Bone Marrow Samples Research Articles

Identification of Therapy-Induced Clonal Evolution and Resistance Pathways in Minimal Residual Clones in Multiple Myeloma through Single-Cell Sequencing.

In multiple myeloma (MM), therapy-induced clonal evolution is associated with treatment resistance and is one of the most important hindrances toward a cure for MM. To further understand the molecular mechanisms controlling the clonal evolution of MM, we applied single-cell RNA sequencing (scRNA-seq) to paired diagnostic and posttreatment bone marrow (BM) samples. scRNA-seq was performed on 38 BM samples from patients with monoclonal gammopathy of undetermined significance (n = 1), MM patients at diagnosis (n = 19), MM posttreatment (n = 17), and one healthy donor (HD). The single-cell transcriptome data of malignant plasma cells (PC) and the surrounding immune microenvironment were analyzed. Profiling by scRNA-seq data revealed three primary trajectories of transcriptional evolution after treatment: clonal elimination in patients with undetectable minimal residual disease (MRD-) and clonal stabilization and clonal selection in detectable MRD (MRD+) patients. We noted a metabolic shift toward fatty acid oxidation in cycling-resistant PCs, whereas selective PCs favored the NF-κB pathway. Intriguingly, when comparing the genetic and transcriptional dynamics, we found a significant correlation between genetic and nongenetic factors in driving the clonal evolution. Furthermore, we identified variations in cellular interactions between malignant PCs and the tumor microenvironment. Selective PCs showed the most robust cellular interactions with the tumor microenvironment. These data suggest that MM cells could rapidly adapt to induction treatment through transcriptional adaptation, metabolic adaptation, and specialized immune evasion. Targeting therapy-induced resistance mechanisms may help to avert refractory disease in MM.

Similarities and differences of bone marrow and peripheral blood samples from acute myeloid leukemia patients in terms of cellular heterogeneity and ex-vivo drug sensitivity.

Bone marrow (BM) evaluation is the de facto standard for diagnosis, molecular analysis, risk stratification, and therapy response assessment in acute myeloid leukemia (AML), but in patients with a high number of circulating blast cells, the peripheral blood (PB) sample could provide similar information as BM. However, there is no large-scale molecular study comparing the two specimens in terms of their gene expression profiles, cellular heterogeneities, and ex-vivo drug sensitivity. We used (i) the BEAT-AML cohort each with detailed molecular data; (ii) cell-type deconvolution to estimate leukemic and immune cell proportions between specimen types; (iii) differential expression (DE) and drug-cell type association analysis; and (iv) logistic regression models to assess the association between induction therapy response, cell-type composition and first-line drug treatment. Results: We identified 207 patients having BM and 116 patients having PB samples. There was a total of 1271 DE genes (false discovery rate<0.05) between BM and PB; the top enriched pathways in terms of DE genes belong to the immune system pathways. Aggregated ex-vivo drug response profiles from the two specimens were largely similar, as were the cellular components, except for the GMP-like cell type (17% in BM vs. 5% in PB, p-value=2×10-7). Among the specimen-specific results, the GMP-like subtype was associated with multiple drug resistance in BM and the ProMono-like subtype in PB. Several cell types were associated with the response to induction therapy, but the impact of specimen type on the interaction of cell type and cytarabine-associated induction therapy was not statistically significant for most cell types. Conclusions: Even though there are molecular and cellular differences between BM and PB samples, they show many similarities in ex-vivo drug response profiles, indicating the clinical utility of the substantially less-invasive PB samples.

Monoclonal gammopathy of clinical signifi cance with osteosclerotic lesions - a case report and a literature review.

Multiple myeloma is a common plasma cell neoplasia usually accompanied by the formation of osteolytic foci, whereas osteosclerotic myeloma is a very rare form of plasma cell dyscrasia. When osteosclerotic myeloma is detected, osteosclerotic foci are usually part of the POEMS syndrome. Osteosclerotic myeloma without other manifestations of the POEMS syndrome is an unusual finding. In a 46-year-old woman, osteosclerotic changes of the temporoparietal region caused soft tissue induration over this lesion, which initiated further investigation. Imaging studies subsequently showed multiple osteosclerotic foci in the skull. Examination of blood proteins revealed 8 g/L of IgG-lambda monoclonal immunoglobulin, subclass IgG1. In search of the cause of the osteosclerotic changes, FDG-PET/CT was performed, which revealed no FDG accumulation, i.e., no other tumor (breast or stomach cancer). Low-dose CT showed irregular bone structure, but not significant osteolytic or osteosclerotic foci. To map the extent of osteosclerotic changes, NaF-PET/CT imagination followed, which revealed multiple spots with high fluoride accumulation. A parietal bone biopsy showed osteosclerosis with minor clonal plasma cell infiltration. Trepanobioptic bone marrow sampling revealed an infiltration of bone marrow with atypical plasma cells in 8%. Flow-cytometric examination of bone marrow showed 0,37% of plasma cells, however predominantly (91%) clonal with lambda expression. MRI of the brain identified asymptomatic meningeal thickening. There was no evidence of POEMS syndrome in the patient; thus, we concluded the diagnosis as monoclonal gammopathy of clinical significance with osteosclerosis which was previously termed osteosclerotic multiple myeloma. Monoclonal gammopathy of clinical significance (MGCS) with osteosclerotic skeletal changes, documented on CT and multiple foci with intensive osteoneogenesis, documented on NaF-PET/CT without evidence of POEMS syndrome, is an extremely rare form of plasma cell dyscrasia. This publication documents the unique clinical manifestations of IgG-lambda type plasma cell proliferation without signs of POEMS syndrome and the role of NaF-PET/CT imaging. Classification of this disease as MGSC with osteosclerotic manifestations is more consistent with the indolent nature of the disease with a significantly better prognosis, compared with multiple myeloma.

Chinese expert consensus on minimal residual disease detection in multiple myeloma based on bone marrow samples (2024)

Multiple myeloma (MM) is the second most common hematologic malignant tumor. Standard holistic treatment model and new drug-based regimens have greatly improved the survival of patients with MM; however, minimal residual disease (MRD) causes relapse in most patients. Therefore, combining MRD testing on the basis of traditional serological efficacy evaluation is necessary to achieve a more accurate assessment of the patient's disease status. At present, next-generation flow cytometry (NGF) and next-generation sequencing (NGS) are the mainstream technologies for detecting MRD based on bone marrow samples. To standardize and normalize MRD detection, the expert group discussed and formulated Chinese expert consensus on the application of NGF and NGS technology for bone marrow MRD detection in patients with MM.

Detection of minimal residual disease in acute myeloid leukemia: evaluating utility and challenges

This study discusses the importance of minimal residual disease (MRD) detection in acute myeloid leukemia (AML) patients using liquid biopsy and next-generation sequencing (NGS). AML prognosis is based on various factors, including genetic alterations. NGS has revealed the molecular complexity of AML and helped refine risk stratification and personalized therapies. The long-term survival rates for AML patients are low, and MRD assessment is crucial in predicting prognosis. Currently, the most common methods for MRD detection are flow cytometry and quantitative PCR, but NGS is being incorporated into clinical practice due to its ability to detect genomic aberrations in the majority of AML patients. Typically, bone marrow samples are used for MRD assessment, but using peripheral blood samples or liquid biopsies would be less invasive. Leukemia originates in the bone marrow, along with the cfDNA obtained from peripheral blood. This study aimed to assess the utility of cell-free DNA (cfDNA) from peripheral blood samples for MRD detection in AML patients. A cohort of 20 AML patients was analyzed using NGS, and a correlation between MRD assessment by cfDNA and circulating tumor cells (CTCs) in paired samples was observed. Furthermore, a higher tumor signal was detected in cfDNA compared to CTCs, indicating greater sensitivity. Challenges for the application of liquid biopsy in MRD assessment were discussed, including the selection of appropriate markers and the sensitivity of certain markers. This study emphasizes the potential of liquid biopsy using cfDNA for MRD detection in AML patients and highlights the need for further research in this area.

Imaging Flow Cytometry and Convolutional Neural Network-Based Classification Enable Discrimination of Hematopoietic and Leukemic Stem Cells in Acute Myeloid Leukemia.

Acute myeloid leukemia (AML) is a heterogenous blood cancer with a dismal prognosis. It emanates from leukemic stem cells (LSCs) arising from the genetic transformation of hematopoietic stem cells (HSCs). LSCs hold prognostic value, but their molecular and immunophenotypic heterogeneity poses challenges: there is no single marker for identifying all LSCs across AML samples. We hypothesized that imaging flow cytometry (IFC) paired with artificial intelligence-driven image analysis could visually distinguish LSCs from HSCs based solely on morphology. Initially, a seven-color IFC panel was employed to immunophenotypically identify LSCs and HSCs in bone marrow samples from five AML patients and ten healthy donors, respectively. Next, we developed convolutional neural network (CNN) models for HSC-LSC discrimination using brightfield (BF), side scatter (SSC), and DNA images. Classification using only BF images achieved 86.96% accuracy, indicating significant morphological differences. Accuracy increased to 93.42% when combining BF with DNA images, highlighting differences in nuclear morphology, although DNA images alone were inadequate for accurate HSC-LSC discrimination. Model development using SSC images revealed minor granularity differences. Performance metrics varied substantially between AML patients, indicating considerable morphologic variations among LSCs. Overall, we demonstrate proof-of-concept results for accurate CNN-based HSC-LSC differentiation, instigating the development of a novel technique within AML monitoring.

Hypermethylation of GSTM5 and its effect on oxidation in myelodysplastic syndrome

AbstractBackgroundHypermethylation of glutathione‐S‐transferase 5 (GSTM5) and its effect on oxidation in the pathogenesis of myelodysplastic syndrome (MDS) were investigated.MethodsGSTM5 methylation was detected in bone marrow (BM) samples from MDS patients, acute myeloid leukemia (AML) patients, and control individuals using methylation‐specific PCR and MassARRAY analysis. Bisulfite sequencing PCR was performed to verify methylation levels, while mRNA levels were determined using reverse transcription polymerase chain reaction. Correlations between GSTM5 methylation and clinical parameters were analyzed. The MDS cell line, SKM‐1, was treated with decitabine, buthionine sulfoximine, or overexpression of GSTM5, and the glutathione level and cell viability were detected.ResultsThe MassARRAY analysis revealed significant differences in GSTM5 methylation levels between the MDS and control groups. GSTM5 methylation levels were significantly increased in the high‐risk subgroup and showed a significant association with MDS progression to AML (hazard ratio = 3.6). Levels of GSTM5 mRNA were significantly decreased in the MDS group, exhibiting a negative correlation with the GSTM5 gene methylation level. Normal BM HS‐5 cells exhibited significantly lower levels of GSTM5 methylation than SKM‐1 cells. Overexpression of GSTM5 in SKM‐1 cells or treatment with buthionine sulfoximine or decitabine resulted in inhibition of proliferation and significantly decreased glutathione levels.ConclusionsGSTM5 plays an anti‐oxidative role in MDS and the tumor suppressor effect of GSTM5 may be mediated by reducing glutathione levels. GSTM5 hypermethylation and low levels of GSTM5 expression may be prognostic markers for MDS.

Effects of fixation and demineralization on histomorphology and DNA amplification of canine bone marrow.

Fixation and demineralization protocols for bone marrow (BM) across diagnostic laboratories are not standardized. How different protocols affect histomorphology and DNA amplification is incompletely understood. In this study, 2 fixatives and 3 demineralization methods were tested on canine BM samples. Twenty replicate sternal samples obtained within 24 hours of death were fixed overnight in either acetic acid-zinc-formalin (AZF) or 10% neutral-buffered formalin (NBF) and demineralized with formic acid for 12 hours. Another 53 samples were fixed in AZF and demineralized with hydrochloric acid for 1-hour, formic acid for 12 hours, or ethylenediamine tetraacetic acid (EDTA) for 24 hours. Histologic sections were scored by 4 raters as of insufficient, marginal, good, or excellent quality. In addition, DNA samples extracted from sections treated with the different fixation and demineralization methods were amplified with 3 sets of primers to conserved regions of T cell receptor gamma and immunoglobulin heavy chain genes. Amplification efficiency was graded based on review of capillary electrophoretograms. There was no significant difference in the histomorphology scores of sections fixed in AZF or NBF. However, EDTA-based demineralization yielded higher histomorphology scores than demineralization with hydrochloric or formic acid, whereas formic acid resulted in higher scores than hydrochloric acid. Demineralization with EDTA yielded DNA amplification in 29 of 36 (81%) samples, whereas demineralization with either acid yielded amplification in only 2 of 72 (3%) samples. Although slightly more time-consuming and labor-intensive, tissue demineralization with EDTA results in superior morphology and is critical for polymerase chain reaction (PCR) amplification with the DNA extraction method described in this article.

Hallmarks of tumor-experienced T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy.

Dysregulation of the bone marrow (BM) niche in multiple myeloma (MM) alters the composition and state of resident immune cells, potentially impeding anti-tumor immunity. One common mechanism of immune inhibition in solid tumors is the induction of exhaustion in tumor-specific T cells. However, the extent of T cell tumor recognition and exhaustion is not well-characterized in MM. As the specific mechanisms of immune evasion are critical for devising effective therapeutic strategies, we deeply profiled the CD8+ T cell compartment of newly-diagnosed MM (NDMM) patients for evidence of tumor reactivity and T cell exhaustion. We applied single-cell multi-omic sequencing and antigen-specific mass cytometry to longitudinal BM and peripheral blood (PB) samples taken from timepoints spanning from diagnosis through induction therapy, autologous stem cell transplant (ASCT), and maintenance therapy. We identified an exhausted-like population that lacked several canonical exhaustion markers, was not significantly enriched in NDMM patients, and consisted of small, nonpersistent clones. We also observed an activated population with increased frequency in the PB of NDMM patients exhibiting phenotypic and clonal features consistent with homeostatic, antigen-nonspecific activation. However, there was no evidence of "tumor-experienced" T cells displaying hallmarks of terminal exhaustion and/or tumor-specific activation/expansion in NDMM patients at any timepoint.

Mutation patterns and prognostic implications in acute myeloid leukemia with chromosomal 7 deletions.

6547 Background: Chromosomal 7 deletions (del7/7q) are the most common adverse cytogenetic event in acute myeloid leukemia and are associated with high rate of relapse. We analyzed gene mutation profiles in del7/7q AML patients who relapsed after initial remission to identify molecular patterns associated with clinical outcomes. Methods: Out of 351 newly diagnosed AML patients with del7/7q, 115 (32%) achieved complete remission after first-line treatment between 2012-2023. Of the 115 patients, 77 (67%) patients relapsed during the study follow-up. Kaplan-Meier and Cox regression were used to analyze survival outcomes. Next-generation sequencing was performed on a targeted panel of 81 genes for 59 patients who relapsed on bone marrow samples at diagnosis and relapse for paired analysis. Results: The median age of the 115 patients at diagnosis was 74 (41-93). Thirty-four patients (30%) received intensive treatment. With 30.8-month median follow-up, the median overall survival (OS) was 10.4 months, with improved survival in patients without TP53 mutation (13.04 vs. 8.6 months, p=0.005) or complex karyotype (12.4 vs. 8.6 months, p=0.03). The median duration of response for the 77 patients who relapsed was 5 months (2-7). Allo-HSCT significantly improved median OS (not reached vs. 8.5 months, P=6e-06), and was identified as the key variable impacting survival in multivariate analysis. TP53 was the most commonly mutated gene at diagnosis (67%) and relapse (71%). Mutations in CBLC and KDM6A were cleared after induction therapy, while BCOR and BCORL1 were commonly acquired at relapse (Table). At diagnosis, a lower co-mutation burden was observed in TP53 mutant patients as compared with wild type (average 1.84 vs. 3.65 respectively, p=0.0001). Patients with mutated TP53 and coexisting mutations in GATA2, NF1, BCORL1, or RUNX1 at diagnosis had shorter relapse free survival (RFS, 2 vs. 5 months, p=0.01) and OS (7.2 vs. 10.4 months, p=0.01) compared to patients with solely mutated TP53 (HR 2.2; 95% CI 1.2-4; P = 0.004). Allo-HSCT significantly improved the OS in patients with mutated TP53 (13 vs. 8 months, p=0.01). Conclusions: Mutated TP53 clones persist from diagnosis to relapse in patients with del7/7q AML. In patients with mutated TP53, co-occurring mutations in GATA2, NF1, BCORL1or RUNX1 at diagnosis were linked to a shorter RFS and indicate a particularly high-risk subgroup that require proceeding to allo-HSCT in CR1 without delay. [Table: see text]

Comparison of immunoglobulin high-throughput sequencing MRD in bone marrow and peripheral blood in pediatric B-ALL: A report from the Children's Oncology Group AALL1731.

10014 Background: Minimal (measurable) residual disease (MRD) at end of induction (EOI) therapy is a strong predictor of outcome in pediatric B-ALL. Currently, EOI MRD is assessed in bone marrow (BM). We hypothesized that the highly sensitive assay, high-throughput sequencing (HTS) of immunoglobulin loci, can effectively monitor MRD in peripheral blood (PB) and may provide a less invasive way to track therapy response. Methods: We conducted HTS MRD on paired EOI BM and PB samples from 808 NCI standard risk (SR) pediatric B-ALL patients enrolled on Children’s Oncology Group study AALL1731 (NCT03914625). We determined the correlation between BM and PB HTS MRD via Spearman’s rank correlations. We calculated the BM/PB MRD ratio and compared these by subgroup using Kruskal-Wallis tests. We defined subgroups by cytogenetics (cyto) ( ETV6::RUNX1, double trisomies of chromosome 4 and 10 (DT), Unfavorable (hypodiploidy, iAMP21, or KMT2A-rearranged), or Neutral (lacking ETV6::RUNX1, DT, or unfavorable)), and risk group (SR-average (AVG) and SR-High). Flow cytometry-defined EOI BM MRD was &lt; 0.01% for all SR-AVG patients (N = 623) and ≥0.01% for selected SR-High patients (N = 185). Results: There was strong correlation between PB and BM HTS MRD with an overall correlation coefficient of 0.75 (P &lt; 0.001). Correlation was similar by cytogenetics: ETV6::RUNX1, 0.69 (N = 63; P &lt; 0.001), DT, 0.75 (N = 147; P &lt; 0.001), Neutral, 0.74 (N = 580; P &lt; 0.001), and Unfavorable, 0.66(N = 18; P = 0.003). For risk groups, correlation for SR-AVG was 0.67 (p &lt; 0.001) and SR-High, 0.64 (p &lt; 0.001). Of the 591 SR-AVG patients with detectable BM HTS MRD, PB HTS MRD was detectable in 474 (80.2%), undetectable in 94 (15.9%) and indeterminate (no leukemic cell detected and &lt; 500,000 total cells in sample) in 23 (3.9%). Among 182 SR-High patients with detectable BM HTS MRD, 175 (96.2%) had detectable PB HTS MRD. Disease burden was higher in the BM than PB with a significantly higher BM/PB ratio in SR-High compared to SR-AVG patients (median 16.5 vs 2.6, P &lt; 0.001). The median BM/PB ratio also varied by cytogenetics with those with Unfavorable cyto having the highest ratio (15.3 vs 6.3 in DT, 3.8 in ETV6::RUNX1, 3.1 in Neutral; P = 0.013). Conclusions: This is the largest analysis of paired B-ALL BM/PB HTS MRD to date. We show strong correlation between PB and BM across risk and cytogenetic groups. The ratio of BM/PB MRD varied and was highest among patients with Unfavorable cyto suggesting BM tropism. Importantly, PB MRD was detectable in nearly all patients with flow EOI BM MRD ≥0.01%, a threshold warranting therapy intensification. However, most patients with EOI BM flow MRD &lt; 0.01% also had detectable PB HTS MRD. Thus, PB HTS MRD may provide a useful adjunct for screening and clinical management of B-ALL patients. Defining a PB HTS MRD threshold useful for risk stratification will require correlation with outcome.

Novel method for the detection of circulating tumor plasma cells in multiple myeloma.

e19520 Background: Multiple Myeloma (MM) is characterized by the proliferation of abnormal plasma cells within the bone marrow. A bone marrow examination is essential for the diagnosis of multiple myeloma. This is a test that causes great pain to patients because it requires collecting and analyzing the bone marrow fluid inside the bone. In addition, there is a disadvantage that it cannot be carried out frequently due to cost issues. Therefore, the development of new diagnostic methods is absolutely necessary. The aim of this study is to access the potential of circulating tumor plasma cells (CTPC) for the diagnosis of MM using CytoGen's Smart Biopsy platform. Methods: Spiking tests using MM cell line (RPMI8226) was conducted with the purpose of making an environment similar to the MM patient's blood. RPMI8226 cells (200 cells) stained with CellTracker were spiked into human blood sample (5mL, healthy donor). Then, spiked cells were isolated by CytoGen’s Smart Biopsy isolator, subsequently recovery rate was accessed by counting of isolated RPMI8226 or immunofluorescence (IF) staining with multiple myeloma-specific marker, CD138. Then, clinical evaluation was performed with bone marrow (3mL) and peripheral blood (5mL) samples of MM patients (n=20). The presence of CTPC in patient samples was tested by IF staining with anti-CD138 antibody. Results: In in vitro experiments to test recovery rate of CTPC using CytoGen's Smart Biopsy isolator, MM cell line’s recovery rate was validated to over 80%. CD138 expression was clearly detected by IF staining of spiking samples of multiple myeloma cell line and was not detected at all in the negative controls. In clinical evaluation study, CTPC was successfully observed after the isolation from bone marrow and peripheral blood using CytoGen's Smart Biopsy isolator by IF staining with CD138. Conclusions: This study shows a novel method for the detection of MM with liquid biopsy. CTPC from liquid biopsy of MM could be isolated using CytoGen's Smart Biopsy isolator with high recovery rate and can clearly be detected with specific marker of MM, CD138 by IF staining. These results suggested that CytoGen's Smart Biopsy platform might be an effective diagnostic tool for the detection of MM. Expanded clinical study will be performed with more MM samples for clinical validation. Clinical trial information: 2013-09-009 .

Multi-drug algorithm to accurately predict best first-line treatments in newly-diagnosed acute myeloid leukemia (AML).

6525 Background: AML is a heterogeneous hematological malignancy with poor prognosis. Several treatments are approved for AML, but clinical trials have shown that current stratification approaches to determine patients’ eligibility produce false positives (treated patients that fail to respond) and negatives (patients not treated but could have responded). Venetoclax + azacitidine (VA) treatment is currently reserved for unfit patients, with younger patients stratified based on their FLT3status, and treated with either intensive chemotherapy (IC), or IC plus midostaurin (MIC). Here, we used phosphoproteomics to build a signature and algorithm that accurately predict which of these approved therapies may be more efficacious for a given patient. Methods: Routine bone marrow and peripheral blood diagnosis samples (s, n=182) were collected across the UK, Austria, Canada and the USA from 138 patients (p) subsequently treated with MIC (n=44/64 p/s), VA (n=40/48 p/s) or IC (n=54/70 p/s). Patients were grouped into Good Responders (GR) and Poor Responders (PR) based on treatment response. For VA, patients that achieved complete remission (CR) were considered GR, while refractory patients were considered PR. For MIC and IC, we considered patients that achieved CR without relapse within 6 months as GR, and those refractory or relapsed within 6 months as PR. Samples were processed for mass spectrometry-based phosphoproteomics. Phosphopeptide abundance data, generated with in-house PiQuant software, was used to identify phosphopeptides that distinguish GR and PR groups in each cohort. Statistical models based on these features were assessed via cross-validation. Results: We compared phosphoproteomes of 182 diagnosis samples from 138 AML patients, from three treatment cohorts (treated with IC, MIC or VA), with each cohort stratified by patients’ response to their respective treatment. Enrichment analysis in each cohort identified several phosphopeptides specific to one of the responder groups, mapping both to proteins with known roles in AML biology (e.g. DNMT3A or RUNX1) and proteins not yet implicated. Next, using machine learning, we identified phosphopeptides that could distinguish between PR and GR, and trained drug response prediction models based on the abundance of these phosphopeptides. In cross-validation, each model stratified patients with log rank p&lt;0.001, HR&lt;0.1 and more than 90% accuracy, greatly outperforming all currently-used stratification methods for first-line AML therapies. Conclusions: We built a suite of predictive models that accurately predict patient response to first-line AML treatment using phosphoproteomic data from routine diagnosis samples. Following validation in independent patient cohorts, this tool will be developed into a single test that predicts treatment response for AML patients, thus addressing an unmet clinical need in this disease.

Molecular characterization and biomarker identification in pediatric B-cell acute lymphoblastic leukemia.

6524 Background: B-cell acute lymphoblastic leukemia (B-ALL) is the most prevalent hematologic malignancy in children and a leading cause of mortality. Despite high cure rates, the management of B-ALL remains challenging due to its high heterogeneity and propensity for relapse. This study aimed to delineate molecular features of pediatric B-ALL and explore the clinical utility of circulating tumor DNA (ctDNA) as a biomarker in B-ALL. Methods: The study analyzed 146 primary pediatric B-ALL patients who were diagnosed from August 2020 to April 2023 and received systemic chemotherapy in Wuhan Children's Hospital. Baseline bone marrow (BM) and plasma samples were collected for next-generation sequencing (NGS) to profile the mutational landscape. BM samples collected on day 19 of the treatment were utilized for minimal residual disease (MRD) testing to assess treatment efficacy. Transcriptomic profiling of baseline BM samples was performed via bulk RNA sequencing. Fisher's exact test and the Wilcoxon rank sum test were utilized to compare categorical and continuous variables between groups, respectively. A two‐tailed P-value&lt;0.05 was considered statistically significant unless indicated otherwise. Results: Transcriptomic analysis revealed that 86.3% of patients (126 out of 146) could be categorized into 13 distinct molecular subtypes, with hyperdiploidy emerging as the predominant subtype. Baseline BM NGS identified gene fusions in 61% of patients, including 37 novel fusions previously unreported in B-ALL. Specifically, the KMT2A-TRIM29 novel fusion was detected and validated in a male child diagnosed with the KMT2A-rearranged subtype. Despite initially responding well to therapy, the patient experienced disease progression after a year, indicating a poor prognosis. We also found that elevated mutant counts and maximum-variant-allele-frequency (maxVAF) in baseline BM were associated with significantly poorer response to chemotherapy ( P=0.0012 and 0.028, respectively). Additionally, MRD-negative patients exhibited upregulated expression of immune-related pathways ( P&lt;0.01) and increased CD8+ T cell infiltration ( P=0.047), indicating a more active immune microenvironment in better responding tumors. Baseline plasma ctDNA, which exhibited high mutational concordance with paired baseline BM samples, also demonstrated significant associations with chemotherapy efficacy, highlighting its potential as a non-invasive tool for disease monitoring and treatment outcome prediction. Conclusions: This study elucidated novel gene fusions and potential biomarkers for treatment response in pediatric B-ALL. Importantly, both baseline plasma ctDNA and BM samples offer promising prognostic insights into chemotherapy responses, paving the way for non-invasive monitoring strategies in the management of pediatric B-ALL.

Meta-analysis of mutational site-specificity and concordance/discordance characteristics of myeloid sarcoma.

6583 Background: Myeloid sarcoma (MS) is an atypical, extramedullary manifestation of acute myeloid leukemia. Next-generation sequencing (NGS) studies have explored mutational profiles of MS tumor sites and bone marrow (BM) samples. However, site-specific molecular patterns and mutational concordance/discordance between MS sites and BM remain unclear. Methods: Relevant studies about MS retrieved from a Pubmed search (1999-2023) with information about MS site involvement and NGS data were included. With R software, a meta-analysis (MA) of descriptive data, MS tumor site, mutations, and mutational concordance/discordance was performed to obtain pooled prevalence estimates using the Freeman-Tukey double arcsine transformation, inverse variance, and random effects model. MA of median age was pooled using the methods of McGrath et al. (2023). Meta-regression (MR) was performed with mixed-effects model. Chi-square test was used for statistical analysis of categorical variables. Results: 87 patients with MS from 10 studies were identified. Median age was 53 years (95% confidence interval [CI]: 48-56), and MS was more common in males (pooled estimate of 67%, 95% CI: 54.8-78.5). Skin was the most common site involved in MS with random effects pooled estimate of prevalence of 39.4% (95% CI: 20.8-59.3), followed by lymph node (10.1%, 95% CI: 1.8-21.8), bone (5%, 95% CI: 0.2-13.3), and soft tissue (2.4%, 95% CI: 0-9.5). Pooled estimates of most common mutated genes were NPM1 (20.3%, 95% CI: 6.2-38), FLT3 (18.3%, 95% CI: 5.5-34.6), TP53 (8.4%, 95% CI: 1.8-17.7), NRAS(6.6%, 95% CI: 0.9-15.4), and IDH2 (4.3% 95% CI: 0-13.4). NPM1 (13/34), FLT3 (7/34), and IDH2 (6/28) were enriched in cutaneous MS. KIT was exclusively enriched in non-cutaneous MS (8/53) compared to cutaneous MS (0/34) (p = 0.017). Although the prevalence of small bowel MS was low (n = 3), FLT3 was mutated in all cases (p &lt; 0.01). Comparing MS tumor site to BM, pooled prevalence of mutation concordance was similar to discordance (49.8% [95% CI: 34.4-65.1] and 50.2% [95% CI: 34.9-65.6], respectively). Most common concordant mutations were FLT3 (5/28) and NRAS (5/28). NPM1 and FLT3 were most common discordant mutations and enriched in MS tumor sites (p &lt; 0.01 and p &lt; 0.05, respectively). NPM1 was a discordant mutation in MS tumor site only. Univariate MR of cutaneous MS found no significant influence from male sex and mutational concordance/discordance. Multivariate MR showed significant interaction with males and mutational discordance toward cutaneous MS (p &lt; 0.01). Conclusions: Our meta-analysis highlights potential site-specific and mutational disparities in MS. Knowledge about such differences may allow the use of targeted therapies against different molecular aberrations, emphasizing the need to sequence both BM and MS sites. Findings suggesting interaction of male sex and mutational discordance in cutaneous MS needs further validation.

Expression of alternatively spliced BCMA RNA with skipping of transmembrane domain.

7514 Background: The TNFRSF17 gene, which encodes for the B cell maturation antigen (BCMA), is a small gene expressed mainly on the surface of plasma cells and some DLBCL cells. This gene is composed of three exons. Exon 1 is responsible for the extracellular domain, exon 2 for the transmembrane domain, and exon 3 for the TRAF binding domain. The BCMA is currently targeted by various types of immunotherapies as a major therapeutic approach for the treatment of multiple myeloma (MM). This includes CAR-T cells, bi-specific antibodies, and antibody-drug conjugates (ADC). However, emerging data indicates that alternative splicing in genes is an important mechanism for expression of different isoforms that may influence antibody-based therapies. We explored the potential of the presence of alternative splicing in BCMA transcripts via sequencing of BCMA RNA in patients with lymphoma or multiple myeloma. Methods: RNA was extracted from 587 fresh bone marrow samples with lymphoid/plasma cell neoplasms or from FFPE samples with lymphoma. In addition, cfRNA was extracted from 260 peripheral blood plasma samples from patients with lymphoma or multiple myeloma. RNA was sequenced using a hybrid capture-targeted RNA panel with analysis focused on TNFRSF17 (BCMA) gene transcript. Quantification of RNA transcript was done using Salmon algorithm. Results: Of the 587 lymphoma/plasma cell samples, 161 (27%) samples showed alternative splicing involving deletion of exon 2 (BCMA∆Ex2). Of the 260 cfRNA samples, 14 (6%) showed BCMA∆Ex2. The median percentage of BCMA∆Ex2 transcripts was 0.7% of total BCMA transcripts in cellular samples as compared with 9% in cfRNA samples. In cellular samples, there was a correlation between levels of BCMA and BCMA∆Ex2 (R=0.63). Cases with higher levels of BCMA had significantly higher levels of BCMA∆Ex2 (P&lt;0.0001, Kruskal-Wallis). In contrast, cfRNA showed no correlation between levels of BCMA and levels of BCMA∆Ex2 (R=021, Spearman) and mildly higher level of BCMA∆Ex2 in cases with higher levels of BCMA (P=0.002, Kruskal-Wallis). Conclusions: BCMA exon 2 skipping is detected in a significant number of patients with multiple myeloma and lymphoma. The percentage of skipping transcripts is low in cells and relatively higher in cfRNA. Since exon 2 skipping deletes the transmembrane domain, this BCMA protein may remain in the cytoplasm or perhaps is secreted as cell-free BCMA protein. The demonstration of relatively higher levels of BCMA∆Ex2 in cfRNA is likely reflecting higher turnover of cells and raises the possibility that cells with this isoform of BCMA are more aggressive than cells without the expression of this isoform. Further studies are needed to explore the clinical relevance of the expression of such abnormal BCMA protein on treatment with the various forms of anti-body-based therapy or CAR-T.

High-Resolution Raman Imaging of >300 Patient-Derived Cells from Nine Different Leukemia Subtypes: A Global Clustering Approach.

Leukemia comprises a diverse group of bone marrow tumors marked by cell proliferation. Current diagnosis involves identifying leukemia subtypes through visual assessment of blood and bone marrow smears, a subjective and time-consuming method. Our study introduces the characterization of different leukemia subtypes using a global clustering approach of Raman hyperspectral maps of cells. We analyzed bone marrow samples from 19 patients, each presenting one of nine distinct leukemia subtypes, by conducting high spatial resolution Raman imaging on 319 cells, generating over 1.3 million spectra in total. An automated preprocessing pipeline followed by a single-step global clustering approach performed over the entire data set identified relevant cellular components (cytoplasm, nucleus, carotenoids, myeloperoxidase (MPO), and hemoglobin (HB)) enabling the unsupervised creation of high-quality pseudostained images at the single-cell level. Furthermore, this approach provided a semiquantitative analysis of cellular component distribution, and multivariate analysis of clustering results revealed the potential of Raman imaging in leukemia research, highlighting both advantages and challenges associated with global clustering.

Long non-coding RNA PXN-AS1 promotes glutamine synthetase-mediated chronic myeloid leukemia BCR::ABL1-independent resistance to Imatinib via cell cycle signaling pathway

BackgroundChronic myeloid leukemia (CML) is a common hematological malignancy, and tyrosine kinase inhibitors (TKIs) represent the primary therapeutic approach for CML. Activation of metabolism signaling pathway has been connected with BCR::ABL1-independent TKIs resistance in CML cells. However, the specific mechanism by which metabolism signaling mediates this drug resistance remains unclear. Here, we identified one relationship between glutamine synthetase (GS) and BCR::ABL1-independent Imatinib resistance in CML cells.MethodsGS and PXN-AS1 in bone marrow samples of CML patients with Imatinib resistance (IR) were screened and detected by whole transcriptome sequencing. GS expression was upregulated using LVs and blocked using shRNAs respectively, then GS expression, Gln content, and cell cycle progression were respectively tested. The CML IR mice model were established by tail vein injection, prognosis of CML IR mice model were evaluated by Kaplan–Meier analysis, the ratio of spleen/body weight, HE staining, and IHC. PXN-AS1 level was blocked using shRNAs, and the effects of PXN-AS1 on CML IR cells in vitro and in vivo were tested the same as GS. Several RNA-RNA tools were used to predict the potential target microRNAs binding to both GS and PXN-AS1. RNA mimics and RNA inhibitors were used to explore the mechanism through which PXN-AS1 regulates miR-635 or miR-635 regulates GS.ResultsGS was highly expressed in the bone marrow samples of CML patients with Imatinib resistance. In addition, the lncRNA PXN-AS1 was found to mediate GS expression and disorder cell cycle in CML IR cells via mTOR signaling pathway. PXN-AS1 regulated GS expression by binding to miR-635. Additionally, knockdown of PXN-AS1 attenuated BCR::ABL1-independent Imatinib resistance in CML cells via PXN-AS1/miR-635/GS/Gln/mTOR signaling pathway.ConclusionsThus, PXN-AS1 promotes GS-mediated BCR::ABL1-independent Imatinib resistance in CML cells via cell cycle signaling pathway.Graphic

TES and SLC40A1 as Potential Biomarkers for Predicting Survival in T-Cell Acute Lymphoblastic Leukemia.

Identifying patients with high-risk T-cell acute lymphoblastic leukemia (T-ALL) is crucial for personalized therapy; however, the lack of robust biomarkers hinders prognosis assessment. To address this issue, our study aimed to screen and validate genes whose expression may serve as predictive indicators of outcomes in T-ALL patients while also investigating the underlying molecular mechanisms. Differentially expressed genes (DEGs) between T-ALL patients and healthy controls were identified by integrating data from three independent public datasets. Functional annotation of these DEGs and protein-protein interactions were also conducted. Further, we enrolled a prospective cohort of T-ALL patients (n = 20) at our center, conducting RNA-seq analysis on their bone marrow samples. Survival-based univariate Cox analysis was employed to identify gene expressions related to survival, and an intersection algorithm was sequentially applied. Furthermore, we validated the identified genes using cases from the Therapeutically Applicable Research to Generate Effective Treatments database, plotting Kaplan-Meier curves for secondary validation. Through the integration of survival-related genes with DEGs identified in T-ALL, our analysis revealed six T-ALL-specific genes, the expression levels of which were linked to prognostic value. Notably, the independent prognostic value of SLC40A1 and TES expression levels was confirmed in both an external cohort and a prospective cohort at our center. In summary, our preliminary study indicates that the expression levels of TES and SLC40A1 genes show promise as potential indicators for predicting survival outcomes in T-ALL patients.

Parallel genomic analysis from paired bone marrow and peripheral blood samples of 200 cytopenic patients

Parallel genomic analysis from paired bone marrow and peripheral blood samples of 200 cytopenic patients