scholarly journals Dynamics of Genetic Landscapes and Clonal Evolution between Patients and PDX Models in Acute Myeloid Leukemia

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 439-439 ◽  
Author(s):  
Naomi Kawashima ◽  
Yuichi Ishikawa ◽  
Akimi Akashi ◽  
Hikaru Hattori ◽  
Yohei Yamaguchi ◽  
...  
Keyword(s):  
Research Funding ◽  
Somatic Mutations ◽  
Clonal Evolution ◽  
Gene Mutations ◽  
Genetic Alterations ◽  
Treatment Resistant ◽  
Engraftment Failure ◽  
Nog Mice ◽  
Primary Leukemia ◽  
Pdx Models

Abstract Introduction: Recent genome-wide studies of leukemia have revealed its clonal architecture and subclonal heterogeneity. Patient-derived xenograft (PDX) models are assumed to capture the cellular and molecular characteristics of human cancer and widely utilized for studying drug response. However, it has not been elucidated whether PDXs faithfully represent the genetic features of primary leukemia. In this study, we monitored the dynamics of somatic mutations in primary leukemia cells and PDX cells to evaluate their genetic stability and clonal selections. Methods: A total of 90 fresh bone marrow or peripheral blood samples from patients with hematological malignancies were intravenously transplanted into NOD/Shi-scid, IL-2Rγnull (NOG) mice at 0.2-15x106 cells per mouse. Targeted sequencing of 54 genes frequently identified in myeloid malignancies was performed in 40 paired genomic DNA of successfully engrafted AML patient and their PDX samples and 20 AML patients with engraftment failure. Clonal diversities were analyzed by comparing variant allele frequencies (VAF) of somatic mutations in 16 sets of serial samples from AML patients at diagnosis and subsequent relapse, and their PDX models. All patients provided written informed consent. Results: Sixty-five of 90 (72%) primary cells (AML; 60, ALL; 5) engrafted in NOG mice at the median of day 112 (29-549) post transplantation. Patient samples with successful establishment of PDX models included significantly higher number of infused cell counts (7.2 vs. 4.9 x 106 cells, P=0.002), higher percentage of blasts (56.2% vs. 38.7%, P=0.04) and harbored activating kinase gene mutations more frequently than those with engraftment failure (83% vs. 40%, P=0.001; Figure 1). Especially, FLT3 (53% vs. 10%, P=0.001), NPM1 (28% vs. 5%, P=0.04), RUNX1 (25% vs. 0%, P=0.01), IDH1 (20% vs. 0%, P=0.03) and ASXL1 (18% vs. 0%, P=0.05) mutations were significantly accumulated in successfully engrafted patients. In terms of the sensitivity to chemotherapy, patients with successful engraftment in NOG mice showed poorer 2-year overall survival than those without engraftment (36.1% vs. 100%, P=0.04; Figure 2). In 40 pairs of AML patients and their PDXs, a total of 172 genetic alterations (101 SNV, 39 frameshift, 32 inframe insertion/deletion) were identified. Mean VAF changes in PDXs compared with patients showed dominant elevation in driver gene mutations including FLT3 (+16.9%), CEBPA (+19.1%) and WT1 (+26.4%) demonstrating the expansion of clones carrying these mutations in PDXs, whereas those of ASXL1 (-2.2%), NPM1 (+4.8%) and DNMT3A (+6.0%) in PDXs were almost the same as primary patient samples, implicating that these mutations are founder events in clonal evolution. VAF of 26 pairs of patients' samples and their PDXs at relapse were more concordant than those of 12 pairs at diagnosis (r2=0.689 vs. 0.550). In 16 sets of AML patients' samples at diagnosis and relapse, and their PDX samples, clonal diversities between primary leukemia at diagnosis and their PDXs were classified into 2 subtypes. In 7/16 models (44%), minor clones detected in patients at diagnosis dominantly expanded to be major clones in their PDX models, whereas major clones persisted in similar VAF between primary leukemia and their PDXs in 9/16 models (56%). These subtypes of clonal diversity between primary leukemia at diagnosis and their PDXs were concordant with clonal evolution between patients at diagnosis and relapse in 12/16 models (75%). Furthermore, in 4/16 models (25%), clones selectively expanded in PDXs were detected as major clones in their patients' first relapsed samples predictively. Conclusions: Our findings indicate the existence of diverse clonal evolution in AML PDX models. Primary AML samples harboring treatment-resistant clones have higher potential of engraftment and growth in NOG mice. Furthermore, PDX models recapitulate the clonal evolution from diagnosis through relapse in treatment-resistant patients. Further understanding of expanded clones in PDX models could reveal the pathogenesis of clonal selection in AML patients. Disclosures Kiyoi: Bristol-Myers Squibb: Honoraria; FUJIFILM Corporation: Research Funding; Zenyaku Kogyo Co., Ltd.: Research Funding; Sanofi K.K.: Research Funding; Celgene Corporation: Research Funding; Sumitomo Dainippon Pharma Co., Ltd.: Research Funding; Phizer Japan Inc.: Research Funding; Kyowa Hakko Kirin Co., Ltd.: Research Funding; Eisai Co., Ltd.: Research Funding; Astellas Pharma Inc.: Research Funding; Otsuka Pharmaceutical Co., Ltd.: Research Funding; Novartis Pharma K.K.: Research Funding; Takeda Pharmaceutical Co., Ltd.: Research Funding; Nippon Shinyaku Co., Ltd.: Research Funding; Chugai Pharmaceutical Co., Ltd.: Research Funding.

scholarly journals Rosai-Dorfman disease in the central nervous system with two isolated lesions originated from a single clone: a case report

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Huawei Jin ◽  
Zhenhua Yu ◽  
Tian Tian ◽  
Guoping Shen ◽  
Weian Chen ◽  
...  
Keyword(s):  
Clonal Evolution ◽  
Gene Mutations ◽  
Genetic Alterations ◽  
Driver Gene ◽  
Whole Exome ◽  
Rosai Dorfman Disease ◽  
Single Clone ◽  
Tumor Mutational Burden ◽  
The Central Nervous System ◽  
Clonal Nature

Abstract Background Rosai–Dorfman disease (RDD) is a rare, benign, idiopathic non-Langerhans cell histiocytosis. Cases of RDD in the CNS are extremely rare but lethal. RDD is thought to represent a reactive process. Recent studies proposed a subset of RDD cases that had a clonal nature. However, its clone origin is poorly understood. Case presentation We present a rare case of RDD in the CNS with two isolated lesions. These two lesions were removed successively after two operations. No seizure nor recurrence appears to date (2 years follow-up). Morphological and immunohistochemical profiles of these two lesions support the diagnosis of RDD. Based on the whole-exome sequencing (WES) data, we found the larger lesion has a higher tumor mutational burden (TMB) and more driver gene mutations than the smaller lesion. We also found seven common truncal mutations in these two lesions, raising the possibility that they might stem from the same ancestor clone. Conclusions Overall, this is the first report about clonal evolution of RDD in the CNS with two isolated lesions. Our findings contribute to the pathology of RDD, and support the notion that a subset of cases with RDD is a clonal histiocytic disorder driven by genetic alterations.

scholarly journals Genetic Mutation in Cytopenic Patients: Distinctive Genomic Profile between Preclinical Vs. Clinical Myelodysplastic Syndrome

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 5429-5429
Author(s):  
Kritanan Songserm ◽  
Amornchai Suksusut ◽  
Sunisa Kongkiatkamon ◽  
Kitsada Wudhikarn ◽  
Chinnachote Teerapakpinyo ◽  
...  
Keyword(s):  
Bone Marrow ◽  
High Risk ◽  
Myelodysplastic Syndrome ◽  
Somatic Mutations ◽  
Conflicts Of Interest ◽  
Gene Mutations ◽  
Genetic Alterations ◽  
Genetic Mutation ◽  
Low Risk ◽  
Genomic Profile

Genetic mutation in cytopenic patients: Distinctive genomic profile between preclinical vs. clinical myelodysplastic syndrome. Introduction Myelodysplastic syndromes (MDS) are heterogeneous groups of clonal hematopoietic disorders. The current diagnosis of MDS is based on morphologic assessments of dysplasia which are subjected to inter-observer variability and cytogenetic abnormalities which are frequently absent. Somatic mutations in myeloid-related genes have been identified in MDS. However, they are also found in idiopathic cytopenia of unknown significance (ICUS) that shows no significant dysplasia. Therefore, we aimed to explore the clinical implications of genetic mutations in ICUS and compared with MDS. The secondary objective was to find association between degree of dysplasia and somatic mutations. Materials and Methods The patients with peripheral cytopenia ≥1 lineage (ANC < 1,800/mm3, hemoglobin < 10 gm/dL, platelet < 100x109/mL) without explainable causes were enrolled. Bone marrow aspirates were evaluated independently by 2 hematologists. Of note, dysplasia are defined by WHO 2008 classification (eg. Erythroid lineage: ring sideroblasts, megaloblastoid change; granulocytic lineage: hypogranularity, pseudopelger-huet anomaly; megakaryocytic lineage: hypolobate, micro-megakaryocyte). The significant dysplasia cut off was 10% in single lineage or more. If there was a discrepancy, the third hematologist would help to reach the final consensus. We extracted DNA from bone marrow and performed next generation sequencing (NGS) that targeted 143 myeloid-related genes. Results Forty-eight patients were enrolled in this study. The median age at diagnosis was 70 years (71-96). Results of bone marrow examinations were categorized by morphology into 3 groups; non-significant dysplasia (dysplasia < 10%) 27%, low risk MDS (IPSS-R ≤3.5) 42% and high-risk MDS/sAML (IPSS-R >3.5/Blast≥20% in BM or peripheral blood) 31%. Most of cases (77%) carried normal cytogenetics while other genetic alterations were complex chromosome (6%), -Y (6%), del(5q) (4%), trisomy 8 (2%), del(20q) (2%), i(17q) (2%). Thirty from 48 cases (62%) harbored more than 1 somatic mutation. Twenty-eight gene mutations were identified. Mutations were detected 1.6 mutation per 1 patient in average. Most frequent somatic mutations were ASXL1:10/80 (12%), TET2:9/80 (11%), MFDS11: 6/80 (7%), TP53:6/80 (7%), and RUNX1:5/80 (6.25%). The proportions of cases with somatic mutations were not different across the groups (no dysplasia 50%, non-significant dysplasia 80% and significant dysplasia 62%). According to mutation types in each group, mutations in epigenetic pathways were the most frequent mutations across all patient subgroups (ICUS 64.7%, low-risk MDS 51.8 %, and high-risk MDS 52.5%). Mutations in transcription factor were predominated in MDS (18.5% and 25.0% in low-risk and high-risk MDS, respectively) compared to ICUS (11.7%). Individual average frequency of gene mutations was significantly different between disease subtype (high risk MDS 2.7 gene/person, low risk MDS 1.1 gene/person, ICUS 1.3 gene/person (P=.038). Higher variant allele frequency (VAF) of mutated genes was significantly observed in high risk MDS (38.3%) compared to low risk MDS (30.8%) and preclinical MDS (29.0%) (P=.03). Conclusion In conclusion, molecular profiling was significantly different between preclinical MDS and MDS groups in terms of types of somatic mutations and VAF. This unique contrast could be used to distinguish between preclinical MDS and clinically significant MDS. In contrast, degree of marrow dysplasia was not associated with number of gene mutations in this study. Prediction for clinical consequent of somatic mutations in CCUS requires long term follow up. Disclosures No relevant conflicts of interest to declare.

scholarly journals Characterization of Myelodysplastic Syndromes (MDS) with T-Cell Large Granular Lymphocyte Proliferations (LGL)

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 113-113 ◽  
Author(s):  
Christa Roe ◽  
Najla Alali ◽  
Eric Padron ◽  
Pearlie K Burnette ◽  
Kendra L. Sweet ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
T Cell ◽  
Peripheral Blood ◽  
Scoring System ◽  
Lower Risk ◽  
Research Funding ◽  
Somatic Mutations ◽  
Gene Mutations ◽  
Significant Difference ◽  
Somatic Gene

Abstract Introduction: MDS include a spectrum of hematopoietic stem cell malignancies characterized by bone marrow failure and dysplastic morphology. LGL is a clonal proliferation of cytotoxic T cells, which manifest as neutropenia, anemia, and thrombocytopenia and is associated with autoimmune disorders. LGL in association with MDS has been previously reported. However, clinicopathological features, prognostic, and predictive factors in those patients diagnosed with both LGL and MDS is not well studied. Methods: We identified patients at Moffitt Cancer Center (MCC) diagnosed with MDS who were previously tested for the presence of LGL clonal populations by peripheral blood flow cytometry at time of first visit. An LGL population was defined by the standard flow cytometry immunophenotype and clonality confirmed by T-cell receptor gamma and beta gene rearrangement.. Next Generation sequencing data was available for 151 patients. Recurrent somatic gene mutations were compared between patients with an LGL clone and those without. Results: Of the 675 patients with MDS tested for LGL in the database, 206 (30.5%) had an LGL clonal population. The mean LGL absolute cell count in the peripheral blood was 335/µL. Table-1 summarizes the baseline characteristics of the two groups. There was no difference in response to azacitidine therapy. Among 50 patients with LGL clone who received azacitidine with available data on response, the rate of hematological improvement or better (HI+) was 38%. The (HI+) was 28% among 105 patients evaluable for response without LGL clone. P .14 The median overall survival (OS) was for patients with no LGL clone was 65 months (mo) compared to 46 mo (p .024). The median OS for lower risk MDS patients (low/int-1 by International Prognostic Scoring System [IPSS]) was 68 mo versus 97 mo for those with or without LGL proliferation, respectively (P .005). In higher risk MDS, there was no difference in median OS between those with or without LGL expansion, respectively (20 mo versus 16 mo, p .7). The median OS for patients with very low/ low Revised-Internatinal Prognostic Scoring System (R-IPSS) was 96 mo if LGL proliferation was detected compared to 128 mo if it was not, (p value .016). For intermediate R-IPSS the median OS was 65 mo and 41 mo with or without LGL proliferation (p .16). Finally, for high/very high R-IPSS the median OS was 18 and 16 mo with or without LGL proliferation, (p .84) In cox regression analysis the presence of an LGL clone was independently prognostic for OS after adjusting for age and R-IPSS, Hazard ratio 1.3, p = .05. Somatic gene mutation data were available for 151 patients; there was no statistically significant difference in the distribution of any mutation except IDH-2 (Table-2). The most common somatic mutations observed among patients with LGL clone were SF3B1 19%, TET-2 16%, U2AF1 13%, IDH-2 13%, RUNX-1 13%, and ASXL-1 10%. In patients without an LGL clone the most common somatic mutations were TET-2 26%, ASXL-1 20%, DNMT3A 16%, TP53 13%, SF3B1 12%. Conclusion: An LGL clone is demonstrable in approximately 30% of patients with MDS in association with advancing age. The presence of LGL proliferation was associated with worse OS in lower risk MDS pts. Although the spectrum of somatic gene mutations were similar, the presence of IDH-2 mutation and absence of DNMT3A or TP53 gene mutationscharacterized LGL+ cases. Table 1. Table 1. Table 2. Table 2. Disclosures Roe: Celgene: Speakers Bureau; Alexion: Speakers Bureau; Seattle Genetics: Speakers Bureau. Sweet:Pfizer: Speakers Bureau; Novartis: Consultancy, Speakers Bureau; Ariad: Consultancy, Speakers Bureau; Incyte Corporation: Research Funding; Karyopharm: Honoraria, Research Funding. Sokol:Seattle Genetics: Consultancy; Spectrum: Consultancy. Komrokji:Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Consultancy, Speakers Bureau; Incyte: Consultancy.

Karyotypic and Genetic Abnormalities Associated with Clonal Evolution in Paroxysmal Nocturnal Hemoglobinuria.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2371-2371
Author(s):  
Hideki Makishima ◽  
Kenichi Yoshida ◽  
Michael J. Clemente ◽  
Masashi Sanada ◽  
Yasunobu Nagata ◽  
...  
Keyword(s):  
Stem Cell ◽  
Research Funding ◽  
Somatic Mutations ◽  
Chromosomal Abnormalities ◽  
Clonal Evolution ◽  
Clonal Expansion ◽  
Novel Mutations ◽  
Jak2 Mutation ◽  
Myeloid Malignancies ◽  
Whole Exome

Abstract Abstract 2371 PNH is a clonal stem cell disease. While nonmalignant, PNH shows certain similarities to MDS and other neoplasms affecting hematopoietic stem and progenitor cells, including persistence of an aberrant clone, clonal expansion, and phenotypic abnormalities. In a small proportion of patients, subtle chromosomal abnormalities can be found and cases of otherwise classical PNH due to microdeletions involving the PIG-A locus have been described, illustrating similarities to other malignant conditions. PIG-A gene mutations lead to defective biosynthesis of GPI anchors and are responsible for the PNH phenotype. Similarly, phenotypic features of stem cells affected by PIG-A mutations are believed to be responsible for the extrinsic growth advantage and clonal expansion in the context of immune mediated suppression of hematopoiesis. While this scenario is plausible, there are also observations suggesting that intrinsic factors may be also involved. For instance, PNH persists after successful immunosuppression, often for many years, suggesting activation of stem cell maintenance genes. Furthermore, PNH clones can also be encountered (albeit at a very low frequency) in healthy individuals, and PNH can present in a pure form without aplastic anemia. Such extrinsic factors may include additional, secondary genetic events such as somatic mutations. Supporting this theory, clonal rearrangement of chromosome 12, which leads to overexpression of the transcription factor HMGA2 gene, were found in cells with the PIG-A mutation from 2 PNH cases. Also, we recently reported 3 PNH cases with JAK2 V617F mutation, who presented with a MPN phenotype and thrombosis. We theorized that study of clonal architecture in PNH will reveal clues as to the pathogenesis of clonal evolution of the PNH stem cell. We applied next generation whole exome sequencing to detect somatic mutations in PNH cases (N=6). The subsequent validation set included 45 PNH cases. PNH and non-PNH cells were sorted using magnetic beads. DNA from both fractions was analyzed by whole exome sequencing and results of the non-PNH cells were subtracted from the results of the PNH clone. We found biallelic PIG-A mutations in 2 female cases and a single mutation in each male case. In an index female case with thrombosis, a novel somatic heterozygous mutation of NTNG1 (P24S) was detected, while the patient was negative for the JAK2 mutation. Allelic frequency with the NTNG1 mutation (53/160 sequence reads (33%)) was larger than that with a concomitant heterozygous PIG-A mutation (intron 5 splice donor site G<A) (78/333 reads (23%)). In this case, the size of the other heterozygous PIG-A mutation (G68E) was less (31/194 (16%)) than the other PNH clone. These findings suggest that there are 2 different PNH clones in one case and that the NTNG1 mutation might be acquired before PIG-A gene was mutated. Moreover, NTNG1 encodes a GPI-anchored cell membrane protein and the mutation (P24S) was located in the predicted signal peptide. All together, 3 novel mutations were discovered, including MAGEC1 (C747Y) and BRPF1 (N797S) mutations. Of note, BRPF1 mutations have been also reported in AML. Interestingly, BRPF1 encodes a component of MOZ/MORF complex, positively regulating the transcription of RUNX1. To screen pathogenic karyotypic lesions in PNH clonal expansions, we combined metaphase cytogenetics and single nucleotide polymorphism arrays. We detected 14 somatic chromosomal abnormalities in 13 out of 26 PNH cases (50%). Of note is that a microdeletion on 2q13 resulted in the loss of an apoptosis-inducing gene BCL2L11, suggesting a contribution to growth advantage. Somatic UPD lesions strongly suggest the presence of homozygous mutations, for example the SET nuclear oncogene, which is located in UPD9q32qter was observed in another PNH case. Overall, the discovery of these novel mutations, as well the previously described JAK2 mutation, indicates that the pathophysiology of PNH clonal evolution partially overlaps that of other myeloid malignancies. In sum, various novel somatic karyotypic abnormalities and mutations are frequently detected in PNH clones using technology with comprehensive and high resolution. Some of these aberrations play a similar role in the clonal evolution of myeloid malignancies. These results suggest new therapeutic strategies similar to those for other myeloid malignancies should be considered in PNH cases with addition mutations. Disclosures: Makishima: Scott Hamilton CARES Initiative: Research Funding. Maciejewski:NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding.

The Presence Of Leukemogenic Mutational Events In Paroxysmal Nocturnal Hemoglobinuria Suggests That Clonal Architecture Of Bone Marrow Failure Is Similar To Myelodysplastic Syndrome

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 804-804
Author(s):  
Wenyi Shen ◽  
Bartlomiej P. Przychodzen ◽  
Michael J. Clemente ◽  
Brittney Dienes ◽  
Tetsuichi Yoshisato ◽  
...  
Keyword(s):  
Stem Cell ◽  
Aplastic Anemia ◽  
Research Funding ◽  
Somatic Mutations ◽  
Gene Mutations ◽  
Trisomy 8 ◽  
Clonal Architecture ◽  
Whole Exome ◽  
Tet2 Mutation ◽  
Pnh Clone

Abstract While PNH is characterized by clonality, it has not been considered a malignant disorder. Nevertheless, the similarities to some forms of MDS are clearly apparent, and include clonal hematopoiesis with the prescence of a somatic mutation, persistence and expansion of an aberrant stem cell clone, and frequent antedescent aplastic anemia. Somatic PIG-A gene mutations, the hallmark of PNH, lead to a defective GPI-anchor biosynthesis with a resultant deficiency of the GPI-anchored proteins, and is believed to be responsible for an extrinsic growth advantage. While this scenario is plausible, our research indicates that intrinsic factors may also be involved. Such factors may include additional, secondary genetic events, such as somatic mutations, which may coexist with PIG-A mutations, suggesting that the clonal architecture of PNH is more complex. For the purpose of this project we hypothesized that the evolution of a PNH clone may be associated with additional mutational events. Our genetic analysis involved 50 patients with PNH: the average PNH clone size by flow cytometry was 76%, 19 of these patients have history of antecedent aplastic anemia. We first performed paired whole exome sequencing (WES) of sorted PNH and wild type cells in 12 PNH patients and confirmed 34 somatic events in PNH-derived DNA, including 19 missense, 4 nonsense, 8 frameshift and 3 splice site mutations (a total of 22 genes). An additional 38 cases were used to examine the prevalence of these mutations. We detected somatic PIGA mutations (5 SNVs and 8 indels) in 9/12 PNH fractions (1 negative case contained a 616 kb delXp22.2 microdeletion involving the PIGA locus). Deep sequencing demonstrates the presence two independent PIGA mutations in 1/3 of the patients; semisolid culture experiments followed by sequencing of single CFUs confirmed that 2 independent PNH clones were present. Most significantly, by WES we found and confirmed additional somatic mutations (other than PIG-A) in PNH clones, including TET2 (p.E1250X), MAGEC1 (p.C747Y), BRPF1 (p.N797S), KDM3B (p.L125I), STAC3 (p.F97V) and NTNG1 (p.P24S). In 38 PNH cases studied by deep NGS sequencing, additional 2 somatic homozygous JAK2 (p.V617F), TET2 (p.S1556fs), SUZ12 (intron 2 splice), DHX29 (K498N), MECOM (P18S), and BCOR (Q1606X) mutations were found. Using targeted deep NGS of individual colonies, clonal architecture was analyzed in 9/12 WES cases. Clonal analysis of these cases revealed that PIGA mutations were often acquired in a later stage (6/9) preceeded by mutations in other genes (including NTNG1, CELSR1, STAC3, TET2, SLC20A1). For instance, in one PNH case, the PNH ancestral event was a novel MAN1A2 mutation, which was followed by the appearance of subclonal PIGA mutations, thus creating 2 independent subclones. In another illustrative case, somatic SYNE2 and PEX14 gene mutations were the initial events, followed by a PIGA mutation and an additional subclonal FBN1 mutation. Several somatic mutations were present in both PNH and WT cells and thus likely predated PIGA mutations. These mutations included TET2, SUZ12 and JAK2. In one case we determined that mutant fractions for TET2 and STAC3 mutations were larger than the PIGA mutant fraction with the TET2 mutation also present in the PNH- fraction (CD59+), indicating that PNH, in this case, evolved after the TET2 mutation as a subclone. However, in another case, dysplastic changes were identified along with trisomy 8. FISH analysis resolved that trisomy 8 was only present in the PNH- fraction, suggesting that in this patient, PNH evolved independent of the acquisition of trisomy 8. In sum, using whole exome sequencing, targeted deep NGS sequencing and single colony sequencing, we found that PNH, analogous to myeloid neoplasia, has a complex clonal architecture. Furthermore, the PIG-A mutation is frequently not the sole genetic lesion. Additional somatic mutations may help to further clarify the mechanism of clonal expansions, persistence of the mutated PNH stem cell, clinical diversity of PNH, and distinct behavior of PNH clones in individual patients. Disclosures: Maciejewski: NIH: Research Funding; Aplastic anemia&MDS International Foundation: Research Funding. Makishima:AA & MDS international foundation: Research Funding; Scott Hamilton CARES grant: Research Funding.

Comprehensive Analyses of Genetic Features Identify Coordinate Signatures in Diffuse Large B-Cell Lymphoma

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3922-3922
Author(s):  
Bjoern Chapuy ◽  
Andrew J Dunford ◽  
Chip Stewart ◽  
Atanas Kamburov ◽  
Jaegil Kim ◽  
...  
Keyword(s):  
B Cell ◽  
Board Of Directors ◽  
Research Funding ◽  
Somatic Mutations ◽  
Chromosomal Rearrangements ◽  
Low Frequency ◽  
B Cell Lymphoma ◽  
Genetic Alterations ◽  
B Cell Differentiation ◽  
Advisory Committees

Abstract Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous disease characterized by multiple low-frequency alterations including somatic mutations, copy number alterations (CNAs) and chromosomal rearrangements. We sought to identify previously unrecognized low-frequency genetic events, integrate recurrent alterations into comprehensive signatures and associate these signatures with clinical parameters. For these reasons, our multi-institutional international group assembled a cohort of 304 primary DLBCLs from newly diagnosed patients, 87% of whom were uniformly treated with state-of-the-art therapy (rituximab-containing CHOP regimen) and had long term followup. Tumors were subjected to whole exome sequencing with an extended bait set that included custom probes designed to capture recurrent chromosomal rearrangements. In this cohort, 47% of samples had available transcriptional profiling and assignment to associated disease subtypes. Analytical pipelines developed at the Broad Institute were used to detect mutations (MuTect), CNAs (Recapseq+Allelic Capseq) and chromosomal rearrangements (dRanger+Breakpointer) and assess clonality (Absolute). To analyze formalin-fixed paraffin-embedded tumors without paired normals we developed a method which utilized 8334 unrelated normal samples to stringently filter recurrent germline events and artifacts. Significant mutational drivers were identified using the MutSig2CV algorithm and recurrent CNAs were assessed with GISTIC2.0. In addition, we utilized a recently developed algorithm, CLUMPS2, to prioritize somatic mutations which cluster in 3-dimensional protein structure. With this approach, we identified > 90 recurrently mutated genes, 34 focal amplifications and 41 focal deletions, 20 arm-level events and > 200 chromosomal rearrangements in the DLBCL series. Of note, 33% of the mutational drivers were also perturbed by chromosomal rearrangements or CNAs, underscoring the importance of a comprehensive genetic analysis. In the large DLBCL series, we identified several previously unrecognized but potentially targetable alterations including mutations in NOTCH2 (8%) and TET2 (5%). The majority of identified chromosomal rearrangements involved translocations of potent regulatory regions to intact gene coding sequences. The most frequently rearrangements involved Ig regulatory elements which were translocated to BCL2, MYC, BCL6 and several additional genes with known roles in germinal center B-cell biology. After identifying recurrent somatic mutations, CNAs and chromosomal rearrangements, we performed hierarchical clustering and identified subsets of DLBCLs with comprehensive signatures comprised of specific alterations. A large subset of tumors shared recurrent alterations previously associated with follicular lymphoma including mutations of chromatin modifiers such as CREBBP, MLL2, and EZH2 in association with alterations of TNFRSF14 and GNA13 and translocations of BCL2. This cluster was enriched in GCB-type DLBCLs and contained a subset with select genetic alterations associated with an unfavorable outcome. An additional cohort of tumors was characterized by alterations perturbing B-cell differentiation including recurrent BCL6 translocations or alterations of PRDM1. A subset of these DLBCLs had alterations of NOTCH2 and additional pathway components or mutations of MYD88 in association with TNFAIP3, CD70 and EBF1, a master regulator of B-cell differentiation. An additional group of DLBCLs exhibited frequent MYD88 mutations in association with alterations of CD79B, PIM1, TBL1XR1 and ETV6 and BCL2 copy gain; these tumors were highly enriched for ABC-type DLBCLs. This coordinate signature and additional alterations of p53 pathway components were associated with outcome. We explored bases for the identified genetic alterations in DLBCL by performing an in silico mutational signature analysis. The most frequent mutational signatures were those of spontaneous deamination (aging) and AID with rare cases of microsatellite instability. We also assessed the clonality of identified genetic features to define cancer cell fraction and establish the timing of specific genetic events. The comprehensive genetic signatures of clinically annotated DLBCLs provide new insights regarding approaches to targeted therapy. Disclosures Link: Kite Pharma: Research Funding; Genentech: Consultancy, Research Funding. Rodig:Perkin Elmer: Membership on an entity's Board of Directors or advisory committees; BMS: Research Funding. Pfreundschuh:Boehringer Ingelheim, Celegene, Roche, Spectrum: Other: Advisory board; Roche: Honoraria; Amgen, Roche, Spectrum: Research Funding. Shipp:Gilead: Consultancy; Sanofi: Research Funding; BMS: Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Membership on an entity's Board of Directors or advisory committees; Bayer: Membership on an entity's Board of Directors or advisory committees, Research Funding.

scholarly journals Signaling Gene Mutations Are Characterized By Diverse Patterns of Expansion and Contraction during Progression from MDS to Secondary AML

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 2-3
Author(s):  
Andrew J Menssen ◽  
Ajay Khanna ◽  
Christopher A Miller ◽  
Gue Su Chang ◽  
Jin J Shao ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Research Funding ◽  
Limit Of Detection ◽  
Clonal Evolution ◽  
Gene Mutations ◽  
Transcription Factor Gene ◽  
High Coverage ◽  
Factor Gene ◽  
Multiple Signaling ◽  
Skin Samples

Background: Previous studies indicate that mutations in signaling (e.g., receptor tyrosine kinases and RAS pathway members) and transcription factor genes are more common in secondary acute myeloid leukemia (sAML) than myelodysplastic syndrome (MDS), suggesting a role in disease progression. However, our understanding of the timing and order of mutation acquisition in these genes remains incomplete without analyzing paired MDS and sAML samples from the same patient. Defining the role of signaling gene mutations during progression should provide biologic insight into clonal evolution and help define prognostic markers for MDS progression. Methods: We banked paired MDS and sAML (and matched skin) samples from 44 patients (median time to progression: 306 days, range 21-3568). We sequenced 44 sAML (+ skin) samples for 285 recurrently mutated genes (RMGs) and 12 samples were selected for enhanced whole genome sequencing (eWGS, genome with deep exome coverage) of MDS and sAML samples (+ skin) to determine clonal hierarchy. Somatic mutations in these 12 samples were validated with high coverage error-corrected sequencing, and clonality was defined in MDS and sAML samples using mutation variant allele frequencies (VAFs). Additionally, error-corrected sequencing for all sAML RMG mutations, plus 40 additional genes, was performed on 43 of the MDS samples. Single cell DNA sequencing (scDNAseq, Mission Bio) was performed on 6 samples. Results: We identified 32 signaling gene mutations in 15 of the 44 sAML samples, with only 11 of 32 mutations (34%) detected in the initial, paired MDS sample (limit of detection; &lt;0.1% VAF). This was significantly less than the percentage of sAML transcription factor gene mutations present at MDS (17 of 23, 74%, p=0.006). We used eWGS data to define clonal hierarchies for 12 patients, and found that both signaling and transcription factor gene mutations were in subclones (9 of 9, and 7 of 8 clones, respectively), with signaling gene mutations occurring as terminal events during clonal evolution. Finally, 8 of 9 subclones with signaling gene mutations expanded at progression. Together, the data confirm that both signaling and transcription factor mutations occur in subclones, but with a preferred order of mutation acquisition. We next asked if low-level (&lt;1% VAF) signaling gene mutations were present in MDS samples. Using error-corrected sequencing, we identified 22 signaling gene mutations that were present at MDS and absent at sAML (avg VAF: 0.8%; range 0.05%-11.7%). Combined with sAML-defined signaling genes, 33 total signaling gene mutations were detected at MDS in 19 patients, but only 11 (33%) were present after progression. We observed 5 distinct patterns of clonal evolution for signaling genes: 1) MDS mutations persist and expand at sAML (n=6), 2) ≥2 mutations are present at MDS, at least one mutation persists (and expands) and another contracts at sAML (n=4), 3) MDS mutations contract and a new mutation emerges at sAML (n=2), 4) MDS mutations collapse at sAML (n=7), and 5) no MDS mutations, but ≥1 mutation emerges at sAML (n=5). These diverse patterns of clonal evolution suggest that MDS cells undergo strong selective pressure to acquire a signaling gene mutation, but only mutations in the correct context contribute to progression. Finally, we observed that several MDS (n=6) and sAML (n=10) samples had multiple signaling gene mutations, and it was not always clear whether they occurred in the same subclone. We performed scDNAseq of 6 sAML samples with multiple signaling gene mutations (2-4/case). In 5 of 6 cases the signaling gene mutations did not occur in the same subclone. One sample contained 2 subclones with a NRAS and a PTPN11 mutation, with a separate subclone harboring an additional NRAS mutation. In sum, the co-occurrence of two signaling gene mutations in the same subclone is rare, indicating that the presence of multiple signaling gene mutations may be functionally redundant or detrimental to leukemia cells. Conclusions: Rare cells containing signaling gene mutations are present in nearly half of MDS patients who progress to sAML. The high frequency of signaling gene mutations and diverse patterns of clonal evolution (including the loss of one mutation and acquisition of another), suggest that signaling genes are a major driver of progression to sAML. The paucity of subclones with multiple signaling gene mutations suggests a therapeutic vulnerability for mutant cells. Disclosures DiPersio: Magenta Therapeutics: Membership on an entity's Board of Directors or advisory committees. Jacoby:AbbVie: Research Funding; Jazz Pharmaceuticals: Research Funding.

scholarly journals Genetic Alterations at Diagnosis Predict Outcome of AML Patients Age 60 or Older Undergoing Allogeneic Transplantation in First Remission

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 48-48 ◽  
Author(s):  
H. Moses Murdock ◽  
Haesook T. Kim ◽  
Bryan Hambley ◽  
Pankit Vachhani ◽  
Nathan Denlinger ◽  
...  
Keyword(s):  
High Risk ◽  
Board Of Directors ◽  
Genetic Risk ◽  
Research Funding ◽  
Gene Mutations ◽  
Genetic Alterations ◽  
Advisory Committees ◽  
Genetic Characteristics ◽  
The Impact ◽  
Advisory Role

Background: Older age is associated with inferior outcomes after allogeneic hematopoietic stem cell transplantation (HSCT) for acute myeloid leukemia (AML). High risk genetic characteristics are common among older patients and linked to poor outcomes in the non-transplant setting. An enhanced understanding of genetic risk may thus provide a basis for improving transplant outcomes in these patients. We evaluated the impact of leukemia genetic characteristics at diagnosis on HSCT outcomes in a multi-center cohort of AML patients age 60 or older receiving HSCT in first complete remission (CR1). Methods: We performed targeted sequencing of 112 genes on diagnostic leukemia samples from 257 patients with AML age 60 or older who received allogeneic HSCT in CR1 at 5 US transplant centers. Median age at diagnosis and HSCT were 65 (range 59-76) and 66 (range 60-76), respectively. 31% had clinically defined secondary AML, 11% had therapy-related AML, and 23% had adverse cytogenetics by 2017 ELN classification. Most (84%) were treated with anthracycline-based induction chemotherapy, while 16% received non-intensive induction. Conditioning was either reduced-intensity or non-myeloablative in 94% of patients. Median follow-up for survivors was 3.7 years; 3-year overall survival (OS) and leukemia-free survival (LFS) were 48% and 44%, respectively. Results: All patients had recurrent genetic alterations at the time of diagnosis, including 251 (98%) with gene mutations and 6 with only cytogenetic abnormalities. The most frequent gene mutations were DNMT3A (25%), NPM1 (23%), FLT3-ITD (22%), ASXL1 (21%), TET2 (21%), RUNX1 (20%), and SRSF2 (18%). Secondary-type mutations associated with antecedent MDS occurred in 42%, and 10% had TP53 mutations. As expected, secondary-type and TP53 mutations were associated with clinically-defined secondary AML (p&lt;0.001), need for reinduction (p=0.03), and CR with incomplete count recovery (p= 0.03). Despite the older age at leukemia diagnosis, putative germline pathogenic variants were identified in 22 (8.6%) patients, including 17 (6.6%) with DDX41 mutations (13/17 with somatic mutation of the second allele), and 5 with TERT or TERC variants not found in population databases. We evaluated the impact of gene mutations on LFS using univariable and multivariable Cox models and developed a hierarchical model of 3 molecular genetic risk groups according to the hazard ratios (Fig 1A): (1) patients with TP53 mutation or JAK2 mutation or FLT3-ITD/NPM1-WT (high risk), (2) patients without high risk mutations who have DNMT3A or GATA2 or DDX41 mutations (low risk) (3) patients without high- or low-risk mutations (intermediate risk), with 3-year LFS of 8%, 65%, and 47% (p&lt;0.001), respectively. Next, we combined molecular genetic and cytogenetic risk to derive a final genetic model comprised of 4 groups with distinct 3-year LFS (69%, 50%, 27%, and 0%) (Fig 1B). Poor LFS in the very high-risk group was due almost entirely to relapse (3-year relapse rate &gt; 90%), but was driven by a combination of relapse and non-relapse mortality in the intermediate and high-risk groups (Fig 2). Conclusion: Genetic characteristics at diagnosis are highly associated with OS and LFS in AML patients age 60 or older who undergo allogeneic transplantation in CR1. We identify patients with low genetic risk and remarkably good outcomes who may be candidates for strategies aimed at reducing toxicity, and those with very high-risk genetics who have limited benefit from current transplant approaches. Among intermediate and high-risk patients, the impact of disease genetics on LFS is mostly due to relapse, suggesting that a model incorporating measurement of residual disease in CR1 and after transplantation could enable a more dynamic estimation of risk. Disclosures Perales: Bristol-Meyers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees; Incyte: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Nektar Therapeutics: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Omeros: Honoraria, Membership on an entity's Board of Directors or advisory committees; Bellicum: Honoraria, Membership on an entity's Board of Directors or advisory committees; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees; NexImmune: Membership on an entity's Board of Directors or advisory committees; MolMed: Membership on an entity's Board of Directors or advisory committees; Merck: Consultancy, Honoraria; Medigene: Membership on an entity's Board of Directors or advisory committees; Servier: Membership on an entity's Board of Directors or advisory committees; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Kyte/Gilead: Research Funding; Miltenyi: Research Funding. Koreth:Equillium: Consultancy; Amgen: Consultancy; Cugene: Consultancy. Ho:Jazz Pharmaceuticals: Consultancy. Soiffer:Mana therapeutic: Consultancy; Kiadis: Other: supervisory board; Juno, kiadis: Membership on an entity's Board of Directors or advisory committees, Other: DSMB; Gilead, Mana therapeutic, Cugene, Jazz: Consultancy; Jazz: Consultancy; Cugene: Consultancy. Carroll:Astellas Pharmaceuticals: Research Funding; Incyte: Research Funding; Janssen Pharmaceuticals: Consultancy. Vasu:Boehringer Ingelheim: Other: Travel support; Seattle Genetics: Other: Clinical trial support. Wang:Abbvie: Other: Advisory role; Kite: Other: Advisory role; Jazz: Other: Advisory role; Astellas: Other: Advisory role, Speakers Bureau; celyad: Other: Advisory role; Pfizer: Other: Advisory role, Speakers Bureau; Stemline: Other: Advisory role, Speakers Bureau; Daiichi: Other: Advisory role; Amgen: Other: Advisory role; Agios: Other: Advisory role. Devine:Kiadis Pharma: Other: Protocol development (via institution); Bristol Myers: Other: Grant for monitoring support & travel support; Magenta Therapeutics: Other: Travel support for advisory board; My employer (National Marrow Donor Program) has equity interest in Magenta. Lindsley:Jazz Pharmaceuticals: Research Funding; Takeda Pharmaceuticals: Consultancy; Medlmmune: Research Funding.

scholarly journals Longitudinal Assessment of Circulating Tumor Mutational Burden Using a Next-Generation Sequencing Cancer Gene Panel: A Potential Biomarker of Response to Programmed Cell Death 1 (PD-1) Blockade in Patients with Relapsed/Refractory Classical Hodgkin Lymphoma

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 131-131 ◽  
Author(s):  
Martina Di Trani ◽  
Ettore Rizzo ◽  
Silvia Locatelli ◽  
Fabrizio Marino ◽  
Vanessa Cristaldi ◽  
...  
Keyword(s):  
Research Funding ◽  
Somatic Mutations ◽  
Clonal Evolution ◽  
Advisory Board ◽  
Classical Hodgkin Lymphoma ◽  
Scientific Advisory Board ◽  
Dna Mutations ◽  
Programmed Cell Death 1 ◽  
Scientific Advisory ◽  
Generation Sequencing

Introduction: The programmed cell death 1 (PD-1) monoclonal antibodies (MoAbs) nivolumab and pembrolizumab induce response rates exceeding 70% in relapsed/refractory (R/R) classical Hodgkin lymphoma (cHL). The lack of response to PD-1 MoAbs, and the relapse occurring in most patients who had responded to PD-1 blockade suggest that tools to identify the determinants of response/resistance to PD-1 MoAbs are urgently required. We hypothesized that the characterization of the mutational profile of circulating tumor DNA (ctDNA) could represent a valuable tool to track clonal evolution-driven resistance to checkpoint inhibitors. Patients and Methods: 21 R/R cHL (median age, 32 years; range, 19-51) who had received a median of 5 (range, 3-7) chemotherapy lines, including autologous stem cell transplantation (77%) and brentuximab vedotin (100%), were treated with PD-1 MoAbs. Blood samples were profiled by CAPP-Seq strategy. We analyzed ctDNA and paired DNA from peripheral blood mononuclear cells (PBMCs), as source of germline DNA to filter out polymorphism and sequencing errors. A targeted resequencing panel optimized to include the coding exons and splice sites of 133 genes (320 Kb) that are recurrently mutated in B-cell lymphomas was used. Libraries were prepared from ctDNA and germline gDNA according to the CAPP-seq targeted enrichment strategy (Nimblegen-Roche) and subjected to ultra-deep-next generation sequencing (NGS) using the Nextseq 500 platform (Illumina). The sequencing was performed to obtain a depth of coverage &gt;2000x in &gt;80% of the target region in all samples, which allowed a sensitivity of 3x10-3. A stringent and completely automated bioinformatic pipeline was applied to call non-synonymous somatic mutations, using the somatic function of VarScan2. Results: After a median of 26 (range, 9-63) cycles of PD-1 inhibitors best response was complete remission (CR) for 9 patients (42%), partial remission (PR) for 6 (29%) and progressive disease (PD) for 6 (29%). Patients achieving PR experienced a disease control lasting for 4.5 to 24 months and subsequently underwent PD. Plasma and PBMC samples were collected at baseline, every five cycles of therapy, and end-of-therapy (EOT). At baseline, 18 of 21 patients could be successfully genotyped, whereas three were not. Evaluable patients showed a mean (±SD) number of mutated genes and mutations per patient of 7.3±5.1 (range, 2-22) and 9.9±8.4 (range, 2-37), respectively. Genes recurrently affected by non-synonymous somatic mutations in &gt;20% of R/R cHL included STAT6 (45%), SOCS1 (40%), ITPKB (35%), GNA13 (35%), TP53 (20%), TNFAIP3 (15%). At baseline, no association of distinct DNA mutations with resistance to PD-1 inhibitors could be demonstrated. Signaling pathways targeted by DNA mutations included JAK-STAT, NF-κB, PI3K-AKT, cytokine, NOTCH, immune evasion. The concentration of ctDNA reported as haploid genome equivalent per ml (hGE/ml) was 592.2 (range, 2-2,746), with values of hGE/ml detected in PD patients being significantly higher as compared to CR patients (P=.0437). As compared to cycle 0, the hGE/ml of ctDNA at cycle 5 showed a significant reduction (592.2 vs. 67, P&lt;.0008) which was followed by further hGE/ml decline in CR patients (to 14 P=.05) and further hGE/ml increase in PD patients (to 1,300 P=.1). At cycle 5, all CR/PR patients showed complete disappearance of baseline mutations, which were replaced by completely novel clones. In all CR/PR patients, this pattern of "clonal reshaping" was repeatedly detected over time. In striking contrast, at cycle 5, PD patients showed the persistence of baseline mutations. In all PD patients, this pattern of "clonal persistence", was repeatedly detected over time. In 4 patients, resistance to PD-1 inhibitors was associated with the appearance of a TP53 mutated clone. Although, a formal correlation of circulating DNA mutations with standard FDG-PET imaging was outside the objective of this study, both the "clonal reshaping" and "clonal persistence" patterns could be demonstrated to correlate with the results of FDG-PET. Conclusions: Analysis of ctDNA allows detecting tumor-specific mutations in R/R cHL. The longitudinal tracking of circulating DNA mutations in these patients identifies two different patterns of clonal evolution associated with sensitivity (clonal reshaping) or resistance (clonal persistence) to checkpoint blockade. Disclosures Santoro: Eisai: Consultancy, Speakers Bureau; Novartis: Speakers Bureau; Lilly: Speakers Bureau; Sandoz: Speakers Bureau; Pfizer: Consultancy, Speakers Bureau; Arqule: Consultancy, Speakers Bureau; Gilead: Consultancy, Speakers Bureau; AstraZeneca: Speakers Bureau; Celgene: Speakers Bureau; Servier: Consultancy, Speakers Bureau; Takeda: Speakers Bureau; BMS: Speakers Bureau; Roche: Speakers Bureau; Abb-Vie: Speakers Bureau; Amgen: Speakers Bureau; BMS: Consultancy; Bayer: Consultancy, Speakers Bureau; MSD: Speakers Bureau. Rossi:Gilead: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Honoraria, Other: Scientific advisory board; Janseen: Honoraria, Other: Scientific advisory board; Roche: Honoraria, Other: Scientific advisory board; Astra Zeneca: Honoraria, Other: Scientific advisory board. Carlo-Stella:ADC Therapeutics: Consultancy, Other: Travel, accommodations, Research Funding; Sanofi: Consultancy, Research Funding; Celgene: Research Funding; Janssen Oncology: Honoraria; MSD: Honoraria; Servier: Consultancy, Honoraria, Other: Travel, accommodations; Amgen: Honoraria; Boehringer Ingelheim: Consultancy; Novartis: Consultancy, Research Funding; F. Hoffmann-La Roche Ltd: Honoraria, Other: Travel, accommodations, Research Funding; BMS: Honoraria; Janssen: Other: Travel, accommodations; Takeda: Other: Travel, accommodations; Rhizen Pharmaceuticals: Research Funding; AstraZeneca: Honoraria; Genenta Science srl: Consultancy.

scholarly journals Establishment of prediction models for lung cancer NOG/PDX models: A guideline for machine learning in small biomedical datasets

2020 ◽  
Author(s):  
Haoyue Guo ◽  
Li Diao ◽  
Hui Qi ◽  
Chunlei Dai ◽  
Yu Chen ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Logistic Regression ◽  
Prediction Models ◽  
Gene Mutations ◽  
Gradient Boosting ◽  
Support Vector ◽  
Stepwise Logistic Regression ◽  
Extreme Gradient Boosting ◽  
Nog Mice ◽  
Pdx Models

Abstract Background: Targeted therapy and immune checkpoint inhibitors are the most promising treatments for lung cancers but still facing multiple challenges, including resistance and individual difference. Therefore, patient-derived tumor xenografts (PDX) models are developed for drug discovery and screening. NOG mice is under the destruction of the interleukin-2 (IL-2) receptor common gamma chain, which is appropriate for building PDX models to test immunotherapies. However, current studies have little understanding of the causes of genotype mismatches in PDX or NOG/PDX models, which leads to a massive economic and time loss.Methods: Lung cancer tissues from 53 patients were obtained and engrafted into NOG mice. All of the patients' tumors and NOG/PDX models were detected for common gene mutations. Seventeen clinicopathological features were organized and input to stepwise logistic regression based on the lowest Akaike information criterion (AIC), least absolute shrinkage and selection operator (LASSO)-logistic regression, support vector machine recursive feature elimination (SVM-RFE), eXtreme Gradient Boosting (XGBoost), Gradient Boosting & Categorical Features (CatBoost), and synthetic minority over-sampling technique (SMOTE). Finally, the performance of all models was evaluated by the accuracy, area under the receiver operating characteristic curve (AUC), and F1 score in 100 testing groups.Results: Fifty-three lung cancer NOG/PDX models were successfully established, with a genotype matching rate of 79.2% (42/53). Two multivariable logistic regressions revealed that age, the number of driver mutations, epidermal growth factor receptor (EGFR) gene mutations, the type of prior chemotherapy, prior tyrosine kinase inhibitors (TKIs) therapy, and the source were potent predictors. Moreover, CatBoost (mean accuracy=0.960; mean AUC=0.939; mean F1 score=0.908) and 8-feature SVM (mean accuracy=0.950; mean AUC=0.934; mean F1 score=0.903) showed the best performance compared with the other algorithms. Moreover, the combination of SMOTE with SVM significantly improved the predictive capability (mean accuracy: 0.961 vs. 0.958, P=0.025; mean AUC: 0.940 vs. 0.935, P=0.045; mean F1 score: 0.909 vs. 0.903, P=0.047).Conclusions: We established an optimal predictive model to screen lung cancer patients for NOG/PDX models, and also offered a general approach for building prediction models in small unbalanced biomedical samples.

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