Generation of iPSC and isogenic gene-corrected lines from a patient with RPS7 (c.277_279delGTC)-mutated Diamond-Blackfan anemia syndrome

Stem Cell Research · 2026-01-07

Diamond-Blackfan anemia syndrome (DBAS) is a heterogeneous genetic bone marrow failure disorder characterized by erythroid hypoplasia in young children. Most forms of DBAS are caused by heterozygous loss-of-function mutations in one of the 24 different ribosomal protein genes. We generated an iPSC line from a patient with a heterozygous RPS7 (c.277_279delGTC) mutation, along with a corresponding isogenic cell line wherein the mutation was corrected using Cas9-mediated homology-directed repair.

Endothelial Cell Secretome Alterations Induced by Inflammatory Stress

bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-15

Endothelial cells detect pathogens through pattern recognition receptors, such as Toll-like receptor 4 (TLR4), which triggers the synthesis and secretion of molecules that initiate the innate immune response. Proteins bearing signal peptides are secreted through the classical endoplasmic reticulum (ER)-Golgi-dependent route, whereas select signal-peptide-lacking cytoplasmic proteins are secreted via less well-characterized ER-Golgi-independent mechanisms, collectively termed unconventional cytoplasmic protein secretion (UCPS). To systematically characterize the secretome of human umbilical vein-derived endothelial cells (HUVECs) and delineate the contribution of UCPS, we performed deep quantitative proteomics on HUVEC cell lysates and conditioned medium before and after TLR4 stimulation with lipopolysaccharide (LPS). Of 5205 proteins detected in either fraction, 381 were enriched in the conditioned medium and therefore classified as secreted. Of these, 333 proteins (87.4%) were secreted via the conventional pathway, and 48 (12.6%) were secreted via UCPS, 43 of which were not previously associated with this process. Predicted functions of UCPS-secreted proteins include redox regulation, proteostasis, cytoskeletal remodeling, and innate immune signaling. We confirmed that α-globin (HBA1), which functions as a redox sensor and regulator of nitric oxide in endothelial cells, is secreted constitutively by UCPS and at higher levels following inflammatory activation. Notably, UCPS cargo identity showed poor concordance with current computational predictors, underscoring the need for empirical datasets. Overall, our findings suggest that the HUVEC secretome includes both conventionally and unconventionally secreted proteins that regulate coagulation, angiogenesis, and immune function. Our findings establish a high-quality secretome dataset for HUVECs, providing a novel resource for future efforts to define the molecular determinants governing UCPS cargo selection and trafficking related to endothelial cell function.

Development of Polygenic Risk Score for Persistent Albuminuria in Children and Adults With Sickle Cell Anemia

American Journal of Hematology · 2025-04-05 · 2 citations

ABSTRACT Albuminuria is associated with high‐risk apolipoprotein‐L1 variants ( APOL1 G1/G2) in patients with sickle cell anemia (SCA). However, this gene variant does not account for all chronic kidney disease (CKD) risk. We hypothesized that we could develop a polygenic risk score (PRS) for CKD in SCA, combining APOL1 G1/G2 with other candidate genes that modify SCA severity and further stratify patients into risk categories based on this risk score. Variants in APOL1 , HMOX1 (rs743811), BCL11A (rs1424407), and α‐thalassemia ( α −3.7 ) were identified in children with SCA enrolled in the Sickle Cell Clinical Research and Intervention Program longitudinal cohort (SCCRIP). We individually tested the association of these variants with persistent albuminuria, tested a three‐variant PRS (PRS‐3) ( APOL1 , BCL11A (rs1424407), and α −3.7 ), and developed a four‐variant PRS (PRS‐4) after adding HMOX1 (rs743811) to PRS‐3 using the summation of high‐risk alleles. An adult SCA cohort from the University of Illinois, Chicago (UIC), was used for validation. Persistent albuminuria was defined as having a urine albumin‐to‐creatinine ratio (UACR) ≥ 30 mg/g on at least 2 of 3 consecutive measurements. In both cohorts, APOL1 risk variants increased the risk while α‐thalassemia protected against persistent albuminuria. PRS‐4 was significantly associated with persistent albuminuria (SCCRIP: p = 0.004; UIC: p = 0.00016). When stratifying patients into three and four risk categories based on the PRS, 58% and 86% of the high‐risk (PRS‐3) and 54% and 89% of very high‐risk (PRS‐4) categories developed persistent albuminuria cases in the SCCRIP and UIC cohorts, respectively. A PRS may identify high‐risk SCA patients for albuminuria. Applying this PRS to guide the early implementation of disease modifiers and renoprotective therapies may help reduce the burden of SCA‐related CKD. Trial Registration: NCT02098863

Corrigendum to STAT1 promotes megakaryopoiesis downstream of GATA-1 in mice

Journal of Clinical Investigation · 2025-07-14

Transcriptome and chromatin accessibility divergence during differentiation of a bipotential progenitor cell population to erythroblasts and megakaryocytes

Journal of Biological Chemistry · 2025-10-15

Changes in gene expression drive differentiation along cell lineages, and shifts in gene expression are associated with alterations in chromatin accessibility reflecting activation or repression. We used deep sequencing of polyadenylated RNA to map the transcriptomes of the megakaryocyte-erythroid progenitor (MEP) and its two daughter lineages, erythroblasts (ERYs) and megakaryocytes (MEGs), in mice to reveal insights into differentiation. Transcriptome comparisons revealed that MEPs already expressed much of the MEG program while continuing to express genes associated with parallel myeloid lineages. By contrast, ERYs underwent an extensive program of gene induction along with repression of pan-hematopoietic and MEG genes. Maps of transcription factor occupancy also indicated distinct modes of regulation for the MEG and ERY programs, with MEG genes preferentially occupied by hematopoietic transcription factors in multipotent progenitors and continued occupancy postcommitment, in contrast to erythroid genes that were primarily occupied in committed ERY. Previous work revealed a surprising discordance in the clustering of MEP with other hematopoietic cell types by RNA-Seq versus chromatin states. We combined the differential expression data with chromatin accessibility across blood cell types to identify trends that contribute to this discordance. Specifically, candidate cis-regulatory elements in some ERY-specific genes were precociously actuated in the bipotential cell populations, and some other genes were expressed in both the MEP population and MEG, but their candidate cis-regulatory elements have less chromatin accessibility in MEP. This discordance in cell-type clustering by different modalities of functional genomics may reflect different contributions of subpopulations in the MEP to the particular modalities measured.

PARADIGM: ST. JUDE INITIATIVE TO ADVANCE DEVELOPMENT OF INDIVIDUALIZED BASE AND PRIME EDITING THERAPIES FOR BONE MARROW FAILURE SYNDROMES

EJC Paediatric Oncology · 2025-11-05

AMBRA1 performs a balancing act in β-thalassemia

Blood · 2025-03-06

to, those at risk of dying of the disease.The study supports the view 9 but does not prove (due to study design) that BRAF V600E is a prognostic factor in childhood LCH since almost all study subjects with SHI were positive for BRAF V600E .Also, the study suggests that the presence of BRAF V600E is a treatment factor in childhood LCH; by looking at treatment outcome over time, the beneficial impact of MAPKi is strongly implied.Prospective trials will be needed to determine when and how best to deploy these drugs.In our opinion, these trials are urgently needed and long overdue.

Divergence between transcriptomes and chromatin accessibility during differentiation from a bipotential progenitor cell population to erythroblasts and megakaryocytes

bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-03

Abstract Changes in gene expression drive differentiation along distinct cell lineages, and these shifts in gene expression are associated with alterations in chromatin accessibility and modifications reflecting activation or repression. We used deep sequencing of polyA+ RNA to map the transcriptomes of the megakaryocyte-erythroid progenitor (MEP) and cells of its two daughter lineages, erythroblasts (ERY) and megakaryocytes (MEG) in mice to reveal insights into differentiation. Transcriptome comparisons revealed that MEPs already expressed much of the MEG program while continuing to express genes associated with parallel myeloid lineages. By contrast, ERY underwent an extensive program of gene induction along with repression of pan-hematopoietic and MEG genes. Maps of transcription factor (TF) occupancy also indicated distinct modes of regulation for the MEG and ERY programs, with MEG genes preferentially occupied by hematopoietic TFs in multipotent progenitors and continued occupancy post-commitment, in contrast to erythroid genes that were primarily occupied in committed ERY. Previous work had indicated a surprising discordance in the clustering of MEP with other hematopoietic cell types by RNA-seq versus chromatin states. We combined the differential expression data with chromatin accessibility across blood cell types to identify trends that contribute to this discordance. Specifically, candidate cis-regulatory elements (cCREs) in some ERY-specific genes were precociously actuated in the bipotential cell populations, and some other genes were expressed in both the MEP population and MEG but their cCREs have less chromatin accessibility in MEP. This discordance in cell type clustering by different modalities of functional genomics may reflect the different contributions of subpopulations in the MEP to the different modalities measured.

KDIGO-defined kidney dysfunction predicts long-term outcomes in a multicenter cohort of adults with sickle cell disease

Blood Advances · 2025-08-19 · 1 citations

ABSTRACT: Approximately 15% of deaths in adults with sickle cell disease (SCD) are attributed to kidney failure. Although urine albumin-to-creatinine ratio (UACR) is recommended to screen for kidney damage, its utility in predicting long-term complications in SCD remains unclear. We investigated whether "Kidney Disease: Improving Global Outcomes (KDIGO)" algorithms used to assess kidney disease in the general population predicted chronic kidney disease (CKD) progression and mortality in a longitudinal cohort of 379 adults with SCD from 2 academic institutions. KDIGO criteria include UACR detected in 2 consecutive measurements ≥3 months apart and a heat map integrating UACR with estimated glomerular filtration rate. KDIGO-defined CKD was present in 39.8% of individuals in our SCD cohort. Over a median follow-up of 3.3 years, incremental KDIGO-defined UACR category independently predicted a twofold greater risk of CKD progression and 1.8-fold greater risk of mortality (P ≤ .05). KDIGO-defined CKD heat map strengthened the ability to predict CKD progression and mortality risk (P ≤ .0087). Our data provide clinical support for the screening utility of UACR based on repeated abnormal values ≥3 months apart. The KDIGO heat map further refines the risk of long-term outcomes among adults with SCD and should be applied to guide future studies for monitoring and intervention strategies.

Personalized Care for Pancreatic Cancer: Harnessing Patient-Derived Organoids

Journal of Gastrointestinal Cancer · 2025-05-10