title: INTEGRATED ATAC-SEQ AND RNA-SEQ ANALYSIS IDENTIFIES KEY REGULATORY ELEMENTS IN FEEDER CELL-ACTIVATED NK CELLS [ATAC-seq]

city: Minneapolis

first: Pedram

last: Motallebnejad

state: MN

address: 421 Washington Ave SE

institute: University of Minnesota

summary: NK cells can potentially be used in allogeneic immunotherapy; however, for such use as off-the-shelf medicines, NK cells need to undergo ex vivo expansion, typically through activation with feeder cells, to generate enough cells for clinical applications. Upon stimulation with feeder cells, NK cells undergo profound changes in gene expression, altering their metabolic activity, cell cycle progression, and growth behavior. After examining the transcriptome and chromatin accessibility of NK cells before and 7 days after feeder cell activation, significant alterations were seen. These changes are even more pronounced in genome regions closer to enhancers. Several transcription factors, including AP-1, IRF4, STATs, T-bet, Eomes, and bHLHE40, which play key roles in NK cell development and immune response, exhibited differential binding activity between unstimulated and day 7 NK cells. Gene sets composed of target genes downstream of these transcription factors were also enriched at day 7, implying their involvement in NK cell activation. Moreover, we compared potential super-enhancer regions in NK cells before and after coculture, combined with the transcriptional activity of nearby genes. We identified stable and transcriptionally active super-enhancers in unstimulated and day 7 NK cells, as well as those that form or disappear after coculture initiation. The transcriptomic and epigenetic characterization of NK cells presented in this study could facilitate the ex vivo expansion and engineering of functionally superior NK cells.

overall_design: To investigate the changes in chomatin accessibility of NK cells that are activated with K562 feeder cells engineered to express membrane-bound IL-21 and 4-1BB-L, we carried out ATAC-seq on NK cells before stimulation (unstimulated samples) and 7 days after coculture with NK cells. We utilized 3 different donors for the analysis. We then performed transcription factor footprinting and motif enrichment analysis on the samples. Finally, we identified potential super-enhancers by stitching the peaks that are located in proximity in genomic regions.

first: Zion

last: Lee

first: Jen

last: One

first: Samira

last: Azarin

first: Wei-Shou

last: Hu


title: IgD expressed in nucleus of Pro-B cells promotes Pro-B cells proliferation by regulating E2F3 expression [ChIP-seq]

status: Public on May 22 2025

city: Beijing

first: Yixiao

last: Zhang

address: Xueyuan Road, No.38

country: China

institute: Peking Unversity

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Immunoglobulin D (IgD) has historically been considered as a surface marker of mature B cell with its specific function being undefined. Until now, no evidence had been presented to suggest that IgD is also expressed in pro-B cells. Here, we developed a mouse model with a targeted deletion of IgD, and assessed the production of the IgM, IgG and IgA, as well as the generation of the antigen specific antibodies. The findings indicated no significant differences in these Ig levels between wild type and IgD-deficient mice. However, we observed a notable reduction in the number of mature B cells, which led us to the surprising discovery that this decrease in B cell count begins at the pro-B cell stage. More significantly, we identified that IgD, in its intact tetrapeptide structure, is expressed in the nucleus of pro-B cells. Functionally, IgD appears to promote the proliferation of pro-B cells. Mechanically, IgD exhibits a transcription factor-like activity, and directly binds to the promoter region of E2f3, a pro-proliferative transcription factor. IgD drives the expression of E2f3, thereby promoting the proliferation of pro-B cells. This novel insight into the physiological significance of IgD in B cell development has important implications for our understanding of immune system function.

overall_design: Sorting of pro-B cells from WT mice, and using a specific antibody against IgD, we conducted chromatin immunoprecipitation (ChIP)-seq experiments, with isotype IgG (mouse IgG) serving as a control..


title: Phagocyte-Associated Pathobionts in Crohn's Disease

city: Miami

first: Maria

middle: T

last: Abreu

state: Florida

address: 1475 NW 12th Ave floor 1

department: Gastroenterology

country: USA

institute: University of Miami

type: Expression profiling by high throughput sequencing

summary: This study evaluated lamina propria phagocyte gene expression and the associated microbiome in samples from Crohn's disease patients and controls.

overall_design: Gut mucosal biopsies were collected from the terminal ileum and ascending colon of Crohn's disease patients and non-IBD controls. Phagocytes were isolated from digested biopsies using magnetic column sorting for CD11b+ cells. RNA was extracted from these cells and sequenced.

first: G

middle: E

last: Jacobsen

first: M


title: Genetic variation modulates aberrant DNA hypomethylation in naïve pluripotent stem cells.

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

summary: We observed markedly different DNA methylation chances in response to MAP kinase inhibition between 129 and B6J mESCs. We reasoned that these differences at least in part are driven by the differential expression of DNA methylation regulators and conducted RNA sequencing experiments.

overall_design: Mouse ES cells of B6J or 129 background were cultured in complete ES cell media with  serum/LIF.DMSO or 1uM of Mek inhibitor (iMEK-PD 0325901) was added to the culture from Day 0 to Day 5 daily. RNA was extracted at the end of 5 days of treatment and processed for RNA sequencing.

first: Matthias

last: Stadtfeld


title: The level of H2BK5acK10acK15ac affects the repair of DSBs  in  Schizosaccharomyces pombe

city: nanjing

first: Guangchun

last: Lu

address: wenyuan road

institute: Nanjing Normal University

summary: To investigate the different of gene expression between H2BK5RK10RK15R, H2BK5AK10AK15A, H2BK5QK10QK15Q and wild strain, and then, we performed the gene expression analysis from the RNA-Seq data.

overall_design: Gene expression analysis of the  H2BK5RK10RK15R, H2BK5AK10AK15A and H2BK5QK10QK15Q mutant strains were compared with the wild-type.

first: Gang

last: Feng


title: NanoCMSer: A Clinically Applicable Tool for Stratification of Colorectal Cancer Samples [March2024.CODE]

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: Colorectal cancer (CRC) is a significant contributor to global cancer-related mortality, emphasizing the critical need for advanced predictive biomarkers to guide treatment decisions. In our pursuit of identifying novel biomarkers, as part of an international consortium, we have previously categorized CRCs into four transcriptome-based consensus molecular subtypes (CMS1-4). These subtypes show promise for predicting outcomes and facilitating biological investigations. To streamline the integration of CMS classification into clinical practice, where routinely formalin-fixed paraffin-embedded (FFPE) samples are used, we developed NanoCMSer. This NanoString-based CMS classifier reliably stratifies both fresh-frozen (FF) and FFPE samples using a concise panel of just 55 genes. Employing domain adaptation methods during training enhanced the generalizability of the classifier, resulting in high accuracy for both FF and FFPE samples. For FF NanoString-based datasets, an accuracy of 95% and for FFPE NanoString-based datasets an accuracy of 92% was achieved, which is the highest reported for FFPE tissues. Furthermore, using the NanoCMSer, a 96% accuracy across a comprehensive collection of 1,976 RNAseq-based samples from 23 datasets aggregated in this study was determined.  Additionally, our findings highlight that even with a limited number of genes, the biological relevance of predictions at the individual sample level can be still identified, with distinct CMS biology readily recognizable upon conducting enrichment analysis. Furthermore, our observations revealed a substantial difference in 5-year recurrence free survival (RFS) for CMS2  and CMS3  patients in stage III compared to II (CMS2 21% more recurrences, CMS3 31% more recurrences), while this difference is less pronounced for CMS1 and CMS4 with 11% and 9%, respectively. We posit NanoCMSer as a robust tool with potential applications to assess the CMS status of CRCs in both tumor biology and clinical practice, accessible through the NanoCMSer R package.

first: Jan

middle: P

last: Medema


title: NanoCMSer: A Clinically Applicable Tool for Stratification of Colorectal Cancer Samples [March2024.MATCH]


title: NanoCMSer: A Clinically Applicable Tool for Stratification of Colorectal Cancer Samples [March2024]


title: NanoCMSer: A Clinically Applicable Stratification Tool for Stratification of Colorectal Cancer Samples [III]

summary: Colorectal cancer (CRC) is a significant contributor to global cancer-related mortality, emphasizing the critical need for advanced predictive biomarkers to guide treatment decisions. In our pursuit of identifying novel biomarkers, as part of an international consortium, we have previously categorized CRCs into four transcriptome-based consensus molecular subtypes (CMS1-4). These subtypes show promise for predicting outcomes and facilitating biological investigations. To streamline the integration of CMS classification into routine clinical practice, particularly on low RNA-quality archival data, we developed NanoCMSer. This NanoString-based CMS classifier reliably stratifies both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples using a concise panel of just 55 genes. Employing domain adaptation methods during training enhanced the generalizability of the classifier, resulting in high accuracy for both FF and FFPE samples. For FF NanoString-based datasets, an accuracy of 95% and for FFPE NanoString-based datasets an accuracy of 92% was achieved, which is the highest reported for FFPE tissues. Furthermore, using the NanoCMSer, a 96% accuracy across a comprehensive collection of 1,976 RNAseq-based samples from 23 datasets aggregated in this study was determined.    Additionally, our findings highlight that even with a limited number of genes, the biological relevance of predictions at the individual sample level can be still identified, with distinct CMS biology readily recognizable upon conducting enrichment analysis. Furthermore, our observations revealed a substantial decline in recurrence free survival (RFS) for CMS2 and CMS3 patients as they progress from stage II to III, while this decline is less pronounced for CMS1 and CMS4. We posit NanoCMSer as a robust tool with potential applications in both tumor biology and clinical practice, accessible through the NanoCMSer R package.

overall_design: FF tissues of Stage III CRC tumors.

first: Simone

last: Weerd


title: NanoCMSer: A Clinically Applicable Stratification Tool for Stratification of Colorectal Cancer Samples [II]

overall_design: FF and FFPE tissues of CRC tumors.


title: NanoCMSer: A Clinically Applicable Stratification Tool for Stratification of Colorectal Cancer Samples

summary: Colorectal cancer (CRC) is a significant contributor to global cancer-related mortality, emphasizing the critical need for advanced predictive biomarkers to guide treatment decisions. In our pursuit of identifying novel biomarkers, as part of an international consortium, we have previously categorized CRCs into four transcriptome-based consensus molecular subtypes (CMS1-4). These subtypes show promise for predicting outcomes and facilitating biological investigations. To streamline the integration of CMS classification into routine clinical practice, particularly on low RNA-quality archival data, we developed NanoCMSer. This NanoString-based CMS classifier reliably stratifies both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples using a concise panel of just 55 genes. Employing domain adaptation methods during training enhanced the generalizability of the classifier, resulting in high accuracy for both FF and FFPE samples. For FF NanoString-based datasets, an accuracy of 95% and for FFPE NanoString-based datasets an accuracy of 92% was achieved, which is the highest reported for FFPE tissues. Furthermore, using the NanoCMSer, a 96% accuracy across a comprehensive collection of 1,976 RNAseq-based samples from 23 datasets aggregated in this study was determined. Additionally, our findings highlight that even with a limited number of genes, the biological relevance of predictions at the individual sample level can be still identified, with distinct CMS biology readily recognizable upon conducting enrichment analysis. Furthermore, our observations revealed a substantial decline in recurrence free survival (RFS) for CMS2 and CMS3 patients as they progress from stage II to III, while this decline is less pronounced for CMS1 and CMS4. We posit NanoCMSer as a robust tool with potential applications in both tumor biology and clinical practice, accessible through the NanoCMSer R package.


title: Maintenance of tolerance after lung transplantation is dependent on the preservation of allograft tissue-resident Foxp3+ T cells

city: Saint Louis

first: Daniel

last: Kreisel

state: MO

address: 425 S Euclid Ave

department: Department of Surgery

institute: Washington University School of Medicine

summary: Mechanisms of allograft tolerance differ between organs. We have previously shown that Foxp3+ T cell (Treg)-enriched bronchus-associated lymphoid tissue is induced in tolerant murine lung allografts and that graft-resident Tregs suppress B cell activation to maintain tolerance. Here, using our previously described retransplant model, we examined whether continuous recruitment of Tregs to the allograft is required to maintain tolerance. We found that graft-infiltrating Tregs migrate to BALT where they interact with graft-resident CD11c+ and Foxp3+ cells. Graft-infiltrating and graft-resident Tregs are likely of thymic origin but have different gene expression profiles at the single cell level. Following retransplantation of a tolerized left lung graft into a non-immunosuppressed B6.Foxp3-DTR secondary recipient, we depleted graft-infiltrating Tregs by administering diphtheria toxin. When graft-infiltrating Tregs are depleted, the lung allograft has gross and histological evidence of rejection and is associated with B cell activation and development of donor-specific alloantibodies in the serum. These phenotypes are rescued when B cell-depleting anti-CD20 antibody is administered, further supporting an antibody-mediated mechanism by which graft-infiltrating Tregs maintain tolerance. Finally, we show that recombinant IL-33 administration can be used to expand the Treg population following murine lung transplant.

overall_design: Lungs from a BALB/c donor transplanted into an immunosuppressed B6 (CD45.2) primary recipient, and then retransplanted into a B6 (CD45.1) secondary recipient at least 30 days later were harvested at 7 days post-retransplant. Lung tissue was digested, and single cell suspensions were prepared. Cells from two transplanted lungs were pooled together. CD45.1+, CD45.2+, and CD45- cells were sorted by flow cytometry to create three separate libraries for single cell RNA sequencing.

first: Wenjun

last: Li

first: Yun Zhu

last: Bai

first: Yuriko

last: Terada

first: Hailey

middle: M

last: Shepherd

first: Junedh

last: Amrute

first: Yuhei

last: Yokoyama

first: Jason

last: Gauthier

first: Katsutaka

last: Mineura

first: Amit

last: Bery

first: Maxim

last: Artyomov

first: Marina

last: Terekhova

first: Alessandro

last: Alessandrini

first: Heth

last: Turnquist

first: Peter

last: Sage

first: Varun

last: Puri

first: Ramsey

last: Hachem

first: Ankit

last: Bharat

first: Kory

middle: J

last: Lavine

first: Andrew

last: Gelman

first: Alexander

middle: S

last: Krupnick

first: Ruben

middle: G

last: Nava


title: Acquired resistance to immunotherapy by physical barriers with cancer cell–expressing collagens in non–small cell lung cancer

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Drug resistance is the principal challenge of cancer therapies, including recently developed immunotherapy. More and more popular use of immunotherapy, especially treatments with immune checkpoint inhibitors (ICIs), witnesses explosively increasing cases of both primary and acquired immunotherapy resistance. While primary resistance has been extensively studied, mechanisms underlying acquired resistance of immunotherapy are less understood. Here we reported that tumor cells could develop acquired resistance to ICI treatment through self-built collagen-containing physical barriers in non-small cell lung cancer (NSCLC). We found that tumor cells expressed high levels of multiple collagen genes, including COL3A1 and COL6A1, and were fully covered with collagen fibers. COL3A1 formed a castle-like structure of a cluster of tumor cells and prevented the infiltration of T cells, while COL6A1 seemed to be an armor-like structure of each tumor cell and protected them from attack by cytotoxic T cells. Genetic or pharmaceutic disruption of these collagens, by warfarin, a commonly used medicine, significantly reversed the acquired resistance. Thus, our data reveal an unprecedented tumor cell-intrinsic mechanism, mediated by collagen-containing physical barriers, of acquired immunotherapy resistance, which immediately suggests a treatment option for patients.

overall_design: ATAC-seq in immunotherapy-sensitive and resistant mouse NSCLC organoids.

first: Manli

last: Wang

first: Xiangyu

first: Yu

last: Liu

first: Chong

last: Chen


title: Transcriptomic characterization of the liver microenvironment in cynomolgus macaques treated with TLR8 agonist.

city: Foster City

first: Cameron

last: Soulette

address: 333 Lakeside Dr

institute: Gilead Sciences

summary: RNA-seq data from liver tissues of cynomolgus macaques treated with TLR8 agonist (0.1, 0.5 or 2.5 mg/kg).

overall_design: Cynomolgus macaques (n = 3/sex/group) were dosed via oral gavage on day 1, 8, 15, 22 and 29 with either vehicle [30% (w/v) polyethylene glycol 300 (PEG 300) and 70% (w/v) reverse osmosis water (pH adjusted to 3.0 ± 0.1)], or 0.1, 0.5 or 2.5 mg/kg/dose TLR8 agonist diluted in vehicle at a dose volume of 2 mL/kg. The animals were anesthetized with sodium pentobarbital and euthanized via exsanguination at approximately 4 h (± 30 min) following dosing on day 29. Liver tissue (≥10 mg) was obtained from the left lateral lobe at terminal sacrifice and flash frozen in liquid nitrogen. Isolation of total cellular RNA and RNA-seq was conducted by Expression Analysis (Durham, NC).


title: scRNAseq from pbmc, ileum, and rectal tissue of healthy and crohns disease individuals

city: La Jolla

first: Eunice

last: Choi

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Crohn’s disease (CD) is a major subtype of inflammatory bowel disease (IBD), a spectrum of chronic intestinal disorders caused by dysregulated immune responses to gut microbiota. We performed Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITEseq) on peripheral blood, colon, and ileal immune cells derived from healthy subjects and patients with Crohn’s disease.

overall_design: Healthy individuals were undergoing colonoscopy as part of routine clinical care for colorectal cancer screening/surveillance or non-inflammatory gastrointestinal symptoms that included constipation or rectal bleeding. Cells were isolated, sorted, partitioned, and sequenced.

first: Duong

last: Han

first: Chiang

last: Natalie

first: Choi

last: Eunice

first: Patel

last: Shefali

first: Olvera

last: Jocelyn

first: Liu

last: Yi

first: Lhsuan

middle: L

last: Yun

first: Yao

last: Priscilla

first: Hsu

last: Paul

first: Wong

last: William

first: Indralingam

last: Cynthia

first: Tsai

last: Matthew

first: Boland

last: Brigid

first: Wang

last: Wei

first: Chang

last: John


title: Optineurin inhibition impedes type II collagen challenged dendritic cell migration

city: Hangzhou

first: Jiajia

last: Wang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Due to the maturation, migration and antigen presentation functions, dendritic cells (DCs) play a central role in the development of many autoimmune diseases, like rheumatoid arthritis, multiple sclerosis and dermatitis. However, the molecular regulatory process of disease- or antigen-specific DC activation remains elusive. We show that deletion of Optineurin (OPTN) effectively impairs type II collagen (CII), the main autoantigen for rheumatoid arthritis, challenged DC migration, thus ameliorating collagen-induced arthritis. Transcriptome analyses indicate that OPTN promotes the expressions of migration related genes. Our findings thus indicate that OPTN is an important regulator of CII-pulsed DC migration, which may be of potential value for the accurate treatment of rheumatoid arthritis.

overall_design: 3 wild type and 3 OPTN knockout CII-stimulated BMDCs

first: Wenxiang

last: Hong

first: Qinjie

last: Weng


title: NanoCMSer: A Clinically Applicable Stratification Tool for Stratification of Colorectal Cancer Samples [IV]

first: Arezo

last: Torang

overall_design:
FFPE tissues of CRC tumors.
Submitter states that RCC files not available for some samples.

first: Simone

last: Weerd

first: Jan

last: Medema


title: Effects of oocyte vitrification on gene expression in the liver and kidney tissues of adult offspring

city: Zhengzhou

first: Lei

last: Zhang

state: Henan

address: No. 7, Weiwu Road

department: Reproductive Medicine Center

institute: Henan Provincial People’s Hospital

summary: Oocyte vitrification is an important assisted reproductive technology (ART) that preserves the fertility of unmarried patients with malignant tumors before radiotherapy and chemotherapy, cases where no sperm are available on ART oocyte collection day, and the development of the oocyte donation program. In recent years, the effects of ART, including the vitrification of oocytes and embryos on the health of offspring, have attracted much attention; however, it is difficult to conduct long-term follow-up and biochemical evaluation in humans. In this study, we detected the effect of oocyte vitrification on gene expression in the organs of adult mice offspring by RNA-sequencing for the first time. Our results showed that only a small amount of gene expression was affected. Seven genes (Tpm3, Hspe1-rs1, Ntrk2, Cyp4a31, Asic5, Cyp4a14, Retsat) were abnormally expressed in the liver, and ten genes (Lbp, Hspe1-rs1, Prxl2b, Pfn3, Gm9008, Bglap3, Col8a1, Hmgcr, Ero1lb, Ifi44l) were abnormal in the kidney. Several genes were related to metabolism and disease occurrence in the liver or kidney. Besides, we paid special attention to the expression of known imprinted genes and DNA methylation-related genes in adult organs, which are susceptible to oocyte cryopreservation only in the preimplantation stage. As a result, some of these transcripts were detected in the liver and kidney, but they were not affected by oocyte vitrification. In conclusion, we first report that oocyte vitrification did not significantly change the global gene expression in offspring organs, including imprinted genes and DNA methylation-related genes; nonetheless, it can still influence the transcription of a few functional genes. The potential adverse effects caused by oocyte vitrification need attention and further study.

overall_design: Comparison of gene expression in offspring organs derived from fresh and vitrified oocytes,respectively.

first: Huanhuan

last: Chen

first: Li

last: Meng

first: Cuilian


title: Identification of disulfidptosis-related subtypes, characterization of tumor microenvironment infiltration, and development of a prognosis model in breast cancer

city: hefei

first: Liang

middle: Jia

last: Hui

address: 218 JiXi Avenue

institute: The First Affiliated Hospital of Anhui Medical University,

summary: Introduction: Breast cancer (BC) is now the most common type of cancer in women. Disulfidptosis is a new regulation of cell death (RCD). RCD dysregulation is causally linked to cancer. However, the comprehensive relationship between disulfidptosis and BC remains unknown. This study aimed to explore the predictive value of disulfidptosis-related genes (DRGs) in BC and their relationship with the TME. Methods: This study obtained 11 disulfidptosis genes (DGs) from previous research by Gan et al. RNA sequencing data of BC were downloaded from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus database (GEO) databases. First, we examined the effect of DG gene mutations and copy number changes on the overall survival of breast cancer samples. We then used the expression profile data of 11 DGs and survival data for consensus clustering, and BC patients were divided into two clusters. Survival analysis, gene set variation analysis (GSVA) and ss GSEA were used to compare the differences between them. Subsequently, DRGs were identified between the clusters used to perform Cox regression and least absolute shrinkage and selection operator regression (LASSO) analyses to construct a prognosis model. Finally, the immune cell infiltration pattern, immunotherapy response, and drug sensitivity of the two subtypes were analyzed. CCK-8 and a colony assay obtained by knocking down genes and gene sequencing were used to validate the model. Result: Two DG clusters were identified based on the expression of 11DGs. Then, 225 DRGs were identified between them. RS, composed of six genes, showed a significant relationship with survival, immune cell infiltration, clinical characteristics, immune checkpoints, immunotherapy response, and drug sensitivity. Low-RS shows a better prognosis and higher immunotherapy response than high-RS. A nomogram with perfect stability constructed using signature and clinical characteristics can predict the survival of each patient. CCK-8 and colony assay obtained by knocking down genes have demonstrated that the knockdown of high-risk genes in the RS model significantly inhibited cell proliferation.  Discussion: This study elucidates the potential relationship between disulfidptosis-related genes and breast cancer and provides new guidance for treating breast cancer.

overall_design: The Tumor Cell Line Comprehensive Analysis Database (DepMap Portal) was utilized to screen for cell lines for further experimental validation (18). Breast cancer cell lines (MDA-MB-468) were obtained from Sichuan Huijixin Biotechnology Co., Ltd. The MDA-MB-468 cells were grown in Dulbecco's Modified Eagle Medium (DMEM) culture medium, supplemented with 10% Fetal Bovine Serum (FBS) in a standard humidified incubator with 5% CO2 at 37°C. The TMEM45A and SHCBP1 specific short hairpin RNAs (shRNAs) were synthesized from Chengdu Youkangjianxing Biotechnology Co., Ltd.  The sequences of shRNAs are as the following: sh- TMEM45A -1: 5ʹ- TGCTGTTGACAGTGAGCGCGGTTAAAGTATTTGAATTTAATAGTGAAGCCACAGATGTATTAAATTCAAATACTTTAACCATGCCTACTGCCTCGGA-3ʹ; sh- TMEM45A -2: 5ʹ- TGCTGTTGACAGTGAGCGCGGTGTACAAAGAGTATTCTGATAGTGAAGCCACAGATGTATCAGAATACTCTTTGTACACCATGCCTACTGCCTCGGAʹ. sh- SHCBP1 -1: 5ʹ-TGCTGTTGACAGTGAGCGCCACATTGATTTTTCAATTGAATAGTGAAGCCACAGATGTATTCAATTGAAAAATCAATGTGATGCCTACTGCCTCGGA-3ʹ; sh- SHCBP1 -2: 5ʹ- TGCTGTTGACAGTGAGCGCCAGCCAAATGTTGATATTAAATAGTGAAGCCACAGATGTATTTAATATCAACATTTGGCTGATGCCTACTGCCTCGGA -3ʹ. The knockdown efficiency was evaluated using real-time quantitative PCR (RT-qPCR) after 48 h transfection. The primer sequences used in the experiment are as follows. For the TMEM45A gene, the primers include qpcr-TMEM45A-F (forward primer): TTGGATGCCCACACTATGA and qpcr-TMEM45A-R (reverse primer): TCCATGGTCAAGGAGTTACA. For the SHCBP1 gene, the primers consist of qpcr-SHCBP1-F (forward primer): CTGGAGTTACAGAAGGATGGTG and qpcr-SHCBP1-R (reverse primer): CCATAGAAGCCTGTGGAATGT. After the knockdown of TMEM45A and SHCBP1 in cell line MDA-MB-468, total mRNA from cells was extracted with TRIzol reagent (TaKaRa, Japan). Then, concentration and purity were evaluated by Nanodrop 2000 (Thermo Fisher, USA). After the RNA was reversely transcribed into cDNA with PrimeScript RT kit (TaKaRa, Japan) according to the instructions, SYBR Premix Ex Taq TM kit (TaKaRa, Japan) was applied for RT-qPCR, with β-actin as the endogenous control gene.


title: Expression data from Wilson disease patients liver

city: Baltimore

first: Som

last: Dev

state: MD

address: 725 N, Wolfe St

department: Physiology, School of Medicine

institute: Johns Hopkins University

summary:
The goal of the study was to analyze gene expression profle from the WD patients who underwent liver transplantation for acute or chronic liver failure. Control specimens were obtained from patients who underwent liver resections for other clinical reasons.
We used microarrays (Affymetrix) to determine the gene expression profile in WD

overall_design: Liver sections were snap frozen in liquid nitrogen and stored. Total RNA was isolated using TRIZOL reagent (Invitrogen, Grand Island, NY) followed by RNeasy cleanup procedure (Qiagen, Valencia, CA). The integrity of isolated RNA was electrophoretically verified by ethidium bromide staining and by optical densities (OD) ratio (OD260nm/280nm>1.8). A total of 15 liver RNA samples (8 biological replicates for control liver and 7 for WD patients) were examined for RNA integrity and concentration on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) using the RNA 6.000 LabChip Kit (Agilent Technologies) according to the manufacturers instructions. Affymetrix GeneChip analysis was conducted at the microarray core facility of the Interdisziplinäres Zentrum für klinische Forschung (IZKF), Leipzig (Faculty of Medicine, University of Leipzig). 2 μg of total RNA were used to prepare double-stranded cDNA (Superscript II, Life Technologies, Gaithersburg, MD) primed with oligo-dT containing an T7 RNA polymerase promoter site (Genset SA, Paris, France). cDNA was purified by phenol- chloroform extraction before in vitro transcription using the IVT labeling kit (Affymetrix, Santa Clara, CA, USA) to synthesize cRNA. After the in vitro transcription, unincorporated nucleotides were removed using the RNeasy kit (QIAGEN). The cRNA was fragmented and hybridized to two different (technical replicates) Human Genome U133 Plus 2.0 (Arrays Affymetrix). The washing and staining of the probe array was performed according to the manufacturer’s instructions. The array was scanned with a third generation Affymetrix GeneChipScanner 3000.

first: S

first: D

last: Huster

last: Lutsenko


title: A distinct mechanism of m6A methylation of mRNA in bacteria compared to in eukaryotes

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

type: Methylation profiling by high throughput sequencing

summary: The aim of the study was to uncover the mechanism behind m6A methylation on E. coli mRNA, and to elude to its functional roles by characterising it and asessing its affects under stress. We carried out m6A sequencing to meet these aims, and conclude that there is no enzymatic mechanism acting directly on the mRNA responsible for m6A installation, and that the modification is most likely non-functional, and appears randomly throughout the transcriptome.

overall_design: m6A-RNA sequencing of wild-type E. coli cells (2 replicates), cells from 4 Keio strains with a single gene knokcout, and from wid-type E. coli cells subjected to heat stress (2 replicates) or oxidative stress (2 replicates), to determine the mechanism behind m6A installation in E. coli and its characteristics under stress

first: Klara

last: Szydlo

first: Leonardo

last: Santos


title: Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [XistTitration_scRNAseq]

status: Public on May 21 2025

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

institute: Max Planck Institute for Molecular Genetics

summary: Developmental genes are controlled by several cis-acting regulatory elements (REs), which in turn respond to multiple trans-acting transcription factors (TFs). Understanding this regulatory complexity has remained a challenge. Here, we combine pooled CRISPR screens with different phenotypic readouts to dissect how a cis-regulatory landscape integrates information from a large number of TFs. We apply our approach to the murine X-inactivation center, which harbors the Xist gene. We identify a large set of Xist-controlling TFs and map their TF-RE wiring at the Xist locus. We show that a transiently expressed group of XX-biased TFs, which includes the X-linked factor ZIC3, control Xist’s promoter-proximal REs. These factors promote initial Xist upregulation in a binary fashion, potentially ensuring female-specific Xist expression. A second set of developmental TFs, which include the epiblast master regulator of the epiblast OTX2, are upregulated slightly later and activate distal REs associated with the lncRNA genes Jpx, Ftx and Xert. We show that this second regulatory axis is required to ensure sufficiently high Xist RNA levels for efficient establishment of X-chromosome inactivation. Our unbiased, systematic approach provides a framework for the comprehensive dissection of regulatory interactions across genomic loci.

overall_design: scRNAseq was performed in TX1072 SP427 XX CasTuner mESCs with guides targeting the Xist TSS or the Xist-regulating REs 61, 85, 93 and 96 following 4 days of 2i/LIF-withdrawal. Gradual Xist repression was induced via the addition of different dTAG concentrations to the medium (0, 1, 2, 4, 8 and 500 nM). The cells were sequenced with 10x Chromium following a MULTIseq protocol. Sample barcodes for de-convoluting the raw .fastq files, as well as filtered counts with assigned samples are included in the supplementary files. The experiment was conducted  in 2 replicates.

first: Gemma

last: Noviello

first: Eleni

last: Kanata

first: Jonathan

last: Froehlich

first: Melissa

last: Bothe

first: Alexandra

last: Martitz

first: Aybuge

last: Altay

first: Jade

last: Scouarnec

first: Vivi-Yun

last: Feng

first: Heleen

last: Mallie

first: Martin

last: Vingron

first: Edda

last: Schulz


title: Hypotensive major health effect of Rubus ulmifolius Schott. and Artemisia campestris L. highlighted by nutrigenomic and cardiovascular studies

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

summary: To evaluate the antihypertensive effect of Artemisia campestris and Rubus ulmifolius, we conducted a nutrigenomic analysis to examine the changes induced by the administration of the aqueous extracts of these plants on gene expression in mice. Cardiovascular effects were discussed together with antitumoral, anti-inflammatory, antimicrobial and eating behavior effects.

overall_design: Mice were fed with an aqueous extract of A. campestis (AEAc) and R. ulmifolius (AERu). The mice gavages consisted in a daily force-feeding of 500 µl of extract solution of Ar, Ru or wather (control - Ctr) besides the standard chow. Three mice for each condition were sacrificed. The central core of the liver left lobe was cut into cubes and immediately frozen on liquid azote and stored as individual samples at -80°C for transcriptomics.

first: Afaf

last: Mehiou

first: Abderrahim

last: Ziyyat

first: Sevser

last: Sahpaz


title: Candida albicans water soluble fractions (CAWS)-induced inflammation response in NOD1-deficient bone marrow derived dendritic cells

city: Tokyo

first: Yoshitaka

last: Kimura

address: Kaga 2-11-1, Itabashi-ku

department: Department of Microbiology and Immunulogy

country: Japan

institute: Teikyo University School of Medicine

summary: Candida albicans water-soluble fraction (CAWS)-induced coronary inflammation increased in NOD1-deficient mice. To investigate the molecular mechanisms underlying the aggravation of inflammation, gene expression in CAWS-stimulated bone marrow-derived dendritic cells (BMDCs) was evaluated.

overall_design: Bone marrow-derived dendritic cells (BMDCs) derived from WT (C57BL/6) and Homozygous NOD1-KO mice were stimulated with 100 μg/mL CAWS. The cells were collected before CAWS stimulation and at 48 h and day8 after stimulation.

first: Miyako

first: Noriko

last: Miura

first: Yusuke

last: Yoshino

first: Hajime

last: Kono


title: Surface CD69-negative bone-marrow resident human memory T cells [ESR transcription]

first: Frederik

middle: Richard

last: Heinrich

address: Chariteplatz 1

department: Bioinformatics

summary: Across tissues, tissue-resident memory T cells have been defined as cells which express CD69 in their cell surface, but not S1PR1, the receptor for the tissue-egress signal sphingosin-1-phosphate (S1P). It is  less clear whether CD69-negative memory T cells are also tissue-resident. Here, we compare transcriptomes and T cell receptor repertoires of individual CD4 and CD8 memory T cells from paired blood and bone marrow of three human donors. CD69- memory T cells of blood and bone marrow share transcriptionally defined clusters, as defined by signature genes reflecting their imprinting during activation. However, cells of related clusters of blood and bone marrow have distinct TCR repertoires, suggesting that they represent distinct compartments of memory, and that the CD69- memory T cells are residents of the bone marrow. Interestingly, the surface CD69- memory T cells of bone marrow do transcribe the CD69 gene, and they express S1PR1, suggesting that they are blindfolded for S1P by dimerization and internalization of CD69 and S1PR1, maintaining them in the tissue.

overall_design: Ex vivo transcriptome and TCR of paired blood and bone marrow memory T cells in the resting state

first: Emilia

last: Schneider

first: Pawel

last: Durek

first: Farzin

last: Mashreghi


title: Nitrogen source-driven regulation of Irpex lacteus for enhanced lignocellulose degradation and microbial protein production in wheat straw

city: Changzhou

first: sainan

last: zhang

state: Jiangsu

address: Gehuzhonglu

institute: Changzhou University

summary: White rot fungi, such as Irpex lacteus, offer significant potential for lignocellulose degradation and protein synthesis in sustainable biofuel and animal feed production,but optimizing nitrogen sources to balance fungal growth, lignin degradation, and protein synthesis remains a critical challenge.This study investigated the effects of ammonium chloride (NH₄Cl) and sodium nitrate (NaNO₃) on I. lacteus fermentation in wheat straw, with a focus on the regulation of nitrogen source.Transcriptomic analysis revealed that NaNO₃ upregulated genes associated with nitrogen uptake and cellulose/hemicellulose degradation,while exerting less repression on key ligninolytic enzymes, such as manganese peroxidase and cytochrome P450, compared to NH₄Cl.These findings suggest that NaNO₃ enhances I. lacteus metabolism by harmonizing lignin degradation with efficient nitrogen conversion.

overall_design: To investigate the effects of different nitrogen sources on the fermentation of wheat straw by the fungus Tricholoma album, a study was conducted where ammonium chloride and sodium nitrate solutions were added as inorganic nitrogen sources. A control group was also set up by adding distilled water. Subsequently, transcriptional sequencing was performed on the fermentation samples.


title: Surface CD69-negative bone-marrow resident human memory T cells [ESR TCR]


title: Nanoengineered STING Mucosal Adjuvant Activates Coordinated Mucosal-Systemic Immunity for Durable Cross-Protective Defense

city: Shanghai

first: Kaicheng

last: Zhou

address: No.826 Zhangheng Road

institute: Fudan University School of Pharmacy

summary: A longstanding barrier in vaccinology has been the inability to reconcile potent mucosal immune activation with systemic tolerability, hindering adjuvant development for over a century. Here, we present NanoCF501, a nanoparticulate STING agonist engineered with respiratory-tuned, clinically safe polymers, which overcomes this fundamental limitation. When co-administered with a multivalent pan-β-coronavirus subunit vaccine, NanoCF501 at 1/20th the systemic adjuvant dose elicits coordinated mucosal-systemic immunity, inducing robust and durable cross-protective responses. These include mucosal secretory IgA and tissue-resident memory T cells alongside systemic neutralizing antibodies, memory B cells, and long-lived plasma cells persisting >12 months in murine models. Non-human primates validate the dual-axis mucosal-systemic coupling, while toxicology studies in rats demonstrate more than 18-fold safety margin and undetectable systemic exposure, underscoring translational viability. Mechanistic interrogation via single-cell transcriptomics reveals that NanoCF501 drives STING-dependent innate immune activation, orchestrating broad transcriptional reprogramming in lung antigen-presenting cells and efficient priming of adaptive T and B cell responses. Notably, NanoCF501 converts conventional quadrivalent influenza subunit vaccines into mucosal immunogenic formulations, demonstrating platform versatility. By integrating rational nanocarrier design with innate immune targeting, this work establishes a universal mucosal vaccination strategy with broad implications for pandemic preparedness and mucosal vaccinology.

overall_design: Single-cell RNA sequencing was performed at two critical timepoints: 24 hours post-primary immunization and 7 days post-secondary immunization. Female BALB/c mice (6-8 weeks old) received either SSM2-only or SSM2 adjuvanted with NanoCF501 using the established immunization protocol. Pulmonary tissues were harvested and mechanically dissociated to prepare single-cell suspensions and analyzed using scRNA-seq.

first: Zezhong

last: Liu

first: Jie

first: Ruiyu

last: Gao

first: Yanqun

last: Wang

first: Meiqin

first: Weijie

first: Yuanzhou

first: Peilan

last: Wei

first: Muzhuo

first: Shaokui

last: Pan

first: Lixiao

last: Xing

first: Guangxu

last: Zhang

first: Wei

last: Xu

first: Qian

first: Xueping

last: Jiang

first: Juan

first: Yubei

first: Yaqun

first: Kai

last: Qi

first: Jing

first: Ming

last: Hsieh

first: Xian

last: Zeng

first: Xinling

first: Ray

last: Yin

first: Fan

last: Wu

first: Jincun

last: Zhao

first: Wanli

first: Shibo

first: Lu

last: Lu


title: An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes [P28]

city: Cambridge

first: Min

last: Dai

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute of MIT and Harvard

summary: Establishing tools that can target and manipulate specific neuronal populations is critical to understanding neural circuits and developing targeted therapies. Recombinant adeno-associated virus (rAAV) is a popular tool for gene delivery and is widely used in basic research as well as gene therapy. Significant effort has been made to develop rAAV tools that can drive cell-type or tissue specific transgene expression. One of the strategies to develop such tools is to incorporate cell-type specific enhancer elements into the rAAV genome. In recent years, we and others have identified a number of enhancers that, when incorporated into rAAV vectors, can restrict the transgene expression to particular neuronal populations. Yet, viral tools to access and manipulate fine neuronal subtypes are still limited. Here, we performed systematic analysis of single cell ATAC-seq and RNA-seq data to identify enhancer candidates for each of the cortical interneuron subtypes.We established a set of enhancer-AAV tools that are highly specific for distinct cortical interneuron populations and striatal cholinergic neurons. These enhancers, when used in the context of different effectors, can target (fluorescent proteins), observe activity (gCaMP) and manipulate (opto- or chemo-genetics) specific neuronal subtypes. We also validated our enhancer-AAV tools across species. Thus, we provide the field with a powerful set of tools to study neural circuits and functions and to develop precise and targeted therapy.

overall_design: To identify potential cell type specific enhancers, we took advantage of the single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) data we have previously generated in the lab. To enrich for GABAergic cells, Dlx6a-Cre::INTACT mice were used. GFP+ nuclei from cortex (anterior lateral motor cortex, ALM) and striatum were isolated by FACS and scATAC-seq data were collected


title: Effect of DOX on miRNA expression in plasma exosomes of breast cancer model mice

city: Beijing

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore and identify the differentially expressed miRNAs in plasma EXOs from DOX-treated and vehicle-treated breast cancer-bearing mice, exosomal miRNA-seq was conducted, and the results revealed that 14 miRNAs were significantly upregulated (fold change≥2, q<0.05).

overall_design: Differentially expressed miRNAs in plasma EXOs from DOX-treated and vehicle-treated breast cancer-bearing mice

first: Ma

last: Yan

first: Han

last: Dong


title: Next Generation Sequencing Facilitates Quantitative Analysis of CD8+ T cells Transcriptomes from MondoAfl/fl and MondoAfl/flCD4cre Mice

city: China

first: Nannan

state: Shanghai

address: 280s chongqing road

institute: Shanghai Jiao Tong University School of Medicine

summary: RNA-seq of CD8+ T cells from MondoAfl/fl and MondoAfl/flCD4cre Mice

overall_design: We sorted CD8+ T cells from MondoAfl/fl and MondoAfl/flCD4cre mice and treated CD8+ T cells with anti-CD3/CD28 for 24 hours.

first: Yemin

last: Zhu

first: Xuemei

last: Tong


title: Next Generation Sequencing Facilitates Qunatitative Analysis of Lactic acid Treated CD8+ T cells Transcriptomes

summary: RNA-seq of CD8+ T cells sorted from peripheral blood mononuclear cells (PBMC) and treated with or without lactic acid.

overall_design: Treating CD8+ T cells with 10mM lactic acid for 24 hours, we conducted RNA-seq.


title: Abundant piRNAs beyond transposon regulation drive germ cell formation and transgenerational piRNA inheritance in Drosophila

city: Kumamoto

first: Shingo

last: Usuki

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics (IMEG)

institute: Kumamoto University

summary: Germ cells transmit genetic information to offspring and maintain the genome of the species. In many animals including Drosophila, germ cell formation relies on maternal determinants in the germ plasm. Several proteins present in the germ plasm of oocytes also localize to the perinuclear nuage in nurse cells, where they contribute to the production of PIWI-interacting RNAs (piRNAs). These piRNAs guide the silencing of transposons, thereby protecting the germline genome from invading mobile elements. Aubergine (Aub) is a germ plasm/nuage protein and a piRNA-directed endonuclease that inactivates transposons. Aub is also essential for germ plasm assembly. The Aub-bound piRNAs in the germ plasm are inherited by the progeny germline and serve as templates for piRNA biogenesis in the next generation. Thus, piRNA production in the nurse cell nuage is thought to be coordinated with germ plasm assembly in the oocyte. However, the underlying mechanism remains unclear. Here, we report that a maternal factor, named tiny pole plasm (tpp), mediates this coordination. In tpp– ovaries, the production of piRNAs, particularly Aub-bound piRNAs, is defective, resulting in reduced Aub localization to the germ plasm and impaired germ cell formation. Notably, the levels of piRNA production required for proper germ plasm activity are much higher than those required for transposon silencing. We propose that the production of abundant piRNAs beyond what is required for transposon silencing in the ovary ensures the transgenerational inheritance of anti-transposon information to progeny via the germ plasm, which is essential for the survival of species.

overall_design: We performed RNA-seq analysis of ovaries from control yw, tpp, aub, 38C∆ 42AB∆, tpp 38C∆ 42AB∆ flies. The reads were aligned to the canonical transposon sequences in the Drosophila genome.

first: Hirono

last: Kina

first: Natsuko

last: Izumi

first: Kazuko

last: Hanyu-Nakamura

first: Takashi

last: Yoshitani

first: Mariko

last: Yamane

first: Hitoshi

last: Niwa

first: Yukihide

last: Tomari

first: Akira

last: Nakamura


title: Expression data from NCI-N87 human gastric epithelial cells, seeded on transwell, treated with Poliprotect (F)

city: Sansepolcro

first: Jacopo

last: Lucci

state: Arezzo

address: Loc. Aboca, 20

country: Italy

institute: Bios-Therapy, Physiological Systems For Health S.p.A

summary:
We evaluate the effects of treatment with the product Poliprotect (F) on human NCI-N87 cells in order to measure the overall activity of the product on biological functions of interest
We used microarrays to detail the transcriptional response obtained by treating NCI-N87 cells with HBSS pH1 (acid-induced damage), HBSS pH7.4 (control pH) , Poliprotect (F)(apical and basolateral treatment)

overall_design: We compared transcriptional response of the insult (pH 1) versus the physiological baseline (pH 7.4) and the transcritional response of Poliprotect (F) + pH1 (apical treatment) versus the physiological baseline (pH 7.4) . Morever we compared transcriptional response of Poliprotect (F) (basolateral treatment) versus the physiological baseline (pH 7.4).

first: Sara

last: Caterbi

first: Angela

last: Guerrini


title: Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [Xist_CRISPR_screens]

first: Till

last: Schwämmle

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: CRISPRi screens targeting transcription factor (TF) genes. Xist-High, -Low and -Negative populations were sorted using flow cytometry following FlowFISH staining for Xist RNA. The TFi library targets 570 TF genes using 11058 sgRNAs. The TFiMini library targets 119 TF genes (FDR <0.2 from the TFi screen) with 1270 individual sgRNAs. Two replicates were collected per screen

first: Gemma

last: Noviello

first: Eleni

last: Kanata

first: Jonathan

last: Froehlich

first: Melissa

last: Bothe

first: Alexandra

last: Martitz

first: Aybuge

last: Altay

first: Jade

last: Scouarnec

first: Vivi-Yun

last: Feng

first: Heleen

last: Mallie

first: Martin

last: Vingron

first: Edda

last: Schulz


title: Analysis of transcription in peripheral blood mononuclear cells from HIV-infected patients receiving antiretroviral therapy

city: Moscow

first: Sergey

last: Ivanov

address: 10, Pogodinskaya street

country: Russia

institute: Institute of Biomedical Chemistry

summary: Human immunodeficiency virus is a cause of progressive infection leading to immune dysfunction. Although antiretroviral treatment can normalize the functional state of immune cells by reducing viral load, for some people the immune efficacy of antiretroviral therapy (ART) is insufficient. The aim of this study was to investigate the transcriptomic changes in peripheral blood mononuclear cells (PBMC) of patients receiving ART. To evaluate the changes in PBMC, we conducted a clinical trial involving HIV-positive patients on ART. PBMC were collected before starting ART and after 24 weeks of treatment with ART along with estimation of viral load and CD4+ and CD8+ T-lymphocytes count. To evaluate the transcriptional profiles, we used RNA sequencing of isolated PBMC. The results showed two-fold differential expression of 70 genes in PBMC induced by ART and 56 genes prediction an increase in CD4+ lymphocytes after therapy. This information can be helpful for understanding molecular mechanisms of host response to ART.

overall_design: RNA-seq profiling of peripheral blood mononuclear cells (PBMC) derived from patients with HIV before initiation of therapy and after 24 weeks of therapy (tenofovir + lamivudine + dolutegravir). CD4, CD8 cell counts, and viral load (copies / ml) were also measured before and after therapy.

first: S

first: D

last: Kireev

first: A

middle: A

last: Pokrovskaya

middle: B

last: Shemshura

last: Lagunin

first: V

middle: V

last: Poroikov

first: O

last: Tarasova


title: Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus

first: Till

last: Schwämmle

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

overall_design: Refer to individual Series

first: Gemma

last: Noviello

last: Kanata


title: Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [RNA-seq]

overall_design: mRNA-seq in TX1072 XX and XO cells during the first 96 hours of 2i/LIF-withdrawal. Three replicates per timepoint and cell line. Only two replicates are available for XO_36h.

first: Eleni

first: Jonathan

last: Froehlich

last: Bothe

last: Martitz


title: Berberine protects against hepatocellular carcinoma progression by regulating intrahepatic T cell heterogeneity

first: chen

last: Xue

state: Zhejiang

address: 866 Yuhangtang Rd

summary: Accumulating evidence suggests that berberine (BBR) exhibits anti-cancer effects in hepatocellular carcinoma (HCC). However, the mechanisms by which BBR regulates the immunological microenvironment in HCC has not been fully elucidated. In this study, we established a mouse model of orthotopic HCC and treated with varying doses of BBR. BBR showed effectiveness in reducing tumor burden in mice with HCC. Cytometry by time-of-flight depicted the alterations in the tumor immune landscape following BBR treatment, revealing the enhancement in the T lymphocytes effector function. In particular, BBR decreased the proportion of TCRbhiPD-1hiCD69+CD27+CD8a+ effector CD8+ T lymphocytes and increased the proportion of Ly6ChiTCRb+CD69+CD27+CD62L+ central memory CD8+ T lymphocytes. Single-cell RNA sequencing further elucidate the effects of BBR on transcriptional profiles of liver immune cell and confirmed the phenotypical heterogeneity of T lymphocytes in HCC immune microenvironment. Additionally, we found that BBR potentially regulated the antitumor immunity in HCC by modulating the receptor-ligand interaction among immune cells mediated by cytokines. In summary, our findings improve the understanding of BBR's impact on protecting against HCC, emphasizing BBR's role in regulating intrahepatic T cell heterogeneity. BBR has the potential to be a promising therapeutic strategy to hinder the advancement of HCC.

overall_design: The HCC mouse models were randomly divided into three groups: HCC mouse models treated with PBC (HC group), HCC mouse models treated with low-dose BBR (LB group), HCC mouse model treated with high-dose BBR (HB group). BBR with a purity of 98% was provided by Meilun Biology (Dalian, China) and administered intraperitoneally to the HCC mouse model. The HB group received 200 μL of a BBR solution at a dosage of 30 mg/kg, while the LB group received 10 mg/kg. The HC group was given an equivalent volume of phosphate buffer saline (PBS). Administration was carried out every other day for a period of 14 days. Cytometry by time-of-flight depicted the alterations in the tumor immune landscape following BBR treatment.Single-cell RNA sequencing further elucidate the effects of BBR on transcriptional profiles of liver immune cell and confirmed the phenotypical heterogeneity of T lymphocytes in HCC immune microenvironment.

first: Jiaxiang

last: Hu


title: Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [Reporter_CRISPR_screens]

overall_design: Reporter CRISPR screens linking Xist-regulating transcription factors (TFs) to Xist-controlling regulatory elements (REs). The CRISPR library targets 119 TF genes with 1270 individual sgRNAs. The assay contains 12 individual CRISPR screens targeting 11 different fluorescent reporter lines (including an RE) and an empty control (noRE). GFP-High (top 10%) and GFP-Low (top 10%) populations were sorted using flow cytometry. Three replicates were collected per screen.

first: Melissa

first: Alexandra

first: Aybuge

last: Altay

first: Jade

last: Scouarnec

last: Feng

last: Mallie

last: Vingron


title: Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [scRNA-seq]

overall_design: scRNAseq was performed in TX1072 XX and TX1072 XX dFtx-Xert -/- mESCs following 4 days of 2i/LIF-withdrawal. The cells were sequenced with 10x Chromium following a MULTIseq protocol. As the libraries were prepared together with an unrelated experiment, the provided FASTQ files were filtered for reads matching assigned cell barcodes (using UMI-tools and seqtk). The setup includes 2 replicates (REP1: 187 WT, 87 DEL cells; REP2 325 WT, 79 DEL cells).

first: Vivi-Yun

first: Heleen

first: Martin

first: Edda

last: Schulz


title: miRNA profiling of plasma-derived exosomes in hereditary angioedema

city: Ulm

first: Linda

last: Hofmann

state: Deutschland

address: Frauensteige 14a, Haus 18

institute: University of Ulm

summary: Exosomes were isolated from plasma of healthy donors (HD) and patients with hereditary angioedema (HAE). miRNA profiling of plasma-derived exosomes was performed using nCounter SPRINT system. miRNA levels were compared between HD and HAE patients.

overall_design: Exosomal miRNA profiles from plasma of n = 11 HD and n = 11 HAE patients were analyzed regarding their differential presence.

first: Robin

last: Lochbaum

first: Janina

last: Hahn

first: Marie-Nicole

last: Theodoraki


title: Molecular basis of GA-independent DELLA regulation by the VIH-type inositol pyrophosphate synthase in a non-vascular land plant

city: Bangalore

first: Debabrata

last: Laha

address: C V Raman Institute

institute: Indian Institute of Science

summary: To study the functional relationship between MpVIH and MpDELLA at molecular level, the system-wide transcriptome profile of the following genotype were analysed: WT, CRISPR/Cas9 knockout lines of MpVIH (Mpvih) and  independent Mpvih transgenic lines with reduced MpDELLA transcripts using an artificial microRNA (Mpvih::amiR-MpDELLA) technology.

overall_design: Transcriptome comparison between WT, Mpvih mutant and amiR-MpDELLA lines in Mpvih background. For each genotype (Mpvih and Mpvih::amiR-MpDELLA) two independent lines were analysed. Each genotype has 3 biological replicates.

first: Hemant

middle: C

last: Naik

first: Priyanshi

last: Rana

first: Srimonta

last: Gayen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Lactic acid Treated Human Treg cells Transcriptomes

first: Nannan

last: Xu

summary: RNA-seq of Treg cells sorted from peripheral blood mononuclear cells (PBMC) and treated with or without lactic acid.

overall_design: we polarized CD4+ T cells from PBMC into inducible Tregs (iTregs) in vitro and treated them with or without 10 mM lactic acid for 24 hours.

first: Yemin

last: Zhu

first: Xuemei

last: Tong


title: An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes

first: Min

last: Dai


title: De novo RNA sequencing of  the gut and cerebral ganglion of Dendrobaena veneta exposed to carbamazepine

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

summary: One of the most widely used drugs in municipal wastewater treatment effluents and soil is carbamazepine, a commonly prescribed antidepressants and antiepileptic drug. Carbamazepine exerts an intrinsic biological activity on the nervous system,  thus may induce ecotoxicological effects on non-target organisms. Earthworms, one of the essential indicator species of soil health, accumulate biosolid fertilisers and wastewater contaminants.  In this project, earthworms (Dendrobaena veneta) were treated with carbamazepine to explore their uptake dynamics, molecular and life cycle endpoints.  By conducting transcriptomic profiling of different tissues in an organism exposed to carbamazepine assists in defining   detoxification and neural system responses in the terrestrial invertebrate.

overall_design: De novo RNA sequencing (RNASeq) was carried out via the HiSeq X Ten platform to define the transcriptomic fingerprints in the gut and cerebral ganglion tissue of earthworms exposed to 0.6 or 10 mg/kg carbamazepine added to the topsoil under laboratory conditions for 28 days.

first: Chubin

last: Zhang

first: Leon

last: Barron


title: Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [Cut&Tag]

first: Till

last: Schwämmle

summary: Developmental genes are controlled by several cis-acting regulatory elements (REs), which in turn respond to multiple trans-acting transcription factors (TFs). Understanding this regulatory complexity has remained a challenge. Here, we combine pooled CRISPR screens with different phenotypic readouts to dissect how a cis-regulatory landscape integrates information from a large number of TFs. We apply our approach to the murine X-inactivation center, which harbors the Xist gene. We identify a large set of Xist-controlling TFs and map their TF-RE wiring at the Xist locus. We show that a transiently expressed group of XX-biased TFs, which includes the X-linked factor ZIC3, control Xist’s promoter-proximal REs. These factors promote initial Xist upregulation in a binary fashion, potentially ensuring female-specific Xist expression. A second set of developmental TFs, which include the epiblast master regulator of the epiblast OTX2, are upregulated slightly later and activate distal REs associated with the lncRNA genes Jpx, Ftx and Xert. We show that this second regulatory axis is required to ensure sufficiently high Xist RNA levels for efficient establishment of X-chromosome inactivation. Our unbiased, systematic approach provides a framework for the comprehensive dissection of regulatory interactions across genomic loci.

overall_design: CUT&Tag for active histone modifications in female mouse embryonic stem cells (mESCs) differentiated for 2 days by 2i/LIF-withdrawal. CRISPRi (dCas9-HDAC4) was used to knockdown the indicated factors. Three replicates per condition are included.

first: Gemma

last: Noviello

first: Eleni

last: Kanata

first: Jonathan

last: Froehlich

first: Melissa

last: Bothe

first: Alexandra

last: Martitz

first: Aybuge

last: Altay

first: Jade

last: Scouarnec

first: Vivi-Yun

last: Feng

first: Heleen

last: Mallie

first: Martin

last: Vingron


title: Regional Lung tissue methylation study

city: Hamilton

first: John

middle: Edward

last: McDonough

state: ON

address: 50 Charlton Ave E

country: Canada

institute: McMaster University

type: Methylation profiling by genome tiling array

summary: Multiple samples from different regions and severities of IPF disease were collected and methylation analysis was performed.

overall_design: The bisulfite conversion of 500 ng genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research), and the bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip Kit using standard Illumina protocol

first: Daniel

last: Kurbanov


title: RNA-seq for the soybean roots at different aluminum levels

city: Guangzhou

first: Guoxuan

last: Liu

address: Wushan

institute: 华南农业大学

overall_design: To further identify the candidate genes of aluminum tolerance, a transcriptional analysis of roots subjected to 0 μM (control) and 50 μM AlCl3 (Al) were conducted.

first: Cuiyue

last: Liang

first: Jiang

last: Tian


title: Genome-wide identification of endogenous NMD-targeted RNAs in human stem cells [UPF3B_NPCs]

city: La Jolla

first: Kun

last: Tan

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

summary: Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that influences several biological processes. Specific features in messenger RNAs (mRNAs) have been found to trigger decay by NMD, leading to the assumption that NMD sensitivity is an intrinsic quality of a given transcript. Here, we provide evidence that, instead, an overriding factor dictating NMD sensitivity is the cell environment. Using several genome-wide techniques to detect NMD-target mRNAs, we find that hundreds of mRNAs are sensitized to NMD as human embryonic stem cells progress to form neural progenitor cells. Another class of mRNAs escape from NMD during this developmental progression. We show that the differential sensitivity to NMD extends to in vivo scenarios, and that the RNA-binding protein, HNRNPL, has a role in cell type-specific NMD. We also addressed another issue in the field-whether NMD factors are core or branch-specific in their action. Surprisingly, we found that UPF3B, an NMD factor critical for the nervous system, shares only 30% of NMD-target transcripts with the core NMD factor UPF2. Together, our findings have implications for how NMD is defined and measured, how NMD acts in different biological contexts, and how different NMD branches influence human diseases.

overall_design: To identify UPF3B-target RNAs in NPCs, we performed bulk RNA sequencing (RNAseq) analysis of NPCs differentiated from hESCs from Ctrl and UPF3B-KO groups.

first: Miles

middle: F

last: Wilkinson


title: High-throughput quantification of cell-surface proteins for accelerated cancer therapeutic discovery

city: Seattle

first: Edie

middle: I

last: Crosse

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: Cell-surface proteins on tumor cells serve as both key targets for immunotherapeutic strategies and markers of blast phenotype and differentiation status. Compounds that modulate surface expression of key immunotherapeutic targets offer an attractive strategy for more robust and precise targeting by immunotherapeutics when delivered as a co-therapy. Similarly, identification of compounds that induce differentiation of tumor blasts over indeterminate self-renewal is an area of great therapeutic promise. Both conventional and newer methods for characterizing cell surface protein expression on tumor cells, including flow cytometry and CITE-Seq, are invaluable for characterizing phenotypes but do not readily scale for high-throughput drug screening. Here we present Surface-plex, a new technology which enables a multiplexed, high-throughput sequencing readout of cell-surface proteins on tumor cells following treatment with thousands of compounds. We applied this technology to acute myeloid leukemia and identified PFI90 as an inducer of the therapeutically targetable antigen CD47 and several compounds as inducers of blast differentiation. Surface-plex thus offers a scalable platform enabling the rapid identification of compounds with therapeutic potential, applicable across cancer types, to accelerate targeted cancer therapeutic development.

overall_design: A high-throughput assay that measures cell surface expression on acute myeloid leukemia (MOLM-13) cells by sequencing antibody-oligo conjugates. The data here are sequencing of antibody feature barcodes for two assays; Assay 1 = MOLM-13 cells treated with 85 compounds (5xreplicates) and Assay 2 = MOLM-13 cells treated with 1101 compounds (4xreplicates).

first: Won

last: Jun Kim

first: Omar

last: Abdel-Wahab

first: Robert

middle: K

last: Bradley


title: Genome-wide identification of endogenous NMD-targeted RNAs in human stem cells [UPF3B_ESCs]

overall_design: To identify UPF3B-target RNAs in hESCs, we performed bulk RNA sequencing (RNAseq) analysis of hESCs from Ctrl and UPF3B-KO groups.


title: Genome-wide identification of endogenous NMD-targeted RNAs in human stem cells [Upf3b_mice]

overall_design: To identify Upf3b-target RNAs in mice in vivo, we performed bulk RNA sequencing (RNAseq) analysis of frontal cortex and cerebellum from Ctrl and Upf3b-KO groups.


title: The Genetic Architecture of Congenital Diarrhea and Enteropathy (CODE)

city: Toronto

first: Aleixo

last: Muise

address: 686 Bay Street, 19-9400 I-M PGCRL

department: Cell Biology

institute: The Hospital for Sick Children

summary: Next-generation sequencing (NGS) has supported precision therapeutic approaches that have improved the lives of children with rare diseases. Patients with congenital diarrhea and enteropathies (CODE) have a particularly difficult disease with high morbidity and mortality. However, there are now several targeted therapies including specific diets, pharmacological treatments, and surgical interventions that are based on an individual’s genetic diagnosis. We performed NGS on a large cohort of 139 infants with suspected monogenic congenital diarrheal disorders and identified known causal variants in 50% of cases, including a new founder NEUROG3 variant. We also uncovered and functionally characterized three novel CODE genes, GRWD1, MYO1A, and MON1A, using cell and zebrafish models.

overall_design:
To investigate the role of grwd1 in the development of congenital diarrhea and enteropathies, we generated grwd1 knockout zebrafish and found that all F0 were lethal. Therefore we used first generation (F0) mosaic grwd1 mutant zebrafish using CRISPR (crispants).
We then performed gene expression profile analysis using data obtained from RNAseq from wild type zebrafish line, and grwd1 crispants at 8 days post fertilization (dpf).
Comparative gene expression profiling analysis between wt and grwd1zebrafish mutant were performed to examine the transcriptomic alterations caused by grwd1 deficiency.

first: Zeenat

last: Gaibee

first: Neil

last: Warner

first: Wenjuan

last: Li

first: Rei

last: Guan


title: Genome-wide identification of endogenous NMD-targeted RNAs in human stem cells [pUPF1_RIPseq_NPCs]

overall_design: Given that the sequential phosphorylation and dephosphorylation of UPF1 is required for NMD, we next performed immunoprecipitation of phosphorylated (p)-UPF1 followed by RNA sequencing (RIPseq) analysis, as an independent criterion to further screen high-confidence NMD-target RNAs.


title: Genome-wide identification of endogenous NMD-targeted RNAs in human stem cells [UPF2_NPCs]

overall_design: To identify UPF2-target RNAs in NPCs, we performed bulk RNA sequencing (RNAseq) analysis of NPCs differentiated from hESCs from four groups: UPF2fl/fl-scramble siRNA (“Ctrl”), UPF2fl/fl-siUPF2 (“UPF2-KD”), UPF2-iKO-scramble siRNA (“UPF2-iKO”), and UPF2-iKO-siUPF2 (“UPF2-iKO & KD”).


title: Genome-wide identification of endogenous NMD-targeted RNAs in human stem cells [pUPF1_RIPseq_ESCs]

overall_design: Given that the sequential phosphorylation and dephosphorylation of UPF1 is required for NMD, we next performed immunoprecipitation of phosphorylated (p)-UPF1 followed by RNA sequencing (RIPseq) analysis, as an independent criterion to further screen high-confidenceNMD-target RNAs.


title: Activated RNAi does not rescue piRNA pathway deficiency in testes

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

summary: RNA interference (RNAi) and PIWI-associated RNAs (piRNA) pathways use small RNAs as sequence-specific guides to repress transposable elements. In mice, the loss of Mili, an essential piRNA pathway factor, causes male sterility associated with mobilization of LINE L1 retrotransposons while female mutants remain fertile. At the same time, mouse oocytes have exceptionally active RNAi thanks to an oocyte-specific variant of RNase III Dicer, which efficiently makes small RNAs from long dsRNA substrates. In oocytes of mice lacking functional MILI and the oocyte-specific Dicer variant, we previously observed that L1 retrotransposons are redundantly targeted by both, RNAi and piRNA pathways. To test whether enhanced RNAi may reduce the Mili mutant phenotype in testes, we used transgenic mice ectopically expressing the oocyte-specific Dicer variant during spermatogenesis. We report here that this genetic modification increases siRNA biogenesis and supports RNAi but is not sufficient to reduce spermatogenic defects caused by the loss of Mili.

overall_design: Bulk small RNA-seq of 9 mouse samples, three different tissues in three different genotypes: - Dicerwt/wt spleen, liver, testes - DicerΔHEL1/wt spleen, liver, testes - DicerTg(O-HA) spleen, liver, testes

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Marcos

last: Kulmann


title: RNA‑seq profiling of mRNA associated with aged related Pathological cardiac hypertrophy

city: beijing

first: Wei

last: Ying

state: beijing

address: beijing

institute: Peking union medical college

summary: To identify differentially expressed genes in age-related heart diseases by RNA sequencing

overall_design: Comparative gene expression profiling analysis of RNA-seq data for young mice and aged mice

first: Ying

last: Wei

first: Dongmei

last: Su


title: RNA-seq for the soybean roots

first: Guoxuan

last: Liu

summary: To further identified the candidate genes remobilization and Mn up-take, a transcriptional analysis of roots subjected to 5 μM (control) and 50 μM MnSO4 (Mn) were conducted.

overall_design: 5 μM (control) and 50 μM MnSO4 (Mn)

first: Cuiyue

last: Liang

first: Jiang

last: Tian


title: Astrocyte-driven suppression of tumor-specific T-cell immunity in glioblastoma

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Glioblastoma (GBM) is the most common and aggressive brain cancer, showing minimal response to available therapies. A highly immunosuppressive tumor microenvironment (TME) contributes to the limited therapeutic response of GBM. Astrocytes are major components of the central nervous system (CNS), with important immunoregulatory roles. However, little is known about the role of astrocytes and their subsets in the immune response to GBM. Using single-cell and bulk RNA sequencing in GBM clinical samples and mouse pre-clinical models, in combination with multiplexed immunofluorescence microscopy, in vivo CRISPR-based cell-specific genetic perturbations, and in vitro mouse and human experimental systems we identified an astrocyte subset that limits tumor-specific immunity by inducing CD8+ and CD4+ T-cell apoptosis via the death receptor ligand TRAIL. Moreover, we identified IL-11 produced by tumor cells as a driver of STAT3-dependent TRAIL expression in GBM-associated astrocytes. pSTAT3+ TRAIL+ astrocytes were co-localized with apoptotic T cells in human GBM samples and were associated with a shorter time to recurrence and overall decreased survival in GBM patients. Conversely, genetic inactivation of the IL-11 receptor or TRAIL in astrocytes extended survival in GBM mouse models and boosted tumor-specific T cells and tumor-associated macrophage responses. Finally, a GBM-targeting oncolytic HSV-1 virus engineered to express a TRAIL-blocking single-chain antibody in the TME extended survival and boosted tumor-specific immunity in GBM pre-clinical models. In summary, we established that IL-11/STAT3-driven astrocytes suppress GBM-specific protective immunity by inducing TRAIL-dependent T-cell apoptosis, and we developed engineered therapeutic viruses to target this novel mechanism of astrocyte-driven tumor immunoevasion.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Sequencing of Different Cell types obtained from TRAIL KD mice and control mice.

first: Camilo

last: Faust Akl

first: Francisco

last: Quintana


title: DNA dioxygenase Tet2 regulates liver regeneration after partial hepatectomy [dateset2]

city: Hangzhou

first: Yiyuan

last: Chen

address: Huansha Road 261#

institute: Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province

summary:
To investigate how liver macrophages regulate liver regeneration after partial hepatectomy, we isolate the macrophages 0, 24, and 48h after partial hepatectomy(PHx).
We performed gene expression profiling analysis using data obtained from RNA-seq of liver macrophages 0,24,48h after partial hepatectomy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 0,24,48h after partial hepatectomy.


title: Genome-wide identification of endogenous NMD-targeted RNAs in human stem cells [UPF2_ESCs]

first: Kun

last: Tan

overall_design: To identify UPF2-target RNAs in hESCs, we performed bulk RNA sequencing (RNAseq) analysis of hESCs from four groups: UPF2fl/fl-scramble siRNA (“Ctrl”), UPF2fl/fl-siUPF2 (“UPF2-KD”), UPF2-iKO-scramble siRNA (“UPF2-iKO”), and UPF2-iKO-siUPF2 (“UPF2-iKO & KD”).

first: Miles

last: Wilkinson


title: DNA dioxygenase Tet2 regulates liver regeneration after partial hepatectomy.

overall_design: Refer to individual Series


title: Disrupted MOS signaling alters meiotic cell cycle regulation and the egg transcriptome

status: Public on May 20 2025

city: Hanover

first: Brittany

last: Goods

state: New Hampshire

address: 15 Thayer Dr.

institute: Dartmouth College

summary: Loss of MOS in female mice disrupts metaphase II arrest, potentially causing infertility and germ cell tumors. Single-egg RNA sequencing revealed widespread gene expression changes in mos -/- eggs, including upregulation of cell cycle regulators like Aurka, Bub3, and Cdk7. Pathways related to RNA metabolism, transcription, and neddylation were also enriched in mos -/- eggs. Notably, the transcriptome of mos -/- eggs differed from that of chemically activated eggs. These results highlight MOS as a key regulator of the meiotic cell cycle and transcriptome integrity essential for oocyte developmental competence.

overall_design: Two- to three-month-old wildtype or mos -/- C57BL/6J female mice were injected intraperitoneally with 5 I.U. of pregnant mare serum gonadotropin 48 hours before oocyte collection. All single eggs used for sequencing were collected 38-40 hours post-GV breakdown. We sequenced 29 wildtype C57BL/6J eggs, 17 chemically activated eggs, and 61 mos -/- C57BL/6J.

first: Gisela

last: Cairo

first: Olha

last: Kholod

first: Olivia

last: Palmer

first: Soni

last: Lacefield


title: Hypercapnia induces long-term DNA methylation changes in skeletal muscle.

city: Nutley

first: Andy

last: Madrid

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health

summary: Skeletal muscle dysfunction and elevated CO2 in the blood, or hypercapnia, are both associated with higher mortality in acute and chronic pulmonary diseases. Hypercapnia causes accelerated protein degradation, reduced protein synthesis, and dysfunctional myogenesis. We have recently reported that hypercapnia-induced skeletal myogenic dysfunction persists after resolution of CO2 exposure, suggesting the existence of durable cellular aberrations in previously hypercapnic cells. No data on lingering myofiber atrophy after hypercapnia resolution currently exist. Hypercapnia and age-induced skeletal muscle loss phenotypically overlap, and myogenic progenitor cells from hypercapnic mice elicit senescence-associated transcriptional programs. While aging is characterized by unique DNA methylation and other epigenetic changes, the potential association of hypercapnia and age-related differential methylation have never been investigated. In the present study, we show that hypercapnic mice elicit protracted muscle deterioration even after returning to normocapnia and demonstrate aberrant DNA methylation in comparison to animals never exposed to elevated CO2. We also show that these DNA methylation changes do not overlap with age-induced alterations.

overall_design: RNA sequencing of skeletal muscle tissue from mice exposed to hypercapnic conditions, six months post-hypercapnia, and mice through three aging stages


title: DNA dioxygenase Tet2 regulates liver regeneration after partial hepatectomy [dataset1]

summary:
To investigate how Tet2 inhibitor (Bobcat339 hydrochloride or 4-Octyl Itaconate) affected the function of primary hepatocytes, we treated peritoneal macrophages with Bobcat339 hydrochloride，4-Octyl Itaconate, and DMSO.
We performed gene expression profiling analysis using data obtained from RNA-seq of primary hepatocytes with three treatments

overall_design: Comparative gene expression profiling analysis of RNA-seq data for treated with Bobcat339 hydrochloride，4-Octyl Itaconate, and DMSO.


title: Therapy of allergic rhinitis using ribavirin spray to clear nasal commensal viruses

city: Shanghai

first: Ye

last: Zhou

address: Xiangyin Road

department: National Key Laboratory of Immunity & Inflammation

institute: Naval Medical University

summary: To elucidate the potential role of commensal viruses in the etiology of AR, we performed a metagenomic analysis of nasal mucosa to identify commensal viruses in the nose of mice. To evaluate the potential role of these commensal viruses in AR, we reduced them in the nose of mice by administrating intranasal drops of vehicle (Vehicle group) or broad-spectrum antiviral drug ribavirin daily, starting at 4-week-old and lasting for three weeks (Ribavirin group). These mice were also administrated with PBS, OVA, or HDM to induce AR.

overall_design: Nasal mucosa was obtained from mice that were administered intranasal drops of either vehicle or ribavirin, together with PBS, OVA, or HDM. The nasal tissue samples were then subjected to metatranscriptomic sequencing to assess the abundance of viruses.

first: Jin

last: Hou


title: H3 Acetylation and H2A.Z Levels Interplay to Regulate Gene Expression and Plant Development

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

summary: H2A.Z is a conserved histone variant that plays essential roles in various DNA-templated processes across eukaryotes. H2A.Z and histone post-translational modifications (PTMs) exert a bidirectional and context-dependent influence on each other. Nevertheless, the functions of the interplay between PTMs and H2A.Z level and the underlying molecular mechanism remain poorly understood. Here, we found that the loss of the histone acetyltransferase GCN5 impedes the overexpression of BSU1 typically observed in nrp1-1 nrp2-2, accompanied by changes in H3 acetylation and H2A.Z levels. Interestingly, the increment in H2A.Z levels typical of nrp1-1 nrp2-2 mutant alleviates the morphological and molecular phenotypes of gcn5. Conversely, H2A.Z-depleted mutants aggravate the phenotype of gcn5. In the gcn5 mutant, the H2A.Z level is globally reduced in the gene bodies, and this reduction is dependent on the histone chaperones NRP1 and NRP2. Additionally, the reduction of H3 acetylation levels caused by GCN5 depletion can be recovered in the nrp1-1 nrp2-2 mutant background, likely due to the over-accumulation of H2A.Z. In conclusion, our genetic, molecular, and genomic findings demonstrate that GCN5-mediated H3 acetylation promotes H2A.Z deposition, H2A.Z over-accumulation recovers the loss of GCN5-mediated H3 acetylation, and this interplay is crucial for regulating gene expression and plant development.

overall_design: ChIP-seq of H3 acetylation and histone H2A.Z in Columbia (WT) and gcn5-7, nrp1-1 nrp2-2, gcn5-7 nrp1-1 nrp2-2 backgrounds.The experimental tissues were collected form 12 day after germination (12DAG) from seedlings cultured on GM medium (1x MS salts, 1% sucrose, pH=5.7).

first: Israel

last: Ausin

first: Yafei

last: Wang

first: Yingpei

last: Su

first: Qin

last: Hu

first: Weiye

last: Qian

first: Min

first: Chao

last: Xu

first: Junjie


title: Sustained neuronal stimulation activates paraventricular thalamus astrocytes for maintenance of chronic neuropathic pain in mice

city: Chengdu

first: Peiwen

last: Jian

state: Sichuan

address: 9F, B2, Tianfu Life Science Park, Second Research Building, West China Hospital, Sichuan University, Chengdu，China

institute: West China Hospital of Sichuan University

summary: Ongoing nociceptive inputs from peripheral tissues and nerve injuries lead to maladaptive alterations in central nervous system, which drive the transition from acute to chronic pain.  Although astrocytes act as dynamic and active players in neuropathic pain states, the contribution of astrocytes in upper brain nucleus in this process remains unclear. Here, we revealed that prolonged neuronal inputs induced by periphery injury leads to astrocyte reactive and downregulation of inward rectifying potassium channel protein 4.1 (Kir4.1) in paraventricular thalamus（PVT）. In turn, reactive PVT astrocytes could maintain the hyperexcitability of neurons, and enhanced projections from PVT to medial prefrontal cortex (mPFC) in the chronicity of neuropathic pain. Notably, we identify a neuro-glial interaction mediating pain chronification in PVT, and clarified Kir4.1 channels as a potential therapeutic target for neuropathic pain treatment.

overall_design: RNA-seq profiling of the PVT（paraventricular thalamus） tissues of two groups of CCI（Chronic constriction injury） model mice (n=30) and wild-type controls (n=30).

first: Yi

last: Zhao

first: Guo

last: Chen

first: Cheng

last: zhou


title: The constitutive 20S proteasome is required for the maintenance and differentiation of spermatogonia in mice

city: Hang Zhou

last: Yu

address: 866 Yuhangtang Rd, Xi Hu Qu

institute: Zhejiang University

summary: Proteasomes undergo dynamic changes in their types and activities during mammalian spermatogenesis. While the spermatogenesis-specific 20S proteasome (s20S), characterized by PSMA8 substitution of PSMA7, is known to be essential for meiosis I completion, the functions of the constitutive PSMA7-containing 20S proteasomes (c20S) in spermatogenesis remain poorly understood. Here, we show that c20S proteasomes are required for the maintenance and differentiation of spermatogonia. PSMA7 is ubiquitously expressed in male germ cells beginning at the early spermatogonial stage, preceding PSMA8 expression. Conditional ablation of Psma7 using Stra8-Cre impairs proteasomal degradation in differentiating spermatogonia, leading to male infertility. Single-cell RNA sequencing analysis reveals that PSMA7-deleted germ cells are arrested at the differentiating spermatogonia stage and fail to enter meiosis. Notably, sufficient overexpression of PSMA8 restores normal spermatogenesis in Psma7-null germ cells, suggesting a potential complementarity of s20S to c20S. Therefore, our results add critical insights into the complex regulation of proteasomal degradation during spermatogenesis.

overall_design: Testes were collected from C57BL/6 mice at postnatal day 13 (PD13), comparing control (Psma7 F/+, WT) and conditional knockout (Psma7 F/-;Stra8-Cre KI/+, Psma7_s8ko) genotypes, and analyzed by scRNA-seq.

first: Anxuan

last: Fang

first: Huiwen

last: Cao

first: Ying

last: Zhang

first: Jiangxu

last: Wu

first: Qianting

first: Liang


title: Development of early-stage alpha-synucleinopathy is not governed by myelin status in mice of either sex

city: Pittsburgh

first: Rehana

last: Leak

state: PA

address: 600 Forbes Ave

department: Pharmacology

institute: Duquesne University

summary: Lewy body disorders are characterized by alpha-synucleinopathic inclusions that tend to develop in neurons extending long, thin, and unmyelinated fibers. It is unknown if this selective vulnerability reflects poor myelination per se. We have observed that preformed fibrils (PFFs) of alpha-synuclein tend to induce pathology in gray matter, even when infused into regions penetrated by white matter bundles. In addition, we found that levels of insoluble, hyperphosphorylated alpha-synuclein correlate inversely with myelin markers in the postmortem amygdala of men—but not women—with Lewy body disease. Thus, we tested if myelin disruption with pharmacologic or genetic tools exacerbates alpha-synucleinopathic lesions in a model of early-stage, limbic Lewy body disease. In genetically outbred CD-1 mice infused with PFFs in the caudal olfactory bulb, the myelin-disruptor cuprizone caused subtle exacerbation of α-synucleinopathy, but without impacting PFF-induced neuron loss or behavior deficits. Furthermore, in C57BL/6J mice heterozygous for myelin basic protein (Mbp+/shi), PFF-induced increases in the insolubility and hyperphosphorylation of alpha-synuclein were not amplified and histological outcomes were not markedly exacerbated. Given our observations of inverse correlations between α-synucleinopathy and myelin markers in the human male amygdala, Lewy body disease may disrupt myelination, rather than poor myelination status regulating the emergence of limbic α-synucleinopathy. This new perspective is reinforced by suppressed expression of select oligodendrocytic markers in the amygdalae of men with Lewy body disease compared to women. Thus, resilient neurons may defy the initial development of Lewy-related pathologies due to properties unrelated to myelination per se.

overall_design: RNA-seq profiling of human olfactory bulb and amygdala samples from patients with Lewy body disorders or age-matched controls, from the NIH NeuroBioBank, where the same IDs can be searched on their portal for more deidentified patient information

first: Rachel

middle: N

last: Clark

first: Reese

middle: E

last: Landes

first: Muslim

last: Abbas

first: Victoria

last: Mistretta

first: Kieran

last: DeLoatch

first: Jun

first: Kelvin

last: Luk

first: Xiaoming


title: Transcriptome Analysis of Pseudogymnoascus destructans Under Copper Stress Conditions Reveals Adaptive Responses and Putative Virulence Factors

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

summary: Copper (Cu) is an essential metal micronutrient, and a fungal pathogens' ability to thrive in diverse niches across a broad range of bioavailable copper levels is vital for host-colonization and fungal-propagation. Recent transcriptomic studies have imple-mented that trace metal acquisition is important for the propagation of the white nose syndrome (WNS) causing fungus, Pseudogymnoascus destructans, on bat hosts. This report characterizes the P. destructans transcriptional response to Cu-withholding and Cu-over-load stress. We identify 583 differently expressed genes (DEGs) that respond to Cu-with-holding stress and 667 DEGs that respond to Cu-overload stress. We find that P. de-structans the Cu-transporter genes CTR1a and CTR1b, as well as two homologs to Crypto-coccus neoformans Cbi1/BIM1 VC83_03095 (BLP2) and VC83_07867 (BLP3) are highly reg-ulated by Cu-withholding stress. We identify a cluster of genes, VC83_01834 – VC83_01837, that are regulated by Cu bioavailability, which we identify as the Cu Re-sponsive gene Cluster (CRC). We find that chronic exposure to elevated Cu levels leads to an increase in genes associated with DNA repair and DNA replication fidelity. A com-parison of our transcriptomic data sets with P. destructans at WNS fungal infection sites reveals several putative fungal virulence factors that respond to environmental copper stress.

overall_design: The Pseudogymnoascus destructans (Pd) strain (MYA4855) was purchased from the American tissue culture collection (ATCC strain number 20631-21) and used for all experiments. The long-term propagation of Pd was carried out using solid Yeast extract-peptone and glucose (YPD) plates at 15ºC and consisted of 10 g/L of yeast extract, 20 g/L of peptone, 20 g/L glucose, and 15 g/L of agar. Metal growth studies were performed using chemically defined growth plates (SC-Ura) which were made using Milli-Q water and 1.8 g/L of yeast nitrogen base, 5g/L ammonium sulfate (NH4SO4), 20 g/L glucose, 100 mg/L histidine, 1.7 g/L of the SC-Ura-His amino acid supplement mixture, and 15 g/L agar. Prior to autoclaving 1 pellet (~200 mg) of NaOH was added to the SC-Ura media prior to autoclave sterilization. The addition of sterile Cu-sulfate and Bathocuproine sulfonic acid sodium salt (BCS) was added to the SC-URA growth media using a 125 mM stock solution after autoclave sterilization at a temperature of approximately 50 ºC. All samples were subsequently used for gene expression profiling

first: Anne

last: Saika

first: McDonald

last: Maranda

first: Lu

last: Yuan

first: Peterson

last: Ryan


title: Transcriptomic study of PGPR-induced Brassica rapa plant gene expression towards aphids

city: Singapore

first: Beng-Soon

last: Teh

address: 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

summary: The aim of this study is to explore the gene expression of Brassica rapa with and without inoculation with PGPR bacteria in response to aphids attack on day 5 and day 10. We expect to find many genes regulated in the root and leaves in response to early and late stage of aphid infestation. Some of these genes are involved in hormone signaling, plant-pathogen interaction, and etc. Our data provides a better understanding of the mechanisms of plant-microbe-insect interactions.

overall_design: RNA-seq study of PGPR-inoculated and non-inoculated plants during aphid infestation on day 5 and day 10.

first: Mayalagu

last: Sevugan

first: Sanjay

last: Swarup


title: Loss of age-associated increase in m6A-modified RNA contributes to GABAergic dysregulation in Alzheimer’s disease

first: Junming

last: Hu

address: 75 E Concord St

institute: Boston University

summary: Dysregulated RNA metabolism is a significant feature of Alzheimer’s disease (AD), yet how post-transcriptional RNA modifications like N6-methyladenosine (m6A) are altered in AD is unknown. Here, we performed deamination adjacent to RNA modification targets (DART-seq) on human dorsolateral prefrontal cortices to assess changes in m6A with nucleotide resolution. In non-AD brains, m6A sites increased with age, predominantly within the 3′UTR of transcripts encoding tripartite synapse proteins. In contrast, AD brains lost the age-associated m6A site increase and exhibited global hypomethylation of transcripts, including MAPT and APP. Hypomethylated genes involved with GABAergic signaling, glutamate transport, and ubiquitin-mediated proteolysis exhibited reduced expression, connecting m6A to synaptic excitotoxicity and disrupted proteostasis in AD. Site-specific m6A levels were linked with GABRA1 expression and protein levels, but this relationship was abolished in AD. Our findings provide insight into post-transcriptional mechanisms of dysregulated RNA metabolism in AD that are related to aging and GABAergic regulation.

overall_design: Human post-mortem dorsolateral prefrontal cortex tissue (Brodmann area 9) was collected from two groups: individuals with pathologically confirmed Alzheimer’s disease (AD; n=19) and age- and sex-matched neurologically normal controls (n=19). DART-seq were performed on all n=38 samples. All n=38 samples were treated with DART-WT enzyme and n=11 from each group were treated with DART-Mut enzyme (see below).

first: Jenna

last: Libera

first: Tuyet-Anh

last: Nguyen

first: Zihan

last: Wang

first: Sophie J. F.

last: van der Spek

first: Kamryn

last: Schult

first: Luke

last: Dorrian

first: Jordan

last: Majka

first: Katarnut

last: Tobunluepop

first: Sambhavi

last: Puri

first: Alexander

last: Kynshov

first: Nicholas M.

last: Kanaan

first: Peter T.

last: Nelson

first: Kate

last: Meyer

first: Lei

last: Hou

first: Xiaoling

last: Zhang

first: Benjamin

last: Wolozin


title: Calcium signals shape metabolic control of H3K27ac and H3K18la to regulate EGA

city: Research Triangle Park

first: Zongli

last: xu

state: NC

address: 111 TW Alexander Dr

department: Epidemiology Branch

institute: NIEHS

summary: Calcium dynamics drive metabolic regulation of epigenetic reprogramming at fertilization and alter EGA resulting in long term effects in offspring.

overall_design: A mouse model (C57B6) of dramatically increased calcium exposure at fertilization in vivo was developed by targeting two plasma membrane calcium pumps, isoforms 1 and 3 (PMCA1 and PMCA3) in mouse oocytes. dKO or Control females were mated to WT males. The liver, adipose tissue and muscle of offspring derived from dKO or control dams was assessed for differences in the methylation landscape of DNA.

first: Virginia

last: Savy

first: Carmen

last: Williams

last: Xu