bluuebunny/crossref_metadata_2025_split huggingface dataset:
CHD4 Promotes Tumor Formation, Survival, and Resistance to Genotoxic Therapeutics in TP53 Mutant T-Cell Acute Lymphoblastic Leukemia Cells through the NuRD Chromatin Remodeling Complex
Authors: Shang Shengzhe , Aijaz Javeria , Ginder Gordon 
Published: December 2023

T-Cell acute leukemia(T-ALL) though generally responsive to current chemotherapy remains incurable in over 50% of adult patients. Importantly, the survival for patients with TP53 mutant T-ALL disease is less than 10%. We have previously shown the role of the Methyl Binding Domain protein 2-Nucleosome Remodeling and Deacetylase (MBD2-NURD) chromatin remodeling complex in triple negative breast cancer cell growth and the role of the NuRD component, Chromatin-helicase-binding protein 4(CHD4), in tumor colony formation and genotoxic resistance in acute myeloid leukemia.
In the present study, we have examined the role of specific NuRD complexes and CHD4 in T-cell acute leukemia cells with mutant TP53. The prototypical NuRD complex possesses both a histone deacetylase (HDCC) sub-complex and an ATPase chromatin remodeling sub-complex containing CHD4 linked to MBD2 or MBD3 of the HDCC. CHD4 is linked to the MBD2/3 anchors of the NuRD complex, via GATAD2A or GATAD2B. Depletion of CHD4 was found to increase the rate of apoptosis in several TP53 mutant T-ALL cell lines including Jurkat, MOLT4, RPMI and CCRF by up to 5 to 10-fold. Likewise, depletion of both MBD2 and MBD3 also increased apoptosis and sensitization to the standard genotoxic chemotherapeutic agent, cytosine arabinoside (Ara-C) but had only minimal effects in normal human CD34+ hematopoietic progenitor cells. Depletion of GATAD2B and GATAD2A by shRNA also resulted in a significantly increased survival of 60 days compared to 20 days in Scramble shRNA controls, in a xenogeneic mouse model of T-ALL. Depletion of CHD4 resulted in a profound (10 to 100-fold) decrease in colony formation of the TP53 mutant T-ALL cell lines in methylcellulose. RNA seq analyses identified the apoptosis, ferroptosis and mitophagy pathways as potential mechanisms for the striking effect of NURD disruption on colony formation.
In summary, CHD4, through the NuRD complex, promotes tumor cell formation, survival and therapeutic resistance of TP53 mutant T-ALL cells. Current efforts are aimed at validating these findings in primary T-ALL cells and structure-function studies to advance development of tool compounds for disrupting the NuRD complex, with the long-term goal of developing improved small molecule therapeutics for treatment resistant acute leukemia.
Apoptotic Pathway Inhibition in Cold-Stored Platelet Concentrates Facilitates Retained Ability to Form Thrombi
Authors: Kirschall Johanna , Marini Irene , Pelzl Lisann , Witzemann Andreas , Wolska Nina , Bakchoul Tamam 
Published: December 2023

Introduction: Platelet concentrates (PCs) are used to treat or prevent bleeding in patients with impaired platelet function or after injury. However, the standard storage of PCs at room-temperature (RT) increases the risk of bacterial contamination and is associated with reduced platelet functionality due to storage lesions. Our group reported that cold-stored PCs have better functionality compared to RT-stored PCs but reduced in vivo circulation time due to cold-induced apoptosis. In order to investigate cold-stored PCs hemostatic functionality with and without apoptosis inhibition, we established an ex vivo model simulating physiological conditions of blood flow to evaluate the contribution of cold-stored PCs in thrombus formation.
Methods: Apheresis-derived PCs were stored for 1, 4, 7 and 10 days under agitation at 4°C or RT either with or without the apoptosis inhibitor G04 (RhoA GTPase inhibitor). Next, PCs were stained with CD41 antibody, recalcified and incubated with TRAP6 (thrombin receptor-activating peptide 6) to initiate thrombus formation. Platelet-depleted whole blood samples from healthy donors were spiked-in with PCs and administered to the microfluidic channels of the ex vivo system (Bioflux), under physiological shear pressure. After five minutes of perfusion the resulting thrombi were imaged and analyzed. Ability to form thrombi was further assessed by thromboelastography and impedance aggregometry.
Results: Platelets from 24h storage PCs showed stable thrombus formation upon activation with TRAP6. Unstimulated platelets did not form any thrombi during the entire period of perfusion. To evaluate the effect of cold storage on platelet functions we analyzed the extent of thrombus formation of PCs stored at RT and 4°C upon CD41 staining. Our results indicate that cold-stored platelets form larger clots under flow conditions and maintain higher functionality compared to PCs stored at RT. Moreover, incubation of cold-stored PCs with the apoptosis inhibitor G04 improved ex vivo thrombus formation compared to PCs stored without the inhibitor, without inducing any adverse effects (Figure 1).
Conclusion: The results indicate that our ex vivo assay, which simulates PC transfusion in thrombocytopenic patients, is suitable to test the hemostatic functions of PCs under physiological flow conditions. We demonstrated that PCs stored at 4°C show better thrombus formation ability upon stimulation by agonists compared to RT-stored PCs and that the ability to form clots under shear stress is still preserved after incubation with the apoptosis inhibitor.
To conclude, cold-storage of PCs in combination with apoptosis inhibition is a promising stragedy to reduce the risk of bacterial contamination and prolong in vivo survival time while preserving platelet's hemostatic functionality.
A SAGA Complex-Specific Dependency in Multiple Myeloma Orchestrates Oncogenic Transcriptional Programs
Authors: Chen Ying-Jiun C , Badiger Bhaskara Govinal , Lu Yue , Dent Sharon 
Published: December 2023

Multiple myeloma (MM) is a malignancy of antibody-producing plasma cells that reside within the bone marrow. Epigenetic factors contribute to the initiation, progression, relapse and clonal heterogeneity in MM, but our knowledge of epigenetic regulators involved in MM development is far from complete. Results from the Cancer Dependency Map (DepMap) Project revealed that several components of the SAGA complex are particularly important for MM cell growth and survival. The SAGA complex serves as a coactivator in transcription and also catalyzes histone acetylation and deubiquitination via its lysine acetyltransferase (KAT) and deubiquitinase (DUB) modules, respectively. Our analysis showed that each SAGA complex component is overexpressed in at least 50% of MM patients. To investigate SAGA-specific functions, we centered on ADA2B, a subunit in the KAT module that specifically functions in the SAGA complex.
We observed reduced cell viability upon ADA2B knockdown and CRISPR/Cas9-mediated knockout in MM cell lines. To identify the underlying transcriptional pathways that ADA2B regulate, we performed transcriptome sequencing using MM cell lines with and without ADA2B depletion. Our results showed several oncogenic pathways, including MYC, E2F and MM-specific MAF oncogenic programs, are tightly regulated by ADA2B. We also discovered that the protein but not transcript levels of MAF and the KATs in SAGA, GCN5 and PCAF, as well as the global level of histone H3 lysine 9 acetylation (H3K9ac) are all prominently decreased upon ADA2B depletion. To investigate whether the global reduction in H3K9ac would alter chromatin accessibility, we performed assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and found decreased accessibility at many cancer marker and cancer-promoting genes.
To decipher the protein domains that are essential for ADA2B function in MM, we generated and expressed mutated versions of ADA2B in MM cell lines. Excitingly, mutations of core hydrophobic amino acid residues in the SANT domain disrupt interactions with GCN5 and PCAF and negatively affect protein stability of ADA2B. Hence, drug inhibitors that target the SANT domain could achieve suppression of ADA2B and MM cell growth.
Our findings uncover novel epigenetic and transcriptional mechanisms controlling MM development, and suggest potential for new epigenetic inhibitors targeting SAGA-specific ADA2B as future treatment modalities for MM.
The Efficacy and Safely of Anticoagulation for the Management of Gonadal Vein Thrombosis
Authors: Brown Cameron , Ng Sarah , Zarka Farah , Delluc Aurélien , Carrier Marc 
Published: December 2023

Background
Gonadal vein thrombosis (GVT) is an uncommon condition that has been associated with different risk factors (e.g., post-partum period, cancer, recent pelvic surgery, etc.). The optimal management of GVT remains unclear. Anticoagulation therapy may help to mitigate the risk of thrombosis extension and recurrent venous thromboembolism (VTE) but may also be associated with bleeding complications.We sought to assess the efficacy and safety of anticoagulation therapy in patients with GVT.
Methods
A systematic search of MEDLINE, EMBASE and PubMed for randomized controlled trials and observational studies was performed . Studies with patients presenting with GVT defined as ovarian vein thrombosis or testicular vein thrombosis and reporting at least one of the desired outcomes were included in the analysis.The primary efficacy outcome was recurrent VTE, and the primary safety outcome was major bleeding episode. Secondary outcomes included clinically relevant non-major bleeding and overall mortality. Incidence rates of the outcomes were pooled using the random effects model and expressed as event per 100 patient-years with its associated 95% confidence intervals (CI) using R software.
Results
The search strategy identified 7084 article records. A total of 13 observational studies (1039 patients) with GVT met the inclusion criteria and were included in the analysis. Only one study reported the incidence of testicular vein thrombosis. Hence, 96% of the total patient population were females with ovarian vein thrombosis. Overall, the incidence rate per 100 patient-years for recurrent VTE was 3.60 (95% CI: 2.12-6.13; I-square 75%; Figure 1). A large majority of studies did not report if recurrent events occurred during or following discontinuation of anticoagulation. Similarly, most studies did not report on major or clinically relevant non-major bleeding events, or overall mortality preventing the possibility of conducting pooled analyses for these outcomes.
Conclusion
GVT seems to be associated with a relatively low risk of recurrent VTE. However, it remains unclear if anticoagulant therapy is associated with a favorable risk/benefit ratio. Future studies (e.g., registries, population-based studies) are needed to investigate the efficacy of anticoagulant and whether it outweighs the risk of bleeding in this patient population.
Risk of Developing Post Thrombotic Syndrome after Deep Vein Thrombosis with Different Anticoagulant Regimens, a Systematic Review and Pooled Analysis
Authors: Brown Cameron , Tokessy Lauren , Delluc Aurélien , Carrier Marc 
Published: December 2023

Background
Post-thrombotic syndrome (PTS) is a chronic condition that arises in up to 20-50% of patients with deep vein thrombosis (DVT) of the lower extremity. Symptoms range from skin color changes and limb heaviness to edema, chronic pain and ulcers. PTS has a significant impact on patients' quality of life. Hence, it is important to optimize DVT management to minimize the incidence and severity of PTS. It is unclear if different anticoagulant therapies (e.g. vitamin K antagonists (VKA), direct oral anticoagulants (DOACs) or low molecular weight heparin (LMWH)) are associated with different risks of PTS.
Objective
We sought to assess the incidence rates of PTS development after a proximal DVT of the lower extremity managed with different anticoagulation regimens.
Methods
A systematic search of MEDLINE, EMBASE and PubMed as well as conference proceedings (inception to June 2023) was performed. Studies were screened and selected if they met the criteria for patients (age ≥18) receiving anticoagulation therapy for a minimum of 3 months after the diagnosis of a proximal DVT of the lower extremity. The primary outcome was development of PTS defined by the Villalta or PRV score of ≥ 5, or as defined by the individual studies. Incidence rates (overall and per type of anticoagulant regimens) were pooled using the random effects model and expressed as event per 100 patient-years with its associated 95% confidence intervals (CI) using R software.
Results
Out of the 2837 identified studies, 77 were reviewed in full text and 21 (n= 4342 patients) were included in the analysis (7 randomized controlled trials, 14 observational studies). There were 17 studies (2834 patients), 12 studies (1212 patients) and 2 studies (296 patients) reporting the outcomes for VKA, DOAC and LMWH, respectively. The crude incidence rates for PTS development are depicted in Figure 1. After adjusting for duration of anticoagulation, the overall incidence of PTS was 16.3 per 100 patient-years (95% CI: 11.1-24.12). The incidence of PTS was 15.1 per 100-patient-years (95% CI: 8.7-26.1), 18.2 per 100 patient-years (95% CI: 9.4-35.1), 24.6 per 100 patient-years (95% CI: 9.2-65.5) for VKA, DOAC and LMWH, respectively. The most used DOAC was rivaroxaban (incidence rate of 12.3 per 100 patient-years (95% CI: 1.6-96.4)).
Conclusions
PTS is a common complication among patients with proximal DVT of the lower extremity. Incidence of PTS development may differ based on the anticoagulant regimen. DOACs seems to be associated with lower incidence PTS development compared to VKA and LMWH. Future clinical trials are needed to confirm these findings.
NFκB Dysregulation in the Bone Marrow Niche Drives Epigenomic Reprogramming of Hematopoietic Stem Cells and Myeloid Bias
Authors: Chia Jennifer J , Singh Apeksha , Lin Yu-Sheng Eason , Tran Tiffany , King Jennifer , Rao Dinesh S. , Hoffmann Alexander 
Published: December 2023

Introduction
Aging and chronic inflammation are known to skew hematopoietic output by favoring myelopoiesis and disfavoring lymphopoiesis. In addition, the bone marrow niche plays critical roles in supporting steady-state hematopoiesis, and alterations in the microenvironment may similarly influence disordered hematopoiesis. The NFkB system is a central, pleiotropic regulator of inflammatory signaling in many cell types. Thus, we reasoned that experimental perturbations of NFκB signaling may be used to study how inflammatory dysregulation affects hematopoiesis.
Methods
We generated a mouse model of inflammatory immune dysregulation, the IκB - mouse ( Nfkbia +/- Nfkbib -/-Nfkbie -/-), and then compared the peripheral blood and bone marrow inflammatory proteins and cell compositions betweenyoung WT, young IκB -,and aged WT mice. Using bone marrow transplantation, we next assayed the effect of an inflamed IκB - recipient niche on the hematopoietic output of WT donor bone marrow. Finally, we performed single cell RNA sequencing (scRNA-seq) and assay for transposase-accessible chromatin sequencing (ATAC-seq) on sorted hematopoietic stem and progenitor cells (HSPC) to characterize the epigenomic and transcriptional changes occurring in WT HSPC from an immune dysregulated environment.
Results
We observed an increase in inflammatory cytokines in both young IκB - and aged WT mice compared to young WT controls, as well as myeloid bias in the peripheral blood leukocytes and bone marrow HPSC. Transplantation studies showed that inflammatory dysregulation in the radio-resistant microenvironment resulted in myeloid-biased hematopoiesis. However, this myeloid bias was lost upon secondary transplantation of bone marrow into a WT recipient. Performed on HSPC from an inflamed microenvironment, our scRNA-seq studies showed myeloid bias at the transcriptional level, and ATAC-seq studies further revealed epigenomic changes, with an increased transcription factor (TF) binding motif accessibility for myeloid-priming TFs in long term HSC.
Conclusions
Our studies establish the IκB - mouse as a new model of chronic inflammatory dysregulation that can be used to study the effects of an inflamed bone marrow microenvironment on hematopoiesis. Furthermore, our findings indicate that dysregulated NFκB signaling in the bone marrow microenvironment leads to myeloid bias in HSPC, and is associated with epigenomic reprogramming at the stem cell level. However, despite this epigenomic reprogramming, we observed that myeloid bias could be reversed upon bone marrow re-transplant into a non-dysregulated niche. Together, these data suggest that further understanding niche-derived inflammatory dysregulation may be a useful in targeting disordered hematopoiesis in chronic inflammatory states such as aging.
Preventing Kidney Failure in Hemolytic Anemias with a Novel Heme and Hemoglobin Scavenger
Authors: Lucas Daniela , Cabrales Pedro , Munoz Carlos J , Gopal Srila , Muller Cynthia R 
Published: December 2023

Pathophysiological conditions characterized by chronic hemolysis, such as genetic and acquired hemolytic diseases, lead to increased levels of circulatory cell-free hemoglobin (fHb), free heme, and iron. The toxicity of free acellular hemoglobin has been a subject of intense study to understand its impact on the human body. fHb's small size allows it to extravasate into various organs, causing damage. The kidney is particularly vulnerable to Hb toxicity as it can filtrate through the kidneys, affecting glomerular filtration rate and leading to kidney failure.
To address this, our group has developed a novel technique using the dorsal window chamber model in Golden Syrian hamsters. This method allows us to non-invasively measure glomerular filtration rate (GFR) using FITC-Sinistrin. The advantage of this approach is that it can assess renal function in awake animals, eliminating the need for anesthesia and minimizing its impact on the assessment.
We also tested the function of ApoHb-Hp, a scavenger for Hb and heme, developed by our group, to see how it protects kidney function from mild and severe hemolysis. Our data involved two sets of experiments. In the first set, we injected groups with 10% of their blood volume, either with Hb alone or along with ApoHb-Hp. In the second set, we performed a 20% volumetric exchange of Hb or ApoHb-Hp with Hb. The results indicated that the group infused with Hb showed a sharp 60% decrease in half-life after 2 hours, but it returned to baseline after 24 hours. On the other hand, the group infused with ApoHb-Hp only showed a 30% decrease, suggesting that Hb is responsible for a more pronounced acute decrease, rather than just the volume change. Furthermore, when comparing the exchange data, both the Hb and ApoHb-Hp groups exhibited a 55% decrease in half-life after 2 hours compared to baseline, attributed to the change in volume. However, at the 24-hour mark, the ApoHb-Hp group returned to baseline, while the Hb group's half-life continued to decrease, reaching an 86% decrease compared to baseline.
In conclusion, our preliminary data indicates that continuous exposure to Hb has a more prolonged effect on the kidney's filtration rate, potentially causing prolonged kidney impairment and irreversible damage. Further research is needed to understand the full implications of these findings and to explore the protective role of ApoHb-Hp in mitigating Hb-induced kidney damage.
Epigenetic and Transcriptional Consequences of PIM Kinase Activity and Inhibition in Diffuse Large B-Cell Lymphoma (DLBCL)
Authors: Debek Sonia , Komar Dorota , Garbicz Filip , Zolyniak Aleksandra , Pawlak Michal , Jablonska Ewa , Szydlowski Maciej , Skrzypczak Magdalena , Radomska Sylwia , Bajor Małgorzata , Serin Nazli , Chapuy Bjoern , Juszczyński Przemysław 
Published: December 2023

The PIM kinase family consists of 3 proto-oncogenic proteins: PIM1, PIM2 and PIM3, expressed in numerous malignancies, including DLBCL. PIM kinases regulate crucial processes, such as proliferation, apoptosis, metabolism, or migration, therefore their inhibition is of great interest as a potential therapeutic strategy. Although recent studies have shed new light on the biological role of PIMs in lymphoid cancers, the details and mechanisms of PIM's oncogenic effects and the consequences of their inhibition in DLBCL remain insufficiently understood. Earlier studies have demonstrated a potential epigenetic role of PIM through histone H3S10 phosphorylation, however, described only at a single locus. The broad genomic role of PIM in modulating transcription in lymphoma cells remains unclear.
We confirmed the effect of PIM inhibition on histone modifications using small molecule inhibitors as well as genetic silencing of PIM kinases in DLBCL cell lines. PIM kinase inhibition changed the global amounts of histone modifications (including histone H4 pan-acetylation), accompanied by lower phosphorylation of RNA polymerase II, suggesting an involvement of PIMs in the RNA polymerase II pause release/elongation phase of transcription.
Local histone acetylation changes in the enhancer (H3K27ac) and promoter (H3K9ac) regions in response to treatment with the pan-PIM inhibitor were also identified, coupled with gene expression profiling in DLBCL cell lines. PIM inhibition decreased the expression of genes controlled by super-enhancers (SE), i.e. wide regulatory regions responsible for the high level of expression of the most important genes for the cell, including oncogenes. The integrated results of epigenomic and transcriptomic analyses explain the changes in expression of genes associated with many pathways, including transcription, inflammatory response, apoptosis, epigenetic mechanisms or DNA damage. The induction of the latter was further experimentally confirmed by the examination of DNA breaks using γH2AX, the activating phosphorylation of CHK2 or comet assays following PIM inhibition.
The conducted studies document an epigenetic function of PIM kinases, and suggest that inhibition of PIM activity leads to alterations in the DLBCL epigenetic landscape and associated changes in transcription. They also indicate that PIM inhibitors can be a therapeutic option in DLBCL.
Study supported aby Foundation For Polish Science TEAM Grant # POIR.04.04.00-00-5C84/17 and Polish National Science Centre Grant # 2018/29/B/NZ5/01471.