Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group.

Next-generation sequencing (NGS) allows sequencing of a high number of nucleotides in a short time frame at an affordable cost. While this technology has been widely implemented, there are no recommendations from scientific societies about its use in oncology practice. The European Society for Medical Oncology (ESMO) is proposing three levels of recommendations for the use of NGS. Based on the current evidence, ESMO recommends routine use of NGS on tumour samples in advanced non-squamous non-small-cell lung cancer (NSCLC), prostate cancers, ovarian cancers and cholangiocarcinoma. In these tumours, large multigene panels could be used if they add acceptable extra cost compared with small panels. In colon cancers, NGS could be an alternative to PCR. In addition, based on the KN158 trial and considering that patients with endometrial and small-cell lung cancers should have broad access to anti-programmed cell death 1 (anti-PD1) antibodies, it is recommended to test tumour mutational burden (TMB) in cervical cancers, well- and moderately-differentiated neuroendocrine tumours, salivary cancers, thyroid cancers and vulvar cancers, as TMB-high predicted response to pembrolizumab in these cancers. Outside the indications of multigene panels, and considering that the use of large panels of genes could lead to few clinically meaningful responders, ESMO acknowledges that a patient and a doctor could decide together to order a large panel of genes, pending no extra cost for the public health care system and if the patient is informed about the low likelihood of benefit. ESMO recommends that the use of off-label drugs matched to genomics is done only if an access programme and a procedure of decision has been developed at the national or regional level. Finally, ESMO recommends that clinical research centres develop multigene sequencing as a tool to screen patients eligible for clinical trials and to accelerate drug development, and prospectively capture the data that could further inform how to optimise the use of this technology.

Reversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2-mutant metastatic breast cancer.

BACKGROUND: Little is known about mechanisms of resistance to poly(adenosine diphosphate-ribose) polymerase inhibitors (PARPi) and platinum chemotherapy in patients with metastatic breast cancer and BRCA1/2 mutations. Further investigation of resistance in clinical cohorts may point to strategies to prevent or overcome treatment failure. PATIENTS AND METHODS: We obtained tumor biopsies from metastatic breast cancer patients with BRCA1/2 deficiency before and after acquired resistance to PARPi or platinum chemotherapy. Whole exome sequencing was carried out on each tumor, germline DNA, and circulating tumor DNA. Tumors underwent RNA sequencing, and immunohistochemical staining for RAD51 foci on tumor sections was carried out for functional assessment of intact homologous recombination (HR). RESULTS: Pre- and post-resistance tumor samples were sequenced from eight patients (four with BRCA1 and four with BRCA2 mutation; four treated with PARPi and four with platinum). Following disease progression on DNA-damaging therapy, four patients (50%) acquired at least one somatic reversion alteration likely to result in functional BRCA1/2 protein detected by tumor or circulating tumor DNA sequencing. Two patients with germline BRCA1 deficiency acquired genomic alterations anticipated to restore HR through increased DNA end resection: loss of TP53BP1 in one patient and amplification of MRE11A in another. RAD51 foci were acquired post-resistance in all patients with genomic reversion, consistent with reconstitution of HR. All patients whose tumors demonstrated RAD51 foci post-resistance were intrinsically resistant to subsequent lines of DNA-damaging therapy. CONCLUSIONS: Genomic reversion in BRCA1/2 was the most commonly observed mechanism of resistance, occurring in four of eight patients. Novel sequence alterations leading to increased DNA end resection were seen in two patients, and may be targetable for therapeutic benefit. The presence of RAD51 foci by immunohistochemistry was consistent with BRCA1/2 protein functional status from genomic data and predicted response to later DNA-damaging therapy, supporting RAD51 focus formation as a clinically useful biomarker.

Prevalence and mutational determinants of high tumor mutation burden in breast cancer.

BACKGROUND: High tumor mutation burden (TMB) can benefit immunotherapy for multiple tumor types, but the prevalence of hypermutated breast cancer is not well described. The aim of this study was to evaluate the frequency, mutational patterns, and genomic profile of hypermutated breast cancer. PATIENTS AND METHODS: We used de-identified data from individuals with primary or metastatic breast cancer from six different publicly available genomic studies. The prevalence of hypermutated breast cancer was determined among 3969 patients' samples that underwent whole exome sequencing or gene panel sequencing. The samples were classified as having high TMB if they had ≥10 mutations per megabase (mut/Mb). An additional eight patients were identified from a Dana-Farber Cancer Institute cohort for inclusion in the hypermutated cohort. Among the patients with high TMB, the mutational patterns and genomic profiles were determined. A subset of patients was treated with regimens containing PD-1 inhibitors. RESULTS: The median TMB was 2.63 mut/Mb. The median TMB significantly varied according to the tumor subtype (HR-/HER2- >HER2+ >HR+/HER2-, P < 0.05) and sample type (metastatic > primary, P = 2.2 × 10-16). Hypermutated tumors were found in 198 patients (5%), with enrichment in metastatic versus primary tumors (8.4% versus 2.9%, P = 6.5 × 10-14). APOBEC activity (59.2%), followed by mismatch repair deficiency (MMRd; 36.4%), were the most common mutational processes among hypermutated tumors. Three patients with hypermutated breast cancer-including two with a dominant APOBEC activity signature and one with a dominant MMRd signature-treated with pembrolizumab-based therapies derived an objective and durable response to therapy. CONCLUSION: Hypermutation occurs in 5% of all breast cancers with enrichment in metastatic tumors. Different mutational signatures are present in this population with APOBEC activity being the most common dominant process. Preliminary data suggest that hypermutated breast cancers are more likely to benefit from PD-1 inhibitors.

Successful whole-exome sequencing from a prostate cancer bone metastasis biopsy.

BACKGROUND: Comprehensive molecular characterization of cancer that has metastasized to bone has proved challenging, which may limit the diagnostic and potential therapeutic opportunities for patients with bone-only metastatic disease. METHODS: We describe successful tissue acquisition, DNA extraction, and whole-exome sequencing from a bone metastasis of a patient with metastatic, castration-resistant prostate cancer (PCa). RESULTS: The resulting high-quality tumor sequencing identified plausibly actionable somatic genomic alterations that dysregulate the phosphoinostide 3-kinase pathway, as well as a theoretically actionable germline variant in the BRCA2 gene. CONCLUSIONS: We demonstrate the feasibility of diagnostic bone metastases profiling and analysis that will be required for the widespread application of prospective 'precision medicine' to men with advanced PCa.

Rvb1p and Rvb2p are essential components of a chromatin remodeling complex that regulates transcription of over 5% of yeast genes.

Eukaryotic Rvb1p and Rvb2p are two highly conserved proteins related to the helicase subset of the AAA+ family of ATPases. Conditional mutants in both genes show rapid changes in the transcription of over 5% of yeast genes, with a similar number of genes being repressed and activated. Both Rvb1p and Rvb2p are required for maintaining the induced state of many inducible promoters. ATP binding and hydrolysis by Rvb1p and Rvb2p is individually essential in vivo, and the two proteins are associated with each other in a high molecular weight complex that shows ATP-dependent chromatin remodeling activity in vitro. Our findings show that Rvb1p and Rvb2p are essential components of a chromatin remodeling complex and determine genes regulated by the complex.

Measuring the incremental cost of clinical cancer research.

PURPOSE: To summarize evidence on the costs of treating patients in clinical trials and to describe the Cost of Cancer Treatment Study, an ongoing effort to produce generalizable estimates of the incremental costs of government-sponsored cancer trials. METHODS: A retrospective study of costs will be conducted with 1,500 cancer patients recruited from a randomly selected sample of institutions in the United States. Patients accrued to either phase II or phase III National Cancer Institute-sponsored clinical trials during a 15-month period will be asked to participate in a study of their health care utilization (n = 750). Costs will be measured approximately 1 year after their trial enrollment from a combination of billing records, medical records, and an in-person survey questionnaire. Similar data will be collected for a comparable group of cancer patients not in trials (n = 750) to provide an estimate of the incremental cost. RESULTS: Evidence suggests insurers limit access to trials because of cost concerns. Public and private efforts are underway to change these policies, but their permanent status is unclear. Previous studies found that treatment costs in clinical trials are similar to costs of standard therapy. However, it is difficult to generalize from these studies because of the unique practice settings, insufficient sample sizes, and the exclusion of potentially important costs. CONCLUSION: Denials of coverage for treatment in a clinical trial limit patient access to trials and could impede clinical research. Preliminary estimates suggest changes to these policies would not be expensive, but these results are not generalizable. The Cost of Cancer Treatment Study is an ongoing effort to provide generalizable estimates of the incremental treatment cost of phase II and phase III cancer trials. The results should be of great interest to insurers and the research community as they consider permanent ways to finance cancer trials.

Imaging of the pediatric orbit.

This article addresses the embryology of the eye, the imaging of common congenital malformations involving the globe, and imaging features of common retro-ocular masses. Clinical entities resulting in alterations in the size and contour, and those producing leukokoria, also are discussed.

Analysis of JNK, Mdm2 and p14(ARF) contribution to the regulation of mutant p53 stability.

Identification of Mdm2 and JNK as proteins that target degradation of wt p53 prompted us to examine their effect on mutant p53, which exhibits a prolonged half-life. Of five mutant p53 forms studied for association with the targeting molecules, two no longer bound to Mdm2 and JNK. Three mutant forms, which exhibit high expression levels, showed lower affinity for association with Mdm2 and JNK in concordance with greater affinity to p14(ARF), which is among the stabilizing p53 molecules. Monitoring mutant p53 stability in vitro confirmed that, while certain forms of mutant p53 are no longer affected by either JNK or Mdm2, others are targeted for degradation by JNK/Mdm2, albeit at lower efficiency when compared with wt p53. Expression of wt p53 in tumor cells revealed a short half-life, suggesting that the targeting molecules are functional. Forced expression of mutant p53 in p53 null cells confirmed pattern of association with JNK/Mdm2 and prolonged half-life, as found in the tumor cells. Over-expression of Mdm2 in either tumor (which do express endogenous functional Mdm2) or in p53 null cells decreased the stability of mutant p53 suggesting that, despite its expression, Mdm2/JNK are insufficient (amount/affinity) for targeting mutant p53 degradation. Based on both in vitro and in vivo analyses, we conclude that the prolonged half-life of mutant p53 depends on the nature of the mutation, which either alters association with targeting molecules, ratio between p53 and targeting/stabilizing molecules or targeting efficiency.

CD19 regulates B cell antigen receptor-mediated MHC class II antigen processing.

In B cells, the processing of antigens in the context of MHC class II molecules is initiated by the binding of antigen to the B cell antigen receptor (BCR). The BCR serves two roles in antigen processing, signaling for enhanced processing and endocytosing bound antigen. CD19 is a B cell surface molecule which has been demonstrated to function in modifying signals generated through the BCR, regulating T-cell dependent B-cell activation. Here we provide evidence that cross-linking CD19 selectively blocked BCR-mediated enhancement of the processing and presentation of antigens taken up by fluid pinocytosis. CD19 cross-linking also inhibited the processing and presentation of antigen internalized bound to the BCR by decreasing the degree and rate of internalization of the BCR and specific antigen and its trafficking to the class II peptide loading compartment. In contrast, CD19 cross-linking did not affect the rate of assembly of SDS-stable peptide class II complexes, indicating that CD19 cross-linking did not have a global effect on membrane trafficking in B cells but rather a selective effect on BCR trafficking. Thus, in addition to a direct role in modulating BCR signaling for B cell proliferation and differentiation, CD19 may indirectly influence B cell activation by regulating antigen processing and B cell interactions with helper T cells.

Regulation of B cell receptor-mediated MHC class II antigen processing by FcgammaRIIB1.

The processing and presentation of Ag by Ag-specific B cells is highly efficient due to the dual function of the B cell Ag receptor (BCR) in both signaling for enhanced processing and endocytosing bound Ag. The BCR for IgG (FcgammaRIIB1) is a potent negative coreceptor of the BCR that blocks Ag-induced B cell proliferation. Here we investigate the influence of the FcgammaRIIB1 on BCR-mediated Ag processing and show that coligating the FcgammaRIIB1 and the BCR negatively regulates both BCR signaling for enhanced Ag processing and BCR-mediated Ag internalization. Treatment of splenic B cells with F(ab')2 anti-Ig significantly enhances APC function compared with the effect of whole anti-Ig; however, whole anti-Ig treatment is effective when binding to the FcgammaRIIB1 was blocked by a FcgammaRII-specific mAb. Processing and presentation of Ag covalently coupled to anti-Ig were significantly decreased compared with Ag coupled to F(ab')2anti-Ig; however, the processing of the two Ag-Ab conjugates was similar in cells that did not express FcgammaRIIB1 and in splenic B cells treated with a FcgammaRII-specific mAb to block Fc binding. Internalization of monovalent Ag by B cells was reduced in the presence of whole anti-Ig as compared with F(ab')2 anti-Ig, but the internalized Ag was correctly targeted to the class II peptide loading compartment. Taken together, these results indicate that the FcgammaRIIB1 is a negative regulator of the BCR-mediated Ag-processing function.

Long-term outcome of cyclocryotherapy for refractory pediatric glaucoma.

OBJECTIVE: To evaluate the success rate and long-term outcome of cyclocryotherapy for refractory pediatric glaucoma. DESIGN: Retrospective interventional case series. PARTICIPANTS: A total of 64 eyes of 49 patients from 2 institutions with pediatric glaucomas resistant to conventional medical and surgical therapies treated with cyclocryotherapy from 1975 to 1996 were included in this review. INTERVENTION: Cyclocryotherapy was performed on eyes with pediatric glaucoma resistant to maximal medical and surgical interventions. Each cyclocryotherapy session was evaluated in terms of area treated, temperature, and number of applications placed. MAIN OUTCOME MEASURES: Criteria for success included intraocular pressure (IOP) of 21 mmHg or less without devastating complications or need for further glaucoma surgery. RESULTS: The mean baseline pretreatment IOP of all eyes was 30.0 +/- 8.1 mmHg. Six months after their last treatment, 42 eyes (66%) were successes. Longer term follow-up (mean, 4.8 +/- 3.3 years) yielded a lower final success rate in 28 eyes (44%). For these 28 eyes, mean IOP was reduced from 30.3 +/- 7.8 mmHg pretreatment to 16.8 +/- 4.0 mmHg after their last cyclocryotherapy treatment session (P < 0.001). The average number of cyclocryotherapy sessions for successful eyes was 4.1 +/- 4.0 (range, 1-17). The mean follow-up time for these successful eyes was 4.9 +/- 3.4 years. Devastating complications attributable to cyclocryotherapy included phthisis (5 eyes) and retinal detachment (5 eyes). Devastating complications occurred more frequently among eyes with aniridia than among all other eyes (nonaniridics) (50% vs. 11%, respectively; P < 0.05). CONCLUSION: Cyclocryotherapy is an effective means of lowering IOP and is a reasonable treatment option in selected pediatric patients with refractory glaucoma. Eyes with aniridia experienced a very high rate of phthisis after cyclocryotherapy and may be poor candidates for this treatment.

Signaling through the B cell antigen receptor regulates discrete steps in the antigen processing pathway.

Antigen processing in B cells is initiated by antigen binding to the surface B cell antigen receptor (BCR). The BCR is a signaling receptor which also functions to endocytose bound antigen for subsequent intracellular processing and presentation with class II molecules. Previously, using subcellular fractionation, we showed that although the surface BCR constitutively traffics from the cell surface to the class II peptide-loading compartment (IIPLC), cross-linking the BCR regulates trafficking, resulting in a more rapid movement of the BCR to the IIPLC (Song et al., 1995, J. Immunol. 155, 4255). The rate of degradation of both the BCR and the bound antigen was also accelerated following BCR cross-linking. Here we provide evidence that the effect of cross-linking the BCR on antigen processing is in part dependent on signal cascades initiated by the BCR. We show that the protein kinase inhibitors Genistein and Chelerythrine, which block BCR signaling, reduce BCR-enhanced antigen processing in a dose-dependent manner. The kinase inhibitors have a small effect on the rate of internalization of the BCR and antigen following BCR cross-linking and significantly decrease the accelerated trafficking to the IIPLC. The increased rate of degradation of the BCR and antigen induced by BCR cross-linking is also decreased by the kinase inhibitors. BCR signaling does not appear to have a global effect on intracellular membrane trafficking as cross-linking the BCR did not alter the rate of trafficking of newly synthesized class II molecules to the IIPLC. Thus, the signaling function of the BCR appears to play a significant role in regulating discrete steps in the intracellular antigen processing pathway.

Developmental changes in subcellular AMPA/GluR receptor populations in rat forebrain.

Forebrains from rats of postnatal days (PND) 2, 7, 14, 21, and 30-40 were subjected to subcellular fractionation and samples from crude mitochondrial (P2, which contain synaptic plasma membranes) and microsomal (P3) fractions were used for SDS-PAGE and Western blotting with antibodies against GluR1, and GluR2/3 subunits of AMPA/GluR receptors. GluR immunoreactivity in P2 fractions increased gradually from PND 2 to PND 30. In contrast, GluR immunoreactivity in P3 fractions increased sharply at early postnatal ages, and was higher than in adults as early as at PND 7. Data were compared to postnatal changes in 3H-AMPA binding reported in various studies. Significant correlations were observed between changes in GluR immunoreactivity in P3 fractions and changes in high-affinity binding on one hand and between changes in GluR immunoreactivity in P2 fractions, and changes in low affinity binding. These data further establish that glutamate receptors present in different subcellular compartments represent different maturational states of the receptors, and suggest that changes in GluR populations could participate in mechanisms of synaptic plasticity.

High- and low-affinity alpha-[3H]amino-3-hydroxy-5-methylisoxazole-4-propionic acid ([3H]AMPA) binding sites represent immature and mature forms of AMPA receptors and are composed of differentially glycosylated subunits.

Quantitative alpha-[3H]amino-3-hydroxy-5-methylisoxazole-4-propionic acid ([3H]AMPA) binding autoradiography was performed on frozen-thawed sections from rat brain after preincubation at 0 or 35 degrees C for 1 h. Preincubation at 35 degrees C instead of 0 degrees C resulted in a selective decrease of [3H]AMPA binding assayed at a low concentration of [3H]AMPA (50 nM) and an enhancement of binding at a high concentration (500 nM). The decrease in [3H]AMPA binding after preincubation at 35 degrees C was accompanied with the loss of the lighter organelles of P3 (microsomal) fractions. These organelles were found to contain a small subpopulation of AMPA/GluR receptors exhibiting a high affinity for [3H]AMPA (K(D) approximately 14 nM), whereas heavier organelles exhibited lower affinity for AMPA (K(D) approximately 190 nM). This small subpopulation of AMPA/GluR receptors contained almost exclusively a structurally distinct species of GluR2/3 subunits with an apparent molecular mass of 103.5 kDa (assessed with anti-GluR2/3, C-terminal antibodies). Experiments using two deglycosylating enzymes, N-glycopeptidase F and endoglycosidase H, clearly indicated that the 103.5-kDa species represented a partially unglycosylated form of GluR2/3 subunits containing the high-mannose type of oligosaccharide moiety, whereas receptors present in synaptosomal fractions were composed of subunits with complex oligosaccharides. A similar result was obtained by using an antibody recognizing the N-terminal domain of GluR2(4). The same enzymatic treatment indicated that GluR1 subunits also exhibited a partially glycosylated form. These data indicate that high-affinity [3H]AMPA binding sites represent nonsynaptic, intracellular membrane-bound AMPA receptors that differ from synaptic receptors by at least the glycosylation state of GluR2 (and GluR1) subunits. In addition, our results provide a relatively simple way of assessing changes in two spatially and structurally distinct [3H]AMPA binding/GluR sites.

Wortmannin, a phosphatidylinositol 3-kinase inhibitor, blocks the assembly of peptide-MHC class II complexes.

Peptide-class II complexes are assembled in endocytic, lysosome-like compartments where newly synthesized class II molecules are targeted from the trans-Golgi network (TGN). Recent studies have implicated phosphatidylinositol 3-kinase (PI3-kinase) as an essential component in membrane trafficking from the TGN to lysosomes. Here, using subcellular fractionation, we show PI3-kinase activity associated with subcellular fractions which contain the class II peptide-loading compartment (IIPLC) in B cells. At concentrations required for inhibition of PI3-kinase activity in vivo, wortmannin blocked the processing and presentation of antigen by B cells to T cells. Treatment of B cells with wortmannin significantly limited the proteolytic degradation of invariant chain and the formation of peptide-class II complexes. Subcellular fractionation coupled with pulse-chase analyses showed that invariant chain and class II molecules trafficked to the IIPLC in wortmannin-treated cells. However, wortmannin prevented the maturation and correct targeting to the IIPLC of cathepsin D, a protease necessary for the degradation of invariant chain and assembly of processed antigen-class II complexes. These results suggest that li-class II complexes traffic to the IIPLC via a pathway that is relatively insensitive to wortmannin, but suggest a role for PI3-kinases in the trafficking of other components necessary for the assembly of processed antigen class II complexes to the IIPLC.

B cell antigen receptor signaling links biochemical changes in the class II peptide-loading compartment to enhanced processing.

In B cells, processing of antigens in the context of MHC class II molecules is initiated by the binding of antigen to the B cell antigen receptor (BCR). BCR-mediated processing is highly efficient, as a consequence of the BCR's linked roles of delivering antigen to the class II peptide-loading compartment and of signaling for increased antigen-processing activity. Evidence is emerging that receptor signaling regulates intracellular transport through the activities of kinases. These in turn have been implicated in the regulation of small mol. wt GTPases which govern membrane transport. Therefore, we investigated the changes in the phosphoprotein and GTPase profiles associated with the class II peptide-loading compartment following BCR cross-linking. We first show that protein kinase inhibitors, known to block BCR signal transduction, inhibit BCR-enhanced antigen processing, demonstrating the critical dependence of enhanced processing on the signaling activity of the BCR. Consistent with this observation, the phosphoprotein profile of the class II peptide-loading compartment underwent rapid and transient changes following BCR cross-linking. We also observed a marked increase in the low mol. wt GTPases associated with the class II peptide-loading compartment within 5 min of BCR cross-linking. The observed changes in both the phosphoprotein and GTPase profiles associated with the peptide-loading compartment were blocked by kinase inhibitors and were not accompanied by overall gross changes in the protein composition of the subcellular compartments. Thus, signal cascades initiated by BCR cross-linking at the plasma membrane are translated into changes in specific subsets of regulatory proteins associated with the peptide-loading compartment.