Prediction of Malingant Plasma Cell Biology Related Survival in AL-Amyloidosis

Background. Survival in AL-amyloidosis is thought to be primarily determined by signs and symptoms caused by deposition of amyloid light chains, most prominently in the heart. In contrast, molecular characteristics of the underlying malignant plasma cell disease have been described, but are mostly considered less important. Aim of our study is to predict malignant plasma cell biology related survival in AL-amyloidosis by establishing the first gene expression based risk stratification (HDAL) and assessing its independence from clinical serum parameter assessing risk. Methods. CD138+-purified plasma cell samples of 919 patients with malignant plasma cell diseases, i.e. 195 AL-amyloidosis and 724 symptomatic myeloma patients were investigated by gene expression profiling, 124 AL-amyloidosis patients by RNA-sequencing. Gene expression profiling data of AL-amyloidosis patients were spitted in a training (TG, n=99) and a validation group (VG, n=96). A two-step model according to Rème et al. was applied on the training group, including a running log rank test for gene selection and a multi-cut-off running log-rank algorithm for optimal cut-off-selection, leading to a selection of 15 genes associated with good and 44 genes with adverse prognosis. The resulting HDAL-score was validated on the independent VG and our myeloma patient cohort using survival estimates for censored data. Differences between curves were assessed using the Log-rank test. The continuous RNA-Seq HDAL-score (R-HDAL) was subsequently derived to validate the survival association of the selected genes. HDAL was tested for independence with serum parameter assessing clinical staging systems by multivariate Cox regression. Results. Categorical split of the HDAL-score delineates three significantly predictive groups of 48%, 29% and 23% of AL-amyloidosis patients with a median survival of 105, 53 and 3 months in the training, and 72, 33 and 6 months in the validation group, respectively. In symptomatic myeloma patients, HDAL significantly stratifies two groups with a median survival of 128 and 78 months. Thus, HDAL is a malignant plasma biology related derived risk stratification. HDAL and R-HDAL are significantly predictive for survival as continuous parameters. Categorial and continuous HDAL are individually independent predictive from clinical staging systems, i.e. Mayo 2004, 2012 and Euro score, and the assessed serum parameters, i.e. NT-ProBNP, cTNT and dFLC. In conclusion, malignant plasma cell biology related and amyloid deposition mediated survivals in AL-amyloidosis are independent. Prognosis driven by the first component can significantly be assessed by transcriptome profiling (HDAL or R-HDAL). We thank U. Hegenbart and S. Schönland for clinical collaboration in this work. Disclosures Moreaux: Diag2Tec: Other: Co-founder of Diag2Tec company.

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AL Amyloidosis — Pathogenesis and Prognosis Are Determined By the Amyloidogenic Potential of the Light Chain and the Molecular Characteristics of Malignant Plasma Cells

Blood ◽

10.1182/blood-2018-187 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 187-187

Author(s):

Anja Seckinger ◽

Ute Hegenbart ◽

Susanne Beck ◽

Martina Emde ◽

Tilmann Bochtler ◽

...

Keyword(s):

Gene Expression ◽

Plasma Cell ◽

Light Chain ◽

Research Funding ◽

Plasma Cells ◽

Memory B Cells ◽

Light Chains ◽

Molecular Characteristics ◽

Al Amyloidosis ◽

Malignant Plasma Cell

Abstract INTRODUCTION. Systemic light chain amyloidosis (AL) is caused by accumulation of plasma cells producing misfolded monoclonal light chains depositing as amyloid fibrils in different organs, most frequently heart and kidney. AIM of our study is first assessing the molecular characteristics of malignant plasma cells from AL-patients in relation to those from MGUS, asymptomatic, and symptomatic myeloma: Are these plasma cells different, does this difference explain amyloidogenicity? Does AL correspond to a certain developmental stage during evolution of symptomatic myeloma? Secondly, to what extent is prognosis determined by amyloid-deposition (organotropism, amount, amyloidogenicity) vs. number and molecular characteristics of malignant plasma cells? PATIENTS & METHODS . Consecutive patients (n=3023) with AL (n=582), MGUS (n=306), asymptomatic (n=444, AMM), or previously untreated, therapy-requiring multiple myeloma (n=1691, MM) were included. CD138-purified plasma cell samples were subjected to iFISH (n=582/306/444/1691), 1297 to gene expression profiling using Affymetrix U133 2.0 plus arrays (n=196/64/272/765), 712 to RNA- (n=124/52/38/489), and 258 to whole exome sequencing (n=115/53/39/51). Samples of normal bone marrow plasma cells, memory B-cells, and polyclonal plasmablasts were used as comparators. The CoMMpass-cohort (n=647) was used as comparator for the mutational spectrum of myeloma. RESULTS . Prognosis. By AL-factors. Expectedly, organ involvement, i.e. heart only vs. kidney only vs. heart+kidney vs. other (overall survival (OS), P=.001), the amount of free light chains (dFLC ≥18 mg/dL, HR=2.56, P=.01), and the cardiac European Mayo IIIB score (I/II/IIIA/IIIB, median OS 110/55/16/3 months, HR=1/1.94/3.73/7.90, P<.001) strongly determine prognosis (Fig. 1A). By malignant plasma cell factors. High proliferation rate (HR=3.58, P=.001) and expression-based risk factors for MM (GEP70 high, HR=2.38, P=.005; Rs-score high HR=4.63, P<.001) identify patients with very adverse prognosis (Fig. 1A). Tumor load, e.g. plasma cell infiltration >10%/>30% (HR=1.31/1.81, P=.01, P=.002) and M-protein ≥ 30g/l (HR=3.01, P=.005), are likewise prognostic (Fig. 1A). In multivariate analysis, all tested AL-specific (European Mayo IIIB score) and malignant plasma cell factors (proliferation or GEP70 and plasma cell infiltration) are independent. Molecular characteristics.iFISH. As MM (96.2%) and AMM (92.8%) AL-patients (93.1%) carry at least one recurrent myeloma typical aberration. The mean number of progression-associated aberrations in AL (n=0.98) fits between MGUS (n=0.85) and AMM (n=1.45) with significant difference compared to AMM (P<.001) unlike to MGUS. Main differences in frequency are found for t(11;14) and hyperdiploidy with a comparable pattern of non-etiologic aberrations. Gene expression (GEP and RNA-seq). Aberrant plasma cells in AL amyloidosis show the least difference with AMM, followed by MGUS and MM. In principal component analysis, AL overlaps with AMM and MGUS, independent of presence or absence of heart involvement (Fig. 1B). Pairwise assessment of similarity using a multivariate generalization of the squared Pearson correlation coefficient shows closest similarity to AMM and MM followed by MGUS, with comparable differences to normal plasma cells, polyclonal plasmablasts, and memory B-cells. Significantly more AL-patients present with higher proliferation rate vs MGUS (P<.001) and AMM (P<.02). AL and MM differ significantly regarding distinct molecular entities as determined by GEP (e.g. TC-classification; Fig. 1C). Mutation spectrum in AL amyloidosis vs. MM. From the 20 most frequently synonymously mutated non-Ig transcripts (CoMMpass-cohort), 16 could likewise be detected in AL amyloidosis, i.e. KRAS, NRAS, IGLL5, DIS3, FAM46C, MUC16, BRAF, TRAF3, PCLO, RYR2, FATA4, CSMD3, TP53, DNAH5, RYR2A, and FLG. CCND1 mutations were significantly more frequent in AL and AMM compared to MM (P=.02). DISCUSSION & CONCLUSION. Pathogenesis and prognosis of AL amyloidosis are explained both by AL-specific and malignant plasma cell characteristics. Aberrant plasma cells in AL amyloidosis show the same aberration- and expression pattern and a "molecular age" between MGUS and AMM, most closely resembling the latter. AL amyloidosis is thus mostly a rather early plasma cell dyscrasia with an unstable and toxic immunoglobulin light chain. Disclosures Seckinger: Celgene: Research Funding; EngMab: Research Funding; Sanofi: Research Funding. Hose:Celgene: Honoraria, Research Funding; Sanofi: Research Funding; EngMab: Research Funding.

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Bioinformatics Analysis of The Expression of ATP Binding Cassette Transporters and The Screening of Regulatory Genes in PTEN/PI3K/Akt/mTOR Signaling Pathway in The Hepatocellular Carcinoma

10.21203/rs.3.rs-674099/v1 ◽

2021 ◽

Author(s):

Tingdan Zheng ◽

Wuqi Song ◽

Aiying Yang

Keyword(s):

Gene Expression ◽

Hepatocellular Carcinoma ◽

Overall Survival ◽

Bioinformatics Analysis ◽

Wilcoxon Test ◽

Rank Test ◽

Short Term ◽

Term Survival ◽

Log Rank Test ◽

Short Term Survival

Abstract Objective Here we performed the Bioinformatics analysis on the data from The Cancer Genome Atlas (TCGA), in order to find the correlation between the expression of ATP Binding Cassette (ABC) Transporters’ genes and hepatocellular carcinoma (HCC) prognosis; Methods Transcriptome profiles and clinical data of HCC were obtained from TCGA database. Package edgeR was used to analyze differential gene expression. Patients were divided into low-ABC expression and high-ABC expression groups based on the median expression level of ABC genes in cancer. The overall survival and short-term survival (n= 341) of the two groups was analyzed using the log-rank test and Wilcoxon test; Results We found that ABC gene expression was correlated with the expression of PIK3C2B (p<0.001, ABCC1: r=0.27; ABCC10: r=0.57; ABCC4: r=0.20; ABCC5: r=0.28; ABCB9: r=0.17; ABCD1: r=0.21). All patients with low-ABC expression showed significantly increased overall survival. Significantly decreased overall survival (Log-rank test: p<0.05, Wilcoxon test: p<0.05) was found in patients with high expression of ABCC1 (HR=1.58), ABCD1 (HR=1.45), ABCC4 (HR=1.56), and ABCC5 (HR=1.64), while decreased short-term survival (Log-rank test: p>0.05, Wilcoxon test: p<0.05) was correlated with the increased expression of ABCC10 (HR=1.29), PIK3C2B (HR=1.29) and ABCB9 (HR=1.23); Conclusions Our findings indicate that the specific ABC gene expression correlates with the prognosis of HCC. Therefore, ABC expression profile could be a potential indicator for HCC patients.

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Gene Expression Profiling Identifies Distinct Subclasses in Core Binding Factor Acute Myeloid Leukemia.

Blood ◽

10.1182/blood.v106.11.673.673 ◽

2005 ◽

Vol 106 (11) ◽

pp. 673-673

Author(s):

Lars Bullinger ◽

Stephan Kurz ◽

Konstanze Dohner ◽

Claudia Scholl ◽

Stefan Frohling ◽

...

Keyword(s):

Gene Expression ◽

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Expression Patterns ◽

The Other ◽

Rank Test ◽

Core Binding Factor ◽

Log Rank Test ◽

Binding Factor ◽

Acute Myeloid

Abstract Recurrent cytogenetic aberrations have been shown to constitute markers of diagnostic and prognostic value in acute myeloid leukemia (AML). However, even within well-defined cytogenetic AML subgroups with an inv(16) or a t(8;21) we see substantial biological and clinical heterogeneity which is not fully reflected by the current classification system. Therefore, we profiled gene expression in a large series of adult AML patients with core binding factor (CBF) leukemia [inv(16) n=55, t(8;21) n=38] using a whole genome DNA microarray platform in order to better characterize this disease on the molecular level. By unsupervised hierarchical clustering based on 8556 filtered genes we observed that our CBF leukemia samples separated primarily into three different subgroups. While two of the subgroups were characterized by inv(16) and t(8;21) cases, respectively, the third subgroup contained a mixture of both cytogenetic groups. There was no obvious correlation with known secondary aberrations or molecular marker like FLT3-ITD, NRAS and KIT mutations between the cases in the mixed subgroup and the others. However, the newly defined inv(16)/t(8;21)-subgroup (n=35) was characterized by distinct clinical behavior with shorter overall survival times (P=0.029; log rank test) compared to the other two groups. Unsupervised analyses within the inv(16) and t(8;21) cases also revealed corresponding inv(16) and t(8;21) subgroups with a strong trend towards inferior outcome (P=0.11 and P=0.09, respectively; log rank test). Since the primary translocation/inversion events themselves are not sufficient for leukemogenesis, distinct patterns of gene expression found within each of these cytogenetic groups may suggest alternative cooperating mutations and deregulated pathways leading to transformation. Therefore, we performed a supervised analysis to determine the characteristic gene expression patterns underlying the cluster-defined subgroups. We identified 528 genes significantly differentially expressed between the newly defined inv(16)/t(8;21)-subgroup and the other CBF cases (significance analysis of microarrays, false discovery rate < 0.001). Potential candidates for cooperating pathways characterizing the mixed inv(16)/t(8;21)-subgroup included e.g. AVO3, a member of the mTOR pathway, oncogene homologs like LYN and BRAF, as well as FOXO1A and IL6ST which have been previously identified to correlate with outcome in AML (Bullinger et al., N Engl J Med350:1605, 2004). In conclusion, while the observed signatures remain to be validated for their functional relevance, both supervised and unsupervised methods provide numerous insights into the pathogenesis of CBF AML, identifying clinically significant patterns of gene expression, as well as candidate target genes involved in leukemogenesis.

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Combining Proteomics and Gene Expression Profiling Identifies Proteins/Genes Associated with Short Overall Survival in Multiple Myeloma

Blood ◽

10.1182/blood.v120.21.197.197 ◽

2012 ◽

Vol 120 (21) ◽

pp. 197-197

Author(s):

Ricky D Edmondson ◽

Shweta S. Chavan ◽

Christoph Heuck ◽

Bart Barlogie

Keyword(s):

Gene Expression ◽

Overall Survival ◽

Multivariate Analyses ◽

Rank Test ◽

P Value ◽

Newly Diagnosed ◽

Training Set ◽

Test Set ◽

Log Rank Test ◽

Test Sets

Abstract Abstract 197 We and others have used gene expression profiling to classify multiple myeloma into high and low risk groups; here, we report the first combined GEP and proteomics study of a large number of baseline samples (n=85) of highly enriched tumor cells from patients with newly diagnosed myeloma. Peptide expression levels from MS data on CD138-selected plasma cells from a discovery set of 85 patients with newly diagnosed myeloma were used to identify proteins that were linked to short survival (OS < 3 years vs OS ≥ 3 years). The proteomics dataset consisted of intensity values for 11,006 peptides (representing 2,155 proteins), where intensity is the quantitative measure of peptide abundance; Peptide intensities were normalized by Z score transformation and significance analysis of microarray (SAM) was applied resulting in the identification 24 peptides as differentially expressed between the two groups (OS < 3 years vs OS ≥ 3 years), with fold change ≥1.5 and FDR <5%. The 24 peptides mapped to 19 unique proteins, and all were present at higher levels in the group with shorter overall survival than in the group with longer overall survival. An independent SAM analysis with parameters identical to the proteomics analysis (fold change ≥1.5; FDR <5%) was performed with the Affymetrix U133Plus2 microarray chip based expression data. This analysis identified 151 probe sets that were differentially expressed between the two groups; 144 probe sets were present at higher levels and seven at lower levels in the group with shorter overall survival. Comparing the SAM analyses of proteomics and GEP data, we identified nine probe sets, corresponding to seven genes, with increased levels of both protein and mRNA in the short lived group. In order to validate these findings from the discovery experiment we used GEP data from a randomized subset of the TT3 patient population as a training set for determining the optimal cut-points for each of the nine probe sets. Thus, TT3 population was randomized into two sub-populations for the training set (two-thirds of the population; n=294) and test set (one-third of the population; n=147); the Total Therapy 2 (TT2) patient population was used as an additional test set (n=441). A running log rank test was performed on the training set for each of the nine probe sets to determine its optimal gene expression cut-point. The cut-points derived from the training set were then applied to TT3 and TT2 test sets to investigate survival differences for the groups separated by the optimal cutpoint for each probe. The overall survival of the groups was visualized using the method of Kaplan and Meier, and a P-value was calculated (based on log-rank test) to determine whether there was a statistically significant difference in survival between the two groups (P ≤0.05). We performed univariate regression analysis using Cox proportional hazard model with the nine probe sets as variables on the TT3 test set. To identify which of the genes corresponding to these nine probes had an independent prognostic value, we performed a multivariate stepwise Cox regression analysis. wherein CACYBP, FABP5, and IQGAP2 retained significance after competing with the remaining probe sets in the analysis. CACYBP had the highest hazard ratio (HR 2.70, P-value 0.01). We then performed the univariate and multivariate analyses on the TT2 test set where CACYBP, CORO1A, ENO1, and STMN1 were selected by the multivariate analysis, and CACYBP had the highest hazard ratio (HR 1.93, P-value 0.004). CACYBP was the only gene selected by multivariate analyses of both test sets. Disclosures: No relevant conflicts of interest to declare.

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Center Experience and Calendar Year Of Transplantation Strongly Influence Short Term Survival After Autologous Peripheral Blood Transplantation In 1315 Patients With Light Chain Amyloidosis: An EBMT Analysis

Blood ◽

10.1182/blood.v122.21.417.417 ◽

2013 ◽

Vol 122 (21) ◽

pp. 417-417

Author(s):

Stefan O Schonland ◽

Ute Hegenbart ◽

Simona Iacobelli ◽

Jennifer Hoek ◽

M Rovira ◽

...

Keyword(s):

Board Of Directors ◽

Performance Status ◽

Rank Test ◽

High Dose ◽

Al Amyloidosis ◽

Advisory Committees ◽

Term Survival ◽

Log Rank Test ◽

One Year ◽

Short Term Survival

Abstract Introduction High-dose chemotherapy and autologous stem cell transplantation (ASCT) is a treatment option for eligible patients with systemic light chain (AL) amyloidosis. Compared to patients with multiple myeloma (MM), the risk for complications and transplant-related mortality is increased. However, in this fragile patient group it is often not possible to distinguish between treatment- and amyloidosis-related deaths in the post-transplant period. The CIBMTR reported a one year survival (1-yr OS) of 66% of patients transplanted between 1995 and 2001. Another multicenter analysis from Great Britain reported a one year survival of 75% (Goodman et al., BJH, 2006); interestingly, they could show a significant reduction of day 100 all-cause mortality from 32% to 13% after 1998. In recent single center studies 1-yr OS was better ranging from 80% to 90% (reviewed by Schönland et al., BMT, 2011). The amyloidosis groups of Mayo Clinic and Boston Medical School could also show a survival improvement over time (Tsai et al., Blood, 2012 and Gertz et al., BMT, 2010). Specific Aim The aim of this retrospective study was to analyze the 1-yr OS after ASCT for patients with AL amyloidosis in Europe. Of special interest were calendar year of transplants and center experience. Methodology Patient-, disease-, and transplant-related variables were collected according to the data entries in the EBMT database. Inclusion criteria were as follows: first autologous transplant with peripheral blood stem cells performed between 1997 and 2010. Center experience was measured for each patient by the number of previous MM ASCT done in the center until the year of AL transplant. Results 1315 patients from 259 centers fulfilled the entry criteria and were included in the analysis (for patient characteristics see table). The conditioning regimen was high-dose melphalan in most cases. Median follow up was 47 months. 1-yr OS after ASCT was 80.7% (CI 78.5 – 82.9). In univariate analysis age, gender, time from diagnosis to ASCT had no influence on 1-yr OS. Bad performance status (57% (50-65) vs. 90% (87-92); p<0.001) and progression/relapse as status at conditioning (61% (53-69) vs. 85% (83-87); p<0.001) significantly reduced 1-yr OS. A strong and significant influence of the transplant period (see figure 1, log-rank test, p<0.001) and higher center experience (see figure 2; log-rank test, p<0.001) could also be demonstrated. Interestingly, the proportion of patients with bad performance status decreased from 28% to 13% in most recent years (p=0.001). These results hold in multivariate analysis. Bad performance status (HR 4.3; p<0.001), progression/relapse as status at conditioning (HR 1.96; p<0.001) and earlier transplant period (HR 1.1; p<0.001) retained their highly significant negative influence on 1-yr OS. In an alternative multivariate model replacing transplant period with center experience, the latter has also a beneficial effect (HR 0.99 for 10 additional previous MM transplants; p=0.015) and all other prognostic factors retained the estimated effects. Conclusion This is the first report from the EBMT about the results of ASCT in AL amyloidosis from 259 European centers and the largest retrospective analysis for this rare entity. It clearly shows that short term survival has been improved over time probably due to better patient selection and increase of center experience. Of note, in the most recent cohort (2009 to 2010) the 1-yr OS was 91% (CI 87-96) supporting the further use of ASCT in eligible AL amyloidosis patients. Disclosures: Leblond: Roche : Consultancy, Honoraria, Membership on an entity’s Board of Directors or advisory committees, Speakers Bureau; Janssen: Honoraria, Membership on an entity’s Board of Directors or advisory committees; Mundipharma: Honoraria, Membership on an entity’s Board of Directors or advisory committees, Speakers Bureau.

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A 13-Glycosylation Gene Signature in Multiple Myeloma Can Predicts Survival and Identifies Candidates for Targeted Therapy (GiMM13)

Blood ◽

10.1182/blood.v128.22.4423.4423 ◽

2016 ◽

Vol 128 (22) ◽

pp. 4423-4423 ◽

Cited By ~ 2

Author(s):

Caoilfhionn Connolly ◽

Alokkumar Jha ◽

Alessandro Natoni ◽

Michael E O'Dwyer

Keyword(s):

Gene Expression ◽

Multiple Myeloma ◽

High Risk ◽

Research Funding ◽

Gene Signature ◽

Gene Set Enrichment Analysis ◽

Rank Test ◽

P Value ◽

Log Rank Test ◽

Novel Approach

Abstract Introduction Advances in genomics have highlighted the potential for individualized prognostication and therapy in multiple myeloma (MM). Previously developed gene expression signatures have identified patients with high risk (Kuiper et al, Blood 2016) however, they provide few insights into underlying disease biology thereby limiting their use in informing treatment decisions. Glycosylation is deregulated in MM (Glavey et al), and potential consequences include altered cell adhesion, signaling, immune evasion and drug resistance. In this study we have utilized RNA sequencing data from the IA7 CoMMpass cohort to characterize the expression profile of genes involved in glycosylation. This represents a novel approach to identify a distinct molecular pathway related to outcome, which is potentially actionable. Methods A pathway based approach was adopted to evaluate genes implicated in glycosylation, including the generation of selectin ligands. A literature review and KEGG pathway analysis of pathways relating to O-glycans, N-glycans, sialic acid metabolism, glycolipid synthesis and metabolism was completed. RNA Cufflinks-gene level FPKM expression of 458 patients enrolled in the IA7 cohort of the Multiple Myeloma Research Foundation (MMRF) CoMMpass trial (NCT145429) were analysed as derivation cohort. We developed expression cut-offs using a novel approach of adjusted existing linear regression model to define the gene expression cut-off by applying 3rd Quartile data (q1+q2/2-qmin). The analysis of overall survival (OS) was completed using adjusted 'kpas' R-package according to our cut-off model. Association between individual transcripts and OS was analyzed with log-rank test. Genes with p-value <0.2 were used in subsequent prioritization analysis. This cut-off methodology was employed to define the nearest neighbor for a gene for Gene Set Enrichment Analysis (GSEA). As far as 4th neighbor above and below the cut off was used to have centrally driven gene selection method for prioritization. The gene signature was validated in GSE2658 (Shaughnessy et al) dataset. Results Initial analysis yielded 184 prospective genes. 147 were significant on univariate analysis. Following further prioritization of these genes, we identified thirteen genes that had significant impact upon outcomes (GiMM13). Figure 1 reveals that GiMM13 signature has a significant correlation with inferior OS (HR 4.66 p-value 0.022). The prognostic impact of stratifying GiMM13 positive (High risk) or GiMM13 negative (Low risk) by ISS stage was evaluated. In Table 1. Kaplan Meier estimates generated for GiMM13 (High) or GiMM13 (Low) stratified by ISS are compared statistically using the log rank test. The prognostic ability of GiMM13 to synthesize distinct subgroups relative to each ISS stage is shown in Figure 2. ISS1-Low is the the lowest risk group with best prognosis. Hazard ratios relative to the ISS1-Low group were 1.8, p-value 0.029 (ISS2-Low), 2.1, p-value 0.031 (ISS3-Low), 4.3, p-value 0.04 (ISS1-HR), 5.9, p-value 0.039 (ISS2-HR) and 3.1, p-value 0.001 (ISS3-HR). The GiMM13 signature enhances the prognostic ability of ISS to identify patients with inferior or superior outcomes respectively. Conclusion While the therapeutic armamentarium for MM has expanded considerably, the significant molecular heterogeneity in the disease still poses a significant challenge. Our data suggests aberrant transcription of glycosylation genes, involved predominantly in selectin ligand synthesis, is associated with inferior survival outcomes and may help identify patients likely to benefit from treatment with agents targeting aberrant glycosylation, e.g. E-selectin inhibitor. Consistent with recent findings in chemoresistant minimal residual disease (MRD) (Paiva et al, Blood 2016), it would appear that O-glycosylation, rather than N-glycosylation is most significantly implicated in this biological processes conferring inferior outcomes. In conclusion, using a novel pathway-based approach to identify a 13-gene signature (GiMM13), we have developed a robust tool that can refine patient prognosis and inform clinical decision-making. Acknowledgment These data were generated as part of the Multiple Myeloma Research Foundation Personalized Medicine Initiatives (https://research.themmrf.org and www.themmrf.org). Disclosures O'Dwyer: Glycomimetics: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Research Funding.

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High expression of CD52 predicts poor prognosis of cytogenetic normal acute myeloid leukemia

10.21203/rs.2.22823/v1 ◽

2020 ◽

Author(s):

Ping Cai ◽

Wenzhi Cai ◽

Xiaoyu Xu ◽

xiaofei Yang ◽

yemin Wang ◽

...

Keyword(s):

Gene Expression ◽

Myeloid Leukemia ◽

Poor Prognosis ◽

Leukemia Cell ◽

Dna Demethylation ◽

Rank Test ◽

Log Rank Test ◽

High Level ◽

Acute Myeloid

Abstract Background: The prognosis of cytogenetic normal acute myeloid leukemia (CN-AML) varies. Finding new biomarkers affecting the prognosis of these patients may bring a new strategy for precise classification and treatment. CD52 play a significant role in chronic lymphocytic leukemia (CLL). However, the potential role of CD52 in CN-AML remains largely elusive. Methods: We analyzed the prognostic role of different expression levels of CD52 in 58 CN-AML from The Cancer Genome Atlas (TCGA) dataset and validate these results with 345 CN-AML patients from Gene Expression Omnibus (GEO) dataset. Results: CN-AML patients with high CD52 mRNA expression have a poorer prognosis compared to low CD52 expression ( event-free survival [EFS], P =0.056; overall survival [OS], P=0.043; log-rank test) and the results was verified by GSE12417 (OS, P=0.0197; log-rank test) and GSE71014 (OS, P=0.0197; log-rank test). Hematopoietic stem cell transplantation (HSCT) may improve prognosis of patients with CD52 high . Multivariate cox regression analysis show that the expression level of CD52 (HR=1.503; 95%CI:1.158-1.949 ; P=0.002) was a prognostic factor independent of age (HR=3.045; 95%CI:1.524-6.086; P=0.002) and FLT3 mutation status (HR=2.219; 95%CI:1.123-4.382; P=0.022). CD52 gene expression show a predictive effect on EFS (1-year survival- area under the curve [AUC]:0.685, 2-year survival-AUC:0.752) and OS (1-year survival-AUC: 0.717, 2-year survival-AUC:0.770). Besides, we also found that there is a significant negative correlation between CD52 mRNA expression and DNA methylation . CD52 DNA demethylation may responsible for the high level of CD52 mRNA. Functional enrichment analysis of differentially expressed genes in CD52 high and CD52 low suggests that leukemia cell adhesion-related pathways may be associated with poor prognosis in CD52 high patients . Conclusions: CD52 gene mRNA overexpression is an independent adverse prognostic factor for CN-AML, which could be reversed by HSCT. CD52 DNA demethylation may responsible for the high level of CD52 mRNA. The poor prognosis of patients with CD52 high may involves in leukemia cell adhesion-related pathways. Whether CD52 monoclonal antibodies play a role in high risk patients need further research.

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Implementing CT tumor volume and CT pleural thickness into future staging systems for malignant pleural mesothelioma

Cancer Imaging ◽

10.1186/s40644-021-00415-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Olivia Lauk ◽

Miriam Patella ◽

Thomas Neuer ◽

Bianca Battilana ◽

Thomas Frauenfelder ◽

...

Keyword(s):

Overall Survival ◽

Malignant Pleural Mesothelioma ◽

Tumor Volume ◽

Tumor Thickness ◽

Rank Test ◽

Pleural Mesothelioma ◽

Tumor Weight ◽

Log Rank Test ◽

Kaplan Meier ◽

Staging Systems

Abstract Objectives Tumor thickness and tumor volume measured by computed tomography (CT) were suggested as valuable prognosticator for patients’ survival diagnosed with malignant pleural mesothelioma (MPM). The purpose was to assess the accuracy of CT scan based preoperatively measured tumor volume and thickness compared to actual tumor weight of resected MPM specimen and pathologically assessed tumor thickness, as well as an analysis of their impact on overall survival (OS). Methods Between 09/2013–08/2018, 74 patients were treated with induction chemotherapy followed by (extended) pleurectomy/decortication ((E)PD). In 53 patients, correlations were made between CT-measured volume and -tumor thickness (cTV and cTT) and actual tumor weight (pTW) based on the available values. Further cTV and pT/IMIG stage were correlated using Pearson correlation. Overall survival (OS) was calculated with Kaplan Meier analysis and tested with log rank test. For correlation with OS Kaplan-Meier curves were made and log rank test was performed for all measurements dichotomized at the median. Results Median pathological tumor volume (pTV) and pTW were 530 ml [130 ml – 1000 ml] and 485 mg [95 g – 982 g] respectively. Median (IQR) cTV was 77.2 ml (35.0–238.0), median cTT was 9.0 mm (6.2–13.7). Significant association was found between cTV and pTV (R = 0.47, p < 0.001) and between cTT and IMIG stage (p = 0,001) at univariate analysis. Multivariate regression analysis revealed, that only cTV correlates with pTV. Median follow-up time was 36.3 months with 30 patients dead at the time of the analysis. Median OS was 23.7 months. 1-year and 3-year survival were 90 and 26% respectively and only the cTV remained statistically associated with OS. Conclusion Preoperatively assessed CT tumor volume and actual tumor volume showed a significant correlation. CT tumor volume may predict pathological tumor volume as a reflection of tumor burden, which supports the integration of CT tumor volume into future staging systems.

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Combining Measurements of Plasma Cell Apoptosis and Proliferation in Multiple Myeloma Identifies Patients with Poor Survival.

Blood ◽

10.1182/blood.v106.11.3410.3410 ◽

2005 ◽

Vol 106 (11) ◽

pp. 3410-3410 ◽

Cited By ~ 1

Author(s):

Shaji Kumar ◽

Michael Timm ◽

Martha Q. Lacy ◽

Angela Dispenzieri ◽

Suzanne R. Hayman ◽

...

Keyword(s):

Overall Survival ◽

Plasma Cell ◽

Cell Apoptosis ◽

Prognostic Value ◽

Median Overall Survival ◽

Plasma Cells ◽

Annexin V ◽

Rank Test ◽

Poor Survival ◽

Log Rank Test

Abstract Background: Multiple Myeloma (MM) is characterized by accumulation of malignant plasma cells with relatively low proliferative and apoptotic rates. The proliferative rate of plasma cells, measured in terms of % plasma cells labeled by bromodeoxyuridine (BrdU) using slide based fluorescence microscopy (plasma cell labeling index or PCLI) has been shown to be a powerful prognostic factor in MM. We have previously shown that the % bone marrow plasma cells in apoptosis (PCAP) determined by a flow cytometry method that uses Annexin V staining or 7-amino Actinomycin D (7-AAD) correlates with disease stage in MM. The goal of this study was to examine the prognostic value of the PCAP. Methods: We studied 145 patients with MM including 74 with newly diagnosed MM, 40 with relapsed MM, and 31 with MM on treatment in whom simultaneous measurements of % plasma cell apoptosis and PCLI were available. The PCLI is expressed as the percentage of cytoplasmic immunoglobulin positive plasma cells that have taken up BrdU. The PCLI was characterized as high when >= 1%. Mononuclear cells isolated from bone marrow aspirate, following red cell lysis with ACK solution, are incubated with CD38-PE and either CD138-FITC or CD45-FITC. This is followed by incubation with 7-AAD and the plasma cells are gated using the CD38/CD45 staining pattern. The Annexin method used a similar strategy, with Annexin V in place of 7-AAD. The percentage of plasma cells in apoptosis (PCAP) was categorized as high when >5%, the median value. Results: The median follow up for the entire group was 34 months (range, 0.1 mo to 9 years) and 112 (77%) had died at the time of analysis. Forty seven patients (32%) had a high PCLI (>=1%). The median overall survival for the patients with high PCLI was 14.6 months versus 42.3 months for those with a low PCLI; P = 0.0005 (log rank test). Seventy-five (51.7%) patients had a high PCAP. The median overall survival for those patients was 28.9 months versus 40.2 months for those with a low PCAP; P = 0.078. We next examined if there was any correlation between a high PCAP and high PCLI and found none; P = NS by (Fisher’s exact test). Additionally in a multivariate Cox model using both PCLI and PCAP, both were independently prognostic for overall survival. We then developed an index by adding PCLI to log transformed PCAP (PCLI + log PCAP). Using a cutoff of 1.5 for the new index we were able identify a group of patients with poor survival. The 59 patients with a high value for the new index had a median survival of 19.3 months vs 46.1 months for the rest (P < 0.0001, log rank test). Conclusion: The measurement of plasma cell apoptosis has prognostic value in patients with MM. More importantly, we have shown that by combining measures of two important biological characteristics of the plasma cell, namely proliferation and apoptosis, patients with a poor prognosis can be identified. Such a prognostication strategy can help stratify patients in clinical trials as well as shed light on the disease biology.

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Plasma Cell Gene-Expression Profiles in Patients with Systemic AL Amyloidosis: Responses to Melphalan and Stem Cell Transplant Are Associated with Differential Expression of Genes Involved in Translation, Protein Degradation and Detoxification.

Blood ◽

10.1182/blood.v106.11.3405.3405 ◽

2005 ◽

Vol 106 (11) ◽

pp. 3405-3405

Author(s):

Raymond L. Comenzo ◽

Ping Zhou ◽

Limin Wang ◽

Stephen D. Nimer ◽

Adam B. Olshen

Keyword(s):

Gene Expression ◽

Protein Degradation ◽

Plasma Cell ◽

Plasma Cells ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Gene Families ◽

Plasma Cell Dyscrasia ◽

Al Amyloidosis ◽

Cell Transplant

Abstract Systemic AL amyloidosis is a plasma cell dyscrasia and protein conformation disorder in which Ig light chains (Ig VL) produced by clonal plasma cells form interstitial amyloid in key viscera causing organ dysfunction and death. Patients with AL usually have < 20% marrow plasma cells with low to nil proliferative indices. Paradoxically the plasma cells appear immune to the toxic amyloid-forming Ig VL possibly due to the robust cytoplasmic protein quality-control processes in plasma cells. A standard approach is to treat with high-dose melphalan and stem cell transplant (SCT) without induction therapy. Post-SCT long-term survival depends on significant reductions of the plasma cell disease and Ig VL levels as measured by the serum free light chain (FLC) assay. At 3 months post-SCT responses of the plasma cell dyscrasia are defined both by standard criteria and by normalization of abnormal FLC ratios. By standard criteria, post-SCT one-third fail to achieve a > 50% reduction in plasma cell disease (NR), one-third achieve a > 50% reduction (PR), and one-third achieve clearance of marrow plasma cells and a complete or near complete response (CR). By FLC criteria, post-SCT one-third achieve normalization (N) of the FLC ratio and two-thirds do not (A). Many factors contribute to this distribution of responses. In order to identify factors specific to AL plasma cells, gene expression profiles (GEP; Affymetrix U133 PLUS 2.0) were obtained after double amplification of RNA from FACS-sorted CD138+/DAPI- plasma cells from untreated patients with AL pre-SCT. Data were vetted based on plasma cell lineage gene expression; samples contaminated with monocytes were not used. Supervised analyses were performed based on responses at 3 months post-SCT, comparing CR (n=4) to PR (n=7) and CR to NR (n=5), and FLC N (n=5; one with CR) to A (n=7; two with CR). Differentially expressed genes between paired sets were identified using the t-test. Genes with p < 0.01 were examined using EASE, a program that identifies over-represented gene families. In the CR-PR and CR-NR comparisons, genes involved in translation, RNA ligation and protein degradation, particularly aminoacyl tRNA synthetases, were significantly over-represented with Bonferroni-adjusted EASE scores (like p-values) < 0.05. In the CR set, tryptophanyl tRNA synthetase, a protein that can also be anti-angiogenic, and IDE, an insulin-degrading enzyme that also degrades Aβ amyloid peptides, were among the most over-expressed. In the FLC N-A comparison, protein transport and detoxification gene families were also significantly over-represented with Bonferroni-adjusted EASE scores < 0.001. In the N set, CCT subunits (chaperones), UBE2B (a ubiquitination enzyme and RAD6 homolog) and glyoxalase I (detoxification) were among the most over-expressed. Our initial hypothesis is that the CR and FLC N responses to melphalan have similar but distinctive GEP related to protein folding, ER stress and protein degradation. The responses of AL plasma cells to Ig VL in the ER may influence the patterns observed, possibly modulating melphalan uptake or activity. Further studies of these differences and functional hypothesis testing are currently underway.

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