bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preclinical Activity of Novel TGF Beta Receptor I Kinase Inhibitors IOA-359 and IOA-360 for Treatment of Anemia in MDS/AML
Authors: Ramachandra Nandini , Vegivinti Charan Thej Reddy , Sahu Srabani , Rivera Bianca , Aminov Sarah , Fromowitz Ariel , Zhang Jinghang , Aodengtuya Fnu , Pradhan Kith , Zhao Rongbao , Schwartz Leya , Thiruthuvanathan Victor , Sanawar Rahul , Rabinovich Emma , Ajibade Opeyemi , Shastri Aditi , Lahn Michael , Verma Amit K. 
Published: December 2023

Background:
Overactivation of the Transforming growth factor beta (TGF-β) superfamily has been associated with bone marrow failure in MDS. TGF-β binds to set of receptors that include the TGF-β receptor I kinase (also known as ALK5), that in turn phosphorylates and activates the downstream SMAD2/3 proteins. Activation of SMAD2/3 transcription factors has been shown to occur in MDS and is associated with anemia. Thus, we wanted to evaluate the preclinical efficacy of novel, clinic-ready, TGF-b receptor I kinase small molecule inhibitors IOA-359 and IOA-360 in MDS models.
Results:
Using the TREEspot™ SCAN Max Kinase Panel of 403 kinases, IOA-359 and IOA-360 were found to be highly selective for ALK5. Both, IOA-359 and IOA-360 have a blocking activity against ALK5 similar to clinical stage ALK5 inhibitors. To evaluate the efficacy of IOA-359 and IOA-360, we first used HEK 293- Blue-TGF-β cells that stably overexpresses a SMAD inducible secreted embryonic alkaline phosphatase (SEAP) reporter. Both IOA-359 and IOA-360 were able to significantly inhibit TGF-β driven reporter at nanomolar doses ( Fig1A). Next, we showed that both ALK5 inhibitors were able to block TGF-β-mediated SMAD2/3 downstream phosphorylation/activation in a dose dependent manner in MDS and leukemic cell lines. Functionally, the ALK5 inhibitors did not lead to any increase in viability or proliferation in leukemic cell lines.
We next tested the efficacy of the novel ALK5 inhibitors in primary patient samples from MDS and AML (N=8). Treatment with both ALK5 inhibitors led to increase in erythroid colony formation in majority of MDS samples in clonogenic assays. Colonies were picked up and examined for erythroid and myeloid differentiation by FACS analysis. We observed that ALK5 inhibition led to increase in Glycophorin A and CD71 expression suggesting enhanced erythroid differentiation ( Fig1B). Myeloid differentiation effects were modest in comparison. Furthermore, in selected samples, addition of Luspatercept led to greater maturation of erythrocytes. Treatment of healthy CD34 + hematopoietic stem and progenitors did not lead to significant changes in differentiation. Lastly, to evaluate downstream effects of ALK5 inhibition, we performed RNAseq analysis in MDS cells. Inhibition with ALK5 inhibitors led to numerous changes in genes affecting cellular differentiation, validating functional changes observed by us.
Conclusion:
Our current results support the preclinical in vitro efficacy of ALK5 inhibitors IOA-359 and IOA-360 alone and in combination with Luspartercept, highlighting their potential for further development and clinical testing in MDS/AML.
Functional Interrogation of Clinically Associated Venetoclax-Sensitive Genes Identifies an Essential Role of Transcription Factor ZNF740 in Therapeutic Response
Authors: Zhang Lixia , Lu Rui 
Published: December 2023

Venetoclax, a targeted inhibitor of BCL-2, has shown therapeutic benefits in acute myeloid leukemia (AML). However, the emergence of drug resistance remains a significant clinical challenge, emphasizing the need for deeper understanding of its mechanisms. While comprehensive transcriptome analyses have identified many genes associated with venetoclax responsiveness, it remains crucial to distinguish between genes that play a direct role and those that are simply associated.
In this study, we focused on genes strongly linked to a positive venetoclax response in primary AML samples using the BeatAML2.0 dataset. We identified ~1,400 top genes whose expression inversely correlated with venetoclax AUC. We theorized that if any of these genes were essential for venetoclax sensitivity, their absence would lead to resistance. To explore their significance, we developed a focused CRISPR knockout library of these ~1,400 genes, with each gene represented by 7 guide RNAs, and an additional 250 guide RNAs as negative controls. We then performed CRISPR screens on AML cell lines, using either DMSO or venetoclax as treatments. Interestingly, the majority of the gene knockouts did not lead to resistance, suggesting that these genes likely have an associative rather than a direct impact on venetoclax sensitivity.
However, our screen did identify several genes that, when depleted, consistently resulted in resistance across different AML cell models. One of the top hits was the zinc finger transcription factor ZNF740, whose expression is strongly correlated with venetoclax AUC ( R = -0.52, p = 2.71e-26). For verification, we used CRISPR approach to knock out ZNF740 in Cas9-expressing OCI-AML2 and MOLM-13 cell lines. We then performed IC 50 and competitive proliferation assays under venetoclax treatment. We found that AML cells without ZNF740 exhibited a markedly higher IC 50 and demonstrated enhanced survival under venetoclax exposure. Conversely, enforced overexpression of ZNF740 rendered hypersensitivity to venetoclax. Intriguingly, our transcriptomic study showed that ZNF740 deletion upregulated monocyte differentiation signature genes, a change previously linked to venetoclax resistance.
Collectively, our findings indicate that ZNF740 serves as a newly identified, clinically relevant transcriptional modulator of venetoclax responsiveness. We are now investigating the molecular targets of ZNF740, particularly its role in guiding AML lineage decisions and its impact on venetoclax response. Gaining insight into ZNF740's function and mechanism could pave the way for innovative strategies to counteract venetoclax resistance observed in clinical settings.
Combination of Circulating Plasma Cells Enhances the Efficacy of R2-ISS Stage System for Risk Stratification of Newly Diagnosed Multiple Myeloma: A Single-Center Real-World Study
Authors: Chu Bin , Wang Yutong , Shi Lei , Sun Kai , Bao Li 
Published: December 2023

Previous studies identified the prognostic significance of quantifying circulating plasma cells (CPCs) by multiparametric flow cytometry (MFC) in newly diagnosed multiple myeloma (NDMM) patients. Recently it was reported that the R2-ISS stage is a simple prognostic staging system allowing a better stratification of patients with intermediate-risk NDMM.
We evaluated if a similar quantification of CPCs could add prognostic value to the R2-ISS classification of 279 consecutive NDMM patients treated in our center from 2017 to 2022. Those patients with R2-ISS stage II and stage III disease were re-classified according to the CPCs numbers ≥0.05% (CPC high) or＜0.05% (CPC low) for the purposes of this study.
The median progression free survival (PFS) for patients were as follows: not reached (R2-ISS I), 43 months (R2-ISS II with CPC low),24 months(R2-ISS II with CPC high), 23 months (R2-ISS III with CPC low),12 months (R2-ISS III with CPC high) and 14 months (R2-ISS IV). The median overall survival (OS) for patients were as follows: not reached (R2-ISS I, R2-ISS II with CPC low, R2-ISS II with CPC high and R2-ISS III with CPC low) , 46 months (R2-ISS III with CPC high) and 32 months (R2-ISS IV).
Finally, ≥ 0.05% CPCs retained its adverse prognostic significance in a multivariable model for PFS and OS. Hence, quantifying CPCs by MFC can potentially enhance the R2-ISS classification of a subset of NDMM patients with stage II and III disease by identifying those patients with a worse than expected survival outcome.
The Role of CABIN1 in the Pathogenesis of Idiopathic Multicentric Castleman Disease
Authors: Laczko Dorottya , Fajgenbaum David C. , Kambayashi Taku 
Published: December 2023

Introduction: Idiopathic Multicentric Castleman Disease (iMCD) is a rare disease characterized by flares of hypercytokinemia, leading to life threatening complications. Although several hypotheses have emerged including autoimmune, immune dysregulation, and/or infectious etiology, to date the exact pathogenesis of iMCD is unknown. IL-6 is thought to be the key cytokine that drives symptoms in a proportion of patients and current standard of care targets IL-6; however, it is only successful in one third of patients. Therefore, there is a dire need to identify additional driver cytokines/pathways to address treatment-refractory cases. Lately, the pathogenic role of CXCL13 in iMCD has emerged, as proteomic studies have shown that serum CXCL13 is elevated in iMCD and a biomarker of response to therapy. Given the heterogeneity of the disease, research into iMCD has been limited by the lack of an animal model. Through whole exome sequencing of an iMCD patient, we recently discovered a potential disease-causing mutation in a protein known as CABIN1. CABIN1 in known to play a role in T cell activation as a negative regulator of calcineurin and MEF2. Using Crispr/Cas9 technology, we generated a mouse model that harbors this gene mutation (CABIN1 V2185M).
Methods: Following LCMV infection or ovalbumin (OVA)-mRNA-LNP immunization serum cytokine levels were measured using Luminex assay or CXCL13 specific ELISA kit. Different immune cell populations and Nur77 levels were assessed by flow cytometry. MEF2D protein levels were determined by Western blot analysis.
Results: Although CABIN1 V2185M mice do not demonstrate spontaneous pathology at baseline, we found that upon LCMV CL13 infection, mice harboring the CABIN1 V2185M mutation displayed significantly higher morbidity and mortality compared to control mice. LCMV-infected CABIN1 V2185M mice displayed elevated serum levels of cytokines/chemokines including IL-6 and CXCL13, which are associated with human iMCD flares. Concurrently, we also measured a robust increase in the frequency of CD4 + T cells expressing CXCR5, which is the receptor for CXCL13. Similar to LCMV CL13, infection with LCMV Armstrong or immunization with OVA-mRNA-LNP also led to an increase in serum CXCL13 levels and CXCR5 +CD4 + T cells in the associated secondary lymphoid organ in CABIN1 V2185M compared to control mice. In terms of the underlying mechanism, we found that T cells of CABIN1 V2185M mice exhibit increased MEF2D protein and expression of a MEF2D-regulated gene, Nur77 following CD3/CD28 stimulation, suggesting that CABIN1 V2185M mutation acts through MEF2 dysregulation in T cells.
Conclusion: Our preliminary data shows that LCMV-infected CABIN1 mutant mice recapitulate the cytokine milieu of human iMCD. Therefore, CABIN1 could be the first ever described mutation that could drive iMCD disease. Furthermore, this mouse model could serve as a model platform to study the underlying pathogenic pathway(s) in iMCD.
Treatment Pattern and Survival of Human Immunodeficiency Virus Infection-Related Lymphoma in China 2008-2021
Authors: Liu Jun , Wang Chaoyu , Yang Tao , Wu Yan , Min Haiyan , Huang Yunhong , Wei Guo , Zhang Wei , Wang Min , Tang Xiaoqiong , Zhou Hui , Liu Yao 
Published: December 2023

Background
Over the past few decades, little has been known about HIV-related lymphoma, and there has been a lack of treatment. However, with the development of cART therapy in the 1990s, the survival of HIV-related lymphoma patients has been significantly improved, but there is still a lack of large-scale data reports on HIV-related lymphoma patients in China.Therefore, we performed a multi-center study to analyze the clinical characteristics and outcomes of HIV-related lymphoma patients in China.
Methods
We retrospectively analyzed the data of 443 patients with human immunodeficiency virus infection-related lymphoma from eleven large academic centers in China from 2008 to 2021.
Results
In the entire cohort, the median age was 47 years (range, 18-90) at lymphoma diagnosis, and 364 patients were male (82.2%).More than half of the patients came from public health treatment centers. The most common type of pathology was DLBCL (61.6%)and BL (10.6%). Most patients had elevated lactate dehydrogenase (56.2%), bulky tumor(30.7%), B symptoms(39.3%), extranodal involvement(52.8%), and advanced Ann Arbor stage (60.3%) at diagnosis. High international prognostic index (IPI) score (3-5) at diagnosis was found in 58.7% of patients. The number of patients with CD4 cell count below 200/μl was 244, accounting for 55.1% of the total. The percentage of patients who gave up chemotherapy was as high as 15.6%.
The median follow-up of our cohort was 10.1 (0.1-160) months. The overall 1-year OS rates 70.2%. Cox univariate analysis showed that education level(HR=0.682, 95%CI 0.468-0.994; p=0.046),B symptoms(HR=0.730, 95%CI 0.562-0.948; p=0.018),PLR(ratio of the number of platelets to the number of lymphocytes)(HR=1.000, 95%CI 1.000-1.001; p=0.044),elevated LDH(HR=0.607, 95%CI 0.463-0.769; p=0.000),extranodal involvement(HR=1.498, 95%CI 1.141-1.968; p=0.004) were independent risk factor for adverse prognosis based on overall survival (OS).The overall 1-year PFS rates was 67.4%.Cox univariate analysis showed that age≥60(HR=1.819, 95%CI 1.197-2.763; p=0.005),anemia(Hb&lt;120g/L)(HR=1.564, 95%CI 1.099-2.226; p=0.013),LDH(HR=3.646, 95%CI 2.115-6.286; p=0.000),CNS involvement(HR=2.209, 95%CI 1.384-3.524; p=0.001) were independent risk factor for adverse prognosis based on progression-free survival(PFS).
Conclusion
This is the largest retrospective study of HIV-associated lymphoma in China to date. Our results show that the proportion of men with HIV infection is much higher than that of women, which is positively correlated with the proportion of HIV infection. Patients with HIV-associated lymphoma have more risk factors at first diagnosis, including late stage, high risk layer, elevated LDH, extranodal involvement, and low CD4 cell count.
Predictive Modeling of Hematopoietic Stem Cell Mobilization and Collection Based on Peripheral Blood Marker
Authors: Ran Longrong , Peng Yu , Zhao Mingyu , Luo Xin , Chen Shuang , Yang Zailin , Liu Yao 
Published: December 2023

Background: Autologous stem cell transplantation (ASCT) is the major transplantation therapy for patients with lymphoma and MM, and the success of auto-HSCT depends on the mobilization efficiency of peripheral blood HSC. In clinical practice, CD34 + cell count in peripheral blood is often monitored to predict the collection effect and determine the collection time. However, prediction of poor mobilizers is still difficult .
Methods: We retrospectively analyzed 108 patients with lymphoma and multiple myeloma(MM) at Chongqing University Cancer Hospital who underwent autologous hematopoietic stem cell (HSC) collection between January 2021 to August 2022. There are two groups: collection success group and collection failure group. Compared the differences of clinical characteristics and impact of peripheral blood related detection indexes before autologous HSC collection. Logistic regression analysis was used to establish a prediction model for the successful collection by multi-marker and further evaluated multi-marker prediction models.
Results : There was no significant difference in sex, disease type, disease stage, age, disease status before mobilization, mobilization drugs and chemotherapy courses between the successful collection group and the failed collection group ( P&gt; 0.05). The proportion of patients with mobilization days less than 5 days was higher in the successful collection group ( P&lt; 0.05). The platelet count (PLT), mononuclear cell count (MNC) and absolute CD34 + cell count in the successful collection group were significantly higher than those in the failure group. The sensitivity, specificity and area under the curve (AUC) of combining three indexes were 80.9%, 95.9% and 0.944, respectively. Applied the Logistic regression models to the absolute count of PLT, MNC and CD34 + cells to construct the multi-marker prediction algorithms. The 3-marker model of PLT+MNC+CD34 + cells had the lowest AIC, BIC and high AUC. A prediction model was established based on the absolute count of PLT, MNC and CD34 + cells.
Conclusion :Patients with less than 5 days of mobilization have a higher success rate of collection. PLT, MNC and CD34 + cell counts before collection can reflect HSC mobilization in patients with lymphoma and MM, and the combination of the three can improve the accuracy of prediction of collection effect.The predictive model based on the absolute number of PLT, MNC and CD34 + cells have good predictive value. Our study suggests that multi-markers are important diagnostic tools for predicting successful collection.
Screening for Intracellular Phosphorylation Cascades That Positively and Negatively Regulate the Self-Renewing Proliferation of Immature HPCs
Authors: Kitada Sayaka , Nishinaka-Arai Yoko , Nishikori Momoko , Niwa Akira , Saito Megumu K 
Published: December 2023

For the purpose of studying hematological diseases involving complex lineages of cells, hematopoietic differentiation using patient-derived iPS cells has already proved to be powerful in the analysis of various diseases. However, in terms of sourcing for the expansion of its use to larger scale studies, the time-consuming and inefficient differentiation process still presents a significant obstacle. In this context, the development of a method that allows the proliferation of progenitor cells (HPCs) which maintains their ability to differentiate into multiple lineages is an important issue.
In vivo, immature multipotent hematopoietic stem cells (HSCs) reside in the bone marrow, where intracellular signals via phosphorylation cascades co-ordinately regulate the expression pattern of transcription factors (TFs), leading to fate decisions within the microenvironment between self-renewal and one-way differentiation into HPCs. In contrast, iPS cell-derived hematopoietic differentiation does not involve HSCs and the microenvironment differs from that of bona fide cells. Therefore, the signal combinations required to amplify iPS cell-derived HPCs without further differentiation should naturally differ from those observed in HSCs in vivo. Based on this assumption, we constructed a CRISPRa and CRISPRi screen for phosphorylation-related genes using iPS cell-derived differentiation to search for factors that enable long-term maintenance of multipotent HPCs.
First, Doxycycline-inducible dCas9-VPR (CRISPRa) or dCas9-KRAB-MecP2 (CRISPRi) expression cassettes were introduced into human iPS cells before, and then acted in combination with the phosphorylation-focused sgRNA libraries at the time when HPCs begin to be produced from mesodermal progenitors during their hematopoietic differentiation. Then, to identify the sgRNAs of interest with single-cell accuracy, colony formation assays were performed by isolating HPCs one by one by single-cell sorting. 2 weeks later, cells were collected only from wells that had formed CFU-Mix. Amplicon-sequences were performed using genomic DNA extracted from those cells and the sgRNAs that significantly contributed to the phenotype were identified by calculating the difference in enrichment with control sgRNAs. As a result, the CRISPRa screen identified a group of intracellular signals related with eight candidate genes known to be specifically activated in immature cells in the normal hematopoiesis. On the other hand, the results of CRISPRi showed that suppression of necroptosis-related signalling probably promotes long-term culture of HPCs in the stroma-free, artificial culture circumstances.
Our results showed the potential to obtain multipotent HPCs from iPS cells over a long period of time and in large quantities, simply by adjusting the intracellular signals without artificial adding or removing of individual genes.
Hypofractionated Radiotherapy in Aggressive B-Cell Lymphoma
Authors: Liu Ting-Bo , Li Xiaofan 
Published: December 2023

Background and purpose: Radiotherapy (RT) is an effective and available local treatment for patients with refractory or relapsed (R/R) aggressive B-cell lymphomas. However, the value of comprehensive hypofractionated RT in this setting has not been confirmed.
Materials and methods : We retrospectively analyzed patients with R/R aggressive B-cell lymphoma who received comprehensive hypofractionated RT between January 2020 and August 2022 at a single institution. The objective response rate (ORR), overall survival (OS), progression-free survival (PFS) and acute side effects were analyzed.
Results : A total of 30 patients were included. The median dose for residual disease was 36 Gy, at a dose per fraction of 2.3-5 Gy. After RT, the ORR and complete response (CR) rates were 90% and 80%, respectively. With a median follow-up of 10 months (range, 2-27 months), 10 patients (33.3%) experienced disease progression and three died. The 1-year OS and PFS rates for all patients were 81.8% and 66.3%, respectively. The majority (8/10) of post-RT progressions involved out-field relapses. Patients with relapsed diseases, no response to systemic therapy, multiple lesions at the time of RT, and no response to RT were associated with out-field relapses. PFS was associated with response to RT (P=0.001) and numbers of residual sites (P&lt;0.001). No serious non-hematological adverse effects (≥grade 3) associated with RT were reported.
Conclusion: These data suggest that comprehensive hypofractionated RT was effective and tolerable for patients with R/R aggressive B-cell lymphoma, especially for those that exhibited localized residual disease.