Erythropoiesis is a tightly regulated process involving rapid cell proliferation with orderly differentiation to ensure production of millions of RBCs. TGF-β1 is a key regulator of erythropoiesis, however, the mechanisms via which it regulates erythropoiesis are not well elucidated. Using myelodysplastic syndromes patient samples, we show that elevated TGF-β1 and SMAD2 signaling correlates with the degree of anemia. Functional studies in primary human HSPCs demonstrate that TGF-β1 exerts a bifurcated effect - suppressing proliferation and inducing premature erythroid differentiation - both of which are rescued by clinical-stage TGFBR1 inhibitor. Through integrative RNA-seq, ChIP-seq, and Micro-C analyses, we find TGF-β1 activates β-globin LCR, driving early differentiation, while concurrently disrupting the MYC enhancer-promoter interaction to block proliferation. We validate erythropoiesis defects in vivo by performing single-cell RNA-seq in a TGF-β1 overexpressing mouse model. Overall, we show that TGF-β1/SMAD2 signaling re-wires chromatin to regulate erythropoiesis by affecting the β-LCR and MYC super enhancer regions.

BACKGROUND:Preterm infants have reduced nephrons at birth and are exposed to hyperoxic environments. The objective was to examine the effects of hyperoxia on renal injury. METHODS:We utilized a mouse model of experimental moderate (60% O2)-severe (100% O2) bronchopulmonary dysplasia (BPD), obtaining kidney tissue on postnatal day 14. The number of glomeruli, glomerulus length, and Bowman's capsule's length were recorded. Cell death and expression of multiple biomarkers were assessed. RESULTS:Morphometric analyses showed a significant decrease in glomeruli in male and female mice from room air (RA) to 60% BPD. Bowman's capsule length was significantly increased from RA to 100% BPD in female kidneys. TUNEL staining, cleaved caspase 3, and 9 expression revealed significantly increased cell death in the kidneys in the moderate and severe BPD models. There was increased expression of Angiopoietin-2 in male kidneys of the moderate BPD group, whereas Angiopoietin-1 and vascular endothelial growth factor were decreased in female mice. In the moderate BPD model, there was upregulation of nuclear factor-kappa B, transforming growth factor-β1, interleukin (IL)-6, and IL-1β in male and female mice. CONCLUSION:We report here that there is significant renal injury and cell death in moderate and severe mouse models of experimental BPD. IMPACT:Neonatal kidneys are still developing at birth. Hyperoxia exposure to the whole mouse also impacts the developing neonatal kidney. There is significant renal injury in moderate and severe mouse models of experimental BPD. This includes morphometric changes in the kidney tissue and increased cell death. In addition, there are significant alterations in the expression of vascular and inflammatory biomarkers.

Bronchopulmonary Dysplasia (BPD) is a neonatal condition primarily affecting babies born prematurely, who have been exposed to invasive ventilation and/or oxygen supplementation. These therapies predispose the immature developing lungs to inflammation and injury to the alveolar epithelium resulting in loss of the alveolar epithelium and thickening of alveolar septa, the two important hallmarks of the pathology of BPD. The expansion and enlargement of the alveolar sacs give the characteristic feature of alveolar simplification in BPD. To measure this alveolar abnormality, we have modified and developed a custom-made Chord Length Fiji plugin, which can easily measure the Chord Length and Septal Thickness on Hematoxylin–Eosin-stained histological lung sections, thus generating an instant morphometry readout for quick interpretation. We validated this plugin in multiple animal experimental models and human neonatal lungs with BPD. We were able to differentiate the morphology under conditions of ventilation or hyperoxia exposure, when compared with untreated controls. We thus conclude that our Chord Length and Septal Thickness plugin can be used in a simplified manner following a less meticulous automated operation. To facilitate global use, we have created a (DOI: https://doi.org/10.5281/zenodo.18323663) so that any user can access it without any restrictions to complete the morphometric measurements. This plugin will be useful for smaller research laboratories with limited budgets and require no access to complex software.

Abstract Purpose: Even though smoking is associated with lung cancer, the exact molecular pathways that link carcinogens with inflammation and oncogenic transformation are not well elucidated. Two major carcinogens in cigarette smoke, nicotine-derived nitrosamine ketone, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), and benzo(α)pyrene (BaP), have not been tested in models that mimic inhaled exposure for prolonged periods of time. Experimental Design: Mouse models were used for intratracheal delivery of NNK and BaP (NB) for 18 months. Tissue microarrays from human lung cancers were evaluated for IL-1 receptor–associated kinase-4 (IRAK4) expression. Functional effects of IRAK4 inhibition were evaluated in cell lines and xenografts. Results: Smoking-associated carcinogen–treated mice developed epithelial dysplasia followed by lung cancers at increased rates relative to controls. Histology revealed myeloid inflammation in murine lung tissues. Lung macrophages showed elevated levels of proinflammatory IL-1β when exposed to cigarette smoking condensate. A key downstream mediator of IL-1β signaling, IRAK4, was overexpressed in murine lung tissues exposed to carcinogens. The majority of human lung cancer samples also exhibited overactivated IRAK4 expression. IRAK4 localized in microtubules in lung cancer cell lines. Using mass spectrometry on isolated microtubules, we observed that IRAK4 inhibition was associated with decreased phosphorylation of tubular motility proteins, including myosin heavy-chain 9. Inhibition of IRAK4 resulted in decreased invasion in lung cancer cell lines and reduced growth of lung cancer xenografts. Conclusions: These data demonstrate that smoking-associated carcinogens can be linked to oncogenic transformation via inflammatory IRAK4 activation.

Supplementary Figure S6. Downregulated phosphorylations after IRAK4 inhibitor treatment.

Supplementary Figure S2. Uncropped Western Blots for Figure 6A data presented in the manuscript. Also see Data Availability Statement.

Supplementary Figure S1. Uncropped Western Blots for Figure 4C data presented in the manuscript. Also see Data Availability Statement.

Supplementary Table S1. Manuscript Figure 1 data - The Excel file has data points for easy access to infer numerical values for data presented in the manuscript. Also see Data Availability Statement.

Anemia is the primary clinical manifestation of myelodysplastic syndromes (MDSs), but the molecular pathogenesis of ineffective erythropoiesis remains incompletely understood. Luspatercept, an activin receptor 2B (ACVRIIB-Fc) ligand trap, has been approved to treat anemia; however, its molecular mechanism of action is unclear. We found that activin receptor 2B (ACVR2B), its ligand growth and differentiation factor 11 (GDF11), and an effector, SMAD2, are upregulated in samples of patients with MDS. GDF11 inhibited human erythropoiesis in vitro and caused anemia in zebrafish, effects that were abrogated by luspatercept. Upon GDF11 stimulation of human erythroid progenitors, SMAD2 binding occurred in the erythroid regulatory regions, including at the GATA1 intron. Intronic SMAD2-binding led to skipping of exon 2 of GATA1, resulting in a shorter, hypomorphic isoform (GATA1s). CRISPR deletion of the SMAD2-binding intronic region decreased GATA1s production upon GDF11 stimulation. Expression of GATA1s in a mouse model led to anemia, rescued by a murine ActRIIB-Fc (RAP-536). Finally, RNA-Seq analysis of samples from the phase 3 MEDALIST trial revealed that responders to luspatercept had a higher proportion of GATA1s compared with nonresponders. Moreover, the increase in RBCs after treatment was linked to a relative decrease in GATA1s isoforms. Our study indicates that GDF11-mediated SMAD2 activation results in an increase in functionally impaired GATA1 isoforms, consequently contributing to anemia and influencing responses to luspatercept in MDS.

Supplementary Figure S5. Annotated MS/MS spectrum of the phosphopeptide of MYH9 modified with serine 1943 phosphorylation. Red and blue lines indicate matches between observed and expected fragment masses (red is the b series, while blue is the y series). Fragments annotated as “-Phos” indicate that the phosphorylation fragmented out of the peptide leaving a diagnostic mass of -96 Da.

Supplementary Figure S4. Immunofluorescence using CD68 Cy5 on mouse lung tissues harvested after 18 months of intratracheal treatment. Magenta stain represent Cy5 stain on CD68 antibody and blue represent nuclear counterstain DAPI. Left, representative image for intratracheal PBS administration. Right, representative image for mice administered NB (NNK and BaP).

Supplementary Table S7. Phosphoproteomics results from purified microtubules in cells treated with vehicle vs CA4948 for 72 hours.

Supplementary Figure S3. Exposure to carcinogens leads to carcinogenesis in murine lungs: Representative histological examples of mouse lung carcinogenesis observed during the study to assess the effect of smoking carcinogens.

While therapies targeting CD19 by antibodies, chimeric antigen receptor T cells (CAR-T), and T cell engagers have improved the response rates in B cell malignancies, the emergence of resistant cell populations with low CD19 expression can lead to relapsed disease. We developed an in vitro model of adaptive resistance facilitated by chronic exposure of leukemia cells to a CD19 immunotoxin. Single-cell RNA-Seq (scRNA-Seq) showed an increase in transcriptionally distinct CD19lo populations among resistant cells. Mass cytometry demonstrated that CD22 was also decreased in these CD19lo-resistant cells. An assay for transposase-accessible chromatin with sequencing (ATAC-Seq) showed decreased chromatin accessibility at promoters of both CD19 and CD22 in the resistant cell populations. Combined loss of both CD19 and CD22 antigens was validated in samples from pediatric and young adult patients with B cell acute lymphoblastic leukemia (B-ALL) that relapsed after CD19 CAR-T-targeted therapy. Functionally, resistant cells were characterized by slower growth and lower basal levels of MEK activation. CD19lo resistant cells exhibited preserved B cell receptor signaling and were more sensitive to both Bruton's tyrosine kinase (BTK) and MEK inhibition. These data demonstrate that resistance to CD19 immunotherapies can result in decreased expression of both CD19 and CD22 and can result in dependency on BTK pathways.

Malignancies are reliant on glutamine as an energy source and a facilitator of aberrant DNA methylation. We demonstrate preclinical synergy of telaglenastat (CB-839), a selective glutaminase inhibitor, combined with azacytidine (AZA), followed by a single-arm, open-label, phase 1b/2 study in persons with advanced myelodysplastic syndrome (MDS). The dual primary endpoints evaluated clinical activity, safety and tolerability; secondary endpoints evaluated pharmacokinetics, pharmacodynamics, overall survival, event-free survival and duration of response. The dose-escalation study included six participants and the dose-expansion study included 24 participants. Therapy was well tolerated and led to an objective response rate of 70% with (marrow) complete remission in 53% of participants and a median overall survival of 11.6 months, with evidence of myeloid differentiation in responders determined by single-cell RNA sequencing. Glutamine transporter solute carrier family 38 member 1 in MDS stem cells was associated with clinical responses and predictive of worse prognosis in a large MDS cohort. These data demonstrate the safety and efficacy of CB-839 and AZA as a combined metabolic and epigenetic approach in MDS. ClinicalTrials.gov identifier: NCT03047993 . DiNardo et al. perform a phase 1b/2 clinical trial of telaglenastat (CB-839) in combination with azacytidine in persons with advanced myelodysplastic syndromes and report on the treatment safety and efficacy, including a definition of clinical responders.

Babies born prematurely with gestational age <28 weeks usually develop a severe pulmonary complication called Bronchopulmonary Dysplasia (BPD) in response to hyperoxia. BPD is a sexually dimorphic pediatric disease with no curative options. Several micro RNAs (miRNAs) are implicated in BPD and are expressed differentially in males and females. Circular (circ) RNAs serve as sponges for their dedicated miRNAs to influence transcription and translation. We tested the dimorphism of these circular RNAs in BPD to assess their biological significance and unravel a circRNA-miRNA-mRNA regulatory axis in response to hyperoxia. Our RNA-Sequencing assay identified approximately 33 000 circRNAs at the alveolar stage of development with only a handful of them being expressed differentially between males and females in the control room air (RA) and hyperoxia-treated (BPD) groups. One circRNA, i.e circNfix was found to be associated with miR204-5p that targets the downstream mRNA target Ntrk2. To prove that circNfix regulates Ntrk2, we silenced circNfix using a GapmeR and found that Ntrk2 was also suppressed, leading to an improved alveolar phenotype in BPD male pups. From the results of our study, we can propose circNfix and Ntrk2 as novel key regulators in the pathogenesis and sexual dimorphism of BPD, while simultaneously proposing the use of circNfix GapmeR towards a potential therapeutic application.

Introduction: Luspatercept is an erythroid maturation agent that promotes late-stage erythropoiesis in patients with LR-MDS. While it is known that luspatercept, a modified activin receptor ligand trap, binds to GDF11 and Activin B, the mechanism by which these ligands trigger a decrease in red blood cell (RBC) formation is unknown. Luspatercept was approved by the FDA following the phase 3 MEDALIST study, but biomarkers of response are currently unknown. Results:In a large cohort of primary MDS CD34+ samples, GDF11 expression was significantly higher in MDS samples than in age-matched healthy controls (183 MDS samples vs 17 controls, P < 0.05). GDF11 was detected in primary MDS sera and was substantially elevated in the refractory anemia (RA) and RA with ring sideroblasts (RARS) MDS subgroups. Activin receptor 2B (ACVR2B), the receptor of GDF11, was also overexpressed in MDS samples, and its expression was confirmed by immunohistochemistry (IHC) in the bone marrows of primary MDS patients. GDF11/ACVR2B activates SMAD2, and we found that the overexpression of SMAD2 in CD34+ cells was associated with more severe anemia in MDS patients. RNA-seq and SMAD2 ChIP-seq analyses were then performed to determine the downstream effects of GDF11 in erythroid progenitors. Human CD34+ primary cells were utilized to generate BFU-E stage erythroid progenitors. We discovered that GDF11 promotes an abnormal erythroid gene expression program characterized by increased expression of pro-apoptotic and early erythroid differentiation-related genes. SMAD2 binding was detected in regulatory regions of early erythroid (including GATA1), proinflammatory, and apoptotic transcripts using ChIP-seq analysis with p-SMAD2. In a zebrafish model, administration of GDF11 caused a decrease in erythroid cells, which was rescued by treatment with luspatercept (Wobus et al. Leukemia 2021 35(10):2936-47). Luspatercept inhibited the phosphorylation and activation of SMAD2 in response to GDF11 stimulation in primary hematopoietic cells and leukemia cell lines. Importantly, luspatercept could reverse the growth-inhibiting effects of MDS-derived sera on primary hematopoietic progenitors. Finally, to identify biomarkers associated with clinical responses, we analyzed phase 3 MEDALIST study samples collected before and after treatment with lupatercept. RNA-seq analysis was performed on bone marrow samples from responders (R; n = 14) and non-responders (NR; n = 9) (Figure). Analysis of pre-treatment/screening bone marrow transcriptomes revealed no significant differences between R and NR in global gene expression. Analysis of splice isoforms between the two cohorts revealed strikingly greater differences. Most differential splicing events were observed in NR (702 in R vs 5232 in NR). The most prevalent splicing modifications were exon skipping events, and most functional pathways affected by differential exon usage were RNA splicing related. GATA1, the master erythroid transcription factor, was spliced differently in R at baseline, which was an intriguing observation. Response to luspatercept was found to be associated with exon 2 skipping, resulting in a shortened isoform of GATA1. R had a greater proportion of the short GATA1 isoform than NR (12% in R versus 6% in NR; P = 0.04). We analyzed ChIP-seq data from primary erythroid cells to determine the effect of GDF11/SMAD2 activation on GATA1 splicing. GDF11 stimulation resulted in SMAD2 binding to the second intron of GATA1. CRISPR-mediated deletion of the SMAD2 binding region in primary erythroid progenitors increased expression of the GATA1 long isoform. Next, we performed a CRISPR-mediated deletion of exon 2 of GATA1, resulting in a predominance of GATA1 short isoform expression and a decrease in erythroid output. In CRISPR-modified primary erythroid cells with a predominant short GATA1 isoform (exon 2-deleted cells), luspatercept was able to reverse the inhibition induced by GDF11. Conclusions: These results demonstrate that MDS cases that respond to luspatercept are associated with a relatively high level of expression of functionally deficient GATA1 short isoform. We further demonstrate that GDF11 stimulates the production of the GATA1 short isoform via SMAD2 binding to intron 2 of the GATA1 gene. The regulation of a GATA1 splicing isoform by GDF11/SMAD2 is associated with clinical responses to luspatercept, according to these novel findings.

CONTEXT.—:Plasmablastic lymphoma (PBL) is a rare aggressive lymphoma, usually positive for CD138 and frequently occurring in the oral cavity of human immunodeficiency virus (HIV) patients. Up to 10% of cases are negative for CD138 and diagnostically very challenging.OBJECTIVE.—:To investigate the appropriate approach to diagnose CD138- plasmablastic lymphoma and avoid misdiagnosis.DESIGN.—:We studied 21 cases of CD138- PBL from multiple large institutes in the United States and 21 cases from the literature.RESULTS.—:CD138- PBLs were positive for different B/plasma cell markers at various percentages: MUM1 (94.4%; 34 of 36), OCT2 (70.6%; 12 of 17), immunoglobulin light chains (68.8%; 22 of 32), CD38 (68.4%; 13 of 19), CD79a (34.2%; 13 of 38), and PAX5 (15.6%; 5 of 32), suggesting that MUM1, OCT2, immunoglobulin light chains, and CD38 are useful markers to help establish the lineage. A total of 83% of cases (30 of 36) were extraoral lesions. Extraoral lesions showed much lower Epstein-Barr virus (EBV) infection rates (16 of 30; 53.3%) and had worse prognosis. MYC was positive in 80% (8 of 10) of EBV+ cases and 40% (2 of 5) EBV- cases, indicating the importance of MYC in pathogenesis, especially in EBV+ cases.CONCLUSIONS.—:Our study emphasizes that CD138- PBLs tend to be extraoral lesions, with much lower EBV infection rates, and diagnostically very challenging. Accurate diagnosis requires a thorough investigation and workup by using appropriate markers.

CONTEXT.— Plasmablastic lymphoma (PBL) is a rare aggressive lymphoma, usually positive for CD138 and frequently occurring in the oral cavity of human immunodeficiency virus (HIV) patients. Up to 10% of cases are negative for CD138 and diagnostically very challenging. OBJECTIVE.— To investigate the appropriate approach to diagnose CD138- plasmablastic lymphoma and avoid misdiagnosis. DESIGN.— We studied 21 cases of CD138- PBL from multiple large institutes in the United States and 21 cases from literature. RESULTS.— CD138- PBLs were positive for different B/plasma cell markers at various percentages: MUM1 (94.4%; 34 of 36), OCT2 (70.6%; 12 of 17), immunoglobulin light chains (68.8%; 22 of 32), CD38 (68.4%; 13 of 19), CD79a (34.2%; 13 of 38), and PAX5 (15.6%; 5 of 32), suggesting that MUM1, OCT2, immunoglobulin light chains, and CD38 are useful markers to help establish the lineage. A total of 83% of cases (30 of 36) were extraoral lesions. Extraoral lesions showed much lower Epstein-Barr virus (EBV) infection rates (16 of 30; 53.3%) and had worse prognosis. MYC was positive in 80% (8 of 10) of EBV+ cases and 40% (2 of 5) EBV- cases, indicating the importance of MYC in pathogenesis, especially in EBV+ cases. CONCLUSIONS.— Our study emphasizes that CD138- PBLs tend to be extraoral lesions, with much lower EBV infection rates, and diagnostically very challenging. Accurate diagnosis requires a thorough investigation and workup by using appropriate markers.

Malignancies can become reliant on glutamine as an alternative energy source and as a facilitator of aberrant DNA methylation, thus implicating glutaminase (GLS) as a potential therapeutic target. We demonstrate preclinical synergy of telaglenastat (CB-839), a selective GLS inhibitor, when combined with azacytidine (AZA), in vitro and in vivo, followed by a phase Ib/II study of the combination in patients with advanced MDS. Treatment with telaglenastat/AZA led to an ORR of 70% with CR/mCRs in 53% patients and a median overall survival of 11.6 months. scRNAseq and flow cytometry demonstrated a myeloid differentiation program at the stem cell level in clinical responders. Expression of non-canonical glutamine transporter, SLC38A1, was found to be overexpressed in MDS stem cells; was associated with clinical responses to telaglenastat/AZA and predictive of worse prognosis in a large MDS cohort. These data demonstrate the safety and efficacy of a combined metabolic and epigenetic approach in MDS.