HSCs), which are vital to tissue homeostasis and vascular repair. While diabetes affects HSC homeostasis overall, the molecular signature of  transcriptome under the conditions of long-standing type 2 diabetes (T2D;>6 months) remains unexplored. We employed the strength of Next generation sequencing to to study the differential pattern of LSK transcriptome under chronic diabetes.

overall_design: mRNA sequencing on LSK cells isolated from the bone marrow of db/m and db/db mice (6 months diabetic).

first: Ashay

last: Bhatwadekar


title: ILC2-derived LIF licences progression from tissue-localized to systemic immunity

city: Cambridge

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

summary: Migration and homing of immune cells are critical for immune surveillance. Efficient trafficking is mediated by cellular expression of combinations of adhesion and chemokine receptors which guide immune cells, in response to chemokine signals, to specific locations within tissues and the lymphatic system. This supports tissue-localized immune reactions and systemic immunity. However, fundamental questions remain as to how these signals are initiated and regulated. Here we show that disruption of leukaemia inhibitory factor (LIF) production from group 2 innate lymphoid cells (ILC2s) prevents immune cells from leaving the lungs and migrating to the lymph nodes. During pulmonary viral infection this dysregulation leads to plasmacytoid dendritic cells becoming retained in the lungs where they improve tissue-localized anti-viral immunity. By comparison, during chronic allergen challenge the accumulation of immune cells in the lung leads to the pronounced formation of tertiary lymphoid structures in the lung, and a failure to seed the lymph nodes. Mechanistically, ILC2-derived LIF induces the production of the chemokine CCL21 from lymphatic endothelial cells lining the pulmonary lymphatic vessels, thereby licencing the homing of CCR7+ immune cells to lymph nodes. Thus, ILC2-derived LIF production dictates the egress of immune cells from the lungs regulating tissue versus systemic immunity and the balance between allergen and viral responsiveness in the lungs.

overall_design: This experiment was designed to analyze the gene expression profiles of lung ILC2s (from PBS challenged mice) and pDCs (from PBS or IL-33 challenged mice). Mice were challenged with IL-33 (Biolegend) (0.25 µg in 40 µl PBS) or PBS (40 µl) intranasally on three consecutive days. Lungs were harvested 24 h after the final dose.ILC2s and pDCs were purified from the lung of IL-33 or PBS intranasally treated mice. Lung tissue was predigested with 750 U ml-1 collagenase I (Gibco) and 0.3 mg ml-1 DNaseI (Sigma-Aldrich) before obtaining a single-cell suspension at 37 °C for 30 min; the tissue was passed through a 70 μm cell strainer.Cells were sorted by flow cytometry into PBS, 50% FCS, and RNA was extracted using the RNeasy Plus Micro kit (Qiagen). After assessment using a Bioanalyzer (Agilent), RNA was processed for RNA-seq using an Ovation RNA-seq System V2 (Nugen), fragmented using the Covaris M220 ultrasonicator and bar-coded using Ovation Ultralow Library Systems (Nugen). Samples were sequenced using an Illumina HiSeq 4000, by running a single-read 50-bp protocol. For the comparison of gene expression of ILC2s from different mouse tissues, the tissues were collected from unchallenged mice and processed as described in extract protocol.

first: Mayuri

last: Gogoi

first: Paula

last: Clark

first: Noe

last: Rodriguez Rodriguez

first: Morgan

last: Heycock

first: Michelle

last: Ko

first: Jane

last: Murphy

first: Victor

last: Chen

first: Shi-Lu

last: Luan

first: Helen

last: Jolin

first: Andrew

last: McKenzie


title: Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation [MeRIP-seq, RNA-seq, Ribo-seq]

city: Shenzhen

first: Hao

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

summary: Dinoflagellates, a class of unicellular eukaryotic phytoplankton, exhibit minimal transcriptional regulation, representing a unique model for exploring gene expression. The biosynthesis, distribution, regulation, and function of mRNA N1-methyladenosine (m1A) remain controversial due to its limited presence in typical eukaryotic mRNA. This study found that m1A, rather than N6-methyladenosine (m6A), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetrically distribution along mature transcripts. In Amphidinium carterae, we identified 6549 m1A sites characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 3196 genes, many involved in regulating carbon and nitrogen metabolism. With enrichment within 3'UTR, dinoflagellate mRNA m1A exhibits negative correlation with translation efficiency. Notably, nitrogen depletion led to a significant decrease in mRNA m1A. Furthermore, our analysis revealed that distinctive patterns of m1A modification influence the expression of metabolism-related genes through translation control. Thus, this study provides a comprehensive map of m1A in dinoflagellate mRNA, highlighting its crucial role as a post-transcriptional regulatory layer and enhancing the understanding of mRNA m1A modification.

overall_design: In order to gain further insight into the roles of m1A, particularly its methylation level, distribution, and how mRNA translation responds to N-depletion stress, we conducted MeRIP-seq, RNA-seq and Ribo-seq under both normal conditions and N-depletion conditions. For the MeRIP-seq, each of the three replicates under normal conditions and N-depletion conditions has an associated input. RNA-seq was also executed to capture the broader transcriptomic landscape, with three replicates for each condition. To delve deeper into the intricacies of mRNA translation in relation to these conditions, Ribo-seq was employed, for which we provide data from two replicates.

first: Chongping

last: Li

first: Ying

first: Yuci

last: Wang

first: Jia

last: Guo

first: Jiawei

last: Xu


title: Single Cell Chromatin Accessibility Profiling on the mouse kidneys with ischemia-reperfusion injury

first: Yoshiharu

last: Muto

summary: We performed single nucleus ATAC (snATAC-seq) to generate cell-type-specific chromatin accessibility atlas of the mouse kidneys with ischemia-reperfusion injury. The single nucleus RNA-seq of the same samples were previously published (GEO139107)

overall_design: We performed single snATAC-seq of the mouse kidneys along a time course after ischemia-reperfusion injury (sham, 4 hr, 12 hr, 2 days, 14 days and 42 days after IRI).

first: Benjamin

last: Humphreys


title: Mouse kidneys with ischemia-reperfusion injury; Human kidneys with acute kidney injury; RELA binding sites in primary human proximal tubular cells

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

overall_design: Refer to individual Series


title: MYBL2 drives prostate cancer plasticity and identifies CDK2 as a therapeutic vulnerability in RB1-loss and neuroendocrine prostate cancer [ATAC-seq]

first: Kun-Lin

last: Ho

overall_design: To investigate the change in chromatin asseccibility landscape in phenotypic plasticity in prostate cancer we performed ATACseq in Pten KO (SKO) and Pten:Rb1 KO (DKO) GEMMs.

first: Leigh

last: Ellis


title: RNAseq analysis of blood from influenza infected patients and healthy controls SIG-2018

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary:
Gene expression changes in the blood was studied by RNAseq; project SIG-2018
Results: Strong differential host reponse after infection with influenza virus compared to healthy controls

overall_design: Peripheral blood was collected from patients, RNA was isolated and sequenced.


title: Next Generation Sequencing Facilitates Quantitative Analysis of db/m and db/db bone marrow derived LSK (Lineage negative Sca1-ckit positive cells) Transcriptomes II

first: Neha

last: Mahajan

overall_design: Micro RNA sequencing on LSK cells isolated from the bone marrow of db/m and db/db mice (6 months diabetic).

first: Ashay

last: Bhatwadekar


title: In vitro assessment of the immunomodulatory effects of probiotic Bacillus strains on chicken PBMCs

status: Public on Jul 29 2024

city: Berlin

first: Filip

last: Larsberg

address: Unter den Linden 6

department: Crop and Animal Sciences

institute: Humboldt-Universität zu Berlin

summary: The beneficial effects of feeding probiotic Bacillus subtilis DSM 32315 (BS) and Bacillus velezensis CECT 5940 (BV) to chickens in vivo are well-documented, with potential immune modulation as a key mechanism. In this study, we investigated the direct interactions of chicken peripheral blood mononuclear cells (PBMCs) with BS or BV in vitro through whole transcriptome profiling and cytokine array analysis. Transcriptome profiling revealed 20 significantly differentially expressed genes (DEGs) in response to both Bacillus treatments, with twelve DEGs identified in BS-treated PBMCs and eight in BV-treated PBMCs. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated significant regulation of immune-related pathways by both BS and BV. Notably, BS treatment upregulated genes associated with immune cell surface markers (CD4, CD25, CD28), anti-inflammatory cytokine interleukin-10 (IL-10), and C-C motif chemokine ligand 5 (CCL5), while downregulating the gene encoding pro-inflammatory IL-16. BV treatment similarly affected genes associated with immune cell surface markers, IL-16, and CCL5, with no impact on the gene encoding IL-10. Both treatments induced higher expression of the gene encoding the avian β-defensin 1 (AvBD1). The results of this in vitro study indicate an immunomodulatory effect of BS and BV in chicken PBMCs by regulating genes involved in anti-inflammatory, bacteriostatic, protective, and pro-inflammatory responses. Consequently, BS and BV may serve to augment the immune system’s capacity to defend against infection by modulating immune responses and cytokine expression. Thus, the administration of these probiotics holds promise for reducing reliance on antimicrobials in farming practices.

overall_design: RNA-sequencing was performed for the comparative gene expression analysis of PBMCs from six different chickens (biological replicates) of pooled experimental (technical) duplicates from each chicken after treatment with either BS, BV or conA or untreated samples (medium).

first: Maximilian

last: Sprechert

first: Deike

last: Hesse

first: Clemens

last: Falker-Gieske

first: Gunnar

last: Loh

first: Gudrun

last: Brockmann

first: Susanne

last: Kreuzer-Redmer


title: Longitudinal transcriptomic analysis reveals persistent enrichment of iron homeostasis and erythrocyte function pathways in severe COVID-19 ARDS

city: COLUMBUS

first: Joseph

last: Bednash

state: OH

address: 473 W 12th Avenue, DHLRI 509

department: Medicine

institute: Ohio State University

summary: The acute respiratory distress syndrome (ARDS) is a common complications of severe COVID-19 and contributes to patient morbidity and mortality. ARDS is a heterogeneous syndrome caused by various insults, and results in acute hypoxemic respiratory failure. Patients with ARDS from COVID-19 may represent a subgroup of ARDS patients with distinct molecular profiles that drive disease outcomes. Here, we hypothesized that longitudinal transcriptomic analysis may identify distinct dynamic pathobiological pathways during COVID-19 ARDS. We identified a patient cohort from an existing ICU biorepository and established three groups for comparison: 1) patients with COVID-19 ARDS that survived hospitalization (COVID survivors, n = 4), 2) patients with COVID-19 ARDS that did not survive hospitalization (COVID non-survivors, n = 5), and 3) patients with ARDS from other causes as a control group (ARDS controls, n = 4). RNA was extracted from peripheral blood mononuclear cells (PBMCs) at 4 time points (Days 1, 3, 7, and 10 following ICU admission) and prepared for RNA sequencing with rRNA depletion and library generation for Illumina. An Illumina NovaSeq X Plus instrument was used to generate 150 base pair paired-end reads, which were aligned to the hg GRCh38.96 reference genome using HiSAT2. Differential expression analysis was performed with DESeq2.

overall_design: Transcriptome profiles via RNA-Seq from peripheral blood mononuclear cells (PBMCs) from ARDS patients with fatal COVID-19, non-fatal COVID-19, and non-COVID controls.

first: Moemen

last: Eltobgy


title: RNAseq analysis of blood from influenza infected patients and healthy controls-SIG2019

summary:
Gene expression changes in the blood was studied by RNAseq; project SIG-2019
Results: Strong differential host reponse after infection with influenza virus compared to healthy controls


title: Single cell RNA sequencing of aging neural progenitors reveals loss of excitatory neuron potential and a population with transcriptional immune response (scRNA-Seq)

city: Lund

first: Henrik

last: Ahlenius

address: Sölvegatan 19

department: Department of Experimental Medical Science

country: Sweden

institute: Lund University

summary: In the adult murine brain, neural stem cells (NSCs) reside in two main niches, the dentate gyrus (DG), and the subventricular zone (SVZ). In the DG, NSCs give rise to intermediate progenitors that differentiate into excitatory neurons, while progenitors in the SVZ migrate to the olfactory bulb (OB) where they mainly differentiate into inhibitory interneurons. Neurogenesis, the production of new neurons, persists throughout life but decrease dramatically during aging, concomitantly with increased inflammation. Many cell types, including microglia, undergo dramatic transcriptional changes but few such changes have been detected in neural progenitors. Furthermore, transcriptional profiles in progenitors from different neurogenic regions have not been compared at single cell level, and little is known about how they are affected by age-related inflammation. We have generated a single cell RNA sequencing dataset enriched for intermediate progenitors, which revealed that most aged neural progenitors only acquire minor transcriptional changes. However, progenitors set to become excitatory neurons decrease faster than others. In addition, a population in the aged SVZ, not detected in the OB, acquired major transcriptional activation related to immune responses. This suggests that differences in age related neurogenic decline between regions is not due to tissue differences but rather cell type specific intrinsic transcriptional programs, and that subset of neuroblasts in the SVZ react strongly to age related inflammatory cues.

overall_design: OB were isolated, and SVZ and DG dissected from brains of adult (3-4 months), mid-aged (12-16 months) and aged (18-24 months) heterozygote Dcx-GFP mice. Tissue from 4-5 mice were pooled, for each region and age respectively, dissociated into a single cell suspension and separated with fluorescence-activated cell sorting (FACS) based on endogenous GFP.

first: Jonas

last: Fritze

first: Stefan

last: Lang

first: Mikael

last: Sommarin

first: Shamit

last: Soneji


title: RNAseq analysis of blood from influenza infected patients and healthy controls

first: Klaus

last: Schughart

summary:
Gene expression changes in the blood was studied by RNAseq
Results: Strong differential host reponse after infection with influenza virus compared to healthy controls
project SIG_2020


title: Single cell RNA sequencing of aging neural progenitors reveals loss of excitatory neuron potential and a population with transcriptional immune response


title: RNAseq analysis of blood from influenza infected patients and healthy controls, project SIG_2022

summary: Goals: Study responses in peripheral blood of patients infected with influenza virus and compare to healthy control. Results: Strong differential host reponse after infection was observed.

overall_design: Gene expression changes in the blood was studied by RNAseq; 19 infected, 22 healthy controls


title: Phase Separation of ARID1A Chromatin Remodeling Factor Promotes Oncogenic Potential of Ewing’s Sarcoma

status: Public on Jul 27 2024

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

summary: We charaterized the effect of ARID1A phase separation on transcriptome/epigenome/3D chromatin structure in Ewing's Sarcoma cancer cell line

overall_design: RNA-seq and ATAC-seq were performed on 6 ARID1A LLPS-positive and 7 ARID1A LLPS-negative A673 cell lines. In situ Hi-C was performed on 2 ARID1A LLPS-positive and 2 negative A673 cell lines.

first: Y

last: Kim

first: J

last: Joo

last: Shin

first: S

last: Baek


title: MicroRNA expression data in the liver of offspring with maternal tobacco exposure

status: Public on Jul 28 2024

city: Iksan

first: Daram

last: Yang

address: 79, Gobong-ro

institute: Jeonbuk National University

summary:
We used microarrays to evaluate effects of prenatal exposure to maternal cigarette smoke on the liver in offspring.
We observed that among miRNAs with >1.5-fold change value, 28 miRNAs were upregulated and 64 miRNAs were downregulated. Among these miRNAs, the most profoundly altered one was miR-34a-5p with a fold change of -4.379 (p = 0.007).

overall_design: On day 6 after pregnancy, pregnant dams were exposed to mainstream cigarette smoke (600 μg/L; CS600) or filtered clean (Cont) air for 2 hours a day, 5 days a week for two weeks using a nose-only exposure system. Male offspring mice were studied at postnatal week 4. Microarray analysis carried out in Cont and CS600 groups without any liver injuries to explore potential hepatic miRNAs that might be affected by maternal smoking.

first: Bumseok


title: Single cell RNA sequencing of aging neural progenitors reveals loss of excitatory neuron potential and a population with transcriptional immune response (RNA-Seq)


title: Germinal Center B cell transcriptional profiles in Mef2b-P297L mutant mice

status: Public on Jul 26 2024

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: The MEF2B transcription factor is frequently mutated in germinal center (GC)-derived B-cell lymphomas. Its N-terminal mutations drive lymphomagenesis by escaping interaction with transcriptional repressors, while the function of C-terminal mutations remains to be elucidated. Here, we show that MEF2B C-tail is physiologically phosphorylated at specific residues and phosphorylation at S324 is impaired by lymphoma-associated mutations. Lack of phosphorylation at S324 enhances the interaction of MEF2B with the SWI/SNF chromatin remodeling complex, leading to higher transcriptional activity. In addition, these mutants show an increased protein stability due to impaired interaction with the CUL3/KLHL12 ubiquitin complex. Mice expressing a phosphorylation-deficient lymphoma-associated MEF2B mutant display GC enlargement and develop GC-derived lymphomas, when crossed with Bcl2 transgenic mice. These results unveil converging mechanisms of action for a diverse spectrum of MEF2B mutations, all leading to its dysregulation and GC B-cell lymphomagenesis. These assorted mechanisms provide additional opportunities for the development of targeted therapeutic approaches.

overall_design: The dataset includes: wild-type mice (WT); mice expressing 1 wt and 1 mutant Mef2b allele in GC B cells (P297L-HET); mice expressing two mutant Mef2b alleles in GC B cells (P297L-HOMO). Three to four mice for each genotype have been analyzed.

first: Katia

last: Basso

first: Antony

middle: B

last: Holmes


title: MEF2B C-terminal mutations enhance transcriptional activity and stability to drive B cell lymphomagenesis


title: EZH2 represses mesenchymal genes and upholds epithelial identity in breast cancer cells

city: Granada

first: Ivan

middle: Fernández

last: Rengel

address: Avenida de la Ilustración 114

country: Spain

institute: GENyO

summary: Emerging studies support that the Polycomb Repressive Complex 2 (PRC2) regulates phenotypic changes of cancer cells by modulating their shifts among metastable states within the epithelial and mesenchymal spectrum. This new role of PRC2 in cancer has been recently proposed to stem from the ability of its catalytic subunit EZH2 to bind and modulate the transcription of a large set of mesenchymal genes during epithelial-mesenchymal transition (EMT) in lung cancer cells. Here, we asked whether this mechanism is conserved across different types of carcinomas. By combining TGF-β-mediate reversible induction of epithelial to mesenchymal transition and pharmacological inhibition of EZH2 activity we demonstrate that EZH2 represses a large set of mesenchymal genes and favours the residence of breast cancer cells towards the more epithelial spectrum during EMT in breast cancer cells.

overall_design: mRNA analysis of breast cancer adenocarcinoma cells treated with EZH2 chemical inhibitors. In addition, MCF-7 cells were exposed to TGF-β-mediate reversible induction of epithelial to mesenchymal transition in the presence or absence of EZH2 inhibitor

first: Amador

last: Gallardo

last: Fernandez-Rengel

first: Andrea

last: Serrano

first: Lourdes

last: Lopez-Onieva

first: David

last: Landeira


title: Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer (RNA-Seq)

status: Public on Jul 25 2024

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

summary: Neuroendocrine-like differentiation of castration-resistant prostate cancer is highly aggressive and independent of the androgen receptor signaling for its progression. During such lineage differentiation, adenocarcinoma adopts basal and neuronal characteristics that alter its clinical progression, limiting its therapeutic opportunities. Inadequate understanding of the molecular mechanism for such transformation also restricts its targeted therapies. Using ATAC-Seq, acetylated-histone ChIP-seq, and RNA-seq, we have characterized the early transformation process and identified chromatin occupancy and gene expression differences between adenocarcinoma and neuroendocrine-like cancer cells. By comparing differentially active promoter signatures during lineage-specific transcriptional events, our results indicate that the transcription factor Pax5 plays a major role in the trans-differentiation processes. Using LuCaP PDX tissues and metastatic prostate cancer TMA, in conjunction with patient RNA-expression databases, we validated that Pax5 is selectively expressed only in neuroendocrine like cancer but not in adenocarcinoma. Further analysis reveals that Pax5 expression is involved in neuronal gene expression and critical for imparting therapy resistance. Further, our results indicate that increased hydroxymethylation at the Pax5 promoter leads to recruitment of the homeobox transcription factor Pbx1 for Pax5 transcription. This is in line with our findings that lineage-specific expression of Pbx1/Pax5 is associated with the development of neuroendocrine-like differentiation. Our study suggests, upon continuous exposure to anti-androgen therapeutic stress, chromatin modifications are associated with Pax5-mediated gene expression to adopt neuroendocrine-like characteristics of advanced prostate cancer.

overall_design: The gene expression was analyzed in triplicate in each conditions. Gene expression was compared either with adenocarcinoma vs neuroendocrine like cell lines or between control and Pax5 depleted condition in neuroendocrine cells. Following Pax5 depletion by siRNA for 48hrs, gene expression was carried out.

first: H

last: Harris

last: Bhattacharya

last: Dutta

first: M


title: Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer (ATAC-Seq)

overall_design: The ATAC-seq was carried in duplicates using adenocarcinoma and NEPC cell lines.


title: ARID1 is required to regulate and reinforce H3K9me2 in sperm cells in Arabidopsis

status: Public on Jul 24 2024

city: Shanghai

first: Lei

last: Li

address: Xinjiangwancheng

institute: Fudan University

summary: Heterochromatin de-condensation in companion gametic cells is conserved in both plants and animals. In plants, microspore undergoes asymmetric pollen mitosis (PMI) to produce a vegetative cell (VC) and a generative cell (GC). Subsequently, the GC undergoes pollen mitosis (PMII) to produce two sperm cells (SC). Consistent with heterochromatin de-condensation in the VC, H3K9me2, a heterochromatin mark, is barely detected in VC. However, how H3K9me2 is differentially regulated during pollen mitosis remains unclear. Here, we show that H3K9me2 is gradually evicted from the VC since PMI but remain unchanged in the GC and SC. ARID1, a pollen-specific transcription factor that facilitates PMII, promotes H3K9me2 maintenance in the GC/SC but slows down its eviction in the VC. The genomic targets of ARID1 mostly overlaps with H3K9me2 loci, and ARID1 recruits H3K9 methyltransferase SUVH6. Our results uncover that differential pattern of H3K9me2 between two cell types is regulated by ARID1 during pollen mitosis.

overall_design: ChIP-seq for H3K9me2 in Col-0 and arid1 was performed with 3 biological replicates each. ChIP-seq for SUVH6-YFP in Col-0 and arid1, CUT&Tag for ARID1-GFP were performed with 2 biological replicates each.

first: Binglian

last: Zheng


title: Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer (ChIP-Seq)

overall_design: The ChIP-seq was carried in duplicate using adenocarcinoma and NEPC cell lines.

first: Achyuth

last: Kalluchi


title: Metabolic and transcriptomic reprogramming in the transition from a proliferative to a quiescent state is mediated by YAP-dependent and YAP-independent mechanisms.

city: Chicago

first: Nissim

last: Hay

state: IL

address: 900 South Ashland Ave

department: BMG

institute: University of Illinois Chicago

summary: To investigate the proliferation-to-quiescence transition we looked at metabolic flux and gene expression in proliferating (P) and quiescent (Q) mouse embryonic fibroblasts.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Proliferating (P) and Quiescent (Q) cells.

first: Kang

last: Soeun

first: Hay

last: Nissim

first: Mark

last: Maienschein-Cline

first: Martinez

last: Carlos


title: Chromatin binding of MEF2B and SMARCA4 in normal human germinal center B cells

first: Riccardo

last: Dalla-Favera

overall_design: Cut&Run analyses of MEF2B and SMARCA4 bound regions in normal human GC B cells.

first: Katia

last: Basso

first: Antony

last: Holmes


title: TLR9 activation in large wound induces tissue repair and hair follicle regeneration via γδT cells

city: Chengdu

first: Xinhui

address: No.14,3Rd Section Of Ren Min Nan Rd.ChengDu,SiChuan 610041,China

institute: Sichuan university

summary: In order to investigate the specific characteristics influenced by the activation of TLR9 in wounds, we employed the single-cell RNA sequencing (scRNA-seq) to visually compare immune cells and inflammatory factors and cytokines under the influence of TLR9.

overall_design: Dorsal skin healed from large circular wound (diameter=1.8cm) of the C57/BL6 mice were collected and analyzed using scRNAseg.

first: Tiantian

last: An

first: Yang

last: Yang

first: Zhaoyu

last: Xu

first: Shuaidong

last: Chen

first: Zumu

last: Yi

first: Chen

last: Deng

first: Feng

last: Zhou

first: Yi

last: Man

last: Hu


title: Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in Myelodysplastic Syndromes and Acute Myeloid Leukemia (Screen)

city: Randwick

first: Julie

last: Thoms

state: NSW

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

country: Australia

institute: UNSW Sydney

summary: Hypomethylating agents (HMAs) are frontline therapies effective at altering the natural course of Myelodysplastic Neoplasms (MDS). However, acquired resistance and treatment failure are hallmarks of HMA therapy. Developing effective and rational HMA-focused combinatorial therapies is challenging as the underlying mechanisms driving HMA efficacy are complex. To address this clinical need, we performed a genome-wide CRISPR-Cas9 screen in a human MDS-derived cell line, MDS-L, and characterized TOPORS as a highly ranked target that synergizes with HMAs to reduce leukemic burden and improve survival in xenograft models. We demonstrated that the depletion of TOPORS mediates sensitivity to HMAs by predisposing leukemic blasts to an impaired DNA damage response (DDR) accompanied by an accumulation of SUMOylated DNMT1 in HMA-treated TOPORS-depleted cells. Importantly, the combination of HMAs with targeting of TOPORS did not functionally impair healthy hematopoiesis. While inhibitors of TOPORS are currently unavailable, we show that inhibition of SUMOylation (upstream of TOPORS functions) with TAK-981 partially phenocopies HMA-sensitivity and DDR impairment. Overall, our data suggest that the combination of HMAs with the inhibition of SUMOylation demonstrates a favourable therapeutic index and represents a rational framework towards the treatment of High-Risk MDS (HR-MDS) or Acute Myeloid Leukemia (AML).

overall_design:
To identify novel genetic determinants that regulate Azacitidine sensitivity in MDS, we performed a genome-wide CRISPR-Cas9 screen using MDS-L cells under AZA selection.
We transduced MDS-L-Cas9 cells with the Brunello sgRNA library and treated transduced cells with 0.3uM AZA or DMSO until the AZA-treatment arm underwent 12 cellular divisions to ensure robust depletion of essential genes.
We performed analyses using the MAGeCKFlute pipeline to identify essential, non-essential, and targeted genes that regulate Azacitidine sensitivity in MDS-L cells.

first: Peter

last: Truong

middle: I

first: Christopher

last: Jolly

first: John

last: Pimanda


title: Gene expression analysis of Saccharomyces cerevisiae subjected to sulfur starvation

city: Gif sur Yvette

first: Delphine

last: Naquin

address: avenue de la terrasse

institute: CNRS

summary:
To determine the genome-wide changes in gene expression associated with depletion of sulfur in S. cerevisiae,  we performed transcriptional profiling using RNA-seq before and at three time points after tranfer in medium without sulfur.
Genes downregulated and upregulated were identified by differential gene expression analysis of the RNA-seq data using DESeq2.

overall_design: RNA-seq was performed on three replicates of yeasts collected before and 40, 80 and 120 min after transfer to sulfur-free medium.

first: Laurent

last: Kuras


title: Intramyocardial Sprouting Tip Cells Specify Coronary Arterialization

first: Elena

last: Cano

address: Robert-Rossle str. 10

institute: Max-Delbruck Center

summary:
The elaborate patterning of coronary arteries critically supports the high metabolic activity of the beating heart. How coronary endothelial cells coordinate hierarchical vascular remodeling and achieve arteriovenous specification remains largely unknown. Understanding the molecular and cellular cues that pattern coronary arteries is crucial to develop innovative therapeutic strategies that restore functional perfusion within the ischemic heart.
Single-cell transcriptomics were used to delineate heterogeneous transcriptional states of the developing and mature coronary endothelium with a focus on sprouting endothelium and arterial cell specification. We discovered that a tip-cell-to-artery specification mechanism drives arterialization of the intramyocardial plexus and endocardial tunnels throughout life. We also identified non-overlapping intramyocardial and subepicardial tip cell populations with differential gene expression profiles and regulatory pathways, suggesting that differential sprouting programs govern the formation and specification of the venous and arterial coronary plexus.

overall_design:
CD31+/CD45- cardiac endothelial fractions were isolated by Fluorescent-Activated Sorting (FACS) of C57Bl6J mouse hearts at different stages. After completion of sorting, 10% DMSO was added and cell suspension frozen at -80ºC. Several rounds of single-cell suspension preparation, sorting and freezing was repeated for embryonic samples in order to get a significant number of cells: 8 weeks old adult animals (n=6), P2 postnatal (n=21), E15 (n=48) and E12 (n=37).
Frozen vials of sorted CD31+/CD45- cells from E12, E15, P2 and 8wo adult hearts were thawed in a water bath at 37ºC. For E12 and E15, a dead cell removal kit (Miltenyi) was applied. For P2 and adult, re-sorting by flow cytometry and selection of live cells was performed. Then, cell suspension  loaded on the Chromium controller (10X Genomics) with a targeted cell recovery of 8000-10000 per reaction. 3′ gene expression libraries were prepared according to the manufacturer’s instructions of the v2 Chromium Single Cell Reagent Kits (10X Genomics).


title: Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in Myelodysplastic Syndromes and Acute Myeloid Leukemia (RNA-Seq)

overall_design:
To investigate the role of TOPORS in regulating AZA sensitivity in MDS, we generated a TOPORS-ko MDS-L cell line using CRISPR-Cas9.
We then performed gene expression profiling analysis using bulk RNA-seq data obtained from control and TOPORS-ko MDS-L cells, treated with AZA or DMSO at D4.
We performed differential gene expression and differential splice event analyses using the resulting RNA-seq datasets.


title: hnRNP R promotes O-GlcNAcylation of eIF4G and facilitates axonal protein synthesis

city: Wuerzburg

first: Michael

last: Briese

state: Bavaria

address: Versbacherstr. 5

department: Institute of Clinical Neurobiology

institute: University Hospital Wuerzburg

summary: Motoneurons critically depend on precise spatial and temporal control of translation for axon growth and the establishment and maintenance of neuromuscular connections. While defects in local translation have been implicated in the pathogenesis of motoneuron disorders, little is known about the mechanisms regulating axonal protein synthesis. Here, we report that motoneurons derived from Hnrnpr knockout mice show reduced axon growth accompanied by lowered synthesis of cytoskeletal and synaptic components in axons. Mutant mice display denervated neuromuscular junctions and impaired motor behavior. In axons, hnRNP R is a component of translation initiation complexes and, through interaction with O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (Ogt), modulates O-GlcNAcylation of eIF4G. Restoring axonal O-GlcNAc levels rescued local protein synthesis and axon growth defects of hnRNP R knockout motoneurons. Together, these findings demonstrate a function of hnRNP R in controlling the local production of key factors required for axon growth and formation of neuromuscular innervations.

overall_design: RNA-seq analysis of the somatodendritic and axonal compartment of wildtype (WT) and hnRNP R knockout (KO) motoneurons cultured in microfluidic chambers.

first: Abdolhossein

last: Zare

first: Saeede

last: Salehi

first: Jakob

last: Bader

first: Cornelius

last: Schneider

first: Utz

last: Fischer

first: Alexander

last: Veh

first: Panagiota

last: Arampatzi

first: Matthias

last: Mann

last: Sendtner


title: Transcriptomic Profiling of Neutrophils and Low-Density Granulocytes in COVID-19 Patients

status: Public on Jul 23 2024

city: Helsinki

first: Tomas

last: Strandin

address: Haartmaninkatu 3

country: Finland

institute: University of Helsinki

summary: The severity of COVID-19 is linked to excessive inflammation. Neutrophils represent a critical arm of the innate immune response and are major mediators of inflammation, but their role in COVID-19 pathophysiology remains poorly understood. We conducted transcriptomic profiling of neutrophils obtained from patients with mild and severe COVID-19, as well as from non-infected healthy controls. Additionally, low-density granulocytes (LDGs) from patients with severe COVID-19 were included to understand their unique role. Transcriptomic analysis of polymorphonuclear cells (PMNs), consisting mainly of mature neutrophils, revealed a striking type I interferon (IFN-I) gene signature in severe COVID-19 patients, contrasting with mild COVID-19 and healthy controls. LDGs from severe COVID-19 patients exhibited an immature neutrophil phenotype and lacked this IFN-I signature. These findings underscore the crucial role of neutrophil inflammasomes in driving inflammation during severe COVID-19. The study provides insights into the pathological mechanisms of severe COVID-19 and highlights potential targets for therapeutic intervention.

overall_design: Neutrophils were isolated from peripheral blood of three different cohorts: patients with severe COVID-19, patients with mild COVID-19, and non-infected healthy controls. Additionally, low-density granulocytes (LDGs) were isolated from patients with severe COVID-19. cDNA synthesis from total RNA was performed using the Takara SMARTseq v4 Ultra-low input RNA kit for Sequencing. This was followed by library preparation using the Illumina Nextera XT Library preparation kit. Unique Dual Index (UDI) setup was used for the Nextera XT libraries. Library quality was assessed using the LabChip GX Touch HT High Sensitivity assay, and libraries were pooled based on the concentration measurements. The pooled libraries were quantified for sequencing using the KAPA Library Quantification Kit and sequenced on the Illumina NovaSeq6000 system using an S1 flow cell. The sequencing read length was 2x101 bp, and the paired-end run was conducted for 200 cycles. The study aims to elucidate the transcriptomic changes in neutrophils and LDGs during SARS-CoV-2 infection and their role in the inflammation associated with severe COVID-19.


title: Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

summary: Expansion of the glutamine tract (poly-Q) in the protein Huntingtin (HTT) causes the neurodegenerative disorder Huntington’s disease (HD). Emerging evidence suggests that mutant HTT (mHTT) disrupts brain development. To gain mechanistic insights into the neurodevelopmental impact of human mHTT, we engineered induced pluripotent stem cells to introduce a biallelic or monoallelic mutant 70Q expansion or to remove the poly-Q tract of HTT. The introduction of 70Q mutation caused aberrant development of cerebral organoids with loss of neural progenitor organization. The early neurodevelopmental signature of mHTT highlighted the dysregulation of the protein coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2), a transcription factor involved in mitochondrial integrated stress response. CHCHD2 repression was associated with abnormal mitochondrial morpho-dynamics that was reverted upon overexpression of CHCHD2. Removing the poly-Q tract from HTT normalized CHCHD2 levels and corrected key mitochondrial defects. Hence, mHTT-mediated disruption of human neurodevelopment is paralleled by aberrant neurometabolic programming mediated by dysregulation of CHCHD2, which could then serve as an early interventional target for HD.

overall_design: Single-cell RNA sequencing (scRNAseq) of the regionalized midbrain organoids at the day 35 of differentiation were prepared for  WT/WT and 70Q/70Q. The data were analyzed in three biological replicates, where each sample was composed of 48 midbrain organoids.


title: LSD1 inhibition improves efficacy of adoptive T cell therapy by enhancing CD8+ T cell responsiveness

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

summary: The lysine-specific histonedemethylase1A(LSD1) has been described to play a role in antitumor immunity; however, the role of LSD1 in shaping CD8+ T cell (CTL) differentiation and function is not understood. Here, we showed that pharmacological inhibition of LSD1 (LSD1i) in CTL elicited phenotypic and functional alterations of the CTL that led to robust antitumor immunity in the context of adoptive T cell therapy (ACT). In addition, the combination of anti-PDL1 therapy with LSD1i-based ACT resulted in a complete tumor eradication and long-lasting tumor-free survival. This study demonstrated that LSD1i together with anti-PDL1 therapy complement each other’s deficiencies and produce a better tumor response in a melanoma model, in which both immune and epigenetic therapy alone have shown limited efficacy. Collectively, these results set the translational potential of modulating LSD1 to improve antitumoral responses generated by ACT and anti-PDL1 therapy, which provide a strong rationale for a combination trial of LSD1i and immunotherapy.

overall_design: Comparative gene expression profiling analysis of CD8+ cells NT and treated with LSD1 inhibitor at 72h timepoint.

first: Silvia

last: Tiberti

first: Teresa

last: Frasconi

last: Manzo

last: Ceccacci


title: The role of the transcriptional co-regulator Lmo4 in CD8+ T cell stemness, memory formation and antitumor immunity

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

summary: We aimed to evaluate if Lmo4 is directly involved in the generation and preservation of stem cell-like T cells and if adoptively transferred Lmo4-overexpressing pmel-1 CD8+ T cells (which identify the shared melanoma-melanocyte differentiation antigen gp100) are therapeutically effective in mice bearing subcutaneous B16-hgp100 melanomas. Moreover, our purpose was to investigate the mechanisms by which Lmo4 regulates CD8+ T cell differentiation.

overall_design:
Gene expression was evaluated by RNA-seq of pmel-1 CD62L-KLRG1- T cells collected 5 d after transfer of 1 x 105 pmel-1 Thy1.1+ and Lmo4-Thy1.1+ CD8+ T cells into wild-type mice infected with gp100-vv (five mice per group)
R package edgeR was used to identify differentially expressed genes

first: Roland

last: Schelker

first: Luca

last: Gattinoni


title: Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure [organoids]

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrück Center for Molecular Medicine

summary: Expansion of the glutamine tract (poly-Q) in the protein Huntingtin (HTT) causes the neurodegenerative disorder Huntington’s disease (HD). Emerging evidence suggests that mutant HTT (mHTT) disrupts brain development. To gain mechanistic insights into the neurodevelopmental impact of human mHTT, we engineered induced pluripotent stem cells to introduce a 70Q expansion or remove the poly-Q tract of HTT. 70Q introduction caused aberrant development of cerebral organoids with loss of neural progenitor organization. The early neurodevelopmental signature of mHTT highlighted the dysregulation of the protein coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2), which is involved in mitochondrial integrated stress response. CHCHD2 repression was associated with abnormal mitochondrial morpho-dynamics and elevated resting energy expenditure. Elimination of the poly-Q tract of HTT normalized CHCHD2 expression and mitochondrial defects. Hence, mHTT-mediated disruption of human neurodevelopment is paralleled by aberrant neurometabolic programming mediated by dysregulation of CHCHD2, which could then serve as an early intervention target for HD.

overall_design: rRNA-depleted RNA was fragmented and processed into strand-specific cDNA libraries using TruSeq Stranded Total LT Sample Prep Kit (Illumina)

first: Selene

last: Lickfett

middle: K

last: Metzger

first: Alessandro

last: Prigione


title: Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure [NGN2]

first: Jakob


title: Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in Myelodysplastic Syndromes and Acute Myeloid Leukemia

first: Julie

last: Thoms

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

overall_design: Refer to individual Series


title: Microarray expression data of HCT116 with treatment (EI-52) or controls (DMSO)

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

institute: Centre Léon Bérard

summary:
The RAS pathway is frequently exploited by cancer cells to sustain their proliferation and survival. ERK is the most distal kinase in the RAS signaling cascade, playing a pivotal role in signaling output.
We performed a transcriptomic analysis to obtain an overview of the consequences of EI-52 (CER) treatment, an inhibitor of ERK protein-protein interaction, on the global cellular transcriptional activity.

overall_design: Messenger RNA was extracted from HCT116, after 18h treatment in triplicate with 6µM of EI52 (CER) or DMSO.

first: François

last: Virard

first: Toufic

last: Renno

first: Isabelle

last: Coste

first: Pierre

last: Saintigny


title: Transcriptomic and epigenomic profiling of Tet TKO neural stem cells to study NSC specification and multipotency

first: Meelad

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: In this study we: (1) identify genes deregulated in wildtype (WT) and Tet triple knockout (TKO) mouse embryonic stem cells (ESC) and neural stem cells (NSC). (2) Profile genome-wide changes in DNA methylation in WT and TKO ESCs and NSCs. (3) Map histone marks H3K4me1 and H3K27ac in WT and TKO ESCs and NSCs. (4) Identify promoter-interacting chromatin loops in WT and TKO NSCs.

overall_design: We investigated the role of TET DNA dioxygenases in regulation of neural stem cell (NSC) specification from mouse embryonic stem cells (ESC) using Tet wildtype (WT) and triple knockout (TKO) ESCs in a NSC differentiation model. Analysis and integration of RNA-seq, WGBS, and CUT&Tag revealed critical roles for TET enzymes in establishment of NSC gene expression, gliogenic competence, and enhancer activation. For all omics experiments, Tet-WT and Tet-TKO ESCs were harvested after pre-plating for 45 minutes to remove feeder cells. Tet-WT and Tet-TKO NSCs were harvested on day 6 (passage 1) of NSC culture. RNA-seq: RNA was extracted from three independent Tet-WT and two independent Tet-TKO ESC and NSC lines (Qiagen RNeasy mini kit). Library preparation and RNA-seq were performed by Novogene (https://en.novogene.com/) on an Illumina Novoseq 6000 platform and 20-30 million reads were generated per sample. WGBS: DNA was extracted from one clone of Tet-WT and Tet-TKO ESC and one clone of Tet-WT and Tet-TKO NSC (Quick-DNA miniprep kit - Zymo, D3024) and subjected to WGBS analysis at BGI genomics company (https://en.genomics.cn/). Lamda DNA spike-in confirmed the efficiency of bisulfite conversion (>99.0%). CUT&Tag: Two clones each of Tet-WT and Tet-TKO ESCs and NSCs were used to profile H3K4me1 and H3K27ac. Cells were crosslinked, bound to Con-A beads, incubated with primary antibody and treated with pre-loaded pA-Tn5 adapter complex. Libraries were prepared with NEBNext HiFi 2x PCR Master mix and sent for 75-bp paired-end sequencing on an Illumina NextSeq 500 platform at the Einstein Epigenomics core following their protocols. Promoter-capture HiC: Cells were crosslinked with 4% PFA and then library preparation, promoter-capture, and sequencing were carried out by Arima Genomics. Libraries were sequenced to a depth of 170-190 million raw read-pairs.  Details of RNA-seq, WGBS, CUT&Tag, and promoter-capture HiC procedure and data analyses are described in detail in the methods section of the manuscript.

first: Ian

last: MacArthur


title: Administration of anti-HIV-1 broadly neutralizing monoclonal antibodies with increased binding affinity to Fcg receptors during acute SHIV infection shapes innate and adaptive cellular immunity

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University


title: Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer

first: Jordan

last: Rowley


title: Neuromodulatory co-expression in cardiac vagal motor neurons of the Dorsal Motor Nucleus of the Vagus [spatial transcriptomics]

status: Public on Jul 22 2024

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

summary: The activity of the cardiac vagal innervation is well known to be crucial to the maintenance of cardiac health, and to protect and recover the heart from injury. Only recently has this role been shown to depend on the activity of the underappreciated Dorsal Motor Nucleus of the Vagus (DMV). By combining neural tracing, transcriptomics, and 3D mapping in male and female Sprague Dawley rats we characterize cardiac-specific neuronal phenotypes in DMV. We find that the DMV cardiac-projecting neurons differentially express PACAP, CART, and synucleins, as well as evidence that they participate in neuromodulatory co-expression involving catecholamines. The significance of these findings is enhanced by previous knowledge of the role of PACAP at the heart and of the other neuromodulators in peripheral vagal targets.

overall_design: Adult male Sprague Dawley rat brainstem 10 µm sections evenly spaced 200 µm apart were put on 2 Visium slides (8 sections total). Permeabilization, barcoding, library construction, and sequencing were performed for each 50 µm barcoded spot. We did this throughout the extent of the brainstem including the DMV at the level of Area Postrema.

first: Eden

last: Hornung

first: Shaina

last: Robbins

first: Sirisha

last: Achanta

first: James

last: Schwaber