RESUMO
BACKGROUND: Despite the effectiveness of the various targeted therapies currently approved for solid tumors, acquired resistance remains a persistent problem that limits the ultimate effectiveness of these treatments. Polyclonal resistance to targeted therapy has been described in multiple solid tumors through high-throughput analysis of multiple tumor tissue samples from a single patient. However, biopsies at the time of acquired resistance to targeted agents may not always be feasible and may not capture the genetic heterogeneity that could exist within a patient. METHODS: We analyzed circulating tumor DNA (ctDNA) with a large next-generation sequencing panel to characterize the landscape of secondary resistance mechanisms in two independent prospective cohorts of patients (STING: n = 626; BIP: n = 437) with solid tumors who were treated with various types of targeted therapies: tyrosine kinase inhibitors, monoclonal antibodies and hormonal therapies. RESULTS: Emerging alterations involved in secondary resistance were observed in the plasma of up 34% of patients regardless of the type of targeted therapy. Alterations were polyclonal in up to 14% of patients. Emerging ctDNA alterations were associated with significantly shorter overall survival for patients with some tumor types. CONCLUSION: This comprehensive landscape of genomic aberrations indicates that genetic alterations involved in secondary resistance to targeted therapy occur frequently and suggests that the detection of such alterations before disease progression may guide personalized treatment and improve patient outcome.
Assuntos
DNA Tumoral Circulante , Neoplasias , Humanos , DNA Tumoral Circulante/genética , Medicina de Precisão , Prognóstico , Estudos Prospectivos , Biomarcadores Tumorais/genética , Mutação , Neoplasias/tratamento farmacológico , Neoplasias/genética , Sequenciamento de Nucleotídeos em Larga EscalaAssuntos
Antígenos de Plaquetas Humanas/imunologia , Peptídeos e Proteínas de Sinalização Intercelular/genética , Isoanticorpos/imunologia , Complicações Hematológicas na Gravidez/etiologia , Complicações Hematológicas na Gravidez/terapia , Trombocitopenia/etiologia , Trombocitopenia/terapia , Regiões 5' não Traduzidas , Adulto , Biomarcadores , Coagulação Sanguínea , Testes de Coagulação Sanguínea , Gerenciamento Clínico , Suscetibilidade a Doenças , Feminino , Estudos de Associação Genética , Predisposição Genética para Doença , Mutação em Linhagem Germinativa , Humanos , Peptídeos e Proteínas de Sinalização Intercelular/metabolismo , Gravidez , Complicações Hematológicas na Gravidez/diagnóstico , Trombocitopenia/diagnósticoRESUMO
HLA-C*06:314 differs from HLA-C*06:02:01:01 by one nucleotide substitution in codon 327 in exon 7.
Assuntos
Genes MHC Classe I , Antígenos HLA-C , Alelos , Códon , Éxons/genética , Antígenos HLA-C/genética , Humanos , Análise de Sequência de DNARESUMO
HLA-DRB1*11:282 differs from HLA-DRB1*11:04:01:01 by one nucleotide substitution in codon 41 in exon 2.
Assuntos
Mutação de Sentido Incorreto , Alelos , Códon , Éxons/genética , Cadeias HLA-DRB1/genética , Humanos , Análise de Sequência de DNARESUMO
HLA-DPB1*1139:01 differs from HLA-DPB1*04:01:01:03 by one nucleotide substitution in codon 15 in exon 2.
Assuntos
Alelos , Sequência de Bases , Cadeias beta de HLA-DP/genética , Humanos , Análise de Sequência de DNARESUMO
HLA-C*05:01:58 differs from HLA-C*05:01:01:02 by a single nucleotide change in codon 112 in exon 3.
Assuntos
Genes MHC Classe I , Antígenos HLA-C , Alelos , Éxons/genética , Antígenos HLA-C/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNARESUMO
HLA-A*01:367 differs from HLA-A*01:01:01:01 by one nucleotide substitution in codon 271 in exon 4.
Assuntos
Antígenos HLA-A , Alelos , Códon , Éxons/genética , Antígenos HLA-A/genética , Humanos , Análise de Sequência de DNARESUMO
HLA-DQA1*03:20 differs from HLA-DQA1*03:03:01:01 by one nucleotide substitution in codon 33 in exon 2.
Assuntos
Alelos , Éxons/genética , Cadeias alfa de HLA-DQ/genética , Humanos , Análise de Sequência de DNARESUMO
HLA-A*36:12 differs from HLA-A*36:01:01:01 by one nucleotide substitution in codon 211 in exon 4.
Assuntos
Antígenos HLA-A , Alelos , Códon , Éxons/genética , Antígenos HLA-A/genética , Humanos , Análise de Sequência de DNARESUMO
HLA-DPA1*01:44 differs from DPA1*01:03:01:04 by one nucleotide substitution in codon 175 in exon 3.
Assuntos
Cadeias alfa de HLA-DP , Alelos , Éxons/genética , Cadeias alfa de HLA-DP/genética , Teste de Histocompatibilidade , HumanosRESUMO
Essentials The c.1544+1G>A mutation was identified in Gypsy Glanzmann thrombasthenia (GT) patients. Gypsy GT patients express normal αv ß3 carrying HPA-1b epitopes. To demonstrate HPA-1a alloimmunization by modified antigen capture assays. Gypsy GT patients could develop anti-HPA-1a alloantibodies against ß3 and αv ß3 . ABSTRACT: Background Glanzmann thrombasthenia (GT) is a rare bleeding disorder caused by the absence or the dysfunction of the platelet αIIb ß3 integrin. A founder mutation in the ITGA2B gene was previously identified in French Gypsy patients. Interestingly, this mutation was strongly linked to the human platelet antigen-1b (HPA-1b). The HPA-1bb Gypsy patients are at risk of isoimmunization against αIIb ß3 , as this complex is not expressed at their platelet surface. Tentatively, they would, however, not have an increased risk of developing anti-HPA-1a alloantibodies by exposure of αIIb ß3 on platelets from random platelet transfusions. However, the ß3 chain can also associate with the αv subunit expressed at the platelet surface. Because Gypsy GT patients express normal αv ß3 carrying HPA-1b epitopes, these patients might develop anti-HPA-1a alloantibodies reacting with αv ß3 and/or ß3 . Objectives/Patients/Methods To demonstrate this hypothesis, sera from HPA-1bb (n = 5) and HPA-1ab (n = 1) Gypsy GT patients were investigated by modified antigen capture assay using platelets or stable transfected cells. Furthermore, stable transfected cells expressing either αIIb ß3 or αv ß3 together with soluble monomeric chimeric ß3 (as absorbent) were used to differentiate anti-ß3 and anti-αv ß3 reactivity. Results Only HPA-1bb patients developed alloantibodies reacting with HPA-1a cells. Further analysis showed that HPA-1bb patients developed anti-HPA-1a alloantibodies reacting with ß3 and/or αv ß3 . Conclusion In this study, we found that HPA-1bb patients who failed to express αIIb ß3 on the platelet surface can develop alloantibodies against HPA-1a reacting with ß3 as well as αv ß3 . This is of particular importance as anti-HPA-1a alloantibodies might cause fetal neonatal alloimmune thrombocytopenia and/or platelet transfusion refractoriness.
Assuntos
Roma (Grupo Étnico) , Trombastenia , Humanos , Imunização , Recém-Nascido , Integrina beta3/genética , Mutação , Complexo Glicoproteico GPIIb-IIIa de Plaquetas , Trombastenia/diagnóstico , Trombastenia/genéticaRESUMO
HLA-DQA1*01:49 differs from HLA-DQA1*01:01:01:06 by one nucleotide substitution in codon 9 in exon 2.
Assuntos
Alelos , Éxons/genética , Cadeias alfa de HLA-DQ/genética , Humanos , Análise de Sequência de DNARESUMO
HLA-DRB3*02:02:23 differs from HLA-DRB3*02:02:01:02 by one nucleotide substitution in codon 218 in exon 4.
Assuntos
Cadeias HLA-DRB3 , Alelos , Códon , Éxons , Cadeias HLA-DRB3/genética , HumanosRESUMO
HLA-DQA1*05:05:05 differs from HLA-DQA1*05:05:01:07 by one nucleotide substitution in codon 111 in exon 3.
Assuntos
Alelos , Éxons/genética , Cadeias alfa de HLA-DQ/genética , Humanos , Análise de Sequência de DNARESUMO
PCR-sequence-specific oligonucleotide (PCR-SSO) is commonly used for HLA-typing. We recently replaced LabType SSO HD kit for HLA-C typing with the XR kit (OneLambda, Inc.). We used 137 patients' samples representing unique most likely HLA-C allele combinations to compare these kits' performance. The XR kit decreased the number of allele ambiguities with a median of 26.1% (first to third quartiles 20% to 36.2%, range 0% to 96.1%). The XR kit did not resolve all the common, intermediate and well-documented HLA allele ambiguities, which may be important in the clinical setting. The XR kit eliminated 23.6% of null allele ambiguities. In conclusion, the HLA-C XR kit provides a moderate yet valuable improvement of HLA-typing resolution in comparison with the HLA-C HD kit.
Assuntos
Antígenos HLA-C , Oligonucleotídeos , Alelos , Genes MHC Classe I , Antígenos HLA-C/genética , Teste de Histocompatibilidade , Humanos , Oligonucleotídeos/genéticaRESUMO
HLA-A*26:199 differs from HLA-A*26:01:01:01 by one nucleotide substitution in codon 261 in exon 4.
Assuntos
Antígenos HLA-A , Alelos , Éxons/genética , Antígenos HLA-A/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNARESUMO
HLA-DRB3*01:86 differs from HLA-DRB3*01:01:02:01 by one nucleotide substitution in codon 225 in exon 4.
Assuntos
Cadeias HLA-DRB3 , Alelos , Sequência de Bases , Éxons/genética , Cadeias HLA-DRB1 , Cadeias HLA-DRB3/genética , Teste de Histocompatibilidade , HumanosRESUMO
HLA-DQB1*04:78 differs from HLA-DQB1*04:02:01:04 by one nucleotide substitution in codon 95 in exon 3.
Assuntos
Alelos , Éxons/genética , Cadeias beta de HLA-DQ/genética , Teste de Histocompatibilidade , HumanosRESUMO
HLA-DPA1*01:03:19 differs from DPA1*01:03:01:02 by one nucleotide substitution in codon 190 in exon 4.
Assuntos
Cadeias alfa de HLA-DP , Alelos , Cadeias alfa de HLA-DP/genética , HumanosRESUMO
HLA genotyping by next-generation sequencing is now widely performed. We aimed at evaluating the performance of the One Lambda AllType kit using Thermo Fisher Scientific reagents on the Ion S5 XL platform. Reads were analyzed using the TypeStream Visual software. We performed 15 runs between April and September 2018 to type DNA at the HLA-A/B/C/DRB1/3/4/5/DQA1/DQB1/DPA1/DPB1 loci from 340 samples and 15 positive controls. We observed only seven (0.1%) critical mistakes among the 6009 alleles typed, corresponding to two allele dropouts, one false heterozygous typing assignment, and four phasing abnormalities. Among the 1793 presumably new alleles detected by the analysis software, 11 displayed exon mismatches, of which nine were confirmed as new alleles and two had been described previously. Intron mismatches were observed among the remaining presumably new alleles, of which 371 were considered as probably new, and 1411 were rejected for at least one sequence feature such as homopolymers (n = 1206), nucleotide doublet repeats (n = 26), low read depth (<200 reads, n = 93), high background (>20%, n = 79), or phasing abnormalities (n = 7). A comparison of the AllType results with those obtained using other methods at the second-field resolution level showed 99.5% (1497/1504) concordance for the HLA-A/B/C/DRB1/DQB1/DPB1 loci. Similar agreement was observed between the HLA-C or HLA-DRB3/4/5 results and common linkage disequilibrium, with 96.6% (657/680) and 97.2% (530/545) concordance, respectively. Therefore, the AllType kit used with the Ion S5 XL platform displayed satisfactory performance for HLA typing in current clinical practice.