bluuebunny/crossref_metadata_2025 huggingface dataset:
Hematopoietic Transcription Factor PU.1 and Enhancer RNA Loup Establish a Feedforward Regulatory Loop Governing Monocyte/Macrophage Biology
Authors: Waliullah A S M , Qiu Kevin , Tran Minh L , Dziegielewska Barbara , Zhang Junyan , Tenen Daniel G. , Goldfarb Adam , Trinh Bon
Published: December 2024

The ETS transcription factor PU.1, known for its precise expression pattern, plays a crucial role in blood development. Deviations from its normal graded levels in hematopoietic lineages are associated with blood-related neoplasms and malignancies. As a transcription factor, PU.1 binds to purine-rich DNA sequences in enhancers and promoters as well as other transcription factors to regulate gene expression. While noncoding genes are increasingly reported to control fundamental biological processes in both normal and malignant hematopoiesis, most of our understanding of PU.1's role comes from its myeloid coding target genes. Furthermore, the role of PU.1 in enhancer regulation has not been systematically explored, highlighting a critical area for future research.

In this study, we investigated the role of PU.1 in enhancer regulation. To that end, we first compiled a comprehensive catalog of putative and verified enhancers from databases and published sources. We then interrogated this catalog with a genome-wide PU.1 occupancy profile in a myeloid cell line. In doing so, we identified a repertoire of PU.1-bound enhancers in myeloid cells. Given that enhancer-associated noncoding RNAs (eRNAs) are increasingly reported to promote enhancer activities, we focused our attention on this group of noncoding genes. By interrogating the list of PU.1-bound enhancers with the PU.1-mediated transcript profile, we revealed a group of eRNAs regulated by PU.1. Among these noncoding genes, to our surprise, was the eRNA LOUP, which we had previously discovered as an RNA inducer of PU.1. We further demonstrated that PU.1 occupies a genomic region within the LOUP locus that exhibits the epigenetic features of a myeloid-specific superenhancer. In addition to its previously described role in regulating myeloid differentiation and inflammatory signaling, we demonstrated that LOUP regulates the expression of surface markers and cytokines tailored to monocyte/macrophage biology. Furthermore, our data also indicated the role of LOUP in microbial clearance.

Taken together, our findings suggest that LOUP and PU.1 are partner regulatory biomolecules within an enhancer-mediated feedforward regulatory loop that induces the expression of each other, thereby regulating monocytic/macrophage differentiation and functions. We are currently investigating RNA and protein biomolecules that control this feedforward regulatory loop and its role in myeloid neoplasms and malignancies. Our study could provide a fundamental mechanistic understanding of hematopoietic enhancer specificity and lay the groundwork for further translational studies aimed at developing new therapeutic approaches for the treatment of inflammatory diseases and hematopoietic malignancies.
Which Patients Will Benefit More?–the Impact of Different Biological Characteristics of High-Risk Acute Myeloid Leukemia on the Efficacy of Maintenance Treatment with Decitabine after Allogeneic Hematopoietic Stem Cell Transplantation
Authors: Liu Jia , Zhu Lidan , Liu Huanfeng , Gao Shichun , Wang Lu , Kong Peiyan , Zhang Xi , Gao Lei
Published: December 2024

Background Relapse is the main cause of death after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in high-risk acute myeloid leukemia (HR-AML). Our center and other 11 HSCT centers in China in the early stage to carry out one clinical research on low-dose Decitabine maintenance treatment to prevent relapse of HR-AML after allo-HSCT. Research has found that maintenance treatment with Decitabine can reduce the relapse rate from 38.3% to 15%.Which HR-AML patients will benefit more for maintenance treatment with Decitabine are worth further exploration in clinical practice.

Methods A retrospective analysis was conducted on 296 patients with HR-AML after allo-HSCT who underwent maintenance treatment with Decitabine for more than 6 courses from February 2019 to June 2022 at our center. The impact of different biological characteristics of HR-AML include age, recurrent genetic abnormalities, mutation gene types, and history of pre-leukemia hematological diseases. The main endpoint of the study is the 2-year relapse rate.

Results Among the 296 patients, 52 were over 60 years old and 244 were under 60 years old, indicating that patients under the age of 60 are more likely to benefit from Decitabine maintenance therapy. Common recurrent genetic abnormalities include: 16 cases of t (8,21), 9 cases of inv (16), 9 cases of t (9,11), 6 cases of inv (3), 30 cases of other abnormalities, and 226 cases of no recurrent genetic abnormalities. After maintenance treatment with Decitabine, the 2-year relapse rate of patients with and without recurrent genetic abnormalities were 12.9% and 20.8%(p=0.043), respectively, indicating that maintenance treatment with Decitabine is effective for patients with recurrent genetic abnormalities. Mutated genes are mainly divided into two categories: methylation related gene mutations (151 cases) and other mutations (145 cases). The 2-year relapse rate of patients with methylation related gene mutations and other mutations were 11.2% and 21.4%, respectively (p=0.012), indicating that maintenance treatment with Decitabine is more effective for patients with methylation related gene mutations. According to the history of pre-leukemia hematological diseases, AML was divided into MDS/MPN transformed AML (54 cases) and primary AML (242 cases). The 2-year relapse rates of the two groups were 14.8% and 17.8% (p=0.12), respectively, and there was no significant difference between the two groups.

Conclusion Maintenance treatment with dexamethasone after high-risk AML transplantation is more effective in patients under 60 years old, recurrent genetic abnormalities, and methylation related gene mutations.
Novel Single-Cell RNA Technology Simplifies Measurement of Anti-BCMA CAR-Ts in Patient Samples
Authors: Chen Szu-Ying , Cienciala Martin , Rashid Tasfia , Patino Escobar Bonell , Berne Laura , Georgiev Daniel , Wiita Arun P
Published: December 2024

Introduction: There is a critical clinical need for a technology capable of characterizing cell therapies at time points post infusion. Targeted single cell RNA sequencing (scRNAseq) of anti-BCMA CAR-T cells was performed using a novel encapsulation and barcoding approach from Sampling Human Inc. This proof-of-concept study establishes the performance capability of BCMA antigen functionalized bioparticles for universal anti-BCMA CAR-T detection and mRNA capture directly from complex samples. The platform employs a highly streamlined and instrument free workflow, enabling routine testing of patient samples and providing high-resolution activity data of therapeutic cells in vivo.

Methods: The platform's performance was assessed using a dilution series of PBMCs from a patient receiving anti-BCMA CAR T-cell therapy and a healthy donor. Each sample, consisting of approximately 10,000 cells, was analyzed through an integrated one-step workflow using anti-BCMA CAR encapsulation reagent. Samples were processed directly into barcoded libraries, foregoing separate enrichment or isolation steps, and were sequenced using a standard NGS pipeline. The results were compared to those obtained from a benchmark workflow that employs FACS isolation, followed by analysis with 10X Genomics 3' kits.

Results: The results from the novel approach show strong alignment with existing single cell technologies that employ cell sorting in series with scRNAseq, based on median genes detected (2120 genes per cell) and transcript counts (2589 UMIs per cell). Notably, the platform consistently exhibited a significantly higher mean cell recovery rate (exceeding 70%) and lower false positive rate (<1% CAR-negative cells), permitting analysis on smaller sample sizes. Moreover, the approach demonstrated a decreased percentage of mitochondrial (MT) transcripts, indicating less cellular stress, and lower variability between samples compared to FACS-based methods.

Conclusion: This novel encapsulation and barcoding method from Sampling Human Inc consolidates scRNAseq of anti-BCMA CAR-T cells into a one-step protocol that greatly reduces the time and cost of analysis. The platform significantly increases access to translational scRNAseq data by eliminating isolation and sorting steps to simplify sample preparation at scale. Continued refinement of this platform promises to significantly improve the precision of CAR T-cell typing, with substantial promise for future applications such as precision re-dosing and advanced CAR T-cell engineering.
Clinical Outcomes for Hematopoietic Stem Cell Transplant Recipients with Anemia: An Analysis of the National Inpatient Sample
Authors: Thor Danielle C , Elias Tony , Polineni Vineet , Brik Ben
Published: December 2024

Background: As hematopoietic stem cell transplant (HSCT) grows in accessibility and utility, it remains imperative to understand outcomes for its recipients. Limited data is available on the comorbid correlations for this steadily increasing patient population. We sought to examine the National Inpatient Sample (NIS) database to describe in-hospital outcomes among patients who received a HSCT and developed anemia.

Methods: Data were extracted from the NIS Database from 2019 and 2020. The NIS was searched for hospitalizations of all patients greater than 18 years old who had previously received a HSCT and were hospitalized thereafter. We then analyzed the outcomes of these patients who developed anemia. Multivariate logistic regression analysis was used to adjust for confounders; SPSS software was used for statistical analysis. The primary outcome was inpatient mortality and secondary outcomes are listed below.

Results: This study included 8,302 patients who had received a HSCT, of which 4888 (58.9%) were found to have anemia. Anemic recipients of a HSCT had slightly higher prevalences of obesity (7.3% versus 7.0%, p<0.001) and smoking (21.1% versus 20.5%, p<0.001), as well as higher prevalences of hypertension (32.4% versus 23.7%, p<0.001) and chronic kidney disease (34.6% versus 21.3%, p<0.001). Multivariate regression demonstrated that anemic recipients of a HSCT had higher inpatient mortality (OR 2.549, CI 2.233-2.910, p<0.001). On secondary analysis, anemic HSCT recipients were found to be more likely to have thrombocytopenia (OR 3.467, CI 3.199-3.757, p<0.001), hypertension (OR 5.141, CI 4.699-5.626, p<0.001), acute kidney failure (OR 3.421, CI 3.187-3.673, p<0.001), all-cause arrhythmias (OR 2.772, CI 2.515-3.056, p<0.001), acute pancreatitis (OR 1.906, CI 1.583-2.294, p<0.001), and pericarditis (OR 3.000, CI 2.478-3.632, p<0.001).

Conclusion: In this nationally-representative, population-based retrospective cohort study, anemic patients who have received a HSCT and were subsequently hospitalized were associated with higher mortality and worse outcomes.
Marriage and Fertility of Patients with Beta Thalassemia Major : A Single Center Experience from Southwest Turkey
Authors: Akgun Cagliyan Gulsum , Izmir Guner Sebnem
Published: December 2024

Introduction:

Infertility and hypogonadotropic hypogonadism are still a significant problem due to iron overload in patients with beta thalassemia major (BTM). In our study, we aim to evaluate the marriage and fertility status of the patients with BTM.

Material and Method:

Adult patients living in Denizli with BTM were included in the study. All of the patients were receiving iron chelator therapy and transfusion regularly. In routine follow up all patients were consulted to the endocrinology. The files of the patients were examined retrospectively. We recorded all datas from the files as age, gender, marriage, divorce or have a child.

Results:

In our study, 82 adult patients with BTM were included. The median age was 26 (Min:18, max:45 years). 43.9% (n:36) of the patients were male and 56.1% (n:46) were female. The median ferritin level was 1352 (304-5464). 47.5% (n:39) of the patients had undergone splenectomy. The rate of hypogonadism was 40.2 % (n:33), hypothyroidism was 17% (n:14), hypoparathyroidism was 8.5% (n:7) and diabetes mellitus was 9.7% (n:8) in the patients.The marriage rate was 25.6% (n:21, 10 men, 11 women). The mean age of marriage was 26 years (18-32 years). The duration of mean marriage duration was 3.4 years (3 months - 6 years). There were no couples with both partners with BTM. 1 marriage was between a couple with BTM and sickle cell anemia. The number of divorced patients with BTM was 2.4% (n:2). There was no significant difference between in terms of ferritin levels between married and single patients. We found that the rate of marriage rate was higher in cases without hypogonadism and it was statistically significant (p<0.001). Only 2 patients of married had hypogonadism (2/21). There was no spontaneous miscarriage in the patients. The number of patients who had a child was 12.1% (n: 10, 4 men and 6 women). The mean of the children was 1.4. The patients having 2 or more children was 4.8% (n: 4).

Discussion: In our country, all couples are scanned for the presence of BTM routinely. Although the tests are easy and accessible, births of babies with BTM are still reported today. Whereas, if the patients with BTM are managed correctly and iron load is reduced, they can marry, start a family and have a healthy child. Unfurtunately, patients with BTM still have not only metabolic problems but also social problems.
Clinical Outcomes for Hematopoietic Stem Cell Transplant Recipients with Hyperlipidemia: An Analysis of the National Inpatient Sample
Authors: Elias Tony , Thor Danielle C , Polineni Vineet , Brik Ben
Published: December 2024

Background: As hematopoietic stem cell transplant (HSCT) grows in accessibility and utility, it remains imperative to understand outcomes for its recipients. Limited data is available on the comorbid correlations for this steadily increasing patient population. We sought to examine the National Inpatient Sample (NIS) database to describe in-hospital outcomes among patients with known hyperlipidemia who received a HSCT.

Methods: Data were extracted from the NIS Database from 2019 and 2020. The NIS was searched for hospitalizations of all patients greater than 18 years old who had previously received a HSCT and were hospitalized thereafter. We then analyzed the outcomes of these patients with hyperlipidemia. Multivariate logistic regression analysis was used to adjust for confounders; SPSS software was used for statistical analysis. The primary outcome was inpatient mortality and secondary outcomes are listed below.

Results: This study included 8,302 patients who had received a HSCT, of which 2641 (31.8%) were found to have hyperlipidemia. These HSCT recipients had a higher prevalence of obesity (9.8% versus 7.0%, p<0.001), hypertension (38.2% versus 23.7%, p<0.001), smoking (26.8% versus 20.5%, p<0.001), and chronic kidney disease (29.7% versus 21.3%, p<0.001). Multivariate regression demonstrated that recipients of a HSCT with hyperlipidemia had higher inpatient mortality (OR 1.329, CI 1.251-1.413, p<0.001). On secondary analysis, HSCT recipients with hyperlipidemia were found to be more likely to have non-alcoholic fatty liver disease (OR 1.607, CI 1.414-1.826, p<0.001), anemia (OR 1.485, CI 1.456-1.514, p<0.001), thrombocytopenia (OR 1.457, CI 1.407-1.508, p<0.001), hypertension (OR 2.057, CI 1.965-2.152, p<0.001), acute kidney failure (OR 1.550, CI 1.499-1.604, p<0.001), all-cause arrhythmias (OR 1.689, CI 1.590-1.795, p<0.001), pericarditis (OR 1.419, CI 1.300-1.549, p<0.001), sepsis (OR 1.439, CI 1.400-1.479), coagulopathies (OR 1.379, CI 1.299-1.463, p<0.001), chronic pulmonary disease (OR 1.805, CI 1.700-1.916, p<0.001), severe liver disease (OR 1.429, CI 1.335-1.530, p<0.001), and acute heart failure (OR 1.905, CI 1.811-2.003, p<0.001).

Conclusion: In this nationally-representative, population-based retrospective cohort study, patients with hyperlipidemia who have received a HSCT and were subsequently hospitalized were associated with higher mortality and worse outcomes.
The Long-Term Effect of L-Glutamine Administration in Sickle Cell Disease Related Liver Damage
Authors: Katoch Omika , Pradhan-Sundd Tirthadipa
Published: December 2024

Introduction: Sickle Cell Disease (SCD) is an autosomal recessive genetic disorder in the β-globin gene resulting from a point mutation at its sixth position where hydrophilic glutamic acid substitute with hydrophobic valine that results in mutated sickled hemoglobin. This mutation, which occurs in both copies of the gene, promotes hemolysis, vaso-occlusion, and sterile inflammation. SCD patients experiences serious health complications including multi organ failure including liver failure. Currently, there are no effective treatment available for SCD related liver problems.

Methods: In the present study, we have studied the long-term effect (for up to eight weeks) of L- glutamine administration (10-12 mg/mL) via drinking water on liver pathophysiology using quantitative liver intravital microscopy, advanced imaging, and biochemical analysis in humanized SCD mice.

Results: We found that oral L-glutamine administration significantly reduced the accumulation of iron, heme, and hemoglobin in liver of SCD mice but had no effect on ameliorating liver vaso-occlusion and liver fibrosis. We also found the reduced expression of Kupffer cells after L-glutamine administration which may led to the failure of the resolution of fibrosis and hepatic cell death. Moreover, the balance between proinflammatory vs anti-inflammatory macrophages were impaired in SCD mice liver post L-glutamine treatment. We also found activation of hepatic stellate cell markers including α-SMA, collagenase 1 and 2 post L-glutamine treatment in SCD mice liver.

Conclusion: Our current study highlights the long-term effects of L-glutamine in SCD mouse liver. Interestingly, despite a considerable decrease in hepatic heme-hemoglobin-iron accumulation, chronic liver injury did not ameliorate post-L-glutamine treatment suggesting the need to investigate the long-term effects of L-glutamine therapy on vaso-occlusion, Kupffer cell expression, hepatic cell death, and liver fibrosis in SCD patients.
Global, Regional, and National Burden of Hodgkin Lymphoma from 1990 to 2021: Estimates from the 2021 Global Burden of Disease Study
Authors: Wang Mengyao , Hu Qian , LI He , Liao Yi , Niu Ting
Published: December 2024

Background: Hodgkin lymphoma (HL) is an uncommon B cell lymphoma.This article aimed to assess the global, regional, and national burden of HL from 1990 to 2021, by gender, age, and social-demographic index (SDI) and to to estimate the trends of HL globally from 1990 to 2021.

Methods: Data on HL, including incidence, mortality, and disability adjusted life-years (DALY), from 1990 to 2021 were obtained from the 2021 Global Burden of Disease study. The trends of HL burden were estimated using age-standardized rate (ASR) and estimated annual percentage change (EAPC).

Results: HL incidences increased by 19.23%, from 54671 in 1990 to 65182 in 2021 while the age-standardized incidence rate (ASIR) declined from 1.12 to 0.79 (EAPC= -1.1; 95% CI, from -1.16 to -1.05 ). Regarding SDI level analysis, the ASIR in all SDI regions demontrated a slight decrease. Incidence showed a bimodal distribution with peak values in patients aged 20-29 years and patients aged 75 years or higher. The number of death cases and DALYs remained stable. The age-standardized death rate (ASDR) decreased by 2.07% (95% CI, from − 2.01% to − 2.14%) per year. And the annual age-standardized DALY rate decreased by 1.88% (95% CI, from − 1.83% to − 1.94%). ASDR and age-standardized DALY rate showed a clear gradient across different SDI levels, with higher SDI regions showing lower age-standardized DALY rate and ASDR compared to lower SDI regions.The incidence, death and DALYs, whether in numbers or ASR, in male subjects was higher than that in female subjects. But the disparity in these indicators between the genders is gradually narrowing over time.

Conclusion: Globally, incidence of HL was stable, while mortality and DALY rate of HL had been decreasing from 1990 to 2021. Despite the reduction in mortality and DALYs across all SDI regions, an observed phenomenon existed, which was high SDI region exhibited the highest incidence but the lowest mortality and DALYs, whereas Low SDI region showed the lowest incidence but the highest mortality and DALYs. This result indicated that advanced diagnostic and therapeutic approaches can effectively improve HL prognosis, reducing both mortality and disability. And more attention should be paid to establish specific strategies in low SDI region to reduce death and DALYs.
Graft-Versus-Host Disease Prophylaxis with Post-Transplant Cyclophosphamide Better Preserves Regulatory T Cell
Authors: Koh Jeong Suk , Heo Buyeon , Lee Seul Bi , Choi Su-Young , Pham Thi Thuy Duong , Lee Sang-Woo , Park Jung-Hyun , Jang Yunseon , Seo Wonhyoung , Lee Myung-Won , Jo Deog-Yeon , Kwon Jaeyul , Song Ik Chan
Published: December 2024

Background: Antithymocytic globulin (ATG) and post-transplant cyclophosphamide (PTCy) are the most commonly used regimens for graft-versus-host disease (GVHD) prophylaxis. However, there is lack of data about the difference of regulatory T cell (Treg) subpopulation between these two regimens.

Method: We collected peripheral blood sample at day+21 after allogeneic hematopoietic stem cell transplantation (Allo-HSCT). We analyzed Treg subpopulation by flow-cytometer and classified Treg into 3 subgroups: naïve, effector and non-suppressive Treg. And we compared overall survival (OS), the cumulative incidence of acute and chronic GVHD, relapse rate between 3 group: ATG, PTCy and ATG plus PTCy group.

Results: We enrolled 68 patients (28 in ATG, 17 in PTCy and 23 in ATG plus PTCy) in total. In ATG group, all patients received human leukocyte antigen (HLA) matched-donor HSCT, whereas in the PTCy group, 12 (70.6%) patients received haplo-identical HSCT, and in ATG plus PTCy group, all patients received haplo-identical HSCT (p<0.001). The conventional CD25+FOXP3+Treg count of CD4+T cell was 6.14% in ATG, 12.96% in PTCy and 14.48% in ATG plus PTCy group, respectively (ATG vs PTCy, p=0.0020/ ATG vs ATG plus PTCy, p<0.0001). The naïve Treg count of CD4+T cell was 5.22% in ATG, 5.64% in PTCy, and 6.17% in ATG plus PTCy group (p=0.4643). The effector Treg count of CD4+T cell was 4.13% in ATG, 5.57% in PTCy, and 5.85% in ATG plus PTCy group (p=0.2816). The non-suppressive Treg count of CD4+T cell was 23.75% in ATG, 19.82% in PTCy, and 21.37% in ATG plus PTCy group (p=0.3767). The cumulative incidence of Grade 2 to 4 acute GVHD was 18.3% in ATG, 38.1% in PTCy, and 4.8% in ATG plus PTCy group (p=0.032). And extensive chronic GVHD was 19.4% in ATG, 28% in PTCy, and 21% in ATG plus PTCy group (p=0.615). OS and relapse rate were not statistically different between three group.

Conclusion: There were more conventional CD25+FOXP3+Tregs in PTCy-containing group than in ATG alone group, which was a result of the fact that there were more naïve and effector Treg in PTCy-containing group. ATG plus PTCy showed better outcomes for acute GVHD. Therefore, ATG plus PTCy is more recommended for the prevention of acute GVHD in haplo-identical HSCT.
Gaps in Access to Diagnostic Studies and Treatments for Patients with Lymphoproliferative Diseases in Chile
Authors: León Pilar , Flores Angulo Carlos , Roa Macarena , Vergara Carmen , Espinoza Marcela
Published: December 2024

Introduction: Chile is a country in Latin America that is classified as high-income by the World Bank Group. However, there are significant wage differences, with half of the country's population concentrated in the lowest income brackets (Fonasa A and B) of the public welfare system, which has coverage for approximately 80% of the population. Additionally, geographical characteristics can lead to the concentration of specialized services in large cities. For these reasons, the study aims to determine the gaps in access to diagnostic studies and treatment for patients with lymphoproliferative diseases in Chile.

Methods: We conducted a cross-sectional study by sending a survey to hematologists in Chile between October and December 2023. The survey included questions about the type of work activity (public or private) and the characteristics of health centers. It consisted of 9 questions related to access to diagnostic studies, staging, and treatment response, and 30 items on access to treatment. We used a 5-point Likert scale (1= never, 2= rarely, 3= sometimes, 4= almost always, 5= always) and dichotomized the answers into low access (1-3) and greater access (4 and 5). Consistency was evaluated using Cronbach's alpha, with values between 0.7 and 0.9 considered optimal. Single and multiple logistic regression analyses were performed, considering the location and type of health center as explanatory variables. Statistical analysis was conducted using the glm function and the psych library in R software.

Results: The survey was answered by 47 hematologists from 14 out of 16 regions, providing information from 59 centers (68% public and 32% private), of which 34% were located in the Metropolitan Region. In the crude models, we found significantly greater access in the Metropolitan Region to PET-CT, tissue flow cytometry, and new drugs compared to other regions. We determined that access in the public system (adjusted for the location of the center) was significantly lower than in the private system for PET-CT at diagnosis (OR 0.12; 95% CI 0.02, 0.52) and interim (OR 0.17; 95% CI 0.02, 0.71). Additionally, we evidenced a 94% and 90% reduction in the chance of access to nivolumab/pembrolizumab (p=0.001) and brentuximab (p=0.001), respectively, in the second line of treatment for patients with Hodgkin's lymphoma, as well as for Bruton's tyrosine kinase inhibitors for patients with chronic lymphocytic leukemia (OR 0.06, p<0.001). The results regarding access to specific treatments for patients with follicular, mantle, and T-cell aggressive lymphomas were similar.

Conclusions: We demonstrate reduced access to diagnostic studies and specific treatments in health centers outside the Metropolitan Region and public hospitals. Identifying these gaps can contribute to developing public policies that reduce these disparities, resulting in better health outcomes.
Protein Language Model-Based Intra-Gene Disparity of Donor HLA Alleles Informs Prognostic Risk in Hematologic Malignancy Patients Undergoing Haplo-Identical HSCT: A Combined Xinqiao-CIBMTR Analysis
Authors: Feng Yimei , Wang Yijie , Li Xiaobo , Di Da , Liu Xiangjun , Zhang Xi
Published: December 2024

It has been suggested that the intra-gene disparity in human leukocyte antigen (HLA) within a donor or recipient may play an important immunological role in haplo-identical hematopoietic stem cell transplantation (haplo-HSCT). Current methods to estimate HLA disparity primarily rely on epitope analysis and amino acid index scores. Recently, AlphaFold and emerging protein language models (PLMs) have highlighted the potential of large-scale deep learning techniques for predicting protein structures and functions. In this study, we utilized the newly proposed Protein-Vec PLM (PMID: 38045331) to extract functional embedding vectors from the amino acid sequences encoded by HLA alleles. With these vectors, we defined a novel PLM-based measure of intra-gene disparity for any allele pair of the same HLA gene within an individual and explored its prognostic value in haplo-HSCT.

We collected data from 425 hematologic malignancy (HM) patients undergoing haplo-HSCT between 2015 and 2022 at Xinqiao Hospital in Chongqing, China. We analyzed the association of PLM-based intra-gene HLA disparity (HLA-A/B/C/DRB1/DQB1) in a donor or recipient with overall survival (OS), disease-free survival (DFS), non-relapse mortality (NRM), and relapse. We validated our results by using a publicly available dataset from CIBMTR IB20-02 (PMID: 34774819), which included 985 HM patients who underwent haplo-HSCT between 2013 and 2017.

Using Cox regression to calculate proportional hazard ratios (HR), with p<0.01 as the threshold for statistical significance, our analysis of the Xinqiao dataset showed that higher disparity of donor HLA-B alleles was significantly associated with worse OS (HR=2.0, 95%CI 1.34-3.0, p=0.0007), worse DFS (HR=1.78, 95%CI 1.27-2.49, p=0.0008), higher NRM (HR=1.77, 95%CI 1.1-2.86, p=0.019), and higher relapse risk (HR=1.78, 95%CI 1.11-2.86, p=0.017). The result was further verified by the CIBMTR dataset, where higher disparity of donor HLA-B alleles was associated with worse OS (HR=1.3, 95%CI 1.09-1.57, p=0.0046), worse DFS (HR=1.20, 95%CI 1.02-1.42, p=0.03), higher NRM (HR=1.33, 95%CI 1.0-1.78, p=0.053), higher relapse risk (HR=1.14, 95%CI 0.93-1.40, p=0.2). Multivariate analysis demonstrated that PLM-based disparity of donor HLA-B alleles was an independent prognostic factor for OS in both Xinqiao and CIBMTR dataset. In contrast, we did not find significant results for intra-gene disparity of HLA-A/C/DRB1/DQB1 alleles in either donors or recipients.

In summary, PLM-based disparity of donor HLA-B alleles might be a potential prognostic factor in haplo-HSCT, and might be used as a novel tool assisting donor selection.
Generation of Hypoimmunogenic Hematopoietic Stem Cells and Their Potential Application in HSCT
Authors: Han Yiwen , Hao Sha , Hu Linping , Rao Shuquan , Hou Zhaoyi , Cheng Tao
Published: December 2024

The mismatch of human leukocyte antigens (HLA) significantly limits the availability of suitable donors, primarily due to the risk of immune rejection in allogeneic hematopoietic stem cell transplantation (allo-HSCT). To improve donor-host matching, we performed precise depletion of HLA gene on human hematopoietic stem cells (HSCs) via CRISPR-Cas9 system. Combining with umbilical cord blood, one of the best optional sources for HSCs, we attempt to create off-the-shelf HSCs that are more accessible and available.

To identify the highly efficient guide RNAs (sgRNAs) capable of addressing the genetic diversity of the Chinese population，we firstly designed a library of sgRNAs targeting HLA-A and HLA-B genes. Finally,screened sgRNAs were found up to 60% HLA-A/B protein knock-down efficiency in HEK293T cell line.

To determine the knock-down efficiency of screened sgRNAs in human HSCs, CD34+ HSPCs from umbilical cord blood were obtained and then transduced with RNP by electroporation. The expression of HLA-A/B was detected by flow cytometry after 3 days' ex vivo culture. The knock-down efficiency of HLA-A/B proteins in CD34+ hematopoietic stem and progenitor cells (HSPCs) achieved up to 90%.

To investigate whether the functions of HSPCs with HLA-A/B knocked out(KO-HSPCs) were impaired in vitro, Colony forming cell (CFC) and multi-lineage differentiation assay were performed and the results. confirmed that the abilities of colony forming, self-renewal and lineage differentiation were well retained. To assess their engraftment and reconstruction potential in vivo, we transplanted both KO-HSPCs and non-edited HSPCs into NOG mice via tail vein injection. Transplantation studies in NOG mice showed higher engraftment with KO-HSPCs compared with non-edited ones in peripheral blood, BM and spleen, respectively. To examine the immunogenicity of KO-HSPCs, we performed CFSE-labeled T cell proliferation assay and CD107a assay. These results indicated that KO-HSPCs did not activateNK cells but effectively dampened the response of CD8+ T cells. Finally, the off-target detection assay was performed to investigate the safety by deep sequencing. All potential off-target sites were considered safety.

Our data demonstrate the feasibility of generating hypoimmunogenic HSCs by precisely editing HLA alleles in cord blood stem cells, thereby increasing accessibility and availability for patients in need of HSCT.
Predictive Value of Maximum Tumor Dissemination (Dmax) in Lymphoma Patients Treated with CD19 Specific CAR T-Cell Therapy
Authors: Kunz Wolfgang G , Blumenberg Viktoria , Rejeski Kai , Sheik Gabriel , Brendel Matthias , Von Bergwelt Michael , Subklewe Marion , Winkelmann Michael
Published: December 2024

CD19 specific chimeric antigen receptor T-cell therapy (CART) has emerged as an effective treatment for relapsed or refractory (r/r) lymphoma. Imaging biomarkers are becoming increasingly important in risk assessment. The maximum distance (Dmax) of lymphoma lesions across the body holds potential as prognostic imaging biomarker in lymphoma treated with conventional therapies but has not been studied in context of CART. We evaluated Dmax at baseline imaging as a prognostic tool for assessment of metabolic and overall response, progression-free survival (PFS) and overall survival (OS).

Consecutive r/r lymphoma patients with PET/CT or CT imaging at baseline (BL) and PET/CT at 3 months follow-up (FU) after CAR T-cell transfusion were included. Dmax was measured in cm at BL. Patients were divided into three equal risk groups according to Dmax: low, intermediate, and high. Ann Arbor stages were calculated as baseline for comparison. The sum of product diameters (SPD) in mm2 of up to 6 target lesions was used to represent tumor burden (TB). Overall response according to Lugano criteria and the Deauville score were determined in FU PET/CT imaging.

Of 103 patients with baseline imaging and measurable Dmax, 63 had a PET/CT after 3 months. Median Dmax was 40.0 cm (IQR: 16.4 - 70.3 cm) at BL. TB decreased in the median from BL with 4,095 mm2 to 770 mm2 at FU imaging. Median TB was significantly higher in the intermediate and high-risk group compared to the low-risk group (p=0.005) with 7,222 mm2 (IQR: 3,355 - 11,941 mm2), 4,649 mm2 (IQR: 2,376 - 10,406 mm2) and 1,739 mm2 (IQR: 715 - 7,402 mm2), respectively. Intermediate and high-risk groups showed significantly higher Ann Arbor stages (p<0.001). The survival analysis revealed a significantly (p=0.030) shorter PFS in the high-risk group compared to the other patients (91 vs 364 days), but no relevant differences in OS (p=0.151), which is comparable to the analysis by grouping according to Ann Arbor stage. In addition, no significant differences in Deauville score and ORR were detected.

Patients with high Dmax showed a shorter PFS, but no significant differences in OS. In addition, there was no superiority over the Ann Arbor stages for risk assessment. Nevertheless, Dmax as an interval-scaled parameter represents a useful alternative to the latter. Dmax in the context of CART as an interval-scaled parameter could be used in multiparametric scores to guide and improve patient care.
APRIL CAR-T Cell Therapy for Relapsed/Refractory Multiple Myeloma: A Phase I Clinical Trial
Authors: Li Wenxiao , Hu Yongxian , Zhang Mingming , Lai Xinyi , Zhao Mengyu , Fu Shan , Hong Ruimin , Chang Alex H. , Huang He
Published: December 2024

Background: Chimeric antigen receptor T (CAR-T) cell therapy targeting B cell maturation antigen (BCMA) is an effective treatment for relapsed/refractory multiple myeloma (r/r MM). However, antigen escape-mediated relapse often occurs. CARs simultaneously targeting two antigens may overcome this limitation. Therefore, we used A proliferation inducing ligand (APRIL) to construct a ligand-base CAR that allows for bispecific targeting of BCMA and transmembrane activator and CAML interactor (TACI) as a novel therapy for r/r MM.

Methods: The APRIL CAR-T was evaluated in a Phase 1 clinical trial (NCT04657861) in patients with BCMA/TACI positive relapsed/refractory multiple myeloma. Safety, efficacy, and APRIL CAR-T cellular kinetics were evaluated.

Results: 9 patients received APRIL CAR-T infusions following a conditioning regimen of cyclophosphamide and fludarabine. The treatment was generally well tolerated, with 6 patients experiencing grade 1 cytokine release syndrome (CRS) and 1 patient experiencing grade 2 CRS, no patient had grades 3-4 CRS , no GvHD and immune effector cell-associated neurotoxicity were observed. The overall response rate was 88.8% (8/9), including 2 (22.2%) with complete remission (CR), 4 (44.4%) with very good partial remission (VGPR), and 2 (22.2%) with partial remission (PR).After a median follow-up of 6.63 months (range, 0.50-13.90 months), 1 patients remained in complete remission,and 1 patient died of a cerebrovascular accident. The median overall survival and relapse-free survival for the patients treated with APRIL CAR-T cells was 8.31 months (95% confidence interval [CI], 0.50-13.90 months) and 2.80 months (95% CI, 0.50-6.63 months), respectively.

Conclusions: The APRIL CAR-T cell-based therapy appeared to be a promising therapeutic approach in r/r MM, based on its antitumor effects and manageable side effects, meanwhile additional strategies are required to sustain the therapeutic response.
Successful Cohorting Strategy in CRE-Positive Hospitalized Patients: A Single Center Experience
Authors: Stagno Fabio , Mirabile Giuseppe , Penna Giuseppa , Cancemi Gabriella , Nasso Maria Elisa , Russo Sabina , Allegra Alessandro
Published: December 2024

Introduction: Patients (pts) with Carbapenem-Resistant Enterobacteriaceae (CRE) colonization have at least a two-fold increased risk of infection than non-CRE colonized pts. Further, CRE colonization is also one of the main sources of CRE transmission in hospitals and communities and pts with hematological malignancies are particularly vulnerable to infections with CRE. In this view we started to screen for CRE colonization every pt who required hospitalization to our Hematology Section by executing a cohorting strategy.

Patients and methods: From January 2024 to July 2024 164 pts were screened at hospitalization. They were 77 males and 87 females; median age was 68.8 years. Hematological malignancies were as follow: MM 34, NHL 42, CLL 23, AML 16, ALL 9, MDS 11, CML 4, HD 5, MPN 12, ITP 5, sickle cell anemia 1, anemia from solid cancer 2.

Results: Median duration of hospitalization days for the all the 164 investigated patients was 9 days. Median white blood cell count was 7,3x103/L, median neutrophil count was 4,0x103/L, median lymphocyte count was 2,0x103/L and median neutrophil to lymphocyte (N/L) ratio was 1.7. Thirty-eight out of 164 pts (23.1%) resulted positive for CRE and were all cohorted. Overall, 43/164 (26.2%) received chemotherapy (CHT) regimens while CHT was administered in 10 CRE positive pts. Fever events (FUO) were 33 out of 164 (20.1%), 25/126 (19.8%) occurred in CRE negative pts whereas 8/38 (21.0%) in CRE positive (p=1.0). No statistical differences were observed between CRE positive and negative pts as for WBC counts (p=0.4) neutrophil count (p=0.5) lymphocyte counts(p=0.07) and N/L ratio (p=0.7). Interestingly, because of the cohorting strategy, median duration of hospitalization days for CRE positive and CRE negative pts was the same (9 days).

Conclusions: Pts with hematological malignancies, because of the underlying disease, the necessary treatment and the frequent use of antibacterial drugs are at risk of CRE infections. Our internal policy of both screening and cohortization strategy allowed us to both minimize FUO events and hospitalization days in CRE positive pts. Further, screening for CRE colonization, although cost-effective, revealed to be cost saving,
Validating Laboratory Accuracy of the Next Generation Sequencing (NGS) Technology As a Newborn Screening Tool for Hemoglobinopathies and Thalassemia in Southeast Asian Population
Authors: Suksangpleng Thidarat , Ekwattanakit Supachai , Riolueang Suchada , Viprakasit Vip
Published: December 2024

Background

Thalassemia and hemoglobinopathies are one of the most important health burden to Thailand and several Southeast Asian countries due to a very high frequency of carriers of these globin disorders in the region. Although, Thailand as one of the leading countries on thalassemia research has established a national program for prevent and control of severe thalassemia syndrome at ante-natal screening follows by prenatal diagnosis in pregnant women. However, such program has several limitations due to a late antenatal care and a lack of public awareness. Early screening at neonatal levels together with data incorporated within our Thailand's national health care database (eGovernment) can improve the national thalassemia control program in a long-term run.

Aims

To evaluate the efficacy and accuracy of using next generation sequencing (NGS) technology as a fast, high through-put and scalable method for thalassemia screening in Southeast Asian setting.

Methods

Newborn peripheral blood (heel prick) were collected for hematologic testing including complete blood count and hemoglobin (Hb) typing. Also, genomic DNA (gDNA) was extracted and then analyzed using conventional multiplex PCR methods including α-GAP multiplex PCR, α-ARMS multiplex PCR and β-ARMS multiplex PCR, which covered > 95% of common mutations of globin genes found in the Thai population. All samples were then analyzed for sequences of α-globin (HBA1 and HBA2) and β-globin (HBB) genes using NGS technology and the combinatorial probe-anchor synthesis sequencing method (BGI VISTATM Thalassemia-Seq panel) and detection by software provided by BGI Biotechnology, Wuhan.

Results

Based on the comparative analysis of α-globin and β-globin gene mutations. The 352 neonatal gDNA samples by multiplex PCR methods and combinatorial probe-anchor synthesis sequencing methods, 335 samples (95%) showed identical results on globin gene mutations. However, the NGS approach has a superior on identification several rare but possible clinical significance variants such as Hb Westmead (2.6%), α-triplication (αααanti3.7, 0.3%) and αααanti3.7/–SEA (0.3%) that were missed using the conventional methods.

Conclusion

Application of NGS technology to detect globin gene mutations that causes thalassemia and hemoglobinopathies showed a promising accurate technology for the future newborn screening program in Thailand and other Southeast Asian countries.
The Role of Next-Generation Sequencing in Predicting Early Relapse for Newly Diagnosed Multiple Myeloma Patients Treated with VRD Regimen
Authors: Cheng Lili , Zhang Fujing , Li Ziping , Zhuang Junling , Cai Hao , Li Hui
Published: December 2024

Background：Bortezomib, lenalidomide, and dexamethasone (VRD) is a standard therapy for newly diagnosed multiple myeloma (NDMM), which achieves over 90% response rate. However, some patients still relapsed in early stage. This study aims to demonstrate the predictive role of NGS in NDMM patients treated by front VRD regimen.Methods: Clinical characteristics of 106 NDMM patients receiving front-line VRD regimen were retrospectively analyzed from September 2019 to June 2023 at Peking Union Medical College Hospital. At baseline, interphase fluorescence in situ hybridization (FISH) was performed in CD138 sorted plasma cells. High-risk cytogenetic abnormalities (HRCA) were defined as 1q21+, del17p, t(4;14), t(14;16). A Next-generation sequencing (NGS) panel including 290 tumor-related genes was performed in plasma cells. Early relapse was defined as relapse within 12 months.Results：The median follow-up time of 106 NDMM patients was 32.6 months. 16 patients developed ER. The most frequently mutated gene in the whole cohort was KRAS (27.4%), followed by NRAS (13.2%), TP53 (7.5%), IGLL (5.7%) and BRAF (3.8%). The ER group, mutated genes including KRAS(4/29,13.8%)，NRAS(1/14,7 %), IGLL(2/6,33.3%) and BRAF(0/4,0%) were not significantly different from those in other patients, expect TP53 mutation(P=0.017). PFS in patients with TP53 or IGLL5 mutations and those with HRCA was worse. Whereas PFS in patients with KRAS, NRAS or BRAF mutations and those without HRCA was even longer. Univariate analysis indicated that the HRCAs and TP53 mutation were negatively associated with PFS and OS, however, KRAS mutation was a protective factor. Multivariate logistic regression analysis suggested that HRCA, KRAS and TP53 mutations were the independent influencing factors of PFS. Patients were further stratified into four groups according to these three conditions: Group I (only KRAS mutation), II (others), III (only TP53 mutation or only HRCA), and IV (TP53 mutation and HRCA). There were significant differences in PFS among the four groups. PFS in Group I was the longest, and Group IV represented the worst with majority relapsing within 12 months(4/5,80%).Conclusions: Although RAS mutation is considered as high-risk factors associated with poor prognosis, our findings suggest that VRD regimen may improve the response and survival in NDMM patients by overcoming KRAS mutation. TP53 mutation and HRCA are still unfavorable predictors. Therefore, NGS data could be a complementary method for risk stratification in MM.
Mortality Trends in Non-Hodgkin Lymphoma Patients with High Body Mass Index: A Comparative Study of the USA and Europe from the Global Burden of Disease Registry (1991-2021)
Authors: Bhanushali Charmi , Babu Kalaivani , Rajarajan Srinishant , Jayakumar Jayalekshmi , Kasire Sripada Preetham , Roy Arya Mariam
Published: December 2024

Background:

Several case-control and prospective cohort studies have shown that obesity [body mass index (BMI), ≥30 kg/m²] is associated with elevated risks of non-Hodgkin lymphoma (NHL). This study aims to examine mortality trends and disability-adjusted life years (DALY) associated with high BMI in NHL; globally, in Western Europe, and within the United States (US) over the period of 1991 to 2021.

Methods:

Data from the Global Burden of Disease database, based on the International Classification of Diseases (ICD) version 10, were utilized. ICD code C85.9. was used to extract data for NHL patients. We extracted age-standardized mortality rates (ASMRs) and DALY per 100,000 population (with 95% confidence intervals) separately for both sexes, considering high BMI as a risk factor for NHL in the US, Western Europe, and globally from 1991 to 2021. Trends were analyzed using Joinpoint regression.

Results:

The US has a significantly higher ASMR compared to Western Europe (0.36, 95% CI- 0.12- 0.62 vs. 0.22, 95% CI 0.07- 0.339) and globally (0.36, 95% CI- 0.12- 0.62 vs. 0.15, 95% CI- 0.05- 0.26) for NHL patients with high BMI. Globally, ASMR showed a modest increase of 7.14% (0.14 to 0.15) from 1991 to 2021. In the US, ASMR decreased by 16.28% (0.43 to 0.36), while there was no significant change in Europe. The US also has a significantly higher DALY compared to Europe (8.78, 95% CI- 2.87- 14.92 vs. 5.47, 95% CI- 1.82- 9.53 in 2021) and globally (8.78, 95% CI- 2.87- 14.92 vs. 4, 95% CI- 1.33- 6.90 in 2021). From 1991 to 2021, DALYs witnessed a 13.31% increase globally (3.53 to 4.00), with the US showing a decrease of 26.59% (11.96 to 8.78) and Europe showing a decrease of 7.29% (5.90 to 5.47).

Sex-specific data indicated that globally, male ASMR due to high BMI-related NHL increased by 20% (0.15 to 0.18) and female ASMR by 10.15% (0.12 to 0.13). In the United States, male ASMR decreased by 11.54% (0.52 to 0.46) while female ASMR decreased by 14.69% (0.36 to 0.28). Western Europe saw no significant change in ASMR for males and females over the years. Globally, DALYs increased by 54.50% for males and 55.89% for females over the study period. In the US, DALYs increased by 5.68% in males and decreased by 3.18% in females.

Conclusion:

This study highlights significant regional differences in NHL mortality and DALY burden related to high BMI. The US shows a decreasing trend in ASMR and DALY despite global increases. However, it is to be noted that the US still has higher ASMR and DALY compared to Europe and global average. The significant disparity in ASMR and DALY between the US, Europe, and globally underscores the need for tailored public health strategies to address obesity-related NHL risks.