Identification Of HER2 Research Articles

Identification of HER2+ malignant cells in gastric tumors from single-cell RNAseq data.

417 Background: Gastric cancer is the 4th leading cause of cancer death worldwide with high incidence in East Asia. Despite recent developments in treatment options, gastric cancer survival rate remains low, partially attribute to tumor heterogeneity. Here we performed a comprehensive single cell analysis of malignant cells from gastric tumor samples. In addition to characterizing heterogenous transcriptional patterns, we developed a framework to identify HER2+ malignant cells, which may complement standard diagnostics for treatment decisions. Methods: Published and in-house generated 10x Genomics single cell RNAseq data in tumor and normal samples from gastric cancer patients were aggregated, including 64 tumor samples and 27 pre-cancerous samples and 12 adjacent normal samples. The R package Seurat (version 4.0) was applied for data QC and downstream analysis. High quality cells were clustered using highly variable genes and cell types were annotated by curated marker genes. To identify malignant epithelial cells, a gastric cancer signature was derived using matched tumor and normal samples from TCGA gastric cancer patients. Gastric tumor samples were also leveraged to develop a HER2 signature and TCGA breast tumor samples were used to validate the signature. HER2+ malignant cells were identified by re-clustering malignant epithelial cells using the HER2 signature. Results: 345,361 high-quality single cells were profiled, representing major cell types within tumor microenvironment. Among 59,861 epithelial cells, 22,770 malignant cells were identified with high expression of a gastric cancer signature. Copy number alterations (aneuploid) were highly enriched in inferred malignant cells compared with non-malignant cells (48.6% vs 1.4%, p<2.2×10-16, Fisher’s exact test). Further clustering analysis identified 10 subclusters with divergent expression of cancer oncogenic pathways, highlighting the vast heterogeneity of tumor origin. A Her2 amplification signature was derived using TCGA gastric cancer cohort (AUC=0.99) and validated in breast cancer cohort (AUC=0.93). Applying this signature to malignant cells, HER2+ cells were identified in a majority of tumors, with various proportions. In an independent data set, the percentage of HER2+ malignant cells is highly concordant with clinical HER2+ status, indicating the potential use of single cell data to supplement HER2+ clinical testing for treatment selection. Conclusions: This meta-analysis of single cell RNAseq data provides a comprehensive snapshot of tumor heterogeneity in gastric cancers, with aberrance in multiple oncogenic pathways observed in patients. The HER2+ cell classifier developed here holds the potential to complement standard clinical testing and enable personalized medicine, warranting further validation.

Suggested application of HER2+ breast tumor phenotype for germline TP53 variant classification within ACMG/AMP guidelines.

Early onset breast cancer is the most common malignancy in women with Li-Fraumeni syndrome, caused by germline TP53 pathogenic variants. It has repeatedly been suggested that breast tumors from TP53 carriers are more likely to be HER2+ than those of noncarriers, but this information has not been incorporated into variant interpretation models for TP53. Breast tumor pathology is already being used quantitatively for assessing pathogenicity of germline variants in other genes, and it has been suggested that this type of evidence can be incorporated into current American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for germline variant classification. Here, by reviewing published data and using internal datasets separated by different age groups, we investigated if breast tumor HER2+ status has utility as a predictor of TP53 germline variant pathogenicity, considering age at diagnosis. Overall, our results showed that the identification of HER2+ breast tumors diagnosed before the age of 40 can be conservatively incorporated into the current TP53-specific ACMG/AMP PP4 criterion, following a point system detailed in this manuscript. Further larger studies will be needed to reassess the value of HER2+ breast tumors diagnosed at a later age.

Innovativeness in breast cancer: The prime example of anti-HER2 agents

Since the identification of HER2 in breast cancer pathogenesis and the introduction of the first drugs targeting this receptor, the humanized monoclonal antibody trastuzumab and the tyrosine kinase inhibitor lapatinib, many advances have been made in the treatment of HER2-positive breast cancer that have led to a progressive improvement in the outcome of patients with early and advanced breast cancer. One of the major achievements is the development of dual HER2 blockade strategies. Evidence from the neoadjuvant and metastatic setting suggests that by combining trastuzumab with other anti-HER2 drugs such as lapatinib or the humanized monoclonal antibody pertuzumab, the efficacy of treatment may be further improved.

Abstract P1-02-05: Identification of HER-2/neu amplification using amplicon based benchtop next generation sequencing

Abstract Introduction Aplicon based next generation sequencing (NGS) assays have the potential to incorporate simultaneous assessment of somatic mutations and copy number variation into a single platform. Although not specifically designed for this purpose, we noted numerous examples of apparent HER-2/neu gene amplification in analyzing results from our mutation profiling 46-gene cancer NGS panel (Life Technologies, South San Francisco, CA). Material and Methods Existing amplicon coverage data from the TorrentSuite 2.0 (Life Technologies) pipeline was accessed and used to generate a HER-2/neu coverage proportion (ratio between all HER-2/neu amplicon reads and all other amplicon reads). This ratio was calculated for 170 unique cases of breast carcinoma. A total of 4 cases were eliminated from analysis due to indeterminate IHC/FISH results. Using a total of 166 cases, we performed ROC curve analysis to determine the sensitivity and specificity of NGS based HER-2/neu amplification compared to that of traditional IHC and FISH testing (MedCalc v8.0). Results The NGS based HER-2/neu coverage proportions in the 166 cases showed a clearly non-normal distribution with an outlier cluster of cases with an elevated NGS HER-2/neu ratio (6 cases with ratios >0.045). The distribution of NGS based HER-2/neu ratios for the entire population ranged from 0.01 to a maximum of 0.34. ROC curve analysis of NGS HER-2/neu proportions compared to IHC/FISH data showed a maximal sensitivity of 75.0% and specificity of 100% at an NGS ratio cut off of ≥0.045. In the 166 cases, 6 showed a HER-2/neu coverage proportion of > 0.045 (range 0.045-0.34). Utilizing the 0.045 NGS ratio cut off value, the population frequency of cases positive for HER2 expression was 3.4%. Of the 160 samples with NGS coverage proportion < 0.045, only two cases were positive by IHC/FISH testing. The correlation between NGS HER-2/neu coverage proportion and IHC/FISH testing was highly significant (Spearman rank correlation r = 0.67, p < 0.0001 CI: 0.58-0.75). Conclusions Even utilizing a limited somatic cancer panel that includes less than 200 amplicons in 46 genes, clinically significant HER-2/neu amplification can be readily identified. This is the first study to describe the functional utility of HER-2/neu amplification detection using a NGS based amplicon assay. This study shows that in addition to mutation analysis, amplification data can be simultaneously obtained, which has striking implications for potential clinical utility and HER-2/neu amplification detection outside of traditional IHC and HER2 testing modalities. Furthermore, utilizing this assay as a primary screening modality could limit the additional expense of multiple single gene testing. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-02-05.

Abstract P4-07-09: An approach to the identification of tumors driven by HER2 using the integrated activity of oncomiR miR-21 along with HER2 enriched genes

Abstract Introduction: The initial identification of HER2 as a driver in a subset of breast cancers was at the level of DNA (amplification), and subsequently noted at the level of transcripts and protein as well. However, the clinical selection of patients for treatment with Trastuzumab, has been through either IHC (protein) or FISH (DNA amplification) and not through transcript abundance. Interestingly, in most studies that have estimated transcript abundance in primary tumors, the proportion of patients that demonstrate increased transcript levels (termed HER2 Enriched) have tended to be slightly larger than the clinical HER2+ category. A more clinically useful measure might be proof of HER2 downstream activity that might help separate tumors being driven significantly by HER2 from ones where its role is supportive. One of the many consequences of HER2 over-expression is activation of the oncomiR, miR-21 via the MAPK pathway. miR-21 in turn is known to epigenetically regulate multiple targets including the tumor suppressors PTEN and PDCD4. While these molecular mechanisms have been demonstrated convincingly in breast cancer cell lines, clinical studies of these alterations in large numbers are yet to be reported. In this study we have examined the relationship between clinical HER2 positivity and miR-21 levels in 124 surgically excised breast cancer specimens. Methods: We selected 124 surgically excised specimens of primary breast cancers from our cohort that by HER2 immunohistochemistry (IHC) comprised 42 positive, 62 negative and 20 equivocal. Relative abundance of miR-21 was assessed using a TaqMan qRT-PCR, with normalization by RNU48. Relative transcript abundance of a set of 6 genes (HER2, GRB7, MLN64 and 3 reference genes) were evaluated by SYBR Green real time qPCR. Results: The majority of tumors that were clinically HER2+ over expressed miR-21. A concordance with an AUC of 96% at 100% sensitivity and 85% specificity was noted. There is a highly significant differential expression of miR-21 between HER2 positive, negative and equivocal samples (P < 0.0001). HER2 enriched score determined by using the expression levels of 3 genes (HER2, GRB7, MLN64) identified 35% (44/124) of the samples to be HER2 enriched. 72% of these (32/44) were also clinical HER2 positive by IHC. As expected, miR-21 was significantly over expressed in these tumors as well (P<0.0001). To identify all samples which might show HER2 downstream activity, a logistic regression model was built using expression of miR-21, HER2, MLN64 and GRB7 as the determinants of HER2 status. The best fitting model classified 91% (38/42) of HER2 +, 95% (59/62) of the HER2 negative accurately with 94% specificity and an AUC of 0.96. The model helped identify 10% of clinical HER2 negative samples (6/20 equivocal & 3/62 HER-2 negative) to have a high probability of being HER2+. Conclusion: Identification of HER2+ tumors with evidence of downstream activity may help identify patients with tumors being driven significantly by HER2 from ones where its role is supportive. The possibility of targeting miR-21 raises the tantalizing prospect of effecting change by altering the epigenetic regulation of multiple targets including tumor-suppressors. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-07-09.

Identification of HER-2/neu peptide p373-382 as a naturally processed immunodominant HLA-A2 binding epitope (46.11)

Abstract HER2 is a prime target for cancer therapeutics due to its high overexpression in tumors. Advanced clinical trials, in breast and prostate cancer, investigating the use of the HLA-A2-binding HER2 peptide p369-377 (E75) as a vaccine are ongoing. In the present study, we investigated the proteasomal processing of p369-377 and other epitopes from HER2. We did not detect processing of p369-377 by either the proteasome or immunoproteasome in vitro, suggesting that tumor cells do not naturally process this epitope from HER2 for presentation on HLA-A2. However, other HER2 peptides were found to be consistently processed by the proteasome and immunoproteasome. One newly identified processed peptide, HER2 p373-382, was found to bind HLA-A2 stronger than p369-377, despite algorithms that predicted p369-377 as a stronger binder. Cytotoxic T lymphocytes (CTL) specific for p373-382 recognized target cells pulsed with either p373-382 or p369-377. CTL specific for p373-382 also lysed HER2+HLA-A2+ human breast cancer cells more efficiently than p369-377-specific CTL. These results suggest that cancer cells are naturally processing and presenting p373-382. Furthermore, our results suggest that T cells generated against p369-377 in previous studies may have been cross-reacting with p373-382. Thus, the newly identified p373-382 peptide may be a more appropriate candidate for vaccines with this new evidence that it is processed and presented by HLA-A2 for recognition by HER2-specific CTL.

Study on breast carcinoma Her2/neu and hormonal receptors status assessed by automated images analysis systems: ACIS III (Dako) and ScanScope (Aperio).

Her-2/neu is overexpressed in 20-30% of breast cancer patients and is associated with a more aggressive disease. Identification of Her-2/c-erbB-2-neu overexpression is based on immunohistochemical [ihc] detection of protein and/or gene amplification in fluorescence in situ hybridization test (FISH). Also Estrogen receptors [ER] and Progesterone receptors [PR] are the prognostic and predictive biomarkers, recently analysed by ihc methods. Subjective, manual scoring of the ihc Her-2/neu expression and expression of the ER/PR reported as the percentage of immunopositive cells are the most common mode of interpretation among pathologists. Automated microscopy and computerised processing have provided increased accuracy in quantification and standardisation. to evaluate the scoring reproducibility of Her-2 /neu ihc expression tested by two automated systems: ACIS (Dako) and ScanScope (Aperio); to estimate the ER/PR expression in ihc staining methods with different anti-ER/anti-PR antibodies (the monoclonal and the ER/PR pharmDx TM Kit) by the ACIS system. Her-2/neu ihc expression was measured in 114 primary invasive breast carcinomas by the manual and the automated scoring (ACIS and Aperio system). 106 slides stained ihc with two types of anti-ER/anti-PR antibodies entered the quantisation. The results of our investigations showed very high reproducibility of Her-2/neu scores in intra- and interobserver analysis by ACIS evaluation. The major concordance was present in strong 3+ ihc cases; very small discordance was shown by cases with low expression of Her-2/neu. The accuracy of scoring by the Aperio was little lower in comparison to ACIS but it might result from the smaller and variable series of samples analysed by Aperio. The concordance in scoring of two automated systems was 86.5% (p<0.0001; gamma=0.887); the discordance was referred only to the lower expression of Her-2/neu. The concordance in manual scoring performed by the single observer and the panel was 84.2% (p<0.0001, gamma = 0.99); the discordance comprised a few cases with strong expression (2+ vs 3+). Very high intra- and interobserver reproducibility of the ER/PR ihc measurements was present in the readers results (referred to the percentage of immunoreactive carcinomatous cell population in the breast carcinomas acc. to the ACIS algorithm). No differences were disclosed in the percentage of ER-immunoreactive and PR-immunoreactive carcinomatous cell populations when used 2 different type of antibodies, in the ACIS automated method.

PEA3 and HER-2/NEU — novel therapeutic targets in endocrine tumours such as breast cancer

Identification of HER-2/NEU — PEA3 positive patients may have important implications in the treatment of breast cancer and could prove an appropriate therapeutic target.

Immunohistochemical Identification of HER-2/ neu Overexpression and CD117 (c-kit) Expression in Multiple Myeloma

Multiple myeloma (MM) is the most common plasma cell dyscrasia. Conventional therapy results in a median survival of 3-5 years. Patients with B-cell disorders and coexistent HER-2/ neu overexpression in solid tumors have a poorer prognosis than those without an underlying B-cell disorder. This, and the recent success of the tyrosine kinase inhibitor, imatinib mesylate in chronic myelogenous leukemia, led us to evaluate the incidence and role of c-kit (CD117) and HER-2/ neu overexpression in MM. We conducted a retrospective study to determine the incidence of HER-2/ neu and c-kit overexpression in MM. HER-2/ neu overexpression was evaluated using the DAKO Hercep test and c-kit overexpression was assessed using conventional immunohistochemistry (IHC); 69 patients with a diagnosis of MM were identified, of whom, 31 patients (19 males and 12 females) had an adequate pathological specimen available for IHC testing; 4 out of 31 patients (12.9%) showed HER-2/ neu overexpression, while 5/31 (16.13%) showed CD117 expression. Two patients (6.45%) showed both HER-2/ neu and c-kit overexpression. Although both HER-2/ neu and c-kit are not expressed very frequently in patients with MM, there appears to be a subgroup of patients in whom, either one or both these oncogenes is overexpressed. Given our small sample size, it is difficult to comment on the effect of CD117 and/or HER-2/ neu overexpression on survival. Future larger studies are needed to define the association in MM and to determine if the presence of one (CD117 or HER-2/ neu ) has an effect on overexpression of the other oncoprotein. Furthermore, it would be beneficial to identify the molecular nature of the interplay between HER-2/ neu and c-kit, if any. Target-directed signal transduction inhibition therapy using tyrosine kinase inhibitors, may be a distinct possibility in a select group of patients with MM.

Identification of HER-2/neu immunogenic epitopes presented by renal cell carcinoma and other human epithelial tumors.

HER-2/neu is a tumor-associated antigen overexpressed in a large variety of human tumors. Eight HER-2/neu peptides displaying HLA-A*0201 anchoring motifs were selected and tested for their binding affinity to HLA-A*0201 and their capacity to elicit cytotoxic T lymphocyte (CTL) responses in both HLA-A*0201 transgenic mice and in HLA-A*0201(+) healthy donors. Two high-affinity (p5 and p48) and one intermediate-affinity (p1023) peptides triggered CTL responses in both transgenic mice and humans, comparable to those observed for the well-known HER2/neu dominant peptide p369. CTL induced in transgenic mice lysed HLA-A*0201(+) RMA cells infected with recombinant HER-2/neu but not cells infected with wild-type vaccinia virus. Human CTL lysed HLA-A*0201(+) HER-2/neu(+) tumor cells of different origins (breast, colon, lung and renal cancer) irrespective of the expression levels of HER-2/neu. Importantly, primed CTL specific for these epitopes were detected in freshly isolated tumor-infiltrating lymphocytes from three renal cell carcinoma patients. Therefore, the HER-2/neu peptides p5, p48 and p1023 may be good candidates for immunotherapy of a broad spectrum of tumors, including renal cell carcinoma.

Identification of HER-2/ neu overexpression and the clinical course of lung carcinoma in non-smokers with chronic lymphocytic leukemia

Patients with CLL have an excess risk of developing second primary malignancies. The etiology of this excess risk is unclear, and has been thought to be related to smoking. HER-2/ neu overexpression has evolved as a prognostic/predictive factor in some solid tumors. We reviewed our experience with non-smokers who had CLL and subsequently developed lung carcinoma, in an effort to better understand the clinical course of these patients, and to evaluate the role of HER-2/ neu overexpression. We reviewed the records of all patients who had a diagnosis of both CLL and lung carcinoma between 1986 and 2000. HER-2/ neu overexpression was estimated by immunohistochemistry (IHC) using the Hercep test (DAKO®). An IHC score of 2+ or greater was considered positive. Overall survival was calculated from the date of diagnosis of lung carcinoma by the Kaplan–Meier product limit method. Fourteen non-smokers in whom a diagnosis of CLL was made at least 6 months prior to the diagnosis of lung carcinoma were identified. The median age for diagnosis of CLL in this group was 67 years while that for lung carcinoma was 70 years. The lung carcinomas included 10 non-small cell (NSCLC) and four small cell (SCLC) carcinomas. Nine specimens (six NSCLC and three SCLC) showed HER-2/ neu overexpression. Interestingly, 90% of patients with advanced stage cancer (stage IIIB/IV NSCLC or extensive SCLC) overexpressed HER-2/ neu. The presence of CLL did not alter outcome in patients with early stage lung cancer. However, after adjustment for age and performance status, patients with advanced stage NSCLC and CLL had a worse than expected outcome. HER-2/ neu overexpression (independent of smoking) may be involved in the development/progression of lung cancer in patients with CLL, and has an associated worse outcome. It is appropriate to consider heightened surveillance of CLL patients for lung carcinoma.

Identification of Her-2/Neu CTL epitopes using double transgenic mice expressing HLA-A2.1 and human CD.8

The Her-2/neu protooncogene is associated with malignant transformation and aggressive disease. Because of its overexpression in tumor cells and because it has been shown to be immunogenic, this protein represents an excellent target for T-cell immunotherapy. By identifying potential HLA-A2.1-binding peptides from the Her-2/neu sequence, peptides were selected as candidate T-cell epitopes. The immunogenicity of each peptide was evaluated by priming double transgenic mice expressing both the human (hu) CD8 and HLA-A2.1 molecules with synthetic peptides corresponding to these sequences. Because of the lack of interaction between murine CD8 and HLA-A2.1, expression of huCD8 on murine cells facilitates recognition of HLA molecules on human tumor cell lines. This led to the identification of two peptides that elicit an A2-restricted CTL response, one of which has not been previously identified. Both peptidespecific CTL populations were able to specifically lyse A2.1 and Her-2/neu expressing human tumor cells originating from a variety of tissues, demonstrating the utility of this murine model in identifying peptides presented by human cells. However, several Her-2/neu peptides previously reported to be immunogenic for human CTL were found not to be immunogenic in transgenic mice. The basis for these discrepancies is discussed.