Circulating tumor DNA landscape and prognostic impact of acquired resistance to targeted therapies in cancer patients: a national center for precision medicine (PRISM) study.

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.

Characterization of the novel HLA-DRB1*11:282 allele by sequencing-based typing.

HLA-DRB1*11:282 differs from HLA-DRB1*11:04:01:01 by one nucleotide substitution in codon 41 in exon 2.

Characterization of the novel HLA-DPB1*1139:01 allele by sequencing-based typing.

HLA-DPB1*1139:01 differs from HLA-DPB1*04:01:01:03 by one nucleotide substitution in codon 15 in exon 2.

Characterization of the novel HLA-C*05:01:58 allele by sequencing-based typing.

HLA-C*05:01:58 differs from HLA-C*05:01:01:02 by a single nucleotide change in codon 112 in exon 3.

Characterization of the novel HLA-A*01:367 allele by sequencing-based typing.

HLA-A*01:367 differs from HLA-A*01:01:01:01 by one nucleotide substitution in codon 271 in exon 4.

Characterization of the novel HLA-DQA1*03:20 allele by sequencing-based typing.

HLA-DQA1*03:20 differs from HLA-DQA1*03:03:01:01 by one nucleotide substitution in codon 33 in exon 2.

Characterization of the novel HLA-A*36:12 allele by sequencing-based typing.

HLA-A*36:12 differs from HLA-A*36:01:01:01 by one nucleotide substitution in codon 211 in exon 4.

Characterization of the novel HLA-C*06:314 allele by sequencing-based typing.

HLA-C*06:314 differs from HLA-C*06:02:01:01 by one nucleotide substitution in codon 327 in exon 7.

Characterization of the novel HLA-DPA1*01:44 allele by sequencing-based typing.

HLA-DPA1*01:44 differs from DPA1*01:03:01:04 by one nucleotide substitution in codon 175 in exon 3.

Immunization against αIIb ß3 and αv ß3 in Glanzmann thrombasthenia patients carrying the French Gypsy mutation.

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.

Characterization of the novel HLA-DQB1*04:78 allele by sequencing-based typing.

HLA-DQB1*04:78 differs from HLA-DQB1*04:02:01:04 by one nucleotide substitution in codon 95 in exon 3.

Characterization of the novel HLA-DRB3*01:86 allele by sequencing-based typing.

HLA-DRB3*01:86 differs from HLA-DRB3*01:01:02:01 by one nucleotide substitution in codon 225 in exon 4.

Improvement in HLA-C typing by a new sequence-specific oligonucleotides kit.

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.

[Relevance of antibodies in hematopoietic stem cell transplantation: Antibodies anti-HLA, anti-platelets, anti-granulocytes, anti-erythrocytes and anti-MICA. Guidelines from the Francophone Society of Bone Marrow Transplantation and Cellular Therapy (SFGM-TC)]. / Importance des anticorps dans la prise en charge de la greffe de cellules souches hématopoïétiques : anticorps anti-HLA, anti-plaquettes, anti-granuleux, anti-érythrocytes et anti-MICA. Recommandations de la Société francophone de greffe de moelle et de thérapie cellulaire (SFGM-TC).

The presence of allo-antibodies in the serum of a recipient awaiting hematopoietic stem cell transplantation (HSCT) may have an impact on transfusion efficiency and/or donor choice, especially in the absence of an identical sibling donor. Prior to transplantation, donor specific anti-HLA (Human Leukocyte Antigen) antibodies (DSA) have a recognized effect on transplant outcome, correlated with the increasing MFI value and with the ability of such antibody to fix the complement fraction. Anti-platelet antibodies (anti-HLA class I and anti-HPA [Human Platelet Antigen]) are better involved in transfusion inefficiency and can be responsible for refractory status. ABO incompatibilities require a specific treatment of the graft in presence of high titer to avoid hemolytic adverse effects. Investigations of these antibodies should be carried out on a regular basis in order to establish appropriate transfusion recommendation, select an alternative donor when possible or adapt the source of cells. After transplantation, in case of delayed recovery or graft rejection, long term aplasia, persistent mixed chimerism or late release, and after elimination of the main clinical causes, a biological assessment targeted on the different type of antibodies will have to be performed in order to orient towards the cause or the appropriate therapy. Further studies should be carried out to determine the impact of anti-MICA antibodies and recipient specific anti-HLA antibodies, on the outcome of the transplantation.

Characterization of the novel HLA-A*26:199 allele by sequencing-based typing.

HLA-A*26:199 differs from HLA-A*26:01:01:01 by one nucleotide substitution in codon 261 in exon 4.

Characterization of the novel HLA-DQA1*05:05:05 allele by sequencing-based typing.

HLA-DQA1*05:05:05 differs from HLA-DQA1*05:05:01:07 by one nucleotide substitution in codon 111 in exon 3.

Characterization of the novel HLA-DQA1*01:49 allele by sequencing-based typing.

HLA-DQA1*01:49 differs from HLA-DQA1*01:01:01:06 by one nucleotide substitution in codon 9 in exon 2.

Characterization of the novel HLA-DPA1*01:03:19 allele by sequencing-based typing.

HLA-DPA1*01:03:19 differs from DPA1*01:03:01:02 by one nucleotide substitution in codon 190 in exon 4.

Evaluation of the AllType kit for HLA typing using the Ion Torrent S5 XL platform.

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.