scholarly journals High-Resolution Genomic Copy Number Analysis on Sequential Samples from the CLL8 Trial: Relation Between Clonal Evolution and Defects in DNA Damage Response?

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1964-1964
Author(s):  
Jennifer Edelmann ◽  
Eugen Tausch ◽  
Johannes Bloehdorn ◽  
Thorsten Zenz ◽  
Kirsten Fischer ◽  
...  
Keyword(s):  
High Risk ◽  
Copy Number ◽  
Clonal Evolution ◽  
Genomic Stability ◽  
Post Treatment ◽  
Time Points ◽  
Sequential Samples ◽  
Pre Treatment ◽  
Over Time ◽  
Observation Period

Abstract Genomic abnormalities have strong prognostic impact in chronic lymphocytic leukemia (CLL). However, clonal evolution has been studied in a limited number of cases and not within the setting of current standard therapy. It was therefore our aim to study changes in the composition of copy number alterations (CNA) over time with and without the influence of chemo(immuno)therapy. Sequential samples of 92 patients enrolled on the CLL8 trial of the GCLLSG were analyzed by Affymetrix® 6.0 single nucleotide polymorphism (SNP) arrays. Since procurement of a relapse sample was a prerequisite for this study, the cohort was not representative for the CLL8 trial [21% CR (N=19), 63% PR (N=58), 13% non response (N=12), 3% missing response (N=3)]. 48 patients received Fludarabine / Cyclophosphamide (FC), 44 patients FC plus Rituximab (FCR). Samples were taken at 3 time points: pre-treatment [N=27], time of first treatment in CLL8 [N=92] and post treatment at relapse / progressive disease [N=74]. The median observation period between samples was 35 months [range: 6-127] for the pre-treatment vs. first treatment and 41 months [range: 5-87] for the first treatment vs. post treatment (relapse) comparisons. The majority of cases maintained genomic stability over time. This applied in particular for the comparison between pre-treatment and first treatment [N=21 of 27; 78%] but also for the comparison between first treatment and relapse [N=49 of 74; 66%]. The cohort was characterized by a high proportion of high-risk genomic abnormalities [30% del(11)(q22.3), 22% TP53 loss and/or mutation in the pre-treatment cohort; 36% del(11)(q22.3), 24% TP53 loss and/or mutation in the post treatment cohort]. The acquisition of novel clonal CNAs was associated with these: In the pre-treatment to first treatment comparison [N=27], only 6 [22%] cases had novel CNAs emerging over time and all of them carried an ATM loss by del(11)(q22.3). Eight cases with ATM and/or TP53 alteration and all cases without high-risk genomic aberrations [N=13] showed no evidence of clonal evolution. In the first treatment to relapse comparison [N=74], 25 [34%] cases had newly acquired CNAs at relapse and 20 of them [80%] carried high-risk genomic abnormalities [44% del(11)(q22.3), 36% TP53 loss and/or mutation]. Only 5 cases lacking ATM or TP53 alteration had newly acquired CNAs. In contrast, genomic stability was observed in 25 cases with high-risk genomic abnormalities [15 cases with del(11)(q22.3), 10 with TP53 loss and/or mutation) and 24 cases without high-risk abnormalities. No statistically significant increased incidence of clonal evolution was observed in IGHV unmutated cases [N=66 of 92] [24 (80%) cases with clonal evolution vs. 42 (70%) cases without clonal evolution, p=0.3]. Nine patients had samples available from all 3 time points. While mainly genomic stability could be observed prior to treatment, 3 cases acquired 3 novel CNAs each after therapy. Comparing both treatment arms in the post treatment cohort [N=74] revealed a higher incidence of clonal evolution after treatment with FCR [FCR: N=16 of 35, 46%; FC: N=9 of 39, 23%; p=0.04] at a similar median observation period [36 and 35 months, respectively]. Also, the mean number of newly acquired CNAs at relapse was higher in the FCR treated group [3.3 vs. 2.6]. With regard to response no statistically significant differences were observed between cases with and without clonal evolution [cases with clonal evolution: 6 (24%) CR, 17 (64%) PR, 2 (8%) non-response; without: 8 (17%) CR, 31 (66%) PR, 8 (17%) non-response, p=0.5]. Loss of clonal lesions was rare, occurring only under the selection pressure of therapy: 16 CNAs in 11 cases were not observed anymore at relapse. 3 of these CNAs were subclonal at time of first treatment [10-20% allelic burden] and might not yet have re-emerged after relapse. 5 CNAs in 4 cases were lost at relapse. The remaining 8 CNAs were del(13q) [N=5] and del(11q) [N=3] that were lost for a probably more advantageous del(13q) / del(11q) clone. The appearance of a more advantageous del(13q) / del(11q) clone was linked to a larger deletion size [N=3] or a larger discontinuous deletion very likely resulting from chromothripsis [N=3]. The results of this study support previous data of a high genomic stability in CLL cases lacking alterations of TP53 and/or ATM. However, application of chemo(immuno)therapy did slightly increase the number of cases acquiring novel clonal CNAs. Disclosures Stilgenbauer: Pharmacyclics, Janssen: Honoraria, Research Funding.

scholarly journals Clonal Heterogeneity and Evolutionary Phylogeny of Critical Cytogenetic Aberrations in Multiple Myeloma

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1608-1608
Author(s):  
Yuting Yan ◽  
Xiaoqi Qin ◽  
Jiahui Liu ◽  
Huishou Fan ◽  
Lanting Liu ◽  
...  
Keyword(s):  
High Risk ◽  
Copy Number ◽  
Prognostic Value ◽  
Clonal Evolution ◽  
Clone Size ◽  
Time Points ◽  
Evolution Pattern ◽  
Group A ◽  
Cytogenetic Evolution ◽  
Time Point

Abstract Single-cell analysis is of significant importance in delineate the exact phylogeny of subclonal population and in discovering subtle diversification. So far studies of intratumor heterogeneity and clonal evolution in multiple myeloma (MM) were largely focused at the bulk tumor population level. Here, we performed quantitative multi-gene fluorescence in situ hybridization (QM-FISH) in 129 longitudinal samples of 57 MM patients. All the patients had newly-diagnosed and relapsed paired samples. An expanded cohort of 188 MM patients underwent conventional FISH (cFISH) to validate the cytogenetic evolution in bulk tumor level. 43 of 57 patients (75.4%) harbored three or four cytogenetic clones at diagnosis. We delineated the phylogeny of subclonal tumor population and derived the evolutionary architecture in each patient.13q deletion and the first 1q gain tended to be earlier cytogenetic alternation, whereas 16q and 17p deletion were acquired later. Patients with clonal stabilization had a significantly improved OS than those with other evolutionary patterns (median OS, 71.2 vs. 39.7 vs. 35.2 vs. 25.5 months, for stable, differential, branching and linear patterns, respectively, p=0.001). Besides, a high degree of consistency and complementarity across QM-FISH and cFISH was observed in evaluation of cytogenetic evolution pattern in MM. In total, at least two time-point cytogenetic evaluations by cFISH were underwent in 188 MM patients. The proportion of patients with high-risk cytogenetic features was 33% at diagnosis and 49% at relapse. The prognostic value of the presence of high-risk aberrations at diagnosis were attenuated over time (HR=1.79, p=0.002 for survival from diagnosis; HR=1.55, p=0.026 for survival from relapse, ). Survival from relapse were greater influenced by the presence of high-risk aberrations at relapse (HR=2.07, figure 5E) rather than present at diagnosis (HR=1.55). The present study investigated the prognostic value of evolution in copy number or clone size of 1q21 gain/amplification during follow-up. The incidence of patients carrying at least three copies of 1q21 was higher after relapse than at diagnosis (69% vs. 55%, p=0.004).Patients were categorized as six groups according to the change patterns in copy number and clone size of 1q21 gain between the two time-point samplings. Patients without 1q21 gain/amplification at both time points (group B) and patients who had obvious decrease in clone size or loss of 1q21 gain at relapse (group A) experienced similar superior outcome (Failure free survival after relapse (2 nd FFS), 18.1 vs. 27.8 months, p=0.469), whereas patients carrying 1q21 gain/amplification at both time points with or without increase (group C,D) in clone size relatively worse survival (2 nd FFS 12.4 and 10.5 months, respectively, p<0.05 compare to group A and B). The remaining patients who had an increase in copy number of 1q21 and those who developed de novo 1q21 gain at relapse were observed poorest outcome (group E and F,2 nd FFS 6.7 and 8.9 months). The interval time between two time-point samplings were similar among groups, whereas the different evolution pattern of 1q21 gain could clearly stratify both overall survival and post-relapse survival (p<0.001). This study shows that QM-FISH is a valuable tool to elucidate the clonal architecture at single cell level. Clonal evolution pattern is of prognostic significance, highlighting the need for repeated cytogenetic evaluation in relapsed MM. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

scholarly journals Mechanisms of Adaptation to Ibrutinib in High Risk Chronic Lymphocytic Leukemia

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 585-585 ◽  
Author(s):  
Valeria Spina ◽  
Gabriela Forestieri ◽  
Antonella Zucchetto ◽  
Alessio Bruscaggin ◽  
Tamara Bittolo ◽  
...  
Keyword(s):  
High Risk ◽  
Chronic Lymphocytic Leukemia ◽  
Nuclear Localization ◽  
Peripheral Blood ◽  
Research Funding ◽  
Clonal Evolution ◽  
Lymphocytic Leukemia ◽  
Adaptation Process ◽  
Over Time ◽  
Stimulation Of

Abstract Introduction. Ibrutinib inhibits the BTK molecule downstream the B-cell receptor (BCR). Though highly active in high risk chronic lymphocytic leukemia (CLL), the most typical response achievable in patients is a minimal residual disease (MRD) positive partial remission (PR) which is maintained until the development of genetically driven resistance caused by the acquisition of mutations in the BTK or PLCG2 genes. The study aims at characterizing the adaptation process allowing residual CLL cells to persist despite BTK inhibition. Methods. The IOSI-EMA-001 study (NCT02827617) is an observational study consisting in the prospective and longitudinal collection of peripheral blood samples and clinical data from high risk CLL patients treated with ibrutinib. Peripheral blood CLL cells longitudinally drawn from patients before treatment start and at fixed timepoints under ibrutinib were monitored by: i) next generation flow cytometry approaches for changes in proliferation rate, surfaceome, and pathway activation; and ii) CAPP-seq targeted deep next generation (sensitivity ~10-3) for clonal evolution. Results. The study cohort comprised 31 high risk CLL patients, including 15 treatment naïve, 16 relapsed, 80% IGHV unmutated, 42% 17p deleted and 55% TP53 mutated. Median duration of ibrutinib treatment was 45 weeks (24-72 weeks). All patients obtained a MRD positive PR that was maintained in all but one who progressed with a PLCG2 mutation (VAF 3%). Compared to baseline, under ibrutinib therapy CLL cells slowed down their proliferation, as suggested by the decreased expression of Ki-67, the reduction of the proliferating fraction (CXCR4dimCD5bright), and the increase of the resting fraction (CXCR4brightCD5dim). Compared to baseline, under ibrutinib therapy CLL cells also upregulated BCR and adhesion/homing proteins, and decreased the expression of BCR inhibitor proteins. Upon stimulation of the BCR with anti-IgM, the downstream path through pBTK and pPLCG2 was inhibited by ibrutinib, while conversely the downstream path through pAKT and pERK was still inducible throughout all the assessed timepoints. The proportion of CLL cells harboring nuclear localization of NF-kB progressively increased over time under ibrutinib. NF-kB nuclear localization was inducible throughout all the assessed timepoints by CD40L stimulation of the non-canonical NF-kB pathway, but not by anti-IgM stimulation of the BCR/canonical NF-kB pathway. Overall, 880 individual mutations were longitudinally discovered and monitored across a total of 121 sequential timepoints collected during ibrutinib treatment. Clonal evolution was observed in (67.7%) cases, a proportion rate previously documented in CLL treated with chemoimmunotherapy. Clonal evolution appeared to be heterogeneous involving different genes without a stereotypic targeting. Consistently, none of the main driver gene mutations was homogeneously selected or suppressed by ibrutinib suggesting that the biological adaptation of CLL cells under ibrutinib is not genetically driven. Clonal evolution propensity was not associated with any of the biomarkers of the disease, and it did not decrease over time under ibrutinib. Conclusions. Taken together these results suggest that residual CLL cells persisting under ibrutinib therapy adapt their phenotype by upregulating adhesion molecules, chemokine receptors and BCR molecules, and by maintaining a competence of BCR signaling through the PI3K/AKT/ERK pathway. The progressive selection of CLL cells having NF-kB in the nucleus, likely due to the BTK independent non-canonical NF-kB pathway, might explain their survival despite ibrutinib therapy. Finally, clonal evolution is not suppressed by ibrutinib chemotherapy, and despite does not seem to be directly involved in such adaptation process, may ultimately favor the acquisition of BTK and PLCG2 ibrutinib resistance mutations. Disclosures Zucca: Celltrion: Consultancy; AstraZeneca: Consultancy. Ghia:Sunesis: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; AbbVie, Inc: Honoraria, Research Funding; Acerta: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Gilead: Honoraria, Research Funding; BeiGene: Honoraria, Research Funding. Montillo:Janssen: Consultancy, Honoraria; Gilead: Consultancy, Honoraria, Speakers Bureau; AbbVie: Consultancy, Honoraria, Speakers Bureau; Roche: Consultancy, Honoraria, Research Funding. Tedeschi:Janssen: Consultancy, Speakers Bureau; Gilead: Consultancy; AbbVie: Consultancy. Gaidano:AbbVie: Consultancy, Honoraria; Gilead: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; Morphosys: Honoraria; Roche: Consultancy, Honoraria.

scholarly journals Strong Predictors of Chromosomal Aberrations and Myeloid Neoplasia Following Immunosuppression Therapy for Severe Aplastic Anemia: A Retrospective Cohort Study

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 601-601
Author(s):  
Emma M. Groarke ◽  
Bhavisha A. Patel ◽  
Ruba Shalhoub ◽  
Fernanda Gutierrez-Rodrigues ◽  
Parth Desai ◽  
...  
Keyword(s):  
High Risk ◽  
Clonal Evolution ◽  
Low Risk ◽  
Competing Risk ◽  
Long Term Outcomes ◽  
Risk Patients ◽  
Risk Evolution ◽  
Pre Treatment ◽  
Myeloid Neoplasia

Abstract Introduction: Immune aplastic anemia (AA) is effectively treated with either immunosuppressive treatment (IST) or allogeneic hematopoietic stem cell transplant (HSCT). Clonal evolution remains the most feared long-term complication after IST. We investigated predictor factors, genetic characteristics, and long-term outcomes of patients who developed either secondary myeloid neoplasia or isolated chromosomal abnormalities without morphologic dysplasia after immunosuppression. Methods: All patients with severe AA treated at the NIH Clinical Center with IST from 1989-2020 who underwent clonal evolution were categorized as "high-risk" (overt myeloid neoplasia, or isolated chromosome 7 abnormality / complex cytogenetics) or "low-risk" (isolated chromosome abnormalities without overt myeloid neoplasia or dysplasia; isolated chromosome 7 abnormality or complex cytogenetics were characterized as high-risk). Univariable analysis was performed using the Fine-Gray competing risk regression model using death as a competing risk to determine predictors of clonal evolution. Classification and regression tree analysis of time to clonal evolution was performed on continuous baseline variables to partition the data based on the best categorical cutoff. Long term outcomes assessed included overall survival (OS) and HSCT. Error corrected next-generation sequencing (ECS) was used to assess for pathogenic somatic variants in known myeloid cancer genes in clonal evolvers both at time of evolution and in serial samples prior when available. Results: Of 659 patients with severe AA included in this study, 95 developed clonal evolution: 59 high-risk and 36 low-risk. Age >48 years at diagnosis and pre-treatment ANC >0.87x10 9/L were strong predictors of high-risk clonal evolution. High-risk clonal evolution was increased in patients aged >48 years, with cumulative incidence (CI) of 13.9% by 5 years compared to patients aged <48 years of 3.8% by 5 years (p<0.001). Baseline ANC >0.87 x10 9/L (independent of age) predicted an even higher risk of evolution; CI for high-risk evolution was 17% by 5 years (p<0.001). Combined high ANC and older age (>48 years) were prognostic of the greatest risk of high-risk evolution, with a hazard ratio (HR) of 5.51; conversely, ANC <0.87 x10 9/L and age <48 years was protective, with HR 0.32. High-risk clonal evolution was not significantly increased by use of eltrombopag with IST versus IST only (p=0.3), but there was an increase when all clonal evolution was considered (p=0.02). Overall survival in high-risk evolution was 35% at 5 years and in low-risk evolution was 84% (p<0.001). Patients with high-risk evolution who underwent HSCT (n=26) had better OS compared to those treated with chemotherapy or supportive care (p=0.005). RUNX1 (13 variants in 8 [35%] patients) and ASXL1 (13 variants in 10 [43%] patients) were the most frequent mutated genes at time of clonal evolution in high-risk patients, and BCOR/L1 (14 variants in 8 [32%] patients) was the most frequently mutated in the low-risk group. Longitudinal data were available in five high-risk and eight low-risk patients. Three of five high-risk patients had acquisition or expansion of RUNX1 clones at evolution. Small RUNX1 variants were present in two patients as early as three years prior to high-risk evolution. Splicing factor genes and RUNX1 somatic variants were detected exclusively in the high-risk group; DNMT3A, BCOR/L1 and ASXL1 gene mutations were present in both groups. Conclusion: Age and pre-treatment ANC strongly predict high-risk clonal evolution in AA patients after IST and may be used determine at-risk patients for long term follow-up. Outcomes in patients with low-risk evolution are favorable but poor in high-risk evolution without HSCT. The clonal landscape differs between high-risk and low-risk evolution; MDS-associated genetic mutations are enriched in high-risk evolution, in particular RUNX1. Further study of the role of RUNX1 in high-risk clonal evolvers may give insight into leukemogenesis in AA. Figure 1: Cumulative incidence (CI) of clonal evolution since immunosuppression with death treated as competing risk. (A) CI for development of all clonal evolution in patients >37 years (B) and high-risk clonal evolution in patients >48 years (C) CI for development of all clonal evolution when baseline ANC >0.87x10 9/L and (D) high-risk clonal evolution when baseline ANC >0.87x10 9/L. Figure 1 Figure 1. Disclosures Young: Novartis: Research Funding.

scholarly journals TP53 Clonal and Subclonal Architecture in Chronic Lymphocytic Leukemia Patients Under Ibrutinib Treatment

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3119-3119
Author(s):  
Ilaria Del Giudice ◽  
Luciana Cafforio ◽  
Luca Vincenzo Cappelli ◽  
Caterina Ilari ◽  
Sara Raponi ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Board Member ◽  
Clonal Evolution ◽  
Single Agent ◽  
Variant Calling ◽  
Advisory Board ◽  
Lymphocytic Leukemia ◽  
Bioinformatics Pipeline ◽  
Time Points ◽  
Over Time

Abstract Introduction. Ibrunitib (IBR) is active in chronic lymphocytic leukemia (CLL) patients (pts) with TP53 aberrations. Few data describing the dynamics of TP53 mutated clones under IBR are available. We analyzed a cohort of 40 treatment-naïve and relapsed CLL pts treated with IBR to investigate the dynamics of clonal and subclonal TP53 mutations (TP53-mut). Methods. Forty pts (Table) underwent a longitudinal TP53 monitoring (117 samples) by ultra-deep sequencing (UDS): 26 received IBR + rituximab (IBR+RTX) in first line as part of the GIMEMA LLC 1114 protocol (IBR exposition: 8 months in 7 pts and 14 months in 19 pts) (cohort 1), while 14 received IBR single agent after a median of 1.5 (range: 1-4) chemo-immunotherapy lines (IBR exposition: 2.1 to 4 years in 12 pts) (cohort 2). Samples were analyzed by UDS on a MiSeq sequencer (Illumina, Inc.) to obtain a 5000X coverage/base. For variant calling, the MiSeq Reporter software and an in-house bioinformatics pipeline were applied. All mutations were checked on the IARC TP53 database and those with a variant allele frequency (VAF) <10% (i.e. subclonal) were confirmed in an independent UDS run. VAF was corrected to cancer cell fraction (CCF) by the proportion of CD19+/CD5+ cells. Results. In cohort 1, 12/26 pts were evaluated at 3 time-points: baseline (T0), +8 (T8) and +14 (T14) months from IBR+RTX, and 14 at T0 and either T8 or T14. At T0, 19/26 pts showed a mean number of 1.5 (range: 1-5) clonal/subclonal TP53-mut/pt, for a total of 28 mutations. Of those, 20/28 (71.4%) were clonal (mean VAF: 57.8%; range: 18-94.8%) and 8/28 (27.6%) were subclonal (mean VAF: 4.4%; range: 1.2-9.2%; VAF≤5% in 6). Seven/26 pts resulted wild-type (WT). Under IBR+RTX, of the 28 TP53-mut corrected to CCF (21 clonal and 7 subclonal), 12 (9 clonal + 3 subclonal) (42.8%) persisted stable, 9 (32.1%) clonal mutations decreased, 6 (21.4%) were lost, one evolved to clonal. No novel clonal or subclonal TP53-mut arose during IBR+RTX. According to CCF, the pts followed 5 patterns: 1) clonal TP53-mut present from T0 and persisting clonal with a stable (n=6) or decreasing CCF (n=7); 2) clonal TP53-mut disappearing during treatment (n=1); 3) subclonal TP53-mut evolving to clonal (n=1, CCF 8% at T0 and 17.5% at T14); 4) subclonal TP53-mut persisting subclonal (n=1); 5) absence of any detectable TP53-mut in all time-points (n=7). In addition, 3 cases showed coexisting clonal and subclonal TP53-mut at T0: in one case 3 TP53-mut remained stable; in another one, 4 TP53-mut, including one clonal, were lost, and one clonal decreased in CCF; in the last case, 1 TP53-mut decreased, 1 remained stable and 1 subclonal disappeared. In cohort 2, before IBR, 10/14 pts showed a mean of 3.1 (range: 1-11) clonal/subclonal TP53-mut/pt, for a total of 31 mutations. Of those, 11/31 (35.5%) were clonal (mean VAF: 31.9%; range: 10.5-78.8%) and 20/31 (64.5%) were subclonal (mean VAF: 2.9%; range: 0.9-6.8%). Four/14 pts were WT. Under IBR, 16/31 (6 clonal+10 subclonal) (51.5%) TP53-mut persisted stable, 2 (6.5%) clonal decreased, 11 (2 clonal+9 subclonal) (35.5%) were lost, 2 (6.5%) subclonal evolved to clonal; 2 novel subclonal mutations emerged. No mutation was identified in the 4 WT pts over time. In both cohorts, most of TP53-mut remained stable (42.8% vs 51.5% in cohort 1 and 2, respectively) or decreased (32.1% vs 6.5%) and 17 (5 clonal and 12 subclonal) were lost (21.4% vs 35.5%) (p=NS). Although the lymphocyte count significantly decreased during IBR+RTX/IBR exposure (cohort 1: 47.1 x 109/L vs 7.5 x 109/L, p<0.0001; cohort 2: 48.5 x 109/L vs 15.3 x 109/L, p=0.015), the mean CCF of the existing mutations remained stable on treatment (cohort 1: 48.1% vs 40.1%, p=0.42; cohort 2: 16.9 % vs 13.02%; p=0.5). Conclusions. Both when used front-line or as a subsequent line of therapy, IBR appears to decrease the TP53 clonal and subclonal numerosity and complexity. Clonal evolution and the occurrence of novel mutations are rare and occur mostly in pre-treated pts. The significant decrease of lymphocytosis with stable CCF, prove the IBR effectiveness both on TP53 mutated and WT CLL cells, regardless of previous therapies. A longer follow-up will better clarify the dynamics of clonal and subclonal TP53-mut and whether the persistent clones may survive over time and give rise to subsequent relapses. Figure. Figure. Disclosures Mauro: abbvie: Other: board member; janssen: Other: board member. Foà:GILEAD: Speakers Bureau; CELTRION: Other: ADVISORY BOARD; INCYTE: Other: ADVISORY BOARD; ROCHE: Other: ADVISORY BOARD, Speakers Bureau; JANSSEN: Other: ADVISORY BOARD, Speakers Bureau; NOVARTIS: Speakers Bureau; CELGENE: Other: ADVISORY BOARD, Speakers Bureau; AMGEN: Other: ADVISORY BOARD; ABBVIE: Other: ADVISORY BOARD, Speakers Bureau.

scholarly journals Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer

2021 ◽  
Author(s):  
Alok K. Tewari ◽  
Alexander T.M. Cheung ◽  
Jett Crowdis ◽  
Jake R. Conway ◽  
Sabrina Y. Camp ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
High Risk ◽  
Clinical Outcomes ◽  
Copy Number ◽  
Residual Disease ◽  
Treatment Strategies ◽  
Localized Prostate Cancer ◽  
Copy Number Loss ◽  
Molecular Features ◽  
Pre Treatment

ABSTRACTHigh-risk localized prostate cancer (HRLPC) is associated with a substantial risk of recurrence and prostate cancer-specific mortality1. Recent clinical trials have shown that intensifying anti-androgen therapies administered prior to prostatectomy can induce pathologic complete responses (pCR) or minimal residual disease (MRD) (<5 mm), together termed exceptional response, although the molecular determinants of these clinical outcomes are largely unknown. Here, we performed whole exome (WES) and whole transcriptome sequencing (RNA-seq) on pre-treatment multi-regional tumor biopsies from exceptional responders (ER: pCR and MRD patients) and non-responders (NR: pathologic T3 or lymph node positive disease) treated with intensive anti-androgen therapies prior to prostatectomy. SPOP mutation and SPOPL copy number loss were exclusively observed in ER, while TP53 mutation and PTEN copy number loss were exclusively observed in NR. These alterations were clonal in all tumor phylogenies per patient. Additionally, transcriptional programs involving androgen signaling and TGFβ signaling were enriched in ER and NR, respectively. The presence of these alterations in routine biopsies from patients with HRLPC may inform the prospective identification of responders to neoadjuvant anti-androgen therapies to improve clinical outcomes and stratify other patients to alternative biologically informed treatment strategies.

scholarly journals Treatment Options for Osteoarthritis of the Ankle: Appropriate Distinction Between Brace Treatment and Arthrodesis

2019 ◽  
Vol 4 (4) ◽  
pp. 2473011419S0021
Author(s):  
Takaaki Hirano ◽  
Yui Akiyama ◽  
Tomoko Karube ◽  
Naoki Haraguchi ◽  
Hisateru Niki ◽  
...  
Keyword(s):  
Physical Function ◽  
Ankle Joint ◽  
Daily Living ◽  
Japanese Society ◽  
Treatment Options ◽  
Post Treatment ◽  
Brace Treatment ◽  
Therapeutic Results ◽  
Pre Treatment ◽  
Observation Period

Category: Ankle Arthritis Introduction/Purpose: Ankle arthrodesis (fusion) for the treatment of osteoarthritis of the ankle (OA) was reported to have good therapeutic results; however, this has not been compared with conservative treatment. At this conference last year, brace treatment using an ankle-foot orthosis, Hiflex Foot Gear (HFG), was also reported to have good therapeutic results, which allows for slight mobility in the ankle joint while providing appropriate level of support for the ankle joint. On this occasion, the therapeutic results of brace treatment and fusion were compared, and treatment options for OA were examined. Methods: Subjects included nine cases and ten feet in a group that was diagnosed with stage IIIb OA or worse according to the Takakura Classification and were treated with HFG (mean age of 70.6 years, mean course observation period of 8.4 months) and nine cases and ten feet in a group that was treated with fusion for the same diagnosis (mean age of 58.1 years, mean course observation period of 25.5 months). The pre-treatment and post-treatment physician-initiated objective evaluation by the Japanese Society for Surgery of the Foot scale (JSSF scale) and patient-reported subjective evaluation by the Japanese Orthopaedic Association/ the Japanese Society for Surgery of the Foot, and subscales of Self-Administered Foot Evaluation Questionnaire (SAFE-Q) were examined, and improvements in each score in two groups were compared (post-treatment vs pre-treatment) by an unpaired t-test. The validity and reliability of JSSF scale and SAFE-Q have been established by psychometric verification Results: The improvement after the treatment for the HFG group and the fusion group was observed. JSSF scores were 16.1 (p < 0.001) and 35.5 (p < 0.001), respectively, and pain and pain-related scores in the SAFE-Q were 20.8 (p = 0.021) and 35.4 (p < 0.001), respectively. Physical function and daily living were 12.8 (p < 0.001) and 18.6 (p = 0.007), respectively, while social functioning scores were 18.0 (p = 0.001) and 32.8 (p = 0.001), respectively. The JSSF score for both groups was significantly improved. In SAFE-Q, physical function and daily living improved significantly in the HFG group, while pain and pain-related improved significantly in the fusion group.

Clonal evolution in locally advanced rectal cancers in response to neoadjuvant chemoradiotherapy.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 3616-3616
Author(s):  
Sinead Toomey ◽  
Aoife Carr ◽  
Jillian Rebecca Gunther ◽  
Joanna Fay ◽  
Anthony O'Grady ◽  
...  
Keyword(s):  
Somatic Mutation ◽  
Clonal Evolution ◽  
Locally Advanced ◽  
Neoadjuvant Chemoradiotherapy ◽  
Advanced Rectal Cancer ◽  
Post Treatment ◽  
Driver Mutations ◽  
Exome Capture ◽  
Poor Responders ◽  
Pre Treatment

3616 Background: Locally advanced rectal cancer, LARC (T3/4 and/or N+) is currently treated with neoadjuvant chemoradiotherapy (NACRT), however clinicopathological response is variable. Monitoring clonal evolution in response to NACRT may identify mutations driving therapeutic resistance or tumor growth after treatment. Methods: Fresh-frozen pre- and post-NACRT tumor and matched normal tissue from LARC patients were stratified into good (RCPath A), intermediate (RCPath B) and poor (RCPath C) responders. Following histological review, targeted exome capture was performed using an Agilent SureSelect Human all Exome V3 kit. Samples were sequenced to a minimum of 100X coverage on an Illumina HiSeq2000, and clonal evolution was assessed in matched pre- and post-NACRT tumor samples. Results: The median somatic mutation burden in pre-treatment samples was 114 (IQR 19-207). Two tumors were microsatellite (MSI) unstable and had elevated mutational burdens. The least evolution occurred in the poor responders, where there was little change in clonal composition after treatment, and driver mutations in genes including TP53 and APC were retained. On average 79% of pre-treatment mutations were retained post-treatment in poor responders and 33% of mutations were retained in intermediate responders. Many of the intermediate responders had loss of driver mutations including TP53 from the pre-treatment sample, but also shared a number of mutations in genes including PIK3CA and BRAF between pre- and post-treatment samples. There was also increased frequency in the post-treatment samples of clones that were not present in the pre-treatment samples. In one intermediate responder, all 47 mutations that were present in the pre-treatment sample including the driver mutations TP53 and APC were absent in the post-treatment sample, while 10 completely new mutations were identified. Conclusions: Dynamic mutational processes occur in LARC following selective pressures of exposure to NACRT, including changes in somatic mutation presence or frequency after treatment, owing to persistence or loss of sub-clones. As NACRT can profoundly affect the LARC genome, monitoring molecular changes during treatment may be clinically useful.

Longitudinal Genomic Analyses In Chronic Lymphocytic Leukemia (CLL) Patients Reveal Clonal Relationship and Genomic Evolution In Disease Progression and After Therapy

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3605-3605
Author(s):  
Esteban Braggio ◽  
Neil E. Kay ◽  
Scott Van Wier ◽  
Stephanie Smoley ◽  
Jeanette Eckel-Passow ◽  
...  
Keyword(s):  
Disease Progression ◽  
Board Of Directors ◽  
Copy Number ◽  
Research Funding ◽  
Clonal Evolution ◽  
The Other ◽  
Genomic Evolution ◽  
Advisory Committees ◽  
Time Points ◽  
Time Point

Abstract Abstract 3605 CLL is a malignant B-cell disorder characterized by the accumulation of small B lymphocytes with a mature appearance in blood, marrow and lymph nodes. Despite effective treatment options, all patients with CLL will eventually relapse after therapy. This could be due in part to the presence of subclones of the CLL cell population that harbor genetic abnormalities, which confer resistance to treatment. The aims of this study were to investigate the clonal evolution in longitudinal samples of CLL patients and to identify genetic alterations associated with disease progression and resistance to therapy. Sequential analyses were performed in 51 samples from 23 patients who were included in a previously reported clinical trial of pentostatin, cyclophosphamide and rituximab (PCR) given every 3 weeks for 6 cycles in previously untreated CLL (Blood 109:2007). In all cases the first sample analyzed was prior to therapy. In 5 of 23 patients, three time points were analyzed: >6 months prior to entry onto PCR trial (time point A), just before starting with the PCR regimen (time point B), and the time of relapse after PCR trial (time point C). Seven patients were analyzed at time points A and B; 9 at time points B and C and 2 at time points A and C. The median time between points A and B was 17.5 months (range 8–48 months) and between points B and C was 20.5 months (7–60 m). All samples were examined by array-based comparative genomic hybridization (aCGH) using the Agilent Sureprint G3 (1 million probe) array. aCGH findings were confirmed by interphase FISH using probes for D13S319 (MIR16–1/MIR15A), RB1, MDM2, CEP12, CEP6, MYB, TP53, NFKBIA, PERP and FGFR1 loci. Overall, we observed a small increase in the number of copy-number abnormalities (CNA) with disease progression. Twenty-two of the 23 patients with paired samples harbored at least one CNA that persisted in all samples, indicating clonal relationship between the sequential samples. In 15 of the 23 patients the tumor clone was stable and no CNA differences between time points were identified. Conversely, genomic evolution was found in 8 patients. In 3 cases the genetic differences were observed pre treatment (between time points A and B) and in the other 5 cases, the observed changes were found after therapy (between time points A and C or between B and C). One remarkable case with genome evolution exhibited two subclones sharing trisomies 12 and 19, but with several unique CNA confined to each subclone. The first subclone was characterized by deletions of 6q, RB1, MIR16-1/MIR15A and 3 other losses, while the second subclone showed homozygous deletion of MIR16–1/MIR15A and 5 other monoallelic deletions. The first subclone was predominant at time points A and B (60–70% of cells), but was present in only 10–20% of cells at time point C as confirmed by FISH. Conversely, the second subclone was observed in ~20% of cells at time points A and B and became predominant after therapy, found in ~80% of cells at time point C. Another case was characterized by deletion 11q32 (including ATM and others) as the sole abnormality at time point B. Significant genomic complexity was observed at time point C, including deletions of 11q32, 9p21 (CDKN2A), 9q12-q33, 14q13.2 (NFKBIA) and 17p (TP53), and gains of 2p16 (REL) and 9q34. Interestingly, the deletion 11q32 from both time points arose independently at each time point, as they exhibited different chromosomal breakpoints and copy number variants. Moreover, the other CNA found at relapse were not identified at diagnosis (confirmed by aCGH and FISH). For evolution of specific CNA, trisomy 12 was found in 5 cases at the first sample analyzed and was stable with no changes between time points. The frequency of deletions 13q14.3 (MIR16-1/MIR15A) and 17p increased at the later time points. Conversely, –6q decreased in frequency across time points (3 cases in time points A–B and 1 case in time point C). In summary, at least 35% of CLL patients exhibited clonal evolution and at least 9% showed evidence of multiple subclones. This subgroup of CLL patients provides an exceptional framework for comprehensive analysis of genome evolution during disease progression before and after therapy. Our observations also support the hypothesis of a common CLL progenitor cell can give rise to clonally related, but genetically evolving subpopulations of tumor cells. Finally, this study may bring novel information regarding the drug resistance pathways utilized by CLL B cell clones post therapy. Disclosures: Kipps: GlaxoSmithKline: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Genentech: Research Funding; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Research Funding; Genzyme: Research Funding; Memgen: Research Funding; Igenica: Consultancy, Membership on an entity's Board of Directors or advisory committees; Sanofi Aventis: Research Funding; Abbott Laboratories: Research Funding. Fonseca:Genzyme: Consultancy; Medtronic: Consultancy; BMS: Consultancy; AMGEN: Consultancy; Otsuka: Consultancy; Celgene: Consultancy, Research Funding; Intellikine: Consultancy; Cylene: Research Funding; Onyx: Research Funding; FISH probes prognostication in myeloma: Patents & Royalties.

An Analysis of the Transcriptional Response of Myelodysplastic Syndrome Stem Cells to Therapy at Single Cell Resolution

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 960-960
Author(s):  
Stephen S. Chung ◽  
Priyanka Vijay ◽  
Diana L. Stern ◽  
Virginia M. Klimek ◽  
Christopher E. Mason ◽  
...  
Keyword(s):  
Single Cells ◽  
Post Treatment ◽  
Differentially Expressed ◽  
Therapeutic Resistance ◽  
Wild Type ◽  
Aberrant Splicing ◽  
Time Points ◽  
Pre Treatment ◽  
Go Terms ◽  
Transcriptional Landscape

Abstract The myelodysplastic syndromes (MDS) are initiated in hematopoietic stem cells (HSCs) that persist despite excellent clinical responses to DNA methyltransferase inhibitors (DNMTIs). Given the likely contributions of genetic and phenotypic heterogeneity to therapeutic resistance, we sought to characterize the response of MDS HSCs to DNMTIs at single cell resolution. We identified patients who received the DNMTI decitabine and either sustained hematologic improvement (n=2) or were non-responders (n=2). Bone marrow (BM) specimens were obtained at pre- and post-treatment time points, as well as from untreated MDS patients (n=2) and age matched controls (n=2). From these specimens, HSCs (Lin-CD34+CD38-CD90+CD45RA-) were FACS-purified and the Fluidigm C1 platform was used to capture 686 single cells, with subsequent RNA-sequencing (Illumina HiSeq2500, 100 bp paired-end). The data was of high quality with an average mapping rate of 80%. We used t-distributed Stochastic Neighbor Embedding (t-SNE) to visualize differences between cells from responders, non-responders, and age matched controls (Fig.1A). This revealed separation between responder and non-responder cells prior to treatment, with non-responders more distant from normal HSCs. Post-treatment samples revealed a shift in responder cells closer to normal HSCs, with non-responder cells remaining distant from normal HSCs. A small number of cells from responders and normal HSCs clustered away from their respective groups and closely with cells from non-responders, highlighting intratumoral transcriptional heterogeneity. We speculate that such cells represent a reservoir for eventual therapeutic resistance in responders. Comparing pre-treatment HSCs from responders and non-responders, we found 455 differentially expressed genes (DEGs, FDR<0.01). DEGs were enriched for gene ontology (GO) terms including mRNA catabolic processes, NMD, and translational elongation, with 12/13 DEGs in the top five GO terms being ribosomal proteins (RPs). Pre-treatment cells formed four clusters based on these genes (Fig.1B), with responders comprising the two highest expressing clusters and non-responders comprising the next to lowest expressing cluster. The lowest expressing cluster was a mixture of cells from responders and non-responders, again suggestive of a source for eventual therapeutic resistance in responders. To assess the effect of decitabine on MDS HSCs agnostic to treatment response, we compared all pre-treatment MDS HSCs with all post-treatment MDS HSCs. We identified 45 DEGs (FDR <0.01) after filtering for high expression (FPKM >4) and removing genes that might reflect disease progression by excluding DEGs between early and late time points of untreated patients. Using these DEGs to cluster all pre- and post-treatment cells, the highest level of clustering separated a pre- and post-treatment cluster (Fig.1C). The pre-treatment cluster was primarily composed of pre-treatment cells from responders, with nearly all pre-treatment cells from non-responders falling in the post-treatment cluster, which also included post-treatment cells from both responders and non-responders. Thus MDS HSCs in responders occupy a unique transcriptional landscape prior to therapy. As aberrant splicing may contribute to MDS pathogenesis, we developed an algorithm to evaluate differential isoform usage in single cells. Comparing MDS HSCs to normal HSCs, we identified 22 genes with differentially expressed isoforms, including seven RPs (Fig.1D). A comparison between SRSF2 mutant (n=3) and wild-type (n=4) patients identified 13 differentially expressed isoforms, including five RPs. This suggests that even MDS HSCs from patients lacking splicing factor mutations may exhibit aberrant splicing, and that these changes may differ from those found in patients with mutated splicing genes. In conclusion, our studies of the transcriptional landscape of single MDS HSCs reveal RP gene signatures that represent novel biomarkers that distinguish MDS from age-matched controls and predict response to DNMTIs. Our studies also demonstrate significant intratumoral heterogeneity in gene expression that may underlie the biology of inevitable therapeutic resistance. Such heterogeneity includes differential isoform usage in both splicing factor mutant and wild type patients, suggesting that aberrant splicing may be a general feature of MDS. Disclosures No relevant conflicts of interest to declare.

scholarly journals Post-azacitidine clone size predicts long-term clinical outcome of patients with myelodysplastic syndromes and related myeloid neoplasms

2021 ◽  
Author(s):  
Seishi Ogawa ◽  
Magnus Tobiasson ◽  
Shinya Sato ◽  
Elsa Bernard ◽  
Shigeki Ohtake ◽  
...  
Keyword(s):  
High Risk ◽  
Clinical Outcome ◽  
Clinical Response ◽  
Post Treatment ◽  
Clone Size ◽  
Myeloid Neoplasms ◽  
Mutational Profiling ◽  
Before And After ◽  
Pre Treatment ◽  
Next Generation Sequencing Ngs

Abstract Azacitidine is a mainstay of therapy for high-risk MDS and other myeloid neoplasms. A significant correlation between azacitidine response and clinical outcome suggests a potential role of mutational profiling based on next-generation sequencing (NGS) before and after therapy in evaluating response and predicting overall survival (OS), which however has not fully elucidated. Here through NGS-based mutational profiling of large cohorts (n=451) of azacitidine-treated patients with high-risk MDS and other myeloid neoplasms, we show significant roles of multi-hit TP53 and germline DDX41 mutations in pre-treatment samples and post-treatment clone size in the evaluation/prediction of azacitidine response and OS after azacitidine therapy, which outperformed the prediction based only on clinical response and IPSS-R score. Post-treatment clone size strongly correlated with clinical response with exception of large persistent mutations frequently affecting TET2 after achieving complete remission and those with DDX41 mutations, which poorly correlated with clinical response. Our results highlight the importance of evaluating mutations in both pre- and post-treatment samples in the assessment of response and the prediction of OS after azacitidine therapy.

Sign in / Sign up

Export Citation Format

Share Document