Proteomics of tumor and serum samples from isocitrate dehydrogenase-wildtype glioblastoma patients: is the detoxification of reactive oxygen species associated with shorter survival?

Proteomics has been little used for the identification of novel prognostic and/or therapeutic markers in isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GB). In this study, we analyzed 50 tumor and 30 serum samples from short- and long-term survivors of IDH-wildtype GB (STS and LTS, respectively) by data-independent acquisition mass spectrometry (DIA-MS)-based proteomics, with the aim of identifying such markers. DIA-MS identified 5422 and 826 normalized proteins in tumor and serum samples, respectively, with only three tumor proteins and 26 serum proteins displaying significant differential expression between the STS and LTS groups. These dysregulated proteins were principally associated with the detoxification of reactive oxygen species (ROS). In particular, GB patients in the STS group had high serum levels of malate dehydrogenase 1 (MDH1) and ribonuclease inhibitor 1 (RNH1) and low tumor levels of fatty acid-binding protein 7 (FABP7), which may have enabled them to maintain low ROS levels, counteracting the effects of the first-line treatment with radiotherapy plus concomitant and adjuvant temozolomide. A blood score built on the levels of MDH1 and RNH1 expression was found to be an independent prognostic factor for survival based on the serum proteome data for a cohort of 96 IDH-wildtype GB patients. This study highlights the utility of circulating MDH1 and RNH1 biomarkers for determining the prognosis of patients with IDH-wildtype GB. Furthermore, the pathways driven by these biomarkers, and the tumor FABP7 pathway, may constitute promising therapeutic targets for blocking ROS detoxification to overcome resistance to chemoradiotherapy in potential GB STS.

Plasma-based analysis of ERBB2 mutational status by multiplex digital PCR in a large series of patients with metastatic breast cancer.

Erb-b2 receptor tyrosine kinase 2 (ERBB2)-activating mutations are therapeutically actionable alterations found in various cancers, including metastatic breast cancer (MBC). We developed multiplex digital PCR assays to detect and quantify ERBB2 mutations in circulating tumor DNA from liquid biopsies. We studied the plasma from 272 patients with hormone-receptor-positive, human epidermal growth factor receptor 2-negative (HR+/HER2-) MBC to detect 17 ERBB2 mutations using a screening assay. The assay was developed on the three-color Crystal dPCR™ naica® platform with a two-step strategy for precise mutation identification. We found that nine patients (3.3%) harbored at least one ERBB2 mutation. The mutation rate was higher in patients with lobular histology (5.9%) compared to invasive breast carcinoma of no special type (2.6%). A total of 12 mutations were found with the following frequencies: L755S (25.00%), V777L (25.00%), S310Y (16.67%), L869R (16.67%), S310F (8.33%), and D769H (8.33%). Matched tumor samples from six patients identified the same mutations with an 83% concordance rate. In summary, our highly sensitive multiplex digital PCR assays are well suited for plasma-based monitoring of ERBB2 mutational status in patients with MBC.

[Relapse with HLA loss after hematopoietic stem cell transplantation with non-HLA identical donor: Guidelines from the Francophone society of bone marrow transplantation and cellular therapy (SFGM-TC)]. / Perte d'hétérozygotie HLA dans les rechutes après greffes de cellules souches hématopoïétiques avec donneur non HLA identique : recommandations de la Société francophone de greffe de moelle et de thérapie cellulaire (SFGM-TC).

Loss of heterozygosity or HLA loss is a genomic-type escape mechanism highlighted in certain types of relapses after allogeneic hematopoietic stem cell transplantation with a non-HLA identical donor, and especially after haplo-identical transplantation. The diagnosis must be made with certainty because the result conditions the therapy. In this article, the different mechanisms and techniques that can be used for the diagnosis of loss of heterozygosity, as well as the therapeutic options are reviewed, making it possible to establish clinico-biological recommendations for the diagnosis confirmation and management of the patients in relapse.

New methods for the quantification of mixed chimerism in transplantation.

Background: Quantification of chimerism showing the proportion of the donor in a recipient is essential for the follow-up of hematopoietic stem cell transplantation but can also be useful to document an immune tolerance situation after solid organ transplantation. Historically, chimerism has been quantified from genomic DNA, but with technological advances, chimerism from donor-derived cell-free DNA seems particularly relevant in solid organ transplantation. Methods: The reference method was until recently the short tandem repeat technique, but new innovative techniques as digital PCR (dPCR) and NGS, have revolutionized the quantification of chimerism, such as the so-called microchimerism analysis. After a short review of chimerism methods, a comparison of chimerism quantification data for two new digital PCR systems (QIAcuity™ dPCR (Qiagen®) and QuantStudio Absolute Q (ThermoFisher®) and two NGS-based chimerism quantification methods (AlloSeq HCT™ (CareDx®) and NGStrack™ (GenDX®)) was performed. Results: These new methods were correlated and concordant to routinely methods (r²=0.9978 and r²=0.9974 for dPCR methods, r²=0.9978 and r²=0.9988 for NGS methods), and had similar high performance (sensitivity, reproductibility, linearity). Conclusion: Finally, the choice of the innovative method of chimerism within the laboratory does not depend on the analytical performances because they are similar but mainly on the amount of activity and the access to instruments and computer services.

Characterization of the novel HLA-DQA1*05:13 allele by next-generation sequencing.

DQA1*05:13 differs from DQA1*05:05:01:04 by one nucleotide substitution at position 37 in exon 1.

Characterization of the novel HLA-B*08:67:02N allele by next-generation sequencing.

HLA-B*08:67:02N differs from B*08:01:01:01 by one nucleotide substitution at position 224 in exon 2.

Characterization of the novel HLA-B*18:181 allele by next-generation sequencing.

B*18:181 differs from B*18:01:01:02 by one nucleotide substitution at position 1043 in exon 6.

Characterization of the novel HLA-DRB1*08:97 allele by next-generation sequencing.

DRB1*08:97 differs from DRB1*08:03:02:01 by one nucleotide substitution at position 485 in exon 3.

Characterization of the novel HLA-DQB1*02:162N allele by next-generation sequencing.

DQB1*02:162N differs from DQB1*02:02:01:01 by one nucleotide substitution at position 276 in exon 2.

Characterization of the novel HLA-C*14:114 allele by next-generation sequencing.

HLA-C*14:114 differs from C*14:02:01:01 by one nucleotide substitution at position 1077 in exon 7.

Characterization of the novel HLA-DQA1*01:38:01:01 allele by next-generation sequencing.

DQA1*01:38:01:01 differs from DQA1*01:02:01:01 by one nucleotide substitution at position 554 in exon 3.

Characterization of the novel HLA-DQA1*01:19 allele by next-generation sequencing.

DQA1*01:19 differs from DQA1*01:02:01:04 by one nucleotide substitution at position 731 in exon 4.

Characterization of the novel HLA-B*07:384 allele by next-generation sequencing.

B*07:384 differs from B*07:02:01:01 by one nucleotide substitution at position 472 in exon 3.

Characterization of the novel HLA-B*35:460Q allele by next-generation sequencing.

B*35:460Q differs from B*35:03:01:01 by one nucleotide substitution at position 406 in exon 3.

Characterization of the novel HLA-DQB1*05:235N allele by next-generation sequencing.

DQB1*05:235N differs from DQB1*05:03:01:01 by one nucleotide substitution at position 123 in exon 2, resulting in a premature stop codon.

Characterization of the novel HLA-DQB1*05:176 allele by next-generation sequencing.

DQB1*05:176 differs from DQB1*05:01:01:03 by one nucleotide substitution at position 184 in exon 2.

Characterization of the novel HLA-DRB1*01:106 allele by next-generation sequencing.

DRB1*01:106 differs from DRB1*01:01:01:01 by one nucleotide substitution at position 355 in exon 2.

Characterization of the novel HLA-DQB1*05:237 allele by next-generation sequencing.

DQB1*05:237 differs from DQB1*05:01:01:01 by one nucleotide substitution at position 67 in exon 1.

Characterization of the novel HLA-C*14:115 allele by next-generation sequencing.

C*14:115 differs from C*14:02:01:01 by one nucleotide substitution at position 1030 in exon 6.

Characterization of the novel HLA-C*03:489 allele by next-generation sequencing.

C*03:489 differs from C*03:02:02:01 by one nucleotide substitution at position 899 in exon 5.