title: ATG conjugation system -dependent and -independent mechanisms underlie lysosomal stress-induced TFEB regulation

city: Kashihara

first: Shuhei

last: Nakamura

state: Nara

address: 840 Shijo-cho

department: Department of Biochemistry

institute: Nara Medical University

summary: Transcription factor EB (TFEB), well characterized as a master regulator of autophagy and lysosomal biogenesis, is translocated to the nucleus and activated by varieties of cellular stresses including starvation and lysosomal damage. However, compared to the starvation condition, the molecular mechanism of TFEB activation by other stress conditions is poorly understood. Previously, we have shown that TFEB activation during lysosomal damage but not starvation condition depends on a subset of autophagy regulators, collectively called ATG conjugation system, whose function is essential for the lipidation of ATG8 proteins. In this study, by time-lapse imaging, we newly identified the presence of ATG conjugation system -independent TFEB regulation which precedes the ATG conjugation system-dependent regulation, designated mode I and mode II, respectively. Consistent with the presence of different modes, our time course transcriptome analysis revealed two different sets of TFEB downstream. Comprehensive interactome analysis of TFEB and subsequent functional screening identified unique regulars of TFEB in each mode: APEX1 for Mode I and CCT7 and/or TRIP6 for Mode II, respectively. APEX1 interacted with TFEB and was required for its protein stability in a manner independent of ATG conjugation system. On the other hand, both CCT7 and TRIP6 were accumulated on lysosomes during lysosomal damage and interacted with TFEB mainly in ATG conjugation system deficient cells, presumably blocking TFEB nuclear translocation. Moreover, we further revealed that TFEB regulatory mechanisms by other cellular stresses such as oxidative stress, proteasome inhibition, mitochondria depolarization, and DNA damage can be classified into either APEX1-mediated Mode I or TRIP6-mediated Mode II. Our results pave the way for a unified understanding TFEB regulatory mechanisms from the perspective of ATG conjugation system under varieties of cellular stresses.

overall_design: WT or ATG7 KO or TFEB KO treated with or without LLOMe in Hela cells

first: Shiori

last: Akayama

first: Tamotsu

last: Yoshimori


title: Placental PFAS concentrations are associated with perturbations of placental DNA methylation

status: Public on Jan 29 2025

city: Atlanta

first: Todd

last: Everson

state: GA

address: 1518 Clifton Road

department: Environmental Health

country: USA

institute: Rollins School of Public Health at Emory University

type: Methylation profiling by genome tiling array

summary: The placenta is crucial for fetal development, is affected by PFAS toxicity, and evidence is accumulating that gestational PFAS perturb the epigenetic activity of the placenta. Gestational PFAS exposure can adversely affect offspring, yet individual and cumulative impacts of PFAS on the placental epigenome remain underexplored. Here, we conducted an epigenome-wide association study (EWAS) to examine the relationships between placental PFAS levels and DNA methylation in a cohort of mother-infant dyads in Arkansas (N = 151). We measured 17 PFAS in human placental tissues and quantified placental DNA methylation levels via the Illumina EPIC Microarray. We tested for differential DNA methylation with individual PFAS, and with mixtures of multiple PFAS. Our results demonstrated that numerous epigenetic loci were perturbed by PFAS, with PFHxS exhibiting the most abundant effects. Mixture analyses suggested cumulative effects of PFOA and PFOS, while PFHxS may act more independently. We additionally explored whether sex-specific effects may be present and concluded that future large studies should explicitly test for sex-specific effects. The genes that are annotated to our PFAS-associated epigenetic loci are primarily involved in growth processes and cardiometabolic health, while some genes are involved in neurodevelopment. These findings shed light on how prenatal PFAS exposures affect birth outcomes and children's health, emphasizing the importance of understanding PFAS mechanisms in the in-utero environment.

overall_design: DNA methylation analysis for placental samples using the Illumina EPICv1 array.

middle: M


title: G-quadruplex DNA suppresses transcription during DNA replication

city: hefei

first: sun

last: xuedan

address: daoxiangcun

country: China

institute: ustc

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In eukaryotic cells, although the B-form double helix is the predominant structure of DNA, various non-B-form DNA structures, including G-quadruplex DNA (G4-DNA), are also widely present. For a long time, G4-DNA has been thought to impede DNA replication due to its unique spatial conformation. However, this study demonstrates that S phase G4-DNA accumulation, far from being a passive byproduct, actively functions as a critical safeguard for genomic stability. Contrary to the traditional view of G4-DNA as a replication barrier, its physiological increase during Early S phase minimizes impact on replication itself. Instead, S phase G4-DNA specifically suppresses transcription by stabilizing the negative elongation factor (NELF) complex, thereby preventing transcription-replication conflicts (TRCs) by spatiotemporally segregating transcription and replication. Replication Factor C3 (RFC3), a component of the replication machinery, directly binds and stabilizes G4-DNA to promote its S phase accumulation. Disruption of RFC3 function or G4-DNA unwinding during S phase releases transcriptional suppression, exacerbating TRCs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: [Cut-tag Experimental Design] The objective of this study is to investigate changes in G4-DNA structures and transcription-associated proteins across different cell cycle phases, as well as to examine the impact of RFC3 knockdown on these elements, using the HCCLM3 human hepatocellular carcinoma cell line. The experiment includes one biological replicate for each condition to capture the CUT&Tag data. In order to achieve these goals, HCCLM3 cells were subjected to thymidine synchronization, allowing us to obtain samples representing various stages of the cell cycle. This synchronization process facilitates the analysis of chromatin features specific to distinct cell cycle phases. Additionally, an shRNA-mediated knockdown of RFC3 was performed on synchronized cells to assess how reduced RFC3 expression affects G4-DNA structures and transcription-related proteins. The focus of this investigation is twofold: first, to elucidate the variations in G4-DNA and associated transcription factors as cells progress through different phases of the cell cycle; second, to determine the effect of RFC3 knockdown on G4-DNA formation and the levels or activity of transcription-related proteins. Unmanipulated HCCLM3 cells, which have not undergone synchronization or RFC3 knockdown, serve as control samples, providing a baseline for comparison. By conducting this study, we aim to gain deeper insights into the dynamics of G4-DNA and transcriptional regulation during the cell cycle and under conditions of RFC3 depletion. [scRNA-seq]The experimental design aims to investigate the alterations in various cell types within mouse hepatocellular carcinoma (HCC) tissue following the knockout of the RFC3 gene. For this purpose, two biological groups were established: one group consists of HCC tissues from mice treated with a control guide RNA (sgCtrl), while the other group comprises HCC tissues from mice subjected to RFC3 knockdown using a specific guide RNA (sgRFC3). By comparing the scRNA-seq profiles between these two groups, we seek to uncover the differential expression patterns and potential functional shifts across distinct cell populations in response to RFC3 depletion. This analysis will provide insights into the role of RFC3 in modulating cellular heterogeneity and tumor microenvironment in liver cancer.[RNA-Seq] The experimental design investigates the changes in gene expression following the knockdown of RFC3 using shRNA in the hepatocellular carcinoma cell line HCCLM3. The primary objective of this experiment is to assess how reducing RFC3 expression affects the transcriptome of these cells. To achieve this, HCCLM3 cells were transfected with shRNA specifically targeting RFC3 to induce gene knockdown. As a control, HCCLM3 cells were also transfected with non-targeting shRNA. Biological triplicates were included for both the experimental and control conditions to ensure the reliability and reproducibility of the results. Each replicate represents an independent biological sample. All samples are derived from the HCCLM3 human liver cancer cell line. RNA was isolated from each replicate, and RNA sequencing (RNA-seq) was performed to quantify gene expression levels before and after RFC3 knockdown. This comprehensive approach aims to identify differentially expressed genes resulting from the reduced RFC3 expression.

first: Xuedan

last: Sun

first: Shixiang

last: Pan

last: Zhang

first: Bo

last: Chu

first: Lianxin

last: Liu


title: Hypoxia impairs decitabine-induced expression of HLA-DR in acute myeloid leukaemia cell lines [Bisulfite-Seq]

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

type: Methylation profiling by high throughput sequencing

summary: Background Hypomethylating agents (HMA), such as azacytidine (AZA) and decitabine (DAC), are epigenetic therapies used to treat some patients with acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). HMAs act in a replication-dependent manner to remove DNA methylation from the genome. However, AML cells targeted by HMA therapy are often quiescent within the bone marrow, where oxygen levels are low. In this study, we investigate the effects of hypoxia on HMA responses in AML cells.  Results AML cell lines (MOLM-13, MV-4-11, HL-60) were treated with DAC (100nM) or AZA (500-2000nM) in normoxic (21% O2) and hypoxic (1% O2) conditions. Hypoxia significantly reduced AML cell growth and colony-forming capacity across all cell lines, with no additional effects observed upon HMA treatment. Hypoxia had no impact on the extent of DNA hypomethylation induced by DAC treatment, but limited AZA-induced loss of methylation from the genome. Transcriptional responses to HMA treatment were also altered, with HMAs failing to up-regulate antigen presentation pathways in hypoxia. In particular, cell surface expression of the MHC class II receptor, HLA-DR, was increased by DAC treatment in normoxia, but not hypoxia. Conclusion Our results suggest that HMA-induced antigen presentation may be impaired by hypoxia. This study highlights the need to consider microenvironmental factors when designing co-treatment strategies to improve HMA therapeutic efficacy.

overall_design:
Leukaemic cell lines (HL-60, MOLM-13 and MV-4-11) were pre-exposed to either normoxic or hypoxic conditions, followed by treatment with hypomethylating agents (HMAs) or without (untreated) as controls. Each condition has three replicates. DNA was isolated from samples after completion of the experiment and methylation levels assessed by PBAT sequencing.

UPDATE: [Aug-01-2025] The MV411 Samples were removed because they were mislabeled as MV-4-11 cells.

first: Sam

last: Humphries

first: Sean

last: Burnard

first: Courtney

last: Eggins

first: Simon

last: Keely

first: Danielle

middle: R

last: Bond

middle: J


title: Hypoxia impairs decitabine-induced expression of HLA-DR in acute myeloid leukaemia cell lines

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

overall_design: Refer to individual Series


title: Changes of energy metabolism-related proteins before and after donor liver transplantation in patients with ischemia-reperfusion injury

status: Public on Jan 23 2025

city: wuhan

first: Zhongshan

last: Lu

address: 169 Donghu Road, Wuchang District

institute: Zhongnan Hospital of Wuhan University

summary: To investigate the molecular mechanisms underlying ischemia-reperfusion (IR) injury in liver transplantation, RNA sequencing (RNA-seq) was performed on liver specimens obtained at various stages: before ischemia and post-reperfusion. The RNA-seq analysis aimed to profile gene expression changes in response to IR injury and identify key molecular pathways involved in liver dysfunction, with a particular focus on energy metabolism-related proteins PPARα. This approach provides a comprehensive understanding of the transcriptional alterations that occur during liver transplantation, highlighting the changes in metabolic pathways such as gluconeogenesis and fatty acid oxidation. These findings may offer insights into therapeutic strategies for mitigating IR-induced damage and enhancing liver transplantation outcomes by targeting energy metabolism pathways.

overall_design: RNA-seq profiling of the donor liver were collected immediately after a period of warm ischemia, and 1 hours after opening the portal vein during liver transplantation

first: Anxiong

first: Zhigao

last: Deng

first: Jun

last: Luo


title: Transcriptomic analysis of gastric cancer cells in response to stable over-expression of SNORA37

status: Public on Jan 22 2025

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Small nucleolar RNAs (snoRNAs) are a highly conserved category of non-coding RNAs that play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of snoRNAs in regulating gastric cancer progression remain to be determined. We identify that as an ELAVL1-generated 129-nt H/ACA box snoRNA derived from host gene methyl-CpG binding domain protein 2 (MBD2), SNORA37 is a driver of gastric cancer progression. To investigate the mechanisms underlying the functions of SNORA37, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human gastric cancer MKN-45 cells in response to stable over-expression of SNORA37. The results showed that stable over-expression of SNORA37 led to 1521 alternative splicing events in MKN-45 cells. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to SNORA37 over-expression in human gastric cancer cells, and these findings will help us understand the pathogenesis of cancer progression.

overall_design: Total RNA of cells stably transfected with empty vector or SNORA37 was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an llumina Novaseg 6000 platform were performed by Wuhan SeqHealth Technology Co., Ltd. (Wuhan, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value less than 0.05.

first: Liduan

last: Zheng


title: Nucleoredoxin enhances stem cell transition to pituitary hormone-producing cells

status: Public on Jan 27 2025

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

institute: University of Michigan

summary: Nucleoredoxin (Nxn) encodes a multi-functional enzyme with oxidoreductase activity that regulates many different signaling pathways in a redox-dependent manner.  It is involved in a variety of cellular processes.  Rare NXN mutations are reported in some individuals with recessive Robinow syndrome, which involves mesomelic short stature, craniofacial dysmorphisms, and incompletely penetrant heart and palate defects.  Here we report that Nxn is expressed in the ventral diencephalon and Rathke’s pouch, and that Nxn deficient mice have pituitary dysmorphology, cleft palate, and craniofacial abnormalities.  Nxn mutant mice exhibit altered WNT signaling and reduced progression of pituitary stem cells to hormone-producing cells.  These results suggest that some patients with Robinow syndrome may have pituitary insufficiency and benefit from evaluation by endocrinologists.

overall_design: Embryonic pituitary glands were dissected at e14.5 and used for transcript analysis by scRNAseq

first: Michelle

middle: L

last: Brinkmeier

first: Leonard

middle: Y

last: Cheung

middle: P

last: O'Connell

first: Eve

last: Rhodes

first: Sally

middle: A

last: Camper

first: Shannon

middle: W

last: Davis


title: Regulation of Hippo signaling and planar cell polarity via distinct regions of the Fat intracellular domain [ds38k]

status: Public on Jan 28 2025

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

summary: The large Drosophila protocadherin Fat (Ft) is a receptor for signal transduction pathways that control growth (Hippo signaling), planar cell polarity (PCP), metabolism and the proximodistal patterning of appendages. The intracellular domain (ICD) of Ft is crucial in implementing its biological functions. Six regions of high conservation (named A-F) within the ICD have been identified, as well as distinct regions mediating Hippo pathway activity that have been functionally characterized via overexpression assays. Here, we make targeted deletions of these highly conserved residues and the putative Hippo- and PCP-regulating domains of endogenous Ft using CRISPR/Cas9. Through transcriptomic, developmental, and phenotypic analyses, we show that different regions of Ft contribute uniquely to chromatin dynamics, tissue morphogenesis, PCP and metabolic regulation. We also demonstrate that different regions of Ft regulate Yorkie activity in opposite directions, finely tuning growth and tissue development. Strikingly, conserved regions D and F are key regulators of Ft’s functions- exhibiting opposing effects on wing morphology and Hippo pathway modulation- and conserved region D is the main regulator of PCP.

overall_design: RNA-seq profiling of imaginal wing discs from third-instar Drosophila larvae. This dataset is used to compare wild-type and ds^38k mutant

first: Jannette

last: Rusch

first: Nattapon

last: Thanintorn


title: Targeting AXL inhibits the growth and metastasis of prostate cancer in bone

city: STANFORD

first: James

last: Brooks

address: 300 PASTEUR DR

institute: STANFORD UNIVERSITY

summary: We evaluated soluble AXL (sAXL or batiraxcept), a decoy receptor that can potently inhibit AXL signaling, as a single agent or in combination with docetaxel or carboplatin to treat prostate cancer (PCa) bone metastases. We used intratibial injection of multiple patient-derived xenografts with different characteristics, reflecting a traditional phase II clinical trial without pre-selection for a particular tumor characteristic. Inhibition of tyrosine kinase receptor AXL was highly effective as a single agent and showed additive effects when combined with docetaxel or carboplatin in suppressing PCa tumor growth in the bone and in suppressing metastasis to the lung. AXL inhibition suppressed critical cancer stem cell gene expression and significantly decreased proliferation and metastasis through suppression of E2F1 and NuSAP1. Our findings provide compelling preclinical data for testing batiraxcept in patients with prostate cancer with bone metastases.

overall_design: To understand the mechanisms by which AXL inhibition suppressed mPCa AC and NEPC in the bone microenvironment, we profiled the transcriptomes of LuCaP PDX bone tumors with or without sAXL treatment alone or combination with docetaxel or carboplatin by RNAseq.

first: Chun-Lung

last: Chiu

first: Dalin

last: Zhang

first: Hongjuan

last: Zhao

first: James D.


title: Spatiotemporal Landscape in Kidney of A Mouse Model of Hyperuricemia at Single-Cell Level [spatial transcriptomics data]

city: Changzhou

first: Chao

last: Tu

state: Jiangsu

address: 185 Juqian Road

department: Department of Internal Medicine

institute: The Third Affiliated Hospital of Soochow University

summary: Our team utilized single-cell RNA sequencing and spatial multi-omics to explore the spatial landscape of kidney in mice with hyperuricemia at single-cell level

overall_design: Male urate oxidase knockout (Uox-KO) mice and male wild-type mice were purchased from GemPharmatech (Nanjing, China). The corporation knocked out exons 2-4 of the mouse Uox gene on the C57BL/6J background to obtain the Uox-KO model. This model is an ideal animal model for screening and evaluating drugs for treating hyperuricemia due to the accumulation of uric acid in mice. our team figured the spatiotemporal atlas of hyperuricemic nephropathy by applying single-cell RNA sequencing, spatial transcriptomics, spatial proteomics and spatial metabolomics in the Uox-KO mouse model.

first: CHAO

last: TU

first: SHUHONG

last: GUAN

first: QIANRU

last: TAO

first: XIAOZHOU

last: HE


title: BRD4 ChIP-Seq in 22Rv1 cells exogenously expressing HNF4G or GFP

status: Public on Jan 18 2025

city: New York

first: Shipra

last: Shukla

state: NY

address: 417 East 68th Street

institute: MSKCC

overall_design: Here, we have mapped BRD4 binding sites in 22Rv1-GFP and 22Rv1-HNF4G overexpressing cells treated with BET inhibitor, ABBV-075 or DMSO control.

first: Yu

last: Chen


title: Bulk-RNA seq of human Leydig cells with rec-WISP2 treatment or WISP2mut overexpression

status: Public on Feb 01 2025

city: Zhuhai

first: Liangyu

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

overall_design:
Human LC were treatment with 100 ng/ml of WISP2 for 48 hours or WISP2mut overexpression
Human LC were treatment with 100 ng/ml of WISP2 for 48 hours or WISP2mut (delete the signal peptide domain) overexpression


title: BET inhibitor Pelabresib and AR inhibitor enzalutamide perturbed pathways in prostate cancer CRPC PDX LuCaP 35CR

summary: To study the effect of inhibiting AR and HNF1A/HNF4G activity either alone or in combination on the growth of CRPC PDX LuCaP 35CR

overall_design: LuCaP 35CR tumors were treated with enzalutamide, pelabresib or a combination of pelabresib and enzalutamide and tumor volumes were compared to vehicle control


title: BET inhibitor Pelabresib and AR inhibitor enzalutamide perturbed pathways in prostate cancer CRPC PDX LuCaP 77CR

summary: To study the effect of inhibiting AR and HNF1A/HNF4G activity either alone or in combination on the growth of CRPC PDX LuCaP 77CR.

overall_design: LuCaP 77CR tumors were treated with enzalutamide, pelabresib or a combination of pelabresib and enzalutamide and tumor volumes were compared to vehicle control


title: Role of different epigenetic drugs in reshaping murine melanoma tumor microenvironment [Array]

status: Public on Jan 31 2025

city: Genova

first: Adriana

middle: Agnese

last: Amaro

state: Italy

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale policlinico San Martino

summary: To highlight the role of epigenetics in immune responses, we exploited a model of melanoma using B16F10 injected subcutaneously in syngeneic C57black6j mice and studied the effect of inhibitors of (i) BET bromodomain (OTX-015) (ii) DNA methyltransferase (DNMT) (guadecitabine) on in vivo tumour growth. OTX-015 showed significant in vivo effects in reducing tumour growth in our setting. Guadecitabine induced MHC class I expression on tumour cells, but the latter also increased immune checkpoint expression on cancer cells. Each epigenetic agent altered the tumour microenvironment (TME), mostly by reducing immune suppression, particularly of Tregs or MDSC, or both. OTX-015 and guadecitabine had strong effects, but in opposite ways. OTX-015 downmodulated antitumour responses, whereas guadecitabine remodeled the TME to be more immune-responsive. Epigenetic therapy may enhance immunotherapy, but specific schedules for treatments need to be studied for each drug. Among the drugs tested, guadecitabine seems to be the most promising drug for successful combination immunotherapy.

overall_design:
Microarray analysis on B16F10 cell line treated or not with OTX-015 (4 Untreated and 4 Treated) and tumor samples derived from mice treated or not with OTX015 (11 Untreated and 10 Treated) or Guadecitabine (5 Untreated and 6 Treated).  Gene expression data.
Contributor: EPigenetic Immune-oncology Consortium Airc (EPICA)

first: Valentina

last: Rigo

first: Rosaria

last: Gangemi

first: Francesco

last: Reggiani

first: Alessia

last: Parodi

first: Daniela

last: Fenoglio

first: Barbara

last: Banelli

first: Simonetta

last: Astigiano

first: Laura

last: Emionite

first: Stefania

last: Martini

first: Giuseppina

last: Conteduca

first: Tiziana

last: Altosole

first: Mariangela

last: Petito

first: Cecilia

last: Profumo

first: Guido

last: Ferlazzo

first: Gilberto

last: Filaci

first: Michele

last: Maio

first: Ulrich

last: Pfeffer

first: Michela

last: Croce


title: Expression profile of 22Rv1 cells with GFP or HNF4G exogenous expression when treated with BETi ABBV-075

first: Shipra

last: Shukla

summary: To study the consequence of HNF4G target genes expression with ABBV-075 treatment in cells that have BETi-independent HNF4G expression, we performed RNA-Seq on 22Rv1 cells that exogenously express HNF4G using GFP expression as control.

overall_design: GFP or HNF4G transgenes were expressed in 22Rv1 cells in BET independent manner and cells were treated with ABBV-075 (25 nM for 24 hrs) or DMSO and global transcriptome was evaluated using RNA-Seq.

first: Yu

last: Chen


title: Gene expression profile at single cell level in prostate cancer PDX, LucaP 70CR  treated with Bromo- and -extraterminal domain (BET) inhibitor Pelabresib and vehicle control

summary: We used single-cell RNA-sequencing to evaluate the effect of BET inhibitor, pelabresib on AR and HNF1A/HNF4G regulated transcriptome in prostate cancer PDX

overall_design: LuCaP 70CR tumors implanted in SCID mice were treated with pelabresib (30 mg/Kg), twice daily for 6 days and were harvested, processed to a single-cell suspension, and subjected to scRNA-seq.


title: BET inhibitor ABBV-075 perturbed pathways in prostate cancer organoid MSK-PCa17

summary: To study global transcriptomic changes with BET inhibition in MSK-PCa17 cells and correlate with growth inhibition

overall_design: MSK-PCa17 organoids  were treated with increasing doses of ABBV-075 for 4 hours


title: Recruitment to the nuclear periphery enhances repression of H3K9me2-marked genes and transposons to shape cell fate [CUT&Run II]

city: San Francisco

first: Harold

last: Marin

state: CA

address: 555 Mission Bay Boulevard South

department: Smith Cardiovascular Institute

institute: University of California San Francisco

summary: Heterochromatic loci marked by histone H3 lysine 9 dimethylation (H3K9me2) are enriched at the nuclear periphery in metazoans, but the effect of spatial position on heterochromatin function has not been defined. Here, we remove three nuclear lamins and lamin B receptor (LBR) in mouse embryonic stem cells (mESCs) and show that heterochromatin detaches from the nuclear periphery. Mutant mESCs sustain naïve pluripotency and maintain H3K9me2 across the genome but cannot repress H3K9me2-marked genes or transposons. Further, mutant cells fail to differentiate into epiblast-like cells (EpiLCs), a transition that requires the expansion of H3K9me2 across the genome.  Mutant EpiLCs can silence naïve pluripotency genes and activate epiblast-stage genes. However, H3K9me2 cannot repress markers of alternative fates, including primitive endoderm. We conclude that the nuclear periphery controls the spatial position, dynamic remodeling, and repressive capacity of H3K9me2-marked heterochromatin to shape cell fate decisions.

overall_design: Cleavage Under Target and Release Under Nuclease (CUT & RUN) for Lamin B1 (LMNB1) and Lamina-associated polypeptide 2 beta isoform (LAP2B) in naive mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLC), and the histone modification tri-methylated lysine 9 on histone H3 (H3K9me3) in naive mESCs.

first: Eric

last: Simental

first: Charlie

last: Allen

last: Martin

last: Panning

first: Bassem

last: Al-Sady

first: Abigail

last: Buchwalter


title: Recruitment to the nuclear periphery enhances repression of H3K9me2-marked genes and transposons to shape cell fate


title: Regulation of Hippo signaling and planar cell polarity via distinct regions of the Fat intracellular domain

first: Helen

last: McNeill

overall_design: RNA-seq profiling of imaginal wing discs from third-instar Drosophila larvae. This dataset is used to compare wild-type, fat nulls, conserved and functional domain mutants

first: Cole

last: Julick

first: Nattapon

last: Thanintorn

first: Yonit

last: Tsatski

first: Megan

last: Glaeser

first: Jannette

last: Rusch


title: Non-small Cell Lung Cancer Brain Metastasis Atlas

status: Public on Jan 17 2025

first: Somnath

last: Tagore

address: 650W, 168th Street

institute: Columbia University

overall_design: Refer to individual Series


title: Non-small Cell Lung Cancer Brain Metastasis Atlas [slide-seq]

summary: We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), pool matched low pass whole genome sequencing (WGS) and single-cell spatial transcriptomics  of  12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors  (PTs) and 31  treatment-naïve NSCLC brain metastases (BMs) . In total, we recovered 277,206  cell transcriptomes in 43 samples. We performed matched spatial sequencing using SlideSeq2 on 14 snRNA-seq samples.

overall_design:
Single-nuclei RNA sequencing of 277,206 cells  from 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors and 31 treatment-naïve NSCLC brain metastses (BMs).
*** submitter declares that the raw data will be deposited in dbGap ***

first: Benjamin

last: Izar

first: Lindsay

last: Caprio


title: sRNA-seq of Aspergillus fumigatus RNAi double knockouts expressing a pksP inverted-repeat transgene

status: Public on Jan 16 2025

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: The RNA interference (RNAi) pathway has evolved numerous functionalities in eukaryotes, with many on display in Kingdom Fungi. RNAi can regulate gene expression, facilitate drug resistance, or even be altogether lost to improve virulence potential in some fungal pathogens. In the WHO fungal priority pathogen, Aspergillus fumigatus, the RNAi system is known to be intact and functional. To extend our limited understanding of A. fumigatus RNAi, we performed a sRNA-seq to assess sRNAs produced in several RNAi double knockouts and a wild type strain expressing a 1200 nt inverted-repeat transgene with complementarity to the pksP gene. The transgene harbors a 500-bp inverted repeat.  We included an uninduced wild type strain with no inverted-repeat transgene as a control. All conditions were performed in mycelium grown for 24 hours in liquid culture.

overall_design:
Small RNA profiling analysis of Aspergillus fumigatus RNAi double knockouts (𝚫dclA/B, 𝚫ppdA/B, 𝚫rrpA/B) and wild type expressing a 1200 nt inverted-repeat transgene with complementarity to the pksP gene, using 24-h-mycelium.

Please note that GSM8721378-GSM8721380 raw files and IRT_sRNA_processed.csv processed data file have been replaced on Aug 11, 2025.

middle: G

first: Xiaoqing

last: Pan

first: Swatika

last: Prabakar

first: Lukas

last: Schrettenbrunner


title: Non-small Cell Lung Cancer Brain Metastasis Atlas [single nuclei RNAseq]

summary: We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS)  of 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors  (PTs) and 31  treatment-naïve NSCLC brain metastases (BMs) . In total, we recovered 277,206  cell transcriptomes in 43 samples.


title: Non-small Cell Lung Cancer Brain Metastasis Atlas [TCR-seq]

summary: We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq)  of 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors  (PTs) and 31  treatment-naïve NSCLC brain metastases (BMs) .


title: Non-small Cell Lung Cancer Brain Metastasis Atlas [lpWGS]

overall_design:
Pool matched lp-WGS was performed in addtion to single-nuclei RNA sequencing of 277,206 cells  from 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors and 31 treatment-naïve NSCLC brain metastases (BMs).Together, this data served to improve the identification of the malignant and non-malignant cell compartments.
*** submitter declares that the raw data will be deposited in dbGap ***


title: Effect of Usp17l knockdown on 2c gene in mouse embryonic stem cells (RNA-Seq)

city: Tianjin

first: Jie

last: Li

address: Wei Jin Road Nankai District No. 94

department: Department of Cell Biology and Genetics

institute: Nankai University

summary:
In order to study the regulation of Usp17l on 2c gene, we established Usp17l knockdown cell lines KD4 and KD9. shRNA targets the common regions of the five subtypes of Usp17l
We then performed gene expression profiling  with the data obtained from the RNA-seq of the 7th generation cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Control cell line and  KD cell lines (Control, KD4, KD9).

first: Panpan

last: Shi

first: Xukun

last: Lu

first: Kairang

last: Jin

first: Linlin

last: Liu

first: Guoxing

last: Yin

first: Dai

last: Heng

first: Jiao

last: Yang

first: Huiyu

first: Xiaoyan

last: Sheng

first: Xiaoying

last: Ye

first: Wei

last: Xie

first: Lin


title: Direct induction of meiosis from human iPSCs under defined conditions

status: Public on Jan 15 2025

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

summary: Meiotic failure is a significant cause of infertility, but the lack of an in vitro model of human meiosis is a barrier to understanding its mechanism. Here, we establish a method to initiate meiosis directly from male or female human induced pluripotent stem cells (iPSCs). DNMT1 inhibition, retinoid signaling activation, and overexpression of regulatory factors (anti-apoptotic BCL2, and pro-meiotic HOXB5, BOLL, or MEIOC) rapidly activates meiosis over a 15-day protocol. Our protocol bypasses the primordial germ cell stage and directly generates cells expressing genes similar to meiotic oogonia, including oogonia markers, all synaptonemal complex components, and meiotic recombination machinery. DNMT1 inhibition rapidly erases DNA methylation, including at imprinting control regions and promoters of meiotic genes. Microscopy shows key aspects of meiosis, including chromosome axis formation and synapsis in live human cells. Our model of human meiosis provides opportunities for studying this critical reproductive process under chemically defined conditions in vitro.

overall_design: A constitutive expression vector for the anti-apoptotic factor BCL2, as well as doxycycline-inducible expression vectors for meiosis-promoting factors (HOXB5, BOLL, and MEIOC), were integrated into three lines of human iPSCs (F2 female, F3 female, and PGP1 male) using PiggyBac transposase. The iPSCs were seeded at 50,000 cells/cm2 on Matrigel-coated plates in mTeSR1 supplemented with 5 µM GSK3484862, 1 µg/mL doxycycline, and 10 µM Y-27632, and incubated at 37 °C. For 6-well plates, 1.5 mL of medium was used per well. After one day, the medium was replaced with APEL2 containing 5 µM GSK3484862 and 1 µg/mL doxycycline. A 50% media change was performed every 2 days. Three days after seeding the cells, they were moved to a 34 °C incubator. GSK3484862 was withdrawn starting on day 7. Cells were harvested on day 15 and cryopreserved in CryoStor CS10 prior to sequencing. One sample was sequenced for each of the three iPSC lines.

last: Pierson Smela

first: Jessica

last: Adams

first: Carl

last: Ma

first: Laura

last: Breimann

first: Bogdan

last: Dobre

first: Ursula

last: Widocki

first: Toshi

last: Shioda

first: George

last: Church


title: Identification of RIFIN binding to KIR receptor from RIFIN expression library of Plasmodium flaicparum.

city: Suita

first: Shiroh

last: Iwanaga

state: Osaka

address: 3-1 Yamadaoka

department: Molecular protozoology

country: Japan

institute: RIMD, Osaka University

summary: To discriminate between our own cells and those of a pathogen, natural killer cells are armed with inhibitory and activating immune receptors. The balance in signalling mediated by these receptors determines whether an NK cell is activated to destroy a target cell. In some cases, such as the KIRs, immune receptors are found in pairs, with inhibitory and activating receptors containing nearly identical extracellular ligand-binding domains, coupled to different intracellular signalling domains1. Previous studies have shown that RIFINs, displayed on surfaces of Plasmodium falciparum-infected erythrocytes, can bind to inhibitory immune receptors and dampen NK cell activation2,3, reducing parasite killing. However, no pathogen-derived ligand has been identified for any activating receptor. Here, we identify a clade of RIFINs that bind to inhibitory immune receptor KIR2DL1 more strongly than KIR2DL1 binds the human ligand, MHC class I. We demonstrate that this interaction mediates inhibitory signaling and suppresses the activation of KIR2DL1-expressing NK cells. We show that KIR2DL1-binding RIFINs are abundant in field-isolated strains from both Africa and Asia and reveal how two RIFINs bind KIR2DL1. We also demonstrate that the RIFIN binding surface of KIR2DL1 is conserved in the cognate activating immune receptor KIR2DS1. We find that KIR2DL1-binding RIFINs can also bind to KIR2DS1, resulting in activation of KIR2DS1-expressing NK cells. This study demonstrates for the first time that activating KIRs can recruit natural killer cells to target a pathogen and reveals a potential role for activating immune receptors in control of malaria infection

overall_design: Amplicon-seq for KIR2DL1-binding RIFIN recovered from sorted infected RBC from RIFIN expression library.

first: Akihito

last: Sakoguchi

first: Matthew

last: Higgins

first: Samuel

last: Chamberlain


title: ChIA-PET from HCT116 (ENCSR635DLF)

status: Public on Jan 14 2025

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
RNAPII ChIA-PET in HCT116, CTCF tag and IAA treated

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptome analysis of primary human hepatocytes-derived organoids [RNA-seq]

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

summary: In this study, we established human hepatocyte organoids (HHOs) that were expanded from primary human hepatocytes (PHH) in a defined medium. Briefly, the cryopreserved primary human hepatocytes (purchased) were thawn in advanced DMEM/F12 (Thermo) or Cryopreserved hepatocyte Recovery Medium (Gibco). Then, the cells were embedded in Matrigel (Corning) and cultured with the expansion medium (EM).  For the eHHOs, expansion medium (EM) was prepared with a basal medium (Advanced DMEM/F12 was supplemented with penicillin/streptomycin, 10 mM HEPES, 2 mM GlutaMAX, 1 ×(Thermo Fisher Scientific), 10 nM gastrin I (Sigma), and 1 mM N-acetylcysteine (Wako, Japan) ) containing the following niche factors: 50 ng/ml mouse recombinant EGF (Thermo Fisher Scientific), 25 ng/mL human recombinant HGF (Peprotech), 100 ng/mL human recombinant FGF-10 (Peprotech), 10 uM Forskolin (Cayman Chemical), 25 ng/ml mouse recombinant noggin (Peprotech), 1 mg/ml human recombinant R-spondin1 (R; R&D), 20% Afamin-Wnt-3A serum-free conditioned medium (W; Mihara et al., 2016), 5 uM A83-01 (Tocris), and 20ng/ml human Oncostatin M (OSM; Peprotech). For dHHOs,  eHHOs were cultured for 10-14 days in differentiation medium (DM), which was EM without OSM and WR, and containing a hormone cocktail (10ng/ml Growth Hormone, 10ng/ml Prolactin, and 100 ng/ml Cortisol) and 10uM DAPT (differentiation medium: DM).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PHHs and their derivative HHO with different culture conditions.

first: Ryo

last: Igarashi

last: Okada

first: Toshiro

last: Sato


title: microRNA profile of high-grade B-cell lymphoma with 11q aberration

city: Warszawa

first: Michalina

last: Zajdel

address: W. K. Roentgena 5

department: Department of Cancer Biology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

summary:
Background: High-grade B-cell lymphoma with 11q aberration (HGBCL-11q) is a rare germinal centre lymphoma with a typical gain/loss pattern on chromosome 11q, but without MYC translocation and with some features resembling Burkitt lymphoma (BL) and HGBCLs or germinal centre derived diffuse large B-cell lymphoma, not otherwise specified (GCB-DLBCL-NOS). The microRNA expression profile of HGBCL-11q is not characterised. We aim to analyse miRNA expression profile in HGBCL-11q, BL and in GCB-DLBCL-NOS.
Methods: Next generation sequencing (NGS)-based microRNA profiling was performed for HGBCL-11q (n=6), BL (n=8), and also GCB-DLBCL-NOS without (n=3) and with MYC rearrangement (MYC-R) (n=7).
Results: We identified 39 and 64 miRNAs differentiating HGBCL-11q from BL, and from GCB-DLBCL-NOS without MYC-R, respectively. We found that the expression level of miR-223-3p, miR-193b-3p, miR-29b-3p and miR-146a-5p simultaneously differentiated HGBCL-11q from BL, as well as from GCB-DLBCL-NOS without MYC-R. We found higher miRNA profile heterogeneity in HGBCL-11q than in BL. The analysis of MYC-regulated miRNA showed different profile in HGBCL-11q and in BL but demonstrated separation of HGBCL-11q and BL from GCB-DLBCL-NOS cases.
Conclusion: microRNA profile of HGBCL-11q is different than that of BL and of GCB-DLBCL-NOS but more heterogeneous compared to BL.

overall_design: To investigate the profile of microRNA expression in HGBL-11q in comparison with BL, and also with GCB DLBCL,NOS without and with MYC rearrangement (MYC-R) we have used total RNA isolated from freshly frozen cell aspirates of above mentioned aggressive lymphomas tumours and performed next generation sequencing.


title: ChIA-PET from GM12878 (ENCSR355CTR)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIA-PET from HCT116 (ENCSR309KYA)


title: ChIA-PET from GM12878 (ENCSR764VXA)


title: Genome editing in kidney organoids

city: Charlestown

first: Ryuji

last: Morizane

address: 149 13th Street

institute: Massachusetts General Hospital

summary: Genome editing has transformative potential for curing human diseases but poses unique challenges due to irreversible DNA alterations. Ensuring safe and effective in vivo editing requires preclinical studies to mitigate risks like genotoxicity, cytotoxicity, and immunogenicity. The kidney, highly susceptible to off-target effects due to its blood flow and exposure to systemic therapies, lacks established human models for assessing gene therapies.  We utilized kidney organoids as a preclinical platform to test CRISPR/Cas9 genome editing via adeno-associated virus (AAV) delivery, a clinical strategy raising safety concerns due to toxic viral titers. We conduced RNA-seq to assess nephrotoxic responses.

overall_design: RNA-seq profiling of untreated, AAV-GFP, and AAV-CRISPR/Cas9 kidney organoids.

first: Navin

last: Gupta


title: Small Molecule-Catalyzed Deamination: Applications in Transcriptome-Wide Profiling of N6-Methyladenosine in RNA (Arabidopsis)

status: Public on Jan 08 2025

city: Chicago

first: Chang

last: Ye

state: Illinois

institute: University of Chicago

summary: We present a novel N-nitrosation strategy for deamination capable of tolerating DNA/RNA biological macromolecules under mild conditions. A cooperative catalysis combining a carbonyl organocatalyst with a Lewis acid catalyst facilitates the formation of a C-nitro intermediate from a primary amine, which, upon rearrangement into N-nitrosamine, leads to selective deamination of unsubstituted canonical DNA/RNA bases under mild conditions. We employed this new approach to deamination of adenine into hypoxanthine, read as guanine by reverse transcriptases or DNA polymerases, while N6-methyladenosine (m6A) sites resist deamination and remain identified as adenine. We therefore report a chemically mild, low-input detection method for adenosine methylation sequencing at base resolution, named Chemical cooperative catalysis-Assisted for m6A sequencing (CAM-seq).

overall_design: CAM-seq were applied to Arabidopsis samples, using polyA enriched RNA.


title: Small Molecule-Catalyzed Deamination: Applications in Transcriptome-Wide Profiling of N6-Methyladenosine in RNA (Maize)

overall_design: CAM-seq were applied to Maize samples, using polyA enriched RNA.


title: ChIA-PET from HCT116 (ENCSR028AOM)


title: Small Molecule-Catalyzed Deamination: Applications in Transcriptome-Wide Profiling of N6-Methyladenosine in RNA (human)

overall_design: CAM-seq were applied to human cell lines samples, using polyA enriched RNA.


title: single-cell transcriptomics in patients with anti-citrullinated peptide antibody-positive early rheumatoid arthritis

status: Public on Jan 13 2025

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

country: South Korea

institute: Catholic University of Korea

summary: Despite known differences in immunologic features between anti-citrullinated peptide antibody (ACPA)-positive (ACPA+) and ACPA-negative (ACPA-) early rheumatoid arthritis (eRA) patients, our understanding is still incomplete. To address this, we performed single-cell RNA sequencing of CD45+ cells from peripheral blood samples of drug-naïve ACPA+ and ACPA- eRA patients and compared distribution and functional characteristics of cell subsets based on ACPA presence.

overall_design: We obtained peripheral blood samples from untreated (drug-naïve), early, and active stage of RA patients who met the 2010 ACR/EULAR Rheumatoid Arthritis classification criteria. Peripheral blood mononuclear cells were isolated using Ficoll-Paque gradient centrifugation. Cell quantity and viability were then determined by Trypan Blue staining. We next conducted scRNA-seq to characterize and compare transcriptome profiles of CD45+ cells from PBMCs obtained from healthy controls (n = 4), drug-naïve ACPA- eRA patients (n = 6), and drug-naïve ACPA+ eRA patients (n = 6). Raw data were processed using BD Rhapsody software. Human transcriptome GRCh38-1.2.0 was used as the reference.

first: Wan-Uk

last: Kim


title: YAP regulates periosteal expansion in early fracture repair.

status: Public on Jan 07 2025

city: Philadelphia

first: Madhura

last: Nijsure

state: Pennsylvania

address: 3450 Hamilton Walk

institute: University of Pennsylvania

summary: Periosteal expansion is a key process in the early stages of bone fracture repair. The periosteum is typically quiescent, but upon fracture it expands, periosteal cells proliferate and contribute to the formation of a cartilaginous callus . The early expansion of the periosteum is tightly regulated at the transcriptional level. However, the molecular mechanisms behind periosteal expansion are unknown. Here, we show that Yes-Associated Protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ) mediate periosteal expansion and periosteal cell proliferation. Bone fracture results in increased numbers of YAP-expressing periosteal cells. Deletion of YAP from Osterix (Osx) expressing periosteal cells impairs early periosteal expansion. Mechanistically, YAP regulates both cell intrinsic and extrinsic transcriptional programs that allow for periosteal expansion. Specifically, we identified Bmp4 as a cell extrinsic factor regulated by YAP, that rescues the impairment of periosteal expansion upon YAP deletion. Together, these data establish YAP mediated molecular mechanisms that allow for periosteal expansion in the early stages of fracture repair.

overall_design: Investigating the role of YAP in modulating the transcriptional landscape in periosteal cells

first: Joel

last: Boerckel


title: EZH2 INHIBITION ENHANCES T CELL IMMUNOTHERAPIES BY INDUCING LYMPHOMA IMMUNOGENICITY AND IMPROVING T CELL FUNCTION (RNA-Seq)

status: Public on Jan 10 2025

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: While T cell immunotherapies have demonstrated effectiveness in a subset of patients with diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL), they are currently administered without guidance regarding whether the underlying biology or immunology is conducive to a durable response. Moreover, mechanisms explaining CAR-T resistance in B cell lymphomas remain largely unknown, and suitable systems to study lymphomas are currently unavailable, making it infeasible. To address these unmet needs, we developed syngeneic animal models reflecting the genetics, epigenetics, and immunology of human FL and DLBCL. We show that treatment of these models with EZH2 inhibitors reprogrammed them to re-express T cell engagement genes and rendered them highly immunogenic. Notably, EZH2 inhibitors did not exhibit deleterious effects on T cells. Instead, they promoted a memory CAR CD8 phenotype and reduced exhaustion, resulting in a superior elimination of lymphoma B cells and decreased tumor burden. Intravital 2-photon imaging of transformed FL bearing mice showed that EZH2 inhibition increased the recruitment of CAR-T into the tumor microenvironment and enhanced the quality of interactions with lymphoma cells, leading to increased killing. Therefore, inhibition of EZH2 enhances CAR-T cell activity through direct effects on CAR-T cells, in addition to rendering lymphoma B cells immunogenic. This offers an innovative approach for enhancing the prognosis of patients with refractory B cell lymphomas, and is currently under evaluation in a clinical trial (NCT05934838)

overall_design: RNAseq in murine germinal center B cells, tFL cell line model, PDX samples

first: Yusuke

last: Isshiki

first: Cem

last: Meydan

first: Ari

last: Melnick


title: EZH2 INHIBITION ENHANCES T CELL IMMUNOTHERAPIES BY INDUCING LYMPHOMA IMMUNOGENICITY AND IMPROVING T CELL FUNCTION

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


title: RNA-seq for NKX2-3 knockout tumor pericytes

status: Public on Jan 05 2025

city: guangzhou

first: xiaoyu

last: wu

state: guangdong

address: huangpu road

institute: jinan university

summary: This study aims to investigate genes regulated by NKX2-3

overall_design: For NKX2-3-knockdown experiments, TPCs derived from CRC patients with liver metastasis were infected with Guide RNA of NKX2-3 for 48 h and selected by puromycin (2 mg/mL). Total RNA was extracted using TRIzol reagent (Life technologies) according to the manufacturer manual. The RNA concentration and integrity were evaluated by NanoDrop 2000. Then, the samples were inspected by agarose gel electrophoresis, Nanodrop and Agilent 2100. Then the fragmented RNA pieces were used to construct library by Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit and sequenced with Illumina Novaseq™ 6000

first: Dongmei

last: Zhang

first: Minfen

last: Chen

first: Xiaobo

last: Li

first: Sishan

last: Yan


title: Gene expression profile at single cell level of meniscus tissue

city: Poznań

first: Monika

last: Mankowska

address: Uniwersytetu Poznańskiego

department: Centre for Applied Technology

institute: Adam Mickiewicz University

summary: The meniscus consists of two zones red-red (outer) and white-white (inner). We used single cell RNA-seq to analyze the differences in the composition of cell types between zones. We also compared the medial and lateral meniscus.

overall_design: Lateral and medial menisci were collected. The tissue was segmented into white-white and red-red zones and single cell RNA-seq was performed.

last: Stefanska

first: Anna

last: Mleczko

first: Julia

last: Semba

first: Lukasz

last: Krych

first: Witold

last: Kot

first: Jakub

middle: D

last: Rybka


title: Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [CUT&Run]

status: Public on Jan 01 2025

city: Kunming

first: Chao

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

summary: ATP-dependent chromatin remodelers establish and arrange nucleosome distribution, modifying accessibility of DNA. Brg1 is exclusive ATPase subunit of mSWI/SNF complex. To understand the dosage dependent function of mSWI/SNF complex. We take an advantage of dTag system to precisely control abundancy of BRG1. We found overall Brg1-binding is sensitive to its abundance nevertheless OCT4-target or H3K27ac region, suggesting Brg1 genome-wide distribution rather than being actively recruited. We also reveal open chromatin dependency on BRG1. The chromatin accessibility of super enhancer shows buffered response on depletion of BRG1, whereas weak enhancer is sensitive. Finally, transcriptomic analysis identified that transcription shows buffered dependencies on BRG1 loss. Overall, our results highlight kinetics differences of BRG1-binding to transcriptome underline BRG1 dosage-sensitive mechanism.

overall_design: To study the kinetics of BRG1 binding, chromatin accessibility, and gene expression, we employed the dTAG system to precisely control Brg1 protein levels in mESCs. We then used Cut&Run, ATAC-seq, and RNA-seq to examine the kinetic changes under different Brg1 protein levels.

first: Yota

last: Hagihara

first: Yi


title: Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [ATAC-Seq]


title: Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [RNA-Seq]


title: Induction of ER stress in SHSY5Y human neuroblastoma cells by thapsigargin treatment

city: Kolkata

first: Saikat

last: Chakrabarti

state: West Bengal

address: CN-6, Sector V

country: India

institute: CSIR-IICB

summary: To identify the impact of ER stress on other cellular organelles, cells were treated with ER stress inducer thapsigargin. Transcriptomic profile revealed increased ER stress levels. Deregulated genes was further screened to identify novel ER stress markers of other organelles. Functional charecterization of novel markers were performed to gain insight of the observation.

overall_design: SHSY5Y human neuroblastoma cells were treated with thapsigargin with 0.5 μΜ conc. for 3hrs. RNA isolation was carried out by TRIzol method followed by RNA sequencing. Differential gene expression analysis was performed to identify the deregulated genes under thapsigargin mediated ER stress.

first: Priyanka

last: Mallick


title: The exosome degrades chromatin-associated RNAs genome-wide and maintains chromatin homeostasis (ATAC-Seq)

city: Valencia

first: Jordi

last: Planells

state: Valencia

address: Doctor Moliner, 50 street

department: Biologia celular, biologia funcional y antropologia fisica

country: Spain

institute: Universitat de València

summary: Eukaryotic genomes produce a large variety of RNAs some of which are present in the chromatin and may affect important processes such as chromatin packaging and gene expression. The RNA exosome controls the levels of chromatin-associated RNAs (caRNAs), but little is known about its role in the regulation of chromatin packaging. The project aims at characterizing the role of the RNA exosome in the maintenance of chromatin packaging in Drosophila melanogaster S2 cells. We have used RNA interference to knock down the exosome catalytic subunits RRP6 and DIS3 (individually or simultaneously) and we have analyzed the effects of the depletions on chromatin accessibility by ATAC-seq.

overall_design: Nuclei from control (GFP-Control) and RNA exosome knockdown (dsRrp6, dsDis3, dsDouble) S2 cells were harvested for ATAC preparaton. All conditions consist of 3 biological replicates

first: Antonio

last: Jordán-Pla

first: Juan

last: Guadalupe

first: Shruti

last: Jain

first: Estelle

last: Proux-Wéra

first: Anne

last: von Euler

first: Vicent

last: Pelechano

first: Neus

last: Visa


title: Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation

last: Zhang

overall_design: Refer to individual Series


title: The exosome degrades chromatin-associated RNAs genome-wide and maintains chromatin homeostasis


title: The exosome degrades chromatin-associated RNAs genome-wide and maintains chromatin homeostasis (RNA-Seq)

summary: Eukaryotic genomes produce a large variety of RNAs some of which are present in the chromatin and may affect important processes such as chromatin packaging and gene expression. Little is known about the role of the RNA exosome in the regulation of such chromatin-associated RNAs (caRNAs). The project aims at 1) identifying caRNAs produced from unique and repetitive sequences in the genome of Drosophila melanogaster S2 cells, and 2) characterize the role of the RNA exosome in controlling caRNA levels. To answer these questions, we have used RNA interference to knock down the exosome catalytic subunits RRP6 and DIS3 (individually or simultaneously) and we have analyzed the effects of the depletions on the chromatin-associated transcriptome by sequencing RNAs purified from a chromatin fraction isolated from S2 cells.

overall_design: RNA from GFP-Control, Rrp6-kd, Dis3-kd and Double-kd (Rrp6+Dis3) was extracted from D. melanogaster S2 cells. Total RNA samples consist of pooled biological triplicates. Chromatin samples consist of 3 biological triplicates sequenced independently.


title: Pomacea canaliculata eye: a new system to study full camera-type eye regeneration [oral tentacles, cephalic, tentacles, eye stalks and extracted retinas]

status: Public on Dec 31 2024

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Eyes are complex, delicate sensory organs that can be irreversibly damaged by disease or aging. Finding solutions to repair eyes has been difficult because no animal model has been available to study the complete regeneration of a camera-type eye. To study camera-type eye regeneration we can study partial or limited regeneration in vertebrates or complete regeneration of different types of eyes with simpler structure in animals with higher regenerative potential. I discovered an invertebrate organism, the freshwater apple snail Pomacea canaliculata, with camera-type eyes, yet capable of full regeneration after complete amputation. After cellular and molecular study of P. canaliculata eye and their regeneration dynamic, we developed tools to edit genes and test their functions. We found that, like in humans, eye development in these animals is controlled by the expression of the gene pax6. It is now possible to unravel the genetic basis of camera-type eye regeneration, which may provide new opportunities for therapeutic interventions. This work represents the foundation to use P. canaliculata as a valuable research system in the field of regeneration, not only to bring more knowledge about complex organs regeneration, but also to shed light, for the first time, on the process of complete camera-type eye regeneration.

overall_design: Pomacea canaliculata amputated oral tentacles, cephalic, tentacles, eye stalks and extracted retinas.

first: Alice

last: Accorsi

first: Eric

last: Ross

first: Brenda

last: Pardo Loredo

first: Melainia

last: McClain

first: Tim

last: Corbin

first: Shane

last: Merryman

last: Sánchez Alvarado


title: Overcoming Nanosilver Resistance: Resensitizing Bacteria and Targeting Evolutionary Mechanisms

city: Beijing

first: Rui

last: Sun

address: No.19, Xinjiekouwai St

department: School of Environment

institute: Beijing Normal University

summary: The rapid spread of antimicrobial resistance poses a critical threat to global health and the environment. Antimicrobial nanomaterials, including silver nanoparticles (AgNPs), are being explored as innovative solutions; however, the emergence of nanoresistance challenges their effectiveness. Understanding resistance mechanisms is essential for developing antievolutionary strategies. AgNPs exhibit diverse resistance mechanisms, and our findings reveal a dynamic transition between these mechanisms: from flagellin-mediated AgNP precipitation (state I) to activation of the copper efflux pump (CusCFBA) system (state II). We designed targeted physicochemical interventions to counteract these mechanisms. Energy supply blocking was effective for state I, while for state II, neutralizing intracellular acidic pH significantly reduced resistance. These strategies reduced nanoresistance/tolerance by up to 10,000-fold. Additionally, resistance evolution can be completely halted by disrupting the energy supply using carbonyl cyanide 3-chlorophenylhydrazone and overactivating sigma E, one of the key envelope stress regulators that govern resistance transitions. Our findings provide practical strategies to overcome nanoresistance, offering a groundbreaking approach to enhance nanoantimicrobials’ efficacy in medical therapies and combat resistance evolution.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: E. coli K12 MG1655  was subjected to 14 days of evolution under intermittent exposure to high concentrations of AgNPs. RNA-seq was performed on cells from days 0, 9, and 14.

first: Ruibin

last: Li

first: Radek

last: Zbořil

first: Chengdong


title: Pomacea canaliculata eye: a new system to study full camera-type eye regeneration [regeneration time-course]

overall_design: Pomacea canaliculata eye regeneration time-course of amputated eye stalks from Intact, 1dpa, 3dpa, 7dpa, 9dpa, 12dpa,15dpa,21dpa and 28dpa animals.

last: Loredo


title: Pomacea canaliculata eye: a new system to study full camera-type eye regeneration


title: Single-cell RNA sequencing of PBMC with and without LILRB3-4SNPs pretransplant and posttransplant

status: Public on Dec 26 2024

city: New York

first: Zeguo

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: Single-cell RNA sequencing were conducted on PBMCs from patients with and without LILRB3-4SNPs risk allele to evaluate the potential effects of this SNP on cell level.

overall_design: Single-cell RNA sequencing were performed on PBMCs isolated from the pretransplant blood of 2 AA recipients (1 with and 1 without LILRB3-4SNPs) and post-transplant (24 months) blood of 2 AA recipients (1 with and 1 without LILRB3-4SNPs) with matched recipient and donor’s demographic and baseline clinical features (age, gender, donor status, HLA mismatches and induction types).

first: Wenlin

last: Wang

first: Weijia


title: RNA sequencing of CTOT19 transplantation patients, and single-cell RNA sequencing of PBMC with and without LILRB3-4SNPs pretransplant and posttransplant


title: Pathogenesis of Graves' Disease Using Single-Cell Sequencing with Thyroid Autoantigens Peptides Stimulation in B Cells

status: Public on Dec 23 2024

city: Kyoto

first: GENKI

last: KOBAYASHI

address: Kamugyoku, Kajii-cho 465

institute: Kyoto Prefectural university of medicine

summary: We used the latest technology, BD Rhapsody, to analyze BCR of PBMCs and intrathyroidal blood mononuclear cells from patients with Graves' disease at the single-cell level.

overall_design: scRNA-Seq - BCR of PBMCs and intrathyroidal blood mononuclear cells from patients with Graves' disease

first: Genki

last: Kobayashi


title: Profound synthetic lethality between SMARCAL1 and FANCM (CRISPR screen)

status: Public on Dec 24 2024

city: toronto

first: Sumin

last: Feng

address: 600 University Avenue

country: Canada

institute: The Lunenfeld-Tanenbaum Research Institute

summary: DNA replication stress is a threat to genome integrity. The large SNF2-family of ATPases participates in preventing and mitigating DNA replication stress by employing their ATP-driven motor to remodel DNA or DNA-bound proteins. To understand the contribution of these ATPases in genome maintenance, we undertook CRISPR-based synthetic lethality screens with three SNF2-type ATPases: SMARCAL1, ZRANB3 and HLTF. Here we show that SMARCAL1 displays a profound synthetic lethal interaction with FANCM, another ATP-dependent translocase involved in DNA replication and genome stability. Their combined loss causes severe genome instability that we link to chromosome breakage at loci enriched in simple repeats, which are known to challenge replication fork progression. Our findings illuminate a critical genetic buffering mechanism that provides an essential function for maintaining genome integrity.

overall_design: Synthetic lethal interaction analysis using data from large-scale genomic CRISPR screens in RPE1-hTERT TP53-/- PACKO Cas9 cell

first: Lisa

last: Hoeg

first: Daniel

last: Durocher


title: Profound synthetic lethality between SMARCAL1 and FANCM (END-Seq)

overall_design: Double strands break analysis using data from END-seq generated from RPE1-hTERT TP53-/- PACKO Cas9 cell


title: Clonorchis sinensis infection alters the methylation and hydroxymethylation of hepatocellular carcinoma

status: Public on Dec 20 2024

city: Nanning

first: Junxian

last: Chen

address: 71, Hedi Road, Qingxiu District

department: Department of Clinical Laboratory

institute: Guangxi Medical University Cancer Hospital

summary: Clonorchis sinensis (Cs) infection is prevalent in Southeast Asia and has been classified as a Group I carcinogen by the International Agency for Research on Cancer, posing significant risks to the human liver and biliary system. While recent studies have linked Cs infection to poorer outcomes in hepatocellular carcinoma (HCC) patients, the precise molecular mechanisms underlying its effect on HCC remain to be fully elucidated. This study investigates the epigenetic changes in Cs-infected HCC using whole-genome bisulfite sequencing and whole-genome oxidative bisulfite sequencing to map 5-methylcytosine and 5-hydroxymethylcytosine profiles at single-nucleotide resolution. We identified 29 differentially methylated regions and 13 differentially hydroxymethylated regions in Cs-infected HCC, which were associated with 28 differentially methylated/hydroxymethylated-associated genes (DAGs/DhAGs). The methylation levels of four promoter Cytosine-phosphate-Guanine (CpG) sites of DAGs/DhAGs were found to correlate with prognosis in Cs-infected HCC, while two key DMR/DhMR-associated genes, DHDH and KCNQ3, were significantly linked to overall survival of HCC. Our study provides the first detailed epigenetic map of Cs-associated HCC, uncovering novel insights into potential biomarkers and therapeutic targets that could enhance prognostic predictions and inform treatment strategies for patients affected by this condition.

first: Weilong

last: Yang

first: Taijun

last: Huang

first: Caibiao

last: Wei

first: Lingling

last: Zhou

first: Yulong

last: Xu

first: Jie

last: Gao

first: Fengfei

last: Liu

first: Jian-Kang

last: Zhu

first: Min

last: Fang


title: Transcriptome and cellular evidence of depot-specific function in beef cattle intramuscular, subcutaneous, and visceral adipose tissues

city: Lubbock

first: Clarissa

last: Strieder-Barboza

state: Texas

address: ESB II, 1006 Canton Ave.

department: Veterinary Sciences

institute: Texas Tech University

summary: Deposition of intramuscular adipose tissue (IMAT; marbling) is one of the primary determinants for beef quality grade within the U.S. However, IMAT accumulation is often secondary to subcuta-neous (SCAT) and visceral (VIAT) adipose tissue deposition, which results in lower product yield. The mechanisms that underlie the differences in the accumulation of IMAT, SCAT, and VIAT are still not fully understood. The aim of this study was to define the depot-specific transcriptome and adipocyte function in IMAT, SCAT and VIAT in beef cattle. Functional transcriptome analysis in-dicated the activation of pathways for greater lipid accumulation and immune function in VIAT and SCAT compared with IMAT. Florescent activated cell sorting analysis identified a greater percentage of adipocyte stem and progenitor cells (ASPC) within IMAT compared to SCAT and VIAT, but lower ASPC's proliferation in vitro, suggesting potential functional defects on IMAT's adipogenic capacity. In vitro culture of adipocytes revealed greater lipid accumulation and insulin responses, and lower lipolysis of SCAT compared to IMAT adipocytes, with VIAT adipocytes having a characteristic of both SCAT, and IMAT adipocytes. Our findings revealed the de-pot-specific transcriptional profile of IMAT, SCAT and VIAT in beef cattle, which were corrobo-rated by differences on adipocyte metabolic function in vitro.

overall_design: Four beef animals (3 steers, 1 heifer) were euthanized following humane slaughter practices using a captive bolt stinner at the Texas Tech University meat Lab and tissue samples were collected immediately after exsanguination and hide removal to prevent tissue contamination. Animal history, age and background were not known. All animals were appraised be-fore slaughter and there was no sign of distress or illness at the time of entering the fa-cility. A section of the Longissimus dorsi (LD) muscle (± 500 g) was excised from the 9-11th rib section, placed into a stainless-steel tray, and immediately placed on ice for performing the dissection of IMAT and SCAT (backfat) samples using tweezers and a scalpel. VIAT samples were collected at evisceration from the greater omentum. Tissue subsamples of approximately 1g each were flash frozen in liquid nitrogen for subsequent RNA sequencing analysis.

first: Alexandra

last: Tegeler

first: Hunter

last: Ford

first: Jean

last: Fiallo-Diez

first: Tainara

last: Michelotti

first: Bradley

last: Johnson

first: Oscar

last: Benitez

first: Dale

last: Woerner


title: CDK7 inhibition suppresses RNA polymerase II re-initiation and triggers degradation of elongation and 3'-end processing factors

status: Public on Dec 19 2024

city: Boulder

first: Olivia

last: Luyties

state: CO

address: 3415 Colorado Ave, JSC Biotech Building

department: Biochemistry

institute: University of Colorado Boulder

summary: CDK7 regulates RNA polymerase II (RNAPII) initiation, elongation, and termination through incompletely-defined mechanisms. Biochemical reconstitution of RNAPII transcription initiation showed that CDK7 inhibition suppressed RNAPII activity by blocking promoter escape and re-initiation and this was Mediator- and TFIID-dependent. These in vitro results were consistent with genomics and transcriptomics experiments in human cells; CDK7 inhibition globally reduced transcription and increased RNAPII promoter-proximal pausing. Moreover, we observed termination defects in CDK7-inhibited cells; unexpectedly, this coincided with rapid, widespread degradation of elongation and 3'-end processing factors. Collectively, these mechanistic insights further define how CDK7 kinase activity regulates RNAPII initiation, termination, and RNA processing.

overall_design: Chromatin immunoprecipitation (ChIP-seq) of human RNA Polymerase II and RNA Polymerase II phosphomarks (p-Ser5, p-Ser2, and p-Ser7) under control and CDK7-inhibited conditions.

first: Jessica

last: Rodino

first: Lynn

last: Sanford

first: Taylor

last: Jones

first: Jenna

middle: K

last: Rimel

first: Grace

middle: S

last: Shelby

first: Finn

last: Brennan

first: Christopher

middle: C

last: Ebmeier

first: Lotte

last: Watts

first: Sabrina

last: Spencer

first: Robin

last: Dowell

first: Dylan

last: Taatjes


title: RNA sequencing of human airway epithelial cultures from cystic fibrosis (CF) and non-CF donors exposed to tumor necrosis factor-alpha and interleukin-17 (TNFα+IL-17) for 5 hours

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

institute: Universty of Iowa

summary: Gene expression was compared between disease conditions (CF vs. non-CF) and treatments (TNFα+IL-17 vs. control) as well as the interaction between disease and treatment.

overall_design: Primary differentiated airway epithelia were treated with TNFα (10ng/ml) and IL-17 (20ng/ml) for 5 hours, prepared for RNA sequencing, and sequenced on Illumina HiSeq 4000 system using 2x150bp paired end SBS chemistry.

first: Tayyab

last: Rehman

first: Andrew

last: Thurman

first: Michael

last: Welsh


title: TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network.

address: 3415 Colorado Ave

summary: We combined cryo-EM, transcriptomics, and a clinically relevant inhibitor to define how the TFIIH-associated CDK7 kinase coordinately controls the cell cycle and RNA polymerase II (RNAPII) transcription. CDK7 inhibition rapidly blocked expression of constitutively active genes, whereas inducible genes were unaffected.  Distinct sets of sequence-specific, DNA-binding transcription factors (TFs) regulate constitutive vs. inducible genes; accordingly, inducible TFs (e.g. HSF1) were refractory to CDK7 inhibition. By contrast, CDK7 was required to maintain activity of a core set of promoter-associated TFs that drive proliferative gene expression programs; these core TFs (n=78) are constitutively active in proliferating cells. Thus, a major biological function for CDK7 is regulation of TFs that drive cell proliferation, revealing an apparent universal mechanism by which CDK7 coordinates RNAPII transcription with cell cycle regulation.

overall_design: Precision run-on sequencing (PRO-seq) in HCT116 cells to evaluate the effects of CDK7 inhibition under basal and IFN-gamma stimulated conditions. There are 2 biological replicates for each condition.

first: Kira

last: Cozzolino


title: The TFIIH kinase CDK7 governs RNA polymerase II initiation, elongation, termination, and RNA processing

summary: In this study we perform precision nuclear run-on sequencing (PRO-seq) to measure the altered transcriptional response upon CDK7 inhibition or RNA-seq to elucidate the response of CDK7 inhibition on steady-state RNA. We performed a heat shock time course in PRO-seq with and without the Syros CDK7 inhibitor SY5609. Matching this data we performed three deeply sequenced RNA-seq experiments with SY5609 that include no heat shock, heat shock with recovery and long heat shock with no recovery. We additionally generated two more RNA-seq datasets in heat shock conditions with another Syros inhibitor, SY5102 and in a CDK7-analog sensitive OV90 cell line treated with 3MBPP1.

overall_design: Examination of the altered transcriptional profile and steady-state RNA response with and without selective CDK7 inhibition upon heat shock stimulation.


title: Detection of ALDOB expression level in clear cell renal cell carcinoma

status: Public on Dec 18 2024

city: Guangzhou

first: Tao

last: Wang

address: 566 Congcheng Avenue

institute: The Fifth Affiliated Hospital of Southern Medical University

summary: Immunohistochemical detection of ALDOB expression levels in clear cell renal cell carcinoma tissues and adjacent normal tissues of 80 patients

overall_design: This study conducted immunohistochemical detection of ALDOB expression levels in 80 patients with clear cell renal cell carcinoma tissue and adjacent normal tissue. It was found that ALDOB is a prognostic marker for clear cell carcinoma


title: Dose-dependent effects of dibutyl phthalate on embryonic development in zebrafish (Danio rerio): The value of integrating concentration gradients in transcriptomic analyses

city: Metz

first: Sophie

last: Prud'homme

address: Bâtiment IBISE, Rue Claude Bernard, Metz

department: Toxicologie de l'Environnement

country: France

institute: Université de Lorraine

summary: This study investigates the effects of dibutyl phthalate (DBP)—a plasticizer commonly detected in surface waters worldwide—on zebrafish (Danio rerio) embryos exposed to a concentration gradient from 0 to 120 hours post-fertilization (’protuding mouth’ stage). The primary objective was to assess the utility of integrating concentration gradients into transcriptomic analyses to uncover the mechanisms of action of environmental contaminants, such as DBP. Using this experimental design, dose-response modelling was applied to estimate the sensitivity and shape of transcriptomic responses across the DBP gradient. Following optimized over-representation analysis, we revealed that the retinoid signaling pathway may be the most sensitive pathway affected by DBP during zebrafish development, potentially leading to significant morphological changes.

overall_design: mRNA-seq profiling of whole zebrafish (Danio rerio) embryos (AB strain) exposed to a dose-gradient [0-5-10-50-100 µg/L] of dibutyl phthalate (DBP). The exposition consisted of five replicates of batches of 30 embryos each, exposed from the '256-cell' stage to the 'protuding mouth' stage. Exposition solutions were prepared as a solvent-free stock solution in fish water.

middle: M

first: Bénédicte

last: Sohm

first: Carole

last: Cossu-Leguille


title: Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms

status: Public on Dec 16 2024

city: New york city

first: Siyu

last: Sun

address: 321 61E street

institute: Memorial Sloan Kettering Cancer Center

summary: To thrive, cancers must navigate acute inflammatory signaling accompanying oncogenic transformation, such as via overexpression of retrotransposable elements. We examined the relationship between immunostimulatory repeat expression, tumor evolution and the tumor-immune microenvironment. Integration of multimodal data from a cohort of pancreatic ductal adenocarcinoma (PDAC) patients revealed expression of specific Alu repeats predicted to form double-stranded RNA (dsRNAs) and trigger RIG-I-like receptor-associated (RLR) type-I interferon (IFN) signaling. Alu-derived dsRNA anti-correlated with pro-tumorigenic macrophage infiltration. We defined two complementary pathways whereby PDAC adapt to such anti-tumorigenic signaling. In mutant p53 tumors, ORF1p from LINE-1 may preferentially bind Alus and decrease their expression, whereas ADAR1 editing primarily reduces dsRNA formation in wild-type p53 tumors. Depletion of either ORF1p or ADAR1 reduced tumor growth in vitro. That tumors utilize multiple pathways to mitigate immunostimulatory repeats implies that the stress from their expression is a fundamental phenomenon to which PDAC, and other tumors, adapt.

overall_design: RNAseq of PDAC cell lines and RIPseq data of L1 ORF1p and ORF2p in embryonal carcinoma cellline

first: J

last: LaCava


title: Astroglial Ezh2 regulates early astrocyte morphogenesis and affects the coverage of astrocyte endfeet on blood vessels

status: Public on Dec 15 2024

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To further investigate how Ezh2 derived from cortical astrocytes regulates cell morphology, RNA-seq analysis was performed to examine transcriptomic changes in cortical astrocytes isolated from Ezh2 conditional knockout mice and wild-type littermates at P5. Approximately 4,900 transcripts exhibited differential expression between Ezh2fl/fl and Ezh2-cKO-Aldh1l1 mouse cortical astrocytes, with a fold change ≥2 and a p-value <0.05. After further screening of the highly expressed gene subset among the differentially expressed genes, we found that the upregulated genes were enriched in processes related to gliogenesis, cell differentiation, and cytoskeletal organization. These findings highlight the critical role of astrocytic Ezh2 in the morphological development of astrocytes.

overall_design: Astrocytes were isolated from the cerebral cortex of Ezh2fl/fl and Ezh2-cKO-Aldh1l1 mice at P5 by magnetic bead sorting (ACSA1-anti), and mRNA was extracted. Separately, including 4 samples of WT1/WT2/cKO1/cKO2 (W1/W2/C1/C2). Agilent 2100 Bioanalyze was used to quality controlled and quantified. Then, mRNA was converted to cDNA and the library was constructed. RNA sequencing analysis was performed using the Illumina HiSeq 2500 platform of Annolog Genomics.

first: Xinghua

last: Zhao


title: Differentially expressed genes after transfection of siMAD2L1 in a human cancer cell line

city: Kagoshima

first: Yuya

last: Tomioka

institute: Kagoshima University

summary: To identify differentially expressed genes in human cancer following siRNA transfection, lung adenocarcinoma cells were subjected to high-throughput sequencing.

overall_design: Human lung adenocarcinoma cells (A549) were treated with siMAD2L1

first: Naohiko

last: Seki


title: Differentially expressed genes after transfection of siRNA in a human cancer cell line (siANLN and siFAM111B)

overall_design: Human lung adenocarcinoma cells (A549) were treated with siRNAs (siANLN and siFAM111B)


title: Differentially expressed genes after transfection of miRNA in a human cancer cell line (miR-195-5p and miR-195-3p)

summary: To identify differentially expressed genes in human cancer following miRNA transfection, lung adenocarcinoma cells were subjected to high-throughput sequencing.

overall_design: Human lung adenocarcinoma cells (A549) were treated with miRNAs (miR-195-5p and miR-195-3p)


title: Profound synthetic lethality between SMARCAL1 and FANCM (RNA-Seq)

first: Sumin

last: Feng

overall_design: Gene expression profiling analysis using data from RNA-seq generated from RPE1-hTERT TP53-/- PACKO Cas9 cell

first: Graziana

last: Pastore

first: Lisa

last: Hoeg

first: Daniel

last: Durocher


title: Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis

city: Los Alamos

first: Eric

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

institute: Los Alamos National Laboratory

summary: Microalgae remain an important feedstock for the production of biofuels and bioproducts. Discovery of new species drives innovation for biotransformation, where bioengineering and other technological advances can significantly optimize performance. Production is predicated on deep knowledge of algal behavior predicted from genomic and phenotypic studies. However, prediction and manipulation of behavior, particularly for scale up, remains a challenge. Understanding the contribution of epigenetic processes to algal function provides another piece of this complex puzzle for achieving bioeconomy goals. Utilizing Nannochloropsis species as a model, we provide a methodological framework for investigating epigenetic processes, specifically DNA methylation, in new species and demonstrate best practices for discerning novel epigenetic modifications. We demonstrate specific forms of DNA methylation can be overlooked by traditional epigenetic analysis strategies. Using high-throughput, lower cost techniques, we provide evidence demonstrating Nannochloropsis gaditana and N. salina lack the most ubiquitous forms of eukaryotic DNA methylation (5mC and 5hmC) and instead employ N6-adenine methylation (6mA), commonly found in bacteria, in their genomes.

sample_organism:
Escherichia coli
Nannochloropsis gaditana
Microchloropsis salina

overall_design: Nannochloropsis salina and gaditana were subjected to nitrogen starvation (Replete, Starved, Deplete), or exposed to different levels of light (photoperiod light or dark). gDNA from nitrogen starved cells was treated with bisulfite and sequenced. Alterantively, Oxford Nanopore sequencing was performed for light and dark conditions and methylation calling performed using dorado and modkit.

first: Christina

last: Steadman

first: Shounak

last: Banerjee

first: Scott

last: Twary


title: Sleep Loss Amplifies the Neuron-Specific Interleukin-1 Receptor Accessory Protein Oncogenic Roles

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

summary: To gain molecular insights into the roles of neuron-specific interleukin-1 receptor accessory protein (AcPb)-dependent responses to sleep disruption (SD), we utilized RNA-seq to compare gene expression in the brains of wild-type (WT) and AcPb-/- mice, both with and without SD.

overall_design: We subjected WT and AcPb-/- mice to sleep disruption (SD) from ZT20-4 using a gentle handling technique (SD-WT [n=4], SD-AcPb [n=4]. Control mice (CTL) from both strains (CTL-WT [n=3], CTL-AcPb-/- [n=5]) were left undisturbed before euthanasia at ZT4. RNA sequencing was performed using total RNA extracted from somatosensory cortex tissues collected post-euthanasia from WT and AcPb-/- mice.

first: Yool

last: Lee

first: Erika

last: English

first: Catherine

last: Schwartzmann

first: James

last: Krueger


title: TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network

first: Taylor

last: Jones

overall_design: RNA-seq in OV90 cells was performed to evaluate the effects of CDK7 inhibition under basal conditions at 4hrs. There are 3 biological replicates for each condition.

first: Nisha

last: Rajagopal


title: Enhancer perturbations reveal divergent responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation

status: Public on Dec 12 2024

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

summary: Single cell perturb-seq. Abstract WIP.

overall_design: Single cell perturb-seq of OCT4 and NANOG enhancer perturbation library on embryonic stem cell and definitive endoderm

first: Jielin

last: Yan

first: Danwei

last: Huangfu


title: The core cellular network modulates immune phenotype switching in hepatitis B

status: Public on Dec 05 2024

city: Harbin

first: meng

last: cui

state: Heilongjiang

address: Xidazhi street

institute: Harbin Institute of Technology

summary: Hepatitis B virus (HBV) is a leading cause of liver-related diseases and mortality. However, immune mechanisms governing the phases of HBV infection remain elusive. Understanding molecular components in hepatitis immunosuppression and progression is essential for developing immunotherapies for functional cure of chronic HBV infection. Our integrative analysis of intrahepatic tissue and peripheral PBMC samples from patients with acute and chronic HBV infection using single-cell RNA sequencing (scRNA-seq) and TCR/BCR sequencing (scTCR/BCR-seq) revealed three distinct lineages of PBMC-derived intrahepatic T lymphocytes (hpCTLs): exhausted GZMK+PDCD1+, short-lived effector KLRG1+, and inactivated GZMB+PRF1+ hpCTLs. Key factors such as FasL/Fas-mediated cytotoxicity, CD28 co-stimulation, and exhaustion status were identified as determinants of hpCTL functionality. Liver-resident DC-SIGN+ macrophages were found to act as antigen-presenting cells that cross-prime hpCTLs in response to IL-2 or as suppressive macrophages by inhibiting T cell immunity through IL-10 and PD-L1 production and Treg recruitment. The intrahepatic core cellular network, including DC-SIGN+ macrophages, CSF1+ST2+ mast cells, AREG+ liver-resident NK cells, CD14+ hepatocytes, and CXCL13+ TFH, was observed to modulate immune tolerance, activation, and suppression in HBV infection. This study inferred the core cellular network involved in immune phenotype switching across different hepatitis B phases and suggested potential immunomodulatory strategies for treating chronic HBV infection.

overall_design:
We performed single-cell RNA sequencing (scRNA-seq) on liver biopsy samples from patients with HBV infection, which included 3 cases in the acute hepatitis (AHB) phase, 5 cases in the immune tolerance (IA) phase, 5 cases in the immune clearance (IC) phase, 5 cases in the immune transition (IT) phase and 3 healthy control cases. Additionally, paired peripheral PBMC samples were analyzed, comprising 3 cases in the AHB phase, 3 cases in the IA phase, 5 cases in the IC phase, and 4 cases in the IT phase.

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Raw files for human/patient samples are being made available in GSA (https://ngdc.cncb.ac.cn/gsa/) for controlled access to the personally identifiable sequence data (BioProject PRJCA031773, with the assigned accession number HRA009171).
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first: Chuangeng

last: Chen

first: Ziqi

last: Zhen

first: Meng

last: Cui


title: Transcriptional landscape of direct reprogramming toward hematopoietic stem cells

status: Public on Dec 09 2024

city: Ann Arbor

first: Lindsey

last: Muir

state: Michigan

address: 1600 Huron Parkway

institute: University of Michigan

summary: Direct reprogramming of human fibroblasts into hematopoietic stem cells (HSCs) offers a promising strategy for generating autologous cells to treat blood and immune disorders. However, low conversion efficiency and incomplete characterization of reprogrammed states limit current protocols. To address this, we assembled a single-cell transcriptomic reference atlas spanning hematopoietic, endothelial, and fibroblast cell types, and evaluated a novel algorithmically predicted transcription factor (TF) recipe—GATA2, GFI1B, FOS, REL, and STAT5A—for induction of HSC-like states. The 5TF recipe increased conversion efficiency of fibroblasts to CD34+ cells by approximately three-fold compared to previous protocols. Long-read single-cell RNA sequencing revealed heterogeneous expression of hematopoietic- and endothelial-associated genes, consistent with partial reprogramming. To benchmark re- programmed cells, we developed an approach to map their transcriptomic positions relative to native and initial cell states within the reference atlas. Finally, we cataloged isoform diversity in reprogrammed cells, suggesting a role for alternative splicing in reprogramming dynamics. These findings highlight both the promise and complexity of direct HSC reprogramming and provide a framework for optimizing future protocols.

overall_design: Direct reprogramming of human fibroblasts into hematopoietic stem cells (HSCs) was investigated using a defined set of five transcription factors (TFs): GATA2, GFI1B, FOS, STAT5A, and REL. TFs were selected using a data-guided control algorithm that identified combinations minimizing transcriptional differences between fibroblasts and HSCs. TFs were delivered via lentiviral vectors encoding doxycycline-inducible expression cassettes, and expression was induced with doxycycline for 48 hours. Cells used in control and reprogramming conditions were maintained between passages 2 and 4 at initiation, and all samples were collected before passage 10. Single-cell RNA sequencing was performed using the 10x Genomics Chromium platform, followed by long-read sequencing using Oxford Nanopore Technologies (ONT) platforms. Three libraries were generated: (1) human neonatal foreskin fibroblasts (ATCC CRL-2522), (2) cells reprogrammed with the 5TF cocktail, (3) primary human bone marrow (ATCC PCS-800-012TM, Lot 80516705). Raw sequencing data were processed using the EPI2ME Labs ‘wf-single-cell’ workflow with the GRCh38 reference genome (version 2024-A).

first: Cooper

last: Stansbury

first: Jillian

last: Cwycyshyn

first: Sarah

last: Golts

first: Joshua

last: Pickard

first: Hyunsu

first: Walter

last: Meixner

first: Indika

last: Rajapakse


title: Microglial SHIP1 controls synaptic pruning in the developing hippocampus via the complement system

city: New york

first: Chiara

last: Pedicone

address: 1425 Madison Ave

department: Genetics  and Genomics

institute: Icahn School of medicine at Mount Sinai

summary: INPP5D, which encodes the lipid phosphatase SHIP1, is one of the most common genes associated with the risk of Alzheimer’s disease and is enriched in microglia in the central nervous system. SHIP1 has been found to be highly expressed in plaque-associated microglia. However, how it regulates microglial function and influences brain physiology has been poorly investigated. Here we show that SHIP1 is not only enriched in microglia associated with amyloid beta plaques, but also in early stages of healthy brain development. By combining in vivo loss-of-function approaches and proteomics, we discovered that conditional knockout mice lacking microglial SHIP1 (cKO) display increased complement and synapse loss in the early postnatal brain. Additionally, SHIP1 KO microglia show reduced morphological complexity, altered transcriptional signatures, and abnormal synaptic pruning, which is dependent on the complement system. Single nucleus RNA-sequencing analysis of the entire hippocampus confirmed decreased interaction for synaptic structure-related pathways in both excitatory and inhibitory neurons. Importantly, cKO mice show cognitive defects in adulthood only when microglial SHIP1 is depleted at early postnatal days, but not when depleted at later stages. Finally, using CRISPR/Cas9 we generated human iPSC-derived microglia lacking SHIP1, and validated the increased engulfment of synaptic structures. Altogether, these findings suggest that SHIP1 is essential for proper microglia-mediated synapse remodeling through the complement system in the early postnatal brain. Disrupting this process has lasting behavioral effects and may provide a link to vulnerability to neurodegeneration.

overall_design: Bulk RNA seq data of iPSC derived microglia from control WT and SHIP1 KO edited lines to define microglia markers and principal component analysis proving lack of SHIP1 does not impair microglia differentiation. Two clones per genotype are included.

first: William

last: Kerr

first: Samuele

last: Marro


title: Single-Cell Antigen Receptor Sequencing in Pigs with Influenza

city: Columbia

first: John

last: Driver

address: 1201 Rollins Street

institute: University of Missouri

summary: Understanding the pulmonary adaptive immune system of pigs is of importance as respiratory pathogens present a major challenge for swine producers and pigs are increasingly used to model human pulmonary diseases. Single-cell RNA sequencing (scRNAseq) has accelerated the characterization of cellular phenotypes in the pig respiratory tract under both healthy and diseased conditions. However, combining scRNAseq with recovery of paired VJ and VDJ T cell receptor (TCR) as well as heavy (IGH) and light (IGL) chains of B cell receptors (BCR) to interrogate receptor repertoires has not to our knowledge been demonstrated for pigs. Here, we developed primers to enrich porcine TCR and BCR chains that are compatible with the 10x Genomics VDJ sequencing protocol. Using these pig-specific assays, we sequenced the T and B cell receptors of cryopreserved lung cells from CD1D-expressing and -deficient pigs after one or two infections with influenza A virus (IAV), a major swine and human respiratory pathogen, to examine whether natural killer T (NKT) cells alter pulmonary TCR and BCR repertoire selection. We also performed paired single-cell RNA and TCR sequencing of FACS-sorted T cells longitudinally sampled from the lungs of IAV-vaccinated and -infected pigs to track clonal expansion in response to IAV exposure. All pigs presented highly diverse repertoires. Pigs re-exposed to influenza antigens from either vaccination or infection exhibited higher numbers of expanded CD4 and CD8 T cell clonotypes with activated phenotypes, suggesting potential IAV reactive T cell populations. Our results demonstrate the utility of high throughput single-cell TCR and BCR sequencing in pigs.

overall_design: Six CD1D-/- and six CD1D-/+ pigs were transferred to biocontainment rooms at 4 weeks of age after being confirmed seronegative for IAV nucleoprotein antibodies by ELISA. At day 0, 3 CD1D-/- and 3 CD1D-/+ pigs were intratracheally infected with 1x106 tissue culture infectious dose (TCID50) of H1N1 A/California/04/2009 (pdmH1N1) in 2mL of DMEM after sedation with a combination of midazolam, butorphanol, and xylazine. Fourteen days later, all 12 pigs were sedated and infected with 1x106 TCID50 of H1N1 A/Missouri/CS20N08/2020 IAV. Five days later all 12 pigs were euthanized by pentobarbital sodium IV injections (150 mg/kg of body weight). At necropsy, the lungs were removed from the thoracic cavity for tissue collection. and euthanized. For the study to collect T cells through successive lung lavages, two pigs (FLU1 and FLU2) were vaccinated with a combination of 1x106 TCID50 of ultraviolet-inactivated pdmH1N1 virus and an oil-in water adjuvant (Emulsigen, 1:5 vaccine volume) at 28 days of age and boosted 15 days later. Both pigs were intratracheally infected with 1x106 TCID50 live pdmH1N1 virus 2 weeks after the booster. Lung fluid was collected 3 days before and 7 days after infection. A third unvaccinated, uninfected pig (NAÏVE) was lavaged at 28 and 33 days of age.