Method of Tissue Acquisition Affects Success of Comprehensive Genomic Profiling in Lung Cancer.

CONTEXT.­: Multiple procedural techniques can be used to obtain tissue to create a formalin-fixed, paraffin-embedded specimen for comprehensive genomic profiling (CGP) in lung cancer. The literature is mixed on whether the procedure affects CGP success. OBJECTIVE.­: To examine whether biopsy procedure affects lung cancer CGP success. DESIGN.­: This was a cross-sectional study of all patients with lung cancer whose specimens were submitted for CGP between January and February 2020. Multiple quality control metrics were used to determine whether cases were successfully profiled. RESULTS.­: In all, 3312 samples were identified. Overall, 67.5% (2236 of 3312) of samples were obtained from biopsies, 13.0% (432 of 3312) from fine-needle aspirations (FNAs), 9.7% (321 of 3312) from resections, 5.3% (174 of 3312) from fluid cytology cell blocks, and 4.5% (149 of 3312) from bone biopsies. Overall, 70.1% (2321 of 3312) of cases passed CGP, 15.4% (510 of 3312) of cases were released as qualified reports, and 14.5% (481 of 3312) of cases failed CGP. Resection samples were the most likely to be successfully sequenced, failing in only 2.8% (9 of 321) of instances, while fluid cytology specimens were the least likely, failing in 23.0% (40 of 174) of instances. Biopsy (14.5% [324 of 2236]), FNA (18.5% [80 of 432]), and bone biopsy (18.8% [28 of 149]) specimens failed at intermediate frequencies. On multivariate logistic regression analysis of CGP success on specimen type, fluid cytology (odds ratio [OR], 0.08; 95% CI, 0.03-0.19), biopsy (OR, 0.25; 95% CI, 0.11-0.52), FNA (OR, 0.14; 95% CI, 0.06-0.32), and bone biopsy (OR, 0.07; 95% CI, 0.03-0.17) specimens had decreased odds of CGP success relative to resection samples. Among patients with successfully sequenced samples, 48.0% were eligible for at least 1 therapy, based on a companion diagnostic or National Comprehensive Cancer Network biomarker. CONCLUSIONS.­: The method of tissue acquisition was an important preanalytic factor that determined whether a sample would be successfully sequenced and whether a clinically actionable genomic alteration would be detected.

Comparison of PD-L1 tumor cell expression with 22C3, 28-8, and SP142 IHC assays across multiple tumor types.

BACKGROUND: Multiple PD-L1 immunohistochemistry (IHC) assays, including DAKO 22C3, DAKO 28-8, and Ventana SP142 PD-L1 IHC assays, have been approved by the Food and Drug Administration as a companion diagnostic (CDx) for various antiprogrammed death-1 and antiprogrammed death ligand 1 (PD-L1) based cancer immunotherapies. Here we present 22C3, 28-8, and SP142 analysis of 418 tumor specimens encountered in routine clinical practice. METHODS: All specimens were tested with 22C3, 28-8, and SP142 assays following the manufacturer's established staining protocols. RESULTS: The same PD-L1 status (defined as tumor cell expression (TC) scores with all three assays ≥1% or all <1%) was observed in 60.0% (251/418) tumor specimens (45.9% (192/418) were triple negative and 14.1% (59/418) were triple positive). A total of 54.1% (226/418) tumor cases were positive with at least one IHC assay (94.2% (213/226), 77.0% (174/226), and 28.8% (65/226) of these were positive for 22C3, 28-8 and SP142, respectively). Among the 40.0% (167/418) tumor cases that showed a different PD-L1 status, 62.3% (104/167) were 22C3+/28-8+/SP142-, and 28.7% (48/167) were 22C3+/28-8-/SP142-. The same PD-L1 status with all three antibody clones was observed in 48.7% (97/199) of NSCLC cases, and among these, 54.6% (53/97) were triple negative and 45.4% (44/97) triple positive. A total of 73.4% (146/199) NSCLC cases were positive with at least one IHC assay (95.2% (n=139/146), 82.2% (n=120/146), and 32.2% (n=47/146) were positive for 22C3, 28-8, and SP142, respectively). Among the 51.3% (102/199) NSCLC cases that showed a different status among the three IHC assays, 67.6% (69/102) were 22C3+/28-8+/SP142-, and 23.5% (24/102) were 22C3+/28-8-/SP142-. A total of 81.1% (43/53) lung squamous cell carcinoma, 72.1% (88/122) of lung adenocarcinoma, 69.6% (16/23) of non-small cell lung cancer (NSCLC) not otherwise specified (NOS), and 50.0% (4/8) of small cell lung carcinoma cases were positive with at least one IHC assay. CONCLUSIONS: Our data suggest that 22C3 is the most sensitive PD-L1 IHC assay for tumor cell expression, followed by 28-8 and in turn by SP-142. These findings represent an additional factor for clinical teams to consider when deciding which PD-L1 IHC assay (and in turn which CDx-associated PD-L1 based immunotherapy) is most appropriate for each individual patient.

Circulating Cell-Free DNA Yield and Circulating-Tumor DNA Quantity from Liquid Biopsies of 12 139 Cancer Patients.

BACKGROUND: The amounts of circulating cell-free DNA (cfDNA) and circulating-tumor DNA (ctDNA) present in peripheral blood liquid biopsies can vary due to preanalytic/analytic variables. In this study, we examined the impact of patient age, sex, stage, and tumor type on cfDNA yield, ctDNA fraction, and estimated ctDNA quantity from a large cohort of clinical liquid biopsy samples. METHODS: We performed a retrospective analysis of 12 139 consecutive samples received for liquid biopsy (FoundationOne® Liquid) clinical testing. RESULTS: Significant differences in both cfDNA yield and estimated ctDNA quantity were observed based on the underlying tumor type that initiated the liquid biopsy analysis and the stage of the patient (P < 0.001). In addition, significant differences in ctDNA quantity were present based in both the patient age and sex (P < 0.001). Importantly, we saw a significantly higher success rate of issuing a clinically useful report in patients with higher levels of cfDNA yield and ctDNA quantity (P < 0.001). CONCLUSIONS: In this study, we show that ctDNA quantity varied significantly based on patient age, sex, stage, and tumor type, which could offer an explanation as to why certain liquid biopsy specimens are more likely to fail sequencing or provide clinically meaningful results. In addition, this could affect future clinical decisions on the blood sample volumes required to allow successful liquid biopsy testing.

Clinicopathologic and Genomic Characterization of PD-L1 Positive Urothelial Carcinomas.

INTRODUCTION: Pembrolizumab was approved with an accompanying companion diagnostic (CDx) assay (PD-L1 DAKO 22C3) for urothelial carcinoma (UC). In this study, we further characterize the clinicopathologic and genomic features of UC that are programmed death-ligand 1 (PD-L1) positive. MATERIALS AND METHODS: The cohort of this study consisted of a total of 528 consecutive UC patients with PD-L1 immunohistochemistry (IHC) and comprehensive genomic profiling (CGP). All PD-L1 IHC testing was performed using the DAKO 22C3 CDx assay for UC. PD-L1 positivity was determined at a combined positive score ≥ 10. RESULTS: A total of 44.5% (235/528) patients with UC were PD-L1positive . A lower PD-L1 positivity rate was detected in primary (42.3%, 148/350) versus metastatic sites (48.9%, 87/178). PD-L1 positivity was dependent on the location of the metastatic sites. CGP revealed PD-L1positive patients had more frequent genomic alterations (GAs) in TP53 (p = .006) and RB1 (p = .003) and less frequent GAs in FGFR3 (p = .001) and MTAP (p = .028). The APOBEC mutational signature and tumor mutational burden (TMB)-high were more common in PD-L1positive patients. By testing patients with UC with CGP, in addition to PD-L1 IHC, an additional 97 patients (18.4%) in the total cohort were eligible for immunotherapy based on TMB status. CONCLUSION: PD-L1positive and PD-L1negative urothelial carcinomas are genomically different. Also, our study provides the framework for future clinical investigation with regard to specimen site selection for PD-L1 testing as well as candidate biomarker genomic alterations that may predict for better response or lack of response to immune checkpoint inhibitors. IMPLICATIONS FOR PRACTICE: In this study, a higher prevalence of TP53 and RB1 alterations and APOBEC mutational signatures in the PD-L1positive urothelial carcinoma disease subset and enrichment of FGFR3 alterations in the PD-L1negative disease subset were found. These data provide the basis for future investigation into the role of these genomic changes as positive and negative predictors of immunotherapy response. Also, differences wer seen in PD-L1 positivity based on the collection site of the sample, which can provide a framework for future clinical trial design and could influence sample selection for PD-L1 testing in patients with urothelial carcinoma when multiple samples are available.

Biomarkers in Breast Cancer: An Integrated Analysis of Comprehensive Genomic Profiling and PD-L1 Immunohistochemistry Biomarkers in 312 Patients with Breast Cancer.

BACKGROUND: We examined the current biomarker landscape in breast cancer when programmed death-ligand 1 (PD-L1) testing is integrated with comprehensive genomic profiling (CGP). MATERIAL AND METHODS: We analyzed data from samples of 312 consecutive patients with breast carcinoma tested with both CGP and PD-L1 (SP142) immunohistochemistry (IHC) during routine clinical care. These samples were stratified into hormone receptor positive (HR+)/human epidermal growth factor receptor negative (HER2-; n = 159), HER2-positive (n = 32), and triple-negative breast cancer (TNBC) cohorts (n = 121). RESULTS: We found that in the TNBC cohort, 43% (52/121) were immunocyte PD-L1-positive, and in the HR+/HER2- cohort, 30% (48/159) had PIK3CA companion diagnostics mutations, and hence were potentially eligible for atezolizumab plus nab-paclitaxel or alpelisib plus fulvestrant, respectively. Of the remaining 212 patients, 10.4% (22/212) had a BRCA1/2 mutation, which, if confirmed by germline testing, would allow olaparib plus talazoparib therapy. Of the remaining 190 patients, 169 (88.9%) were positive for another therapy-associated marker or a marker that would potentially qualify the patient for a clinical trial. In addition, we examined the relationship between immunocyte PD-L1 positivity and different tumor mutation burden (TMB) cutoffs and found that when a TMB cutoff of ≥9 mutations per Mb was applied (cutoff determined based on prior publication), 11.6% (14/121) patients were TMB ≥9 mutations/Mb and of these, TMB ≥9 mutations per Mb, 71.4% (10/14) were also positive for PD-L1 IHC. CONCLUSION: Our integrated PD-L1 and CGP methodology identified 32% of the tested patients as potentially eligible for at least one of the two new Food and Drug Administration approved therapies, atezolizumab or alpelisib, and an additional 61.2% (191/312) had other biomarker-guided potential therapeutic options. IMPLICATIONS FOR PRACTICE: This integrated programmed death-ligand 1 immunohistochemistry and comprehensive genomic profiling methodology identified 32% of the tested patients as eligible for at least one of the two new Food and Drug Administration-approved therapies, atezolizumab or alpelisib, and an additional 61.2% (191/312) had other biomarker-guided potential therapeutic options. These findings suggest new research opportunities to evaluate the predictive utility of other commonly seen PIK3CA mutations in hormone receptor-positive breast cancers and to standardize tumor mutation burden cutoffs to evaluate its potentially predictive role in triple-negative breast cancer.

Reduction and pH dual-sensitive nanovesicles co-delivering doxorubicin and gefitinib for effective tumor therapy.

Owing to the complexity of tumorgenesis, combination therapy has proven to be a viable strategy for cancer treatment in recent years. However, the delivery and site-specific release of different therapeutic agents remain a major challenge in combination therapy. In this study, a polymeric nanovesicle based on a copolymer of polyethylene glycol and a polypeptide derivative was introduced as a vector to simultaneously deliver hydrophobic gefitinib and hydrophilic doxorubicin hydrochloride for multi-target combination therapy. The vesicle incorporating the two drugs exhibited prominent pH/reduction sensitivities to trigger the release of gefitinib and doxorubicin inside cancer cells. The two drugs co-delivered by the polymeric nanovesicle exhibited a joint anticancer effect both in vitro and in vivo. In particular, a remarkable therapeutic effect was demonstrated in animal studies using a mouse N2a neuroblastoma model. This study reveals the potential of reduction and pH dual-responsive nanovesicles bearing gefitinib and doxorubicin as an effective nano-medicine for cancer treatment.

Boundary states in the chiral symmetric systems with a spatial symmetry.

We study topological systems with both a chiral and a spatial symmetry which result in an additional spatial chiral symmetry. We distinguish the topologically nontrivial states according to the chiral symmetries protecting them and study several models in 1D and 3D systems. The perturbations breaking the spatial symmetry can break only one of the two chiral symmetries while the perturbations preserving the spatial symmetry always break or preserve both of them. In 3D systems, besides the 3D symmetries, the topologically nontrivial boundary modes may also be protected by the hidden lower dimensional symmetries. We then figure out the corresponding topological invariants and connect them with the 3D invariants.

Microwave spectra, ab initio calculations, and r0 structural parameters for (methylamino)thiophosphoryl difluoride.

The microwave spectra of (methylamino)thiophosphoryl difluoride, CH(3)NHP(=S)F(2), and two deuterated species, CH(3)NDP(=S)F(2) and CD(3)NHP(=S)F(2), have been investigated in the region from 26.5 to 39.0 GHz. The rotational constants of the ground vibrational state have been determined and have been shown to be only consistent with the trans conformer (CH(3) group antiperiplanar to the P=S bond) with C(s) symmetry. The a-type R branch transitions have been assigned for the trans conformer for the three isotopomers on the basis of the rigid rotor model. Near-trans and near-cis forms without molecular planes of symmetry are predicted by all ab initio calculations with the near-trans form being more stable. However, the double-well potentials governing the interchange between the two enantiomeric near-trans as well as the two near-cis forms are too shallow to accommodate the zero-point energies of the nu(24) asymmetric torsion. Thus, the trans conformation with C(s) symmetry may be more accurate in explaining the microwave experimental data. The "adjusted" r(0) structural parameters have been obtained by systematically adjusting the ab initio MP2(full)/6-311+G(d,p) structure of the trans conformer with C(s) symmetry to fit the microwave rotational constants. The determined heavy atom distances are r(C-N) = 1.459(5), r(P-N) = 1.621(5), r(P=S) = 1.879(5), and r(P-F) = 1.550(5) A, and the heavy atom angles are angleCNP = 124.7(5) degrees , angleNPS = 118.3(5) degrees , angleNPF = 103.2(5) degrees , angleFPS = 117.0(5) degrees , and angleFPF = 94.6(5) degrees . The adjusted r(0) parameters have also been obtained for aminodifluorophosphine, H(2)NPF(2), with a slightly pyramidal -PNH(2) moiety. The results indicate that the previously reported short distance of 0.981(5) A for the N-H(o)(outer) bond from the microwave study is too short, and the adjusted r(0) value of 1.007(3) A is obtained from the combined data. Adjusted r(0) parameters are also reported for (dimethylamino)difluorophosphine, (CH(3))(2)NPF(2), with C(s) symmetry with the PNC(2) portion of the molecule being planar. The previously reported C-H distances from the electron diffraction study are too long, and the anglePNC(i) and angleC(o)NC(i) angles are also found to be in error. These results provide a reasonable explanation why the microwave and electron diffraction results differ for the structures of these latter two molecules.