Evaluation of the international Ki67 working group cut point recommendations for early breast cancer: comparison with 21-gene assay results in a large integrated health care system.

PURPOSE: The International Ki67 Working Group (IKWG) has developed training for immunohistochemistry (IHC) scoring reproducibility and recommends cut points of ≤ 5% and ≥ 30% for prognosis in ER+, HER2-, stage I/II breast cancer. We examined scoring reproducibility following IKWG training and evaluated these cut points for selecting patients for further testing with the 21-gene Recurrence Score (RS) assay. METHODS: We included 307 women aged 50+ years with node-negative, ER+PR+HER2- breast cancer and with available RS results. Slides from the diagnostic biopsy were stained for Ki67 and scored using digital image analysis (IA). Two IHC pathologists underwent IKWG training and visually scored slides, blinded to each other and IA readings. Interobserver reproducibility was examined using intraclass correlation (ICC) and Kappa statistics. RESULTS: Depending on reader, 8.8-16.0% of our cohort had Ki67 ≤ 5% and 11.4-22.5% had scores ≥ 30%. The ICC for Ki67 scores by the two pathologists was 0.82 (95% CI 0.78-0.85); it was 0.79 (95% CI 0.74-0.83) for pathologist 1 and IA and 0.76 (95% CI 0.71-0.80) for pathologist 2 and IA. For Ki67 scores ≤ 5%, the percentages with RS < 26 were 92.6%, 91.8%, and 90.9% for pathologist 1, pathologist 2, and IA, respectively. For Ki67 scores ≥ 30%, the percentages with RS ≥ 26 were 41.5%, 51.4%, and 27.5%, respectively. CONCLUSION: The IKWG's Ki67 training resulted in moderate to strong reproducibility across readers but cut points had only moderate overlap with RS cut points, especially for Ki67 ≥ 30% and RS ≥ 26; thus, their clinical utility for a 21-gene assay testing pathway remains unclear.

Immunohistochemistry and alternative FISH testing in breast cancer with HER2 equivocal amplification.

PURPOSE: While HER2 testing is well established in directing appropriate treatment for breast cancer, a small percentage of cases show equivocal results by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Alternative probes may be used in equivocal cases. We present a single community-based institution's experience in further evaluating these cases. PATIENTS AND METHODS: Between 2014 and 2016, 4255 samples were submitted for HER2 amplification testing by alternative probes, TP53, RAI1, and RARA. Of the patients tested by FISH, 505/3908 (12.9%) also had IHC data. RESULTS: Most (73.9%) FISH equivocal cases remained equivocal after IHC testing. However, 50.5% of equivocal cases were classified as HER2 amplified by alternative probes. Most cases were positive by more than one probe: 78% of positive cases by RAI1 and 73.9% by TP53. There was a significant difference between IHC and FISH alternative testing (p < 0.0001) among the equivocal cases by conventional FISH testing, 44% of IHC negative cases became positive while 36% of the positive IHC cases became negative by alternative FISH testing. Available data showed that 41% of patients were treated with palbociclib and were positive by alternative FISH. CONCLUSION: The prevalence of double HER2 equivocal cases and the discrepancy between IHC and alternative FISH testing suggest that FISH alternative testing using both RAI1 and TP53 probes is necessary for conclusive classification. Because almost half of FISH equivocal cases converted to HER2 amplified upon alternative testing, clinical studies to determine the benefit of anti-HER2 therapy in these patients are urgently needed.

Correlation of MET gene amplification and TP53 mutation with PD-L1 expression in non-small cell lung cancer.

BACKGROUND: The role of MET amplification in lung cancer, particularly in relation to checkpoint inhibition and EGFR WT, has not been fully explored. In this study, we correlated PD-L1 expression with MET amplification and EGFR, KRAS, or TP53 mutation in primary lung cancer. METHODS: In this retrospective study, tissue collected from 471 various tumors, including 397 lung cancers, was tested for MET amplification by FISH with a MET/centromere probe. PD-L1 expression was evaluated using clone SP142 and standard immunohistochemistry, and TP53, KRAS, and EGFR mutations were tested using next generation sequencing. RESULTS: Our results revealed that PD-L1 expression in non-small cell lung cancer is inversely correlated with EGFR mutation (P=0.0003), and positively correlated with TP53 mutation (P=0.0001) and MET amplification (P=0.004). Patients with TP53 mutations had significantly higher MET amplification (P=0.007), and were more likely (P=0.0002) to be EGFR wild type. There was no correlation between KRAS mutation and overall PD-L1 expression, but significant positive correlation between PD-L1 expression and KRAS with TP53 co-mutation (P=0.0002). A cut-off for the ratio of MET: centromere signal was determined as 1.5%, and 4% of lung cancer patients were identified as MET amplified. CONCLUSIONS: This data suggests that in lung cancer both MET and TP53 play direct roles in regulating PD-L1 opposing EGFR. Moreover, KRAS and TP53 co-mutation may cooperate to drive PD-L1 expression in lung cancer. Adding MET or TP53 inhibitors to checkpoint inhibitors may be an attractive combination therapy in patients with lung cancer and MET amplification.

Significant Improvement in Detecting BRAF, KRAS, and EGFR Mutations Using Next-Generation Sequencing as Compared with FDA-Cleared Kits.

INTRODUCTION: We compared mutations detected in EGFR, KRAS, and BRAF genes using next-generation sequencing (NGS) and confirmed by Sanger sequencing with mutations that could be detected by FDA-cleared testing kits. METHODS: Paraffin-embedded tissue from 822 patients was tested for mutations in EGFR, KRAS, and BRAF by NGS. Sanger sequencing of hot spots was used with locked nucleic acid to increase sensitivity for specific hot-spot mutations. This included 442 (54%) lung cancers, 168 (20%) colorectal cancers, 29 (4%) brain tumors, 33 (4%) melanomas, 14 (2%) thyroid cancers, and 16% others (pancreas, head and neck, and cancer of unknown origin). Results were compared with the approved list of detectable mutations in FDA kits for EGFR, KRAS, and BRAF. RESULTS: Of the 101 patients with EGFR abnormalities as detected by NGS, only 58 (57%) were detectable by cobas v2 and only 35 (35%) by therascreen. Therefore, 42 and 65%, respectively, more mutations were detected by NGS, including two patients with EGFR amplification. Of the 117 patients with BRAF mutation detected by NGS, 62 (53%) mutations were within codon 600, detectable by commercial kits, but 55 (47%) of the mutations were outside codon V600, detected by NGS only. Of the 321 patients with mutations in KRAS detected by NGS, 284 (88.5%) had mutations detectable by therascreen and 300 (93.5%) had mutations detectable by cobas. Therefore, 11.5 and 6.5% additional KRAS mutations were detected by NGS, respectively. CONCLUSION: NGS provides significantly more comprehensive testing for mutations as compared with FDA-cleared kits currently available commercially.

Deep Sequencing of Cell-Free Peripheral Blood DNA as a Reliable Method for Confirming the Diagnosis of Myelodysplastic Syndrome.

BACKGROUND: Demonstrating the presence of myelodysplastic syndrome (MDS)-specific molecular abnormalities can aid in diagnosis and patient management. We explored the potential of using peripheral blood (PB) cell-free DNA (cf-DNA) and next-generation sequencing (NGS). MATERIALS AND METHODS: We performed NGS on a panel of 14 target genes using total nucleic acid extracted from the plasma of 16 patients, all of whom had confirmed diagnoses for early MDS with blasts <5%. PB cellular DNA from the same patients was sequenced using conventional Sanger sequencing and NGS. RESULTS: Deep sequencing of the cf-DNA identified one or more mutated gene(s), confirming the diagnosis of MDS in all cases. Five samples (31%) showed abnormalities in cf-DNA by NGS that were not detected by Sanger sequencing on cellular PB DNA. NGS of PB cell DNA showed the same findings as those of cf-DNA in four of five patients, but failed to show a mutation in the RUNX1 gene that was detected in one patient's cf-DNA. Mutant allele frequency was significantly higher in cf-DNA compared with cellular DNA (p = 0.008). CONCLUSION: These data suggest that cf-DNA when analyzed using NGS is a reliable approach for detecting molecular abnormalities in MDS and should be used to determine if bone marrow aspiration and biopsy are necessary.

BCR-JAK2 fusion as a result of a translocation (9;22)(p24;q11.2) in a patient with CML-like myeloproliferative disease.

Translocation (9;22)(q34;q11.2) resulting in BCR/ABL1 fusion at the molecular level is the hallmark of chronic myelogenous leukemia (CML). Variants of the Philadelphia translocation and complex translocations involving BCR have been reported in myeloproliferative disorders (MPD). A rare translocation, t(9;22)(p24;q11.2), resulting in a novel BCR-JAK2 fusion has been reported in a handful of cases of CML and acute myelogenous leukemia (AML). We present clinical-pathological and cytogenetic evaluation of a patient with Philadelphia-chromosome negative CML/MPD harboring a t(9;22)(p24;q11.2) resulting in BCR-JAK2 fusion. Fluorescence in situ hybridization and molecular characterization of the translocation confirmed a BCR-JAK2 fusion and helped delineate the breakpoints upstream of exon 1 of minor cluster region of BCR gene and likely intron 18 of the JAK2 gene, resulting in an in-frame transcript This case provides convincing support, along with two previous case-reports, for a role for activation of the Janus kinase 2 in evolution of myeloproliferative disease. The recurrent, albeit rare, nature of the breakpoints within BCR and JAK2 suggests a potential new diagnostic target that should be interrogated in Ph-negative CML/MPD patients.

Trainable immunohistochemical HER2/neu image analysis: a multisite performance study using 260 breast tissue specimens.

CONTEXT: Aperio Technologies, Inc (Vista, California) provides a new immunohistochemistry (IHC) HER2 Image Analysis (IA) system that allows tuning of the intensity thresholds of the HER2/ neu scoring scheme to adapt to the staining characteristics of different reagents. OBJECTIVE: To compare the trainable IHC HER2 IA system for different reagents to conventional manual microscopy (MM) in a multisite study. DESIGN: Two hundred sixty formalin-fixed, paraffin-embedded breast cancer specimens from 3 clinical sites were assayed: 180 specimens stained with Dako's HercepTest (Carpinteria, California), and 80 specimens stained with Ventana's PATHWAY HER-2/neu (Tucson, California). At each site, 3 pathologists performed a blinded reading of the glass slides with the use of a light microscope. The glass slides were then scanned and after a wash-out period and randomization, the same pathologists outlined a representative set of tumor regions to be analyzed by IHC HER2 IA. Each of the methods, MM and IA, was evaluated separately and comparatively by using κ statistics of negative HER2/neu scores (0, 1+) versus equivocal HER2/neu scores (2+) versus positive HER2/neu scores (3+) among the different pathologists. RESULTS: κ Values for IA and MM were obtained across all sites. MM: 0.565-0.864; IA: 0.895-0.947; MM versus IA: 0.683-0.892 for site 1; MM: 0.771-0.837; IA: 0.726-0.917; MM versus IA: 0.687-0.877 for site 2; MM: 0.463-0.674; IA: 0.864-0.918; MM versus IA: 0.497-0.626 for site 3. CONCLUSION: Aperio's trainable IHC HER2 IA system shows substantial equivalence to MM for Dako's HercepTest and Ventana's PATHWAY HER-2/neu at 3 clinical sites. Image analysis improved interpathologist agreement in the different clinical sites.

Fluorescence in situ hybridization and K-ras analyses improve diagnostic yield of endoscopic ultrasound-guided fine-needle aspiration of solid pancreatic masses.

OBJECTIVES: Endoscopic ultrasound (EUS)-guided fine-needle aspiration (FNA) is the main diagnostic modality for pancreatic mass lesions. However, cytology is often indeterminate, leading to repeat FNAs and delay in care. Here, we evaluate whether combining routine cytology with fluorescence in situ hybridization (FISH) and K-ras/p53 analyses improves diagnostic yield of pancreatic EUS-FNA. METHODS: Fifty EUS-FNAs of pancreatic masses in 46 patients were retrospectively analyzed. Mean follow-up was 68 months. Thirteen initial cytologic samples (26%) were benign, 23 malignant (46%), and 14 atypical (28%). We performed FISH for p16, p53, LPL, c-Myc, MALT1, topoisomerase 2/human epidermal growth factor receptor 2, and EGFR, as well as K-ras/p53 mutational analyses. RESULTS: On final diagnosis, 11 (79%) of atypical FNAs were malignant, and 3 benign (21%). Fluorescence in situ hybridization was negative in all benign and all atypical samples with final benign diagnosis. Fluorescence in situ hybridization plus K-ras analysis correctly identified 60% of atypical FNAs with final malignant diagnosis. Combination of routine cytology with positive FISH and K-ras analyses yielded 87.9% sensitivity, 93.8% specificity, 96.7% positive predictive value, 78.9% negative predictive value, and 89.8% accuracy. CONCLUSIONS: Combining routine cytology with FISH and K-ras analyses improves diagnostic yield of EUS-FNA of solid pancreatic masses. We propose to include these ancillary tests in the workup of atypical cytology from pancreatic EUS-FNA.

Reading immunohistochemical slides on a computer monitor--a multisite performance study using 180 HER2-stained breast carcinomas.

BACKGROUND: With the adoption of digital pathology, image analysis (IA) of immunohistochemistry (IHC) slides can be integrated seamlessly into the digital pathology workflow. A pathologist can now use IA efficiently while reading the digital IHC slides on a computer monitor. Thus, the clinical acceptance of a digital pathology system for IHC quantitation depends both on the performance of the IHC IA, and the ability to manually read digital IHC slides on the monitor. A multisite study was conducted to compare the manual reading of IHC Human Epidermal Growth Factor Receptor 2 (HER2) slides on a monitor, using Aperio Technologies, Inc. ScanScope XT instrument and the Spectrum digital pathology information management system to conventional manual microscopy (MM). DESIGN: A total of 180 breast cancers were immunohistochemically stained using Dako HercepTest and assayed: (site 1) 80 retrospective specimens with equal HER2 score distribution from an academic center, and (site 2) 100 prospective specimens from a reference laboratory. At each site, 3 pathologists carried out a blinded read of the glass slides using a conventional light microscope, and reporting the HER2 score for each. The glass slides were scanned using a 20× objective, and after a wash-out period and randomization of the slides, the same 3 pathologists carried out another blinded read of the same slides, but this time of the digital image of the slides on the monitor, again reporting the HER2 score. Each of the methods: MM and reading digital slides on a computer monitor, from now on called manual digital read (MDR) were evaluated separately and comparatively using Percent Agreement (PA) of negative HER2 scores (0, 1+) versus equivocal (2+) versus positive HER2 scores (3+). RESULTS: Comparable PA values were obtained for MM and MDR IHC HER2 images on the monitor (MM: 76.3% to 91.3%; MDR: 70.0% to 86.0%; MM vs. MDR: 61.3% to 92.5%). CONCLUSIONS: Results of manually reading IHC HER2 slides on a monitor using Aperio Technologies, Inc. digital pathology system show substantial equivalence to those obtained by conventional manual microscopy. The digital slides are easily read on a monitor.

A multisite performance study comparing the reading of immunohistochemical slides on a computer monitor with conventional manual microscopy for estrogen and progesterone receptor analysis.

A multisite study was conducted to assess the performance of the Aperio digital pathology system (Aperio Technologies, Vista, CA) for reading estrogen receptor (ER) and progesterone receptor (PR) slides on a computer monitor. A total of 520 formalin-fixed breast tissue specimens were assayed at 3 clinical sites for ER and PR (260 each). Percentage and average staining intensity of positive nuclei were assessed. At each site, 3 pathologists performed a blinded reading of the glass slides using their microscopes initially and later using digital images on a computer monitor. Comparable percentages of agreements were obtained for manual microscopy (MM) and manual digital slide reading (MDR) (ER, percentage of positive nuclei with cutoffs: MM, 91.3%-99.0%/MDR, 91.3%-100.0%; PR, percentage of positive nuclei with cutoffs: MM, 83.8%-99.0%/MDR, 76.3%-100.0%). Reading ER and PR slides on a computer monitor using the Aperio digital pathology system is equivalent to reading the slides with a conventional light microscope.

A new immunohistochemical ER/PR image analysis system: a multisite performance study.

BACKGROUND: Aperio provides a new image analysis (IA) solution for immunohistochemistry (IHC) as part of its digital pathology system. To be used in a clinical setting, substantial equivalence to scoring by manual microscopy (MM) needs to be shown. A multisite study was conducted to assess the performance of Aperio's IHC IA solution for estrogen receptor (ER) and progesterone receptor (PR). DESIGN: A total of 260 formalin-fixed, paraffin-embedded breast tissue specimens were assayed at 2 clinical sites for ER and PR. The ability to score ER/PR slides in terms of (1) percentage of positive nuclei with cutoffs of 1%, 5%, and 10% and (2) average staining intensity as 0, 1+, 2+, and 3+ score was assessed. At each site, 3 pathologists performed a blinded read of the glass slides using their microscopes. The glass slides were then scanned, and after a wash-out period and randomization of the slides, the pathologists viewed the images on a computer monitor and outlined a representative set of tumor regions to be analyzed by IA. Each of the methods: MM and IA were evaluated separately and comparatively. RESULTS: Comparable or higher percent agreements were obtained for IA compared with MM (ER--percent of positive nuclei with cutoffs: MM: 91.3% to 98.8%/IA: 93.8% to 98.8%/IA vs. MM: 92.5% to 97.5%, and intensity score: MM: 55.0% to 86.3%/IA: 88.8% to 90.0%/IA vs. MM: 63.8% to 86.3%; PR-percent of positive nuclei with cutoffs: MM: 83.8% to 99.0%/IA: 85.0% to 99.0%/IA vs. MM: 81.3% to 99.0%, and intensity score: MM: 58.8% to 88.0%/IA: 68.8% to 88.0%/IA vs. MM: 58.8% to 84.0%). CONCLUSIONS: The study results show that Aperio's digital IHC IA solution for ER/PR is substantially equivalent to scoring by MM.

Neonatal autoimmune disease: influence of CD4+ CD25+ regulatory T cells.

Although previous studies have emphasized the tolerogenic property of murine neonatal immune system, recent studies indicate that neonatal mice are prone to autoimmune disease. This chapter will summarize the evidence for neonatal propensity to autoimmune ovarian disease (AOD) and describe the new finding that autoantibody can trigger a T cell-dependent autoimmune disease in neonatal but not adult mice. Based on depletion or addition of the CD4+ CD25+ T cells, disease resistance of older mice is explicable by the emergence of CD4+ CD25+ regulatory T-cell function after day 5, whereas disease susceptibility is associated with resistance to regulation by CD4+ CD25+ T cells.

Autoimmune ovarian disease induced by immunization with zona pellucida (ZP3) peptide.

Autoimmune ovarian disease is a known cause of human premature ovarian failure. An experimental murine model can be created by immunization with a peptide of ZP3, an ovary-specific glycoprotein. Mice injected with the ZP3 peptide develop histological evidence of ovarian inflammation (oophoritis), as well as antibody to the zona pellucida and T cell responses to the peptide. This unit describes the immunologic properties of the ZP3 peptides, the method of active autoimmune oophoritis induction, and the evaluation and semiquantitation of ovarian pathology. Surgical manipulations of the ovaries have been instrumental in the novel application of this autoimmune model; thus the most useful operations are also detailed. Surgical procedures are included for adult oophrectomy, neonatal ovariectomy, and implantation of ovarian grafts into mice without endogenous ovaries.