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Chubarov AS, Oscorbin IP, Novikova LM, Filipenko ML, Lomzov AA, Pyshnyi DV. Allele-Specific PCR for PIK3CA Mutation Detection Using Phosphoryl Guanidine Modified Primers. Diagnostics (Basel) 2023; 13:diagnostics13020250. [PMID: 36673060 PMCID: PMC9858071 DOI: 10.3390/diagnostics13020250] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Phosphoryl guanidine (PG) is the novel uncharged modification of internucleotide phosphates of oligonucleotides. Incorporating PG modification into PCR primers leads to increased discrimination between wild-type and mutated DNA, providing extraordinary detection limits in an allele-specific real-time polymerase chain reaction (AS-PCR). Herein, we used PG-modification to improve the specificity of AS primers with unfavorable Pyr/Pur primer's 3'-end mismatch in the template/primer complex. Two mutations of the PIK3CA gene (E542K, E545K) were chosen to validate the advantages of the PG modification. Several primers with PG modifications were synthesized for each mutation and assessed using AS-PCR with the plasmid controls and DNA obtained from formalin-fixed paraffin-embedded (FFPE) tissues. The assay allows the detection of 0.5% of mutated DNA on the wild-type DNA plasmid template's background with good specificity. Compared with ddPCR, the primers with PG-modification demonstrated 100% specificity and 100% sensitivity on the DNA from FFPE with mutation presence higher than 0.5%. Our results indicate the high potential of PG-modified primers for point mutation detection. The main principle of the developed methodology can be used to improve the specificity of primers regardless of sequences.
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Oscorbin IP, Beginyazova OP, Khlistun IV, Shamovskaya DV, Oskina NA, Filipenko ML. Development of a multiplex allele-specific qPCR approach for testing PIK3CA mutations in patients with colorectal cancer. Heliyon 2022; 8:e11804. [DOI: 10.1016/j.heliyon.2022.e11804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
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Li H, You C, Yoshikawa M, Yang X, Gu H, Li C, Cui J, Chen X, Ye N, Zhang J, Wang G. A spontaneous thermo-sensitive female sterility mutation in rice enables fully mechanized hybrid breeding. Cell Res 2022; 32:931-945. [PMID: 36068348 PMCID: PMC9525692 DOI: 10.1038/s41422-022-00711-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
Male sterility enables hybrid crop breeding to increase yields and has been extensively studied. But thermo-sensitive female sterility, which is an ideal property that may enable full mechanization in hybrid rice breeding, has rarely been investigated due to the absence of such germplasm. Here we identify the spontaneous thermo-sensitive female sterility 1 (tfs1) mutation that confers complete sterility under regular/high temperature and partial fertility under low temperature as a point mutation in ARGONAUTE7 (AGO7). AGO7 associates with miR390 to form an RNA-Induced Silencing Complex (RISC), which triggers the biogenesis of small interfering RNAs (siRNAs) from TRANS-ACTING3 (TAS3) loci by recruiting SUPPRESSOR OF GENE SILENCING (SGS3) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6) to TAS3 transcripts. These siRNAs are known as tasiR-ARFs as they act in trans to repress auxin response factor genes. The mutant TFS1 (mTFS1) protein is compromised in its ability to load the miR390/miR390* duplex and eject miR390* during RISC formation. Furthermore, tasiR-ARF levels are reduced in tfs1 due to the deficiency in RDR6 but not SGS3 recruitment by mTFS1 RISC under regular/high temperature, while low temperature partially restores mTFS1 function in RDR6 recruitment and tasiR-ARF biogenesis. A miR390 mutant also exhibits female sterility, suggesting that female fertility is controlled by the miR390-AGO7 module. Notably, the tfs1 allele introduced into various elite rice cultivars endows thermo-sensitive female sterility. Moreover, field trials confirm the utility of tfs1 as a restorer line in fully mechanized hybrid rice breeding.
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Affiliation(s)
- Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Manabu Yoshikawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai Tsukuba, Ibaraki, Japan
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Haiyong Gu
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chuanguo Li
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
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Theelen WSME, Kuilman T, Schulze K, Zou W, Krijgsman O, Peters DDGC, Cornelissen S, Monkhorst K, Sarma P, Sumiyoshi T, Amler LC, Willems SM, Blaauwgeers JLG, van Noesel CJM, Peeper DS, van den Heuvel MM, Kowanetz M. Absence of PD-L1 expression on tumor cells in the context of an activated immune infiltrate may indicate impaired IFNγ signaling in non-small cell lung cancer. PLoS One 2019; 14:e0216864. [PMID: 31125352 PMCID: PMC6534376 DOI: 10.1371/journal.pone.0216864] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/30/2019] [Indexed: 11/18/2022] Open
Abstract
Background In non-small cell lung cancer (NSCLC), PD-L1 expression on either tumor cells (TC) or both TC and tumor-infiltrating immune cells (IC) is currently the most used biomarker in cancer immunotherapy. However, the mechanisms involved in PD-L1 regulation are not fully understood. To provide better insight in these mechanisms, a multiangular analysis approach was used to combine protein and mRNA expression with several clinicopathological characteristics. Patients and methods Archival tissues from 640 early stage, resected NSCLC patients were analyzed with immunohistochemistry for expression of PD-L1 and CD8 infiltration. In addition, mutational status and expression of a selection of immune genes involved in the PD-L1/PD-1 axis and T-cell response was determined. Results Tumors with high PD-L1 expression on TC or on IC represent two subsets of NSCLC with minimal overlap. We observed that PD-L1 expression on IC irrespective of expression on TC is a good marker for inflammation within tumors. In the tumors with the highest IC expression and absent TC expression an association with reduced IFNγ downstream signaling in tumor cells was observed. Conclusions These results show that PD-L1 expression on TC and IC are both independent hallmarks of the inflamed phenotype in NSCLC, and TC-negative/IC-high tumors can also be categorized as inflamed. The lack of correlation between PD-L1 TC and IC expression in this subgroup may be caused by impaired IFNγ signaling in tumor cells. These findings may bring a better understanding of the tumor-immune system interaction and the clinical relevance of PD-L1 expression on IC irrespective of PD-L1 expression on TC.
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Affiliation(s)
| | - Thomas Kuilman
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Katja Schulze
- Oncology Biomarker Development, Genentech Inc., South San Francisco, United States of America
| | - Wei Zou
- Biostatistics, Genentech Inc., South San Francisco, United States of America
| | - Oscar Krijgsman
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dennis D. G. C. Peters
- Core Facility Molecular Pathology & Biobanking, Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sten Cornelissen
- Core Facility Molecular Pathology & Biobanking, Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kim Monkhorst
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pranamee Sarma
- Oncology Biomarker Development, Genentech Inc., South San Francisco, United States of America
| | - Teiko Sumiyoshi
- Oncology Biomarker Development, Genentech Inc., South San Francisco, United States of America
| | - Lukas C. Amler
- Oncology Biomarker Development, Genentech Inc., South San Francisco, United States of America
| | - Stefan M. Willems
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | | | - Daniel S. Peeper
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Marcin Kowanetz
- Oncology Biomarker Development, Genentech Inc., South San Francisco, United States of America
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Piskol R, Huw L, Sergin I, Kljin C, Modrusan Z, Kim D, Kljavin N, Tam R, Patel R, Burton J, Penuel E, Qu X, Koeppen H, Sumiyoshi T, de Sauvage F, Lackner MR, de Sousa e Melo F, Kabbarah O. A Clinically Applicable Gene-Expression Classifier Reveals Intrinsic and Extrinsic Contributions to Consensus Molecular Subtypes in Primary and Metastatic Colon Cancer. Clin Cancer Res 2019; 25:4431-4442. [DOI: 10.1158/1078-0432.ccr-18-3032] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/29/2019] [Accepted: 04/15/2019] [Indexed: 01/10/2023]
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Schöffski P, Cresta S, Mayer IA, Wildiers H, Damian S, Gendreau S, Rooney I, Morrissey KM, Spoerke JM, Ng VW, Singel SM, Winer E. A phase Ib study of pictilisib (GDC-0941) in combination with paclitaxel, with and without bevacizumab or trastuzumab, and with letrozole in advanced breast cancer. Breast Cancer Res 2018; 20:109. [PMID: 30185228 PMCID: PMC6125885 DOI: 10.1186/s13058-018-1015-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 07/03/2018] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND This phase Ib study (NCT00960960) evaluated pictilisib (GDC-0941; pan-phosphatidylinositol 3-kinase inhibitor) plus paclitaxel, with and without bevacizumab or trastuzumab, or in combination with letrozole, in patients with locally recurrent or metastatic breast cancer. METHODS This was a three-part multischedule study. Patients in parts 1 and 2, which comprised 3 + 3 dose escalation and cohort expansion stages, received pictilisib (60-330 mg) plus paclitaxel (90 mg/m2) with and without bevacizumab (10 mg/kg) or trastuzumab (2-4 mg/kg). In part 3, patients received pictilisib (260 mg) plus letrozole (2.5 mg). Primary objectives were evaluation of safety and tolerability, identification of dose-limiting toxicities (DLTs) and the maximum tolerated dose (MTD) of pictilisib, and recommendation of a phase II dosing regimen. Secondary endpoints included pharmacokinetics and preliminary antitumor activity. RESULTS Sixty-nine patients were enrolled; all experienced at least one adverse event (AE). Grade ≥ 3 AEs, serious AEs, and AEs leading to death were reported in 50 (72.5%), 21 (30.4%), and 2 (2.9%) patients, respectively. Six (8.7%) patients reported a DLT, and the MTD and recommended phase II pictilisib doses were established where possible. There was no pictilisib-paclitaxel drug-drug interaction. Two (3.4%) patients experienced complete responses, and 17 (29.3%) patients had partial responses. CONCLUSIONS Combining pictilisib with paclitaxel, with and without bevacizumab or trastuzumab, or letrozole, had a manageable safety profile in patients with locally recurrent or metastatic breast cancer. The combination had antitumor activity, and the additive effect of pictilisib supported further investigation in a randomized study. TRIAL REGISTRATION ClinicalTrials.gov, NCT00960960 . Registered on August 13, 2009.
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Affiliation(s)
- Patrick Schöffski
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, Faculty of Medicine, Laboratory of Experimental Oncology, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Sara Cresta
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ingrid A. Mayer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Hans Wildiers
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Silvia Damian
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Steven Gendreau
- Oncology Biomarker Development, Genentech Inc, South San Francisco, CA USA
| | - Isabelle Rooney
- Product Development Oncology, Genentech Inc, South San Francisco, CA USA
| | | | - Jill M. Spoerke
- Oncology Biomarker Development, Genentech Inc, South San Francisco, CA USA
| | - Vivian W. Ng
- Biostatistics, Genentech Inc, South San Francisco, CA USA
| | - Stina M. Singel
- Product Development Oncology, Genentech Inc, South San Francisco, CA USA
| | - Eric Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
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Mutational Aberrations Detected in Mucinous Epithelial Ovarian Cancer of Asian Women. Int J Gynecol Cancer 2018; 28:428-436. [PMID: 29465505 DOI: 10.1097/igc.0000000000001138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Mucinous epithelial ovarian cancers (mEOCs) respond poorly to conventional chemotherapy and have a poor prognosis in advanced stages. The genomic landscape for mEOC in the Asian settings is ill defined. We seek to identify various mutational aberrations present in mEOC and correlate them with clinical outcomes. METHODS A total of 199 cases of mEOC were identified from a prospectively maintained gynecologic oncology tumor database. DNA was extracted and analyzed for KRAS mutations by using Sanger sequencing. Further MassArray sequencing was performed on 45 samples. Clinicopathologic correlation was performed with the results obtained. FINDINGS KRAS mutation status was evaluable in 124 cases. Fifty-five percent (68/124) were KRAS negative, whereas 45% (56/124) harbored a KRAS mutation, lower than that in Western populations. Successful ascertainment of both KRAS and HER2 statuses by Sanger sequencing occurred for 105 cases. The proportion of the double-positive subtype (HER2+ and KRAS positive) was 8% (8/105); double-negative subtype (HER2- and KRAS negative), 34% (36/105); and cases with mutation in either KRAS or HER2, 58% (61/105). The KRAS mutation rate was 44%, 50%, and 29% among Chinese, Indians, and Malays, respectively. There was no significant difference in overall survival (P = 0.952) or progression-free survival (P = 0.635) between KRAS-positive and KRAS-negative patients. Similar results were observed for progression-free survival (P = 0.206) and overall survival (P = 0.440) when outcomes were examined between the 4 groups based on KRAS and HER2 mutation. Patients in the double-negative mutation subgroup had higher risk for death/progression compared with patients in the other 3 mutation subgroups. Further MassARRAY multiplexed profiling was performed in patients with sufficient DNA material (n = 45) and yielded KRAS mutations (n = 16), PDGFRA mutations (n = 3), PIK3CA (n = 1) and KIT (n = 1), and HRAS, FGFR, MET, and NRAS (n = 1 each). CONCLUSIONS Our study provides further knowledge about the mutational aberrations in mEOC in Asian populations. Neither the presence of KRAS mutation nor their correlation with HER2 mutations influenced outcomes.
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Yamasaki M, Funaishi K, Saito N, Sakano A, Fujihara M, Daido W, Ishiyama S, Deguchi N, Taniwaki M, Ohashi N, Hattori N. Putative lung adenocarcinoma with epidermal growth factor receptor mutation presenting as carcinoma of unknown primary site: A case report. Medicine (Baltimore) 2018; 97:e9942. [PMID: 29443782 PMCID: PMC5839817 DOI: 10.1097/md.0000000000009942] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
RATIONALE Only a few cases of putative lung adenocarcinoma presenting as carcinoma of unknown primary site (CUP) with epidermal growth factor receptor (EGFR) mutation have been reported, and the efficacy of EGFR-tyrosine kinase inhibitors (TKIs) for these cases is unclear. PATIENT CONCERNS AND DIAGNOSES A 67-year-old man complained of paresis of the right lower extremity, dysarthria, and memory disturbance. Computed tomography and magnetic resonance imaging showed multiple brain tumors with brain edema and swelling of the left supraclavicular, mediastinal, and upper abdominal lymph nodes. Moreover, a metastatic duodenal tumor was detected via upper gastrointestinal endoscopy examination. The biopsy specimen of the lesion was examined and was diagnosed as adenocarcinoma with CK7 and TTF-1 positivity. Finally, the case was diagnosed as EGFR mutation-positive putative lung adenocarcinoma presenting as CUP. INTERVENTIONS AND OUTCOMES Oral erlotinib, an EGFR-TKI, was administered at 150 mg daily. Five weeks later, the brain lesions and several swollen lymph nodes showed marked improvement, and the symptoms of the patient also improved. Three months later, the duodenal lesion was undetected on upper gastrointestinal endoscopy. After an 8-month follow-up, the patient was well with no disease progression. LESSONS Putative lung adenocarcinoma presenting as CUP may have EGFR mutation, and EGFR-TKI therapy may be effective for such malignancy.
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Affiliation(s)
- Masahiro Yamasaki
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Kunihiko Funaishi
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Naomi Saito
- Department of Respiratory Medicine, Mazda Hospital, Aki-gun
| | | | - Megumu Fujihara
- Department of Pathology, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital
| | - Wakako Daido
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Sayaka Ishiyama
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Naoko Deguchi
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Masaya Taniwaki
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Nobuyuki Ohashi
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
- Ohashi Clinic, Naka-ku
| | - Noboru Hattori
- Department of Molecular and Internal Medicine, Institute of Biomedical & Health Sciences, Hiroshima University, Minami-ku, Hiroshima, Japan
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Kerr K, Dafni U, Schulze K, Thunnissen E, Bubendorf L, Hager H, Finn S, Biernat W, Vliegen L, Losa J, Marchetti A, Cheney R, Warth A, Speel EJ, Blackhall F, Monkhorst K, Jantus Lewintre E, Tischler V, Clark C, Bertran-Alamillo J, Meldgaard P, Gately K, Wrona A, Vandenberghe P, Felip E, De Luca G, Savic S, Muley T, Smit E, Dingemans AM, Priest L, Baas P, Camps C, Weder W, Polydoropoulou V, Geiger T, Kammler R, Sumiyoshi T, Molina M, Shames D, Stahel R, Peters S. Prevalence and clinical association of gene mutations through multiplex mutation testing in patients with NSCLC: results from the ETOP Lungscape Project. Ann Oncol 2018; 29:200-208. [DOI: 10.1093/annonc/mdx629] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Fumagalli D, Wilson TR, Salgado R, Lu X, Yu J, O'Brien C, Walter K, Huw LY, Criscitiello C, Laios I, Jose V, Brown DN, Rothé F, Maetens M, Zardavas D, Savas P, Larsimont D, Piccart-Gebhart MJ, Michiels S, Lackner MR, Sotiriou C, Loi S. Somatic mutation, copy number and transcriptomic profiles of primary and matched metastatic estrogen receptor-positive breast cancers. Ann Oncol 2017; 27:1860-6. [PMID: 27672107 DOI: 10.1093/annonc/mdw286] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/14/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Estrogen receptor-positive (ER+) breast cancers (BCs) constitute the most frequent BC subtype. The molecular landscape of ER+ relapsed disease is not well characterized. In this study, we aimed to describe the genomic evolution between primary (P) and matched metastatic (M) ER+ BCs after failure of adjuvant therapy. MATERIALS AND METHODS A total of 182 ER+ metastatic BC patients with long-term follow-up were identified from a single institution. P tumor tissue was available for all patients, with 88 having matched M material. According to the availability of tumor material, samples were characterized using a 120 mutational hotspot qPCR, a 29 gene copy number aberrations (CNA) and a 400 gene expression panels. ESR1 mutations were assayed by droplet digital PCR. Molecular alterations were correlated with overall survival (OS) using the Cox proportional hazards regression models. RESULTS The median follow-up was 6.4 years (range 0.5-26.6 years). Genomic analysis of P tumors revealed somatic mutations in PIK3CA, KRAS, AKT1, FGFR3, HRAS and BRAF at frequencies of 41%, 6%, 5%, 2%, 1% and 2%, respectively, and CN amplification of CCND1, ZNF703, FGFR1, RSF1 and PAK1 at 23%, 19%, 17%, 12% and 11%, respectively. Mutations and CN amplifications were largely concordant between P and matched M (>84%). ESR1 mutations were found in 10.8% of the M but none of the P. Thirteen genes, among which ESR1, FOXA1, and HIF1A, showed significant differential expression between P and M. In P, the differential expression of 18 genes, among which IDO1, was significantly associated with OS (FDR < 0.1). CONCLUSIONS Despite the large concordance between P and matched M for the evaluated molecular alterations, potential actionable targets such as ESR1 mutations were found only in M. This supports the importance of characterizing the M disease. Other targets we identified, such as HIF1A and IDO1, warrant further investigation in this patient population.
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Affiliation(s)
- D Fumagalli
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Free University of Bruxelles, Brussels, Belgium
| | - T R Wilson
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - R Salgado
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Free University of Bruxelles, Brussels, Belgium
| | - X Lu
- Department of Biostatistics, Genentech Inc., South San Francisco, CA, USA
| | - J Yu
- Department of Biostatistics, Genentech Inc., South San Francisco, CA, USA
| | - C O'Brien
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - K Walter
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - L Y Huw
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - C Criscitiello
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology, Milan, Italy
| | - I Laios
- Department of Pathology, Institut Jules Bordet, Brussels, Belgium
| | - V Jose
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Free University of Bruxelles, Brussels, Belgium
| | - D N Brown
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Free University of Bruxelles, Brussels, Belgium
| | - F Rothé
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Free University of Bruxelles, Brussels, Belgium
| | - M Maetens
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Free University of Bruxelles, Brussels, Belgium
| | - D Zardavas
- Breast International Group, Brussels, Belgium
| | - P Savas
- Division of Clinical Medicine and Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - D Larsimont
- Department of Pathology, Institut Jules Bordet, Brussels, Belgium
| | | | - S Michiels
- Division of Biostatistics and Epidemiology, Institut Gustave Roussy, Villejuif, France INSERM U1018, CESP, University of Paris, Villejuif, France
| | - M R Lackner
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - C Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Free University of Bruxelles, Brussels, Belgium Division of Medical Oncology, Institut Jules Bordet, Brussels, Belgium
| | - S Loi
- Division of Clinical Medicine and Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
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Leong S, Moss RA, Bowles DW, Ware JA, Zhou J, Spoerke JM, Lackner MR, Shankar G, Schutzman JL, van der Noll R, Voest EE, Schellens JHM. A Phase I Dose-Escalation Study of the Safety and Pharmacokinetics of Pictilisib in Combination with Erlotinib in Patients with Advanced Solid Tumors. Oncologist 2017; 22:1491-1499. [PMID: 28798270 DOI: 10.1634/theoncologist.2017-0090] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/06/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) and phosphatidylinositol 3-kinase (PI3K) are involved in the proliferation and survival of many cancer types. Enhanced antitumor activity may be achieved through combined inhibition of these pathways. We report results for pictilisib (GDC-0941, a class I pan-PI3K inhibitor) plus erlotinib (an EGFR tyrosine kinase inhibitor) in patients with advanced solid tumors. MATERIALS AND METHODS A 3 + 3 dose-escalation study was carried out at a starting daily dose of 60 mg pictilisib on days 1-21 of a 28-day cycle and 150 mg erlotinib from day 2 of cycle 1. The primary objectives of the study were to assess safety and tolerability, identify dose-limiting toxicities (DLTs), estimate the maximum tolerated dose, and identify the recommended phase II dose (RP2D). Evaluation of a dose-expansion cohort at the RP2D was performed. RESULTS Fifty-seven patients were treated in the study. All patients experienced at least one adverse event (AE). Grade ≥3 AEs, serious AEs, and deaths were reported in 38 (66.7%), 19 (33.3%), and 4 (7.0%) patients, respectively. DLTs occurred in nine patients across eight cohorts and the RP2D was determined to be 340 mg pictilisib on a "5 days on, 2 days off" schedule plus 100 mg erlotinib. Two patients (3.5%) experienced partial response and 19 (33.3%) had stable disease. CONCLUSION Combining pictilisib with erlotinib in patients with advanced solid tumors is feasible; however, antitumor activity is limited. Additional studies may identify patients likely to benefit from combined inhibition of EGFR and PI3K pathways. IMPLICATIONS FOR PRACTICE Combining drugs targeting different signaling pathways in cancer growth and survival could overcome drug resistance and improve antitumor activity. In this first-in-human study for the combination, addition of the PI3K inhibitor pictilisib to the EGFR tyrosine kinase inhibitor erlotinib resulted in toxicity that led to dose and schedule modifications to identify a tolerable recommended phase II dose of 340 mg pictilisib on a "5 days on, 2 days off" schedule plus 100 mg erlotinib daily. The limited antitumor activity observed, however, suggests that additional studies are needed to identify patients most likely to benefit from combined EGFR and PI3K inhibition.
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Affiliation(s)
- Stephen Leong
- Division of Medical Oncology, University of Colorado Cancer Center, Aurora, Colorado, USA
| | - Rebecca A Moss
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Daniel W Bowles
- Division of Medical Oncology, University of Colorado Cancer Center, Aurora, Colorado, USA
| | - Joseph A Ware
- Genentech, Inc., South San Francisco, California, USA
| | - Jing Zhou
- Genentech, Inc., South San Francisco, California, USA
| | | | | | | | | | - Ruud van der Noll
- Division of Pharmacology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emile E Voest
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan H M Schellens
- Division of Pharmacology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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12
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Rosen LS, LoRusso P, Ma WW, Goldman JW, Weise A, Colevas AD, Adjei A, Yazji S, Shen A, Johnston S, Hsieh HJ, Chan IT, Sikic BI. A first-in-human phase I study to evaluate the MEK1/2 inhibitor, cobimetinib, administered daily in patients with advanced solid tumors. Invest New Drugs 2016; 34:604-13. [PMID: 27424159 DOI: 10.1007/s10637-016-0374-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/03/2016] [Indexed: 12/12/2022]
Abstract
Objective Cobimetinib, a MEK1/2 inhibitor, was administered to patients with advanced solid tumors to assess safety, pharmacokinetics, pharmacodynamics, and anti-tumor activity. Methods For dose-escalation, a 3 + 3 design was used. Oral cobimetinib was administered once daily on a 21-day on/7-day off (21/7) or a 14-day on/14-day off (14/14) schedule. Serial plasma samples were collected for pharmacokinetic (PK) analysis on Day 1 and at steady state. In expansion stages, patients with RAS or RAF mutant tumors were treated at the maximum tolerated dose (MTD) of the 21/7 or 14/14 schedule. Results Ninety-seven patients received cobimetinib. In the 21/7 dose escalation, 36 patients enrolled in 8 cohorts (0.05 mg/kg-80 mg). Dose-limiting toxicities (DLTs) were Grade 4 hepatic encephalopathy, Grade 3 diarrhea, and Grade 3 rash. In the 14/14 dose escalation, 20 patients enrolled in 4 cohorts (60-125 mg). DLTs were Grade 3 rash and Grade 3 blurred vision associated with presence of reversible subretinal fluid. The MTD was 60 mg on 21/7 schedule and 100 mg on 14/14 schedule. Cobimetinib PK showed dose-proportional increases in exposure. The most frequent adverse events attributed to cobimetinib were diarrhea, rash, fatigue, edema, nausea, and vomiting. In patients treated at the 60-mg (21/7) or 100-mg (14/14) dose, one unconfirmed complete response and 6 confirmed partial responses were observed. All responses occurred in melanoma patients; 6 harbored the BRAF(V600E) mutation. Conclusions Cobimetinib is generally well tolerated and durable responses were observed in BRAF(V600E) mutant melanoma patients. Evaluation of cobimetinib in combination with other therapies is ongoing.
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Affiliation(s)
- Lee S Rosen
- David Geffen School of Medicine, UCLA, 2020 Santa Monica Blvd, Suite 600, Santa Monica, CA, 90404, USA.
| | | | - Wen Wee Ma
- Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jonathan W Goldman
- David Geffen School of Medicine, UCLA, 2020 Santa Monica Blvd, Suite 600, Santa Monica, CA, 90404, USA
| | - Amy Weise
- Karmanos Cancer Institute, Detroit, MI, USA
| | | | - Alex Adjei
- Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Salim Yazji
- Exelixis, Inc., South San Francisco, CA, USA.,Baxalta, Cambridge, MA, USA
| | - Angela Shen
- Exelixis, Inc., South San Francisco, CA, USA.,Arvinas, New Haven, CT, USA
| | - Stuart Johnston
- Exelixis, Inc., South San Francisco, CA, USA.,Nektar Therapeutics, San Francisco, CA, USA
| | | | - Iris T Chan
- Genentech, Inc., South San Francisco, CA, USA
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13
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The molecular landscape of high-risk early breast cancer: comprehensive biomarker analysis of a phase III adjuvant population. NPJ Breast Cancer 2016; 2:16022. [PMID: 28721382 PMCID: PMC5515335 DOI: 10.1038/npjbcancer.2016.22] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 06/03/2016] [Accepted: 06/10/2016] [Indexed: 01/22/2023] Open
Abstract
Breast cancer is a heterogeneous disease and patients are managed clinically based on ER, PR, HER2 expression, and key risk factors. We sought to characterize the molecular landscape of high-risk breast cancer patients enrolled onto an adjuvant chemotherapy study to understand how disease subsets and tumor immune status impact survival. DNA and RNA were extracted from 861 breast cancer samples from patients enrolled onto the United States Oncology trial 01062. Samples were characterized using multiplex gene expression, copy number, and qPCR mutation assays. HR+ patients with a PIK3CA mutant tumor had a favorable disease-free survival (DFS; HR 0.66, P=0.05), however, the prognostic effect was specific to luminal A patients (Luminal A: HR 0.67, P=0.1; Luminal B: HR 1.01, P=0.98). Molecular subtyping of triple-negative breast cancers (TNBCs) suggested that the mesenchymal subtype had the worst DFS, whereas the immunomodulatory subtype had the best DFS. Profiling of immunologic genes revealed that TNBC tumors (n=280) displaying an activated T-cell signature had a longer DFS following adjuvant chemotherapy (HR 0.59, P=0.04), while a distinct set of immune genes was associated with DFS in HR+ cancers. Utilizing a discovery approach, we identified genes associated with a high risk of recurrence in HR+ patients, which were validated in an independent data set. Molecular classification based on PAM50 and TNBC subtyping stratified clinical high-risk patients into distinct prognostic subsets. Patients with high expression of immune-related genes showed superior DFS in both HR+ and TNBC. These results may inform patient management and drug development in early breast cancer.
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14
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Dolly SO, Wagner AJ, Bendell JC, Kindler HL, Krug LM, Seiwert TY, Zauderer MG, Lolkema MP, Apt D, Yeh RF, Fredrickson JO, Spoerke JM, Koeppen H, Ware JA, Lauchle JO, Burris HA, de Bono JS. Phase I Study of Apitolisib (GDC-0980), Dual Phosphatidylinositol-3-Kinase and Mammalian Target of Rapamycin Kinase Inhibitor, in Patients with Advanced Solid Tumors. Clin Cancer Res 2016; 22:2874-84. [PMID: 26787751 DOI: 10.1158/1078-0432.ccr-15-2225] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/13/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE This first-in-human phase I trial assessed the safety, tolerability, and preliminary antitumor activity of apitolisib (GDC-0980), a dual inhibitor of class I PI3K, and mTOR kinases. EXPERIMENTAL DESIGN Once-daily oral apitolisib was administered to patients with solid tumors for days 1 to 21 or 1 to 28 of 28-day cycles. Pharmacokinetic and pharmacodynamic parameters were assessed. RESULTS Overall, 120 patients were treated at doses between 2 and 70 mg. The commonest ≥G3 toxicities related to apitolisib at the recommended phase 2 dose (RP2D) at 40 mg once daily included hyperglycemia (18%), rash (14%), liver dysfunction (12%), diarrhea (10%), pneumonitis (8%), mucosal inflammation (6%), and fatigue (4%). Dose-limiting toxicities (1 patient each) were G4 fasting hyperglycemia at 40 mg (21/28 schedule) and G3 maculopapular rash and G3 fasting hyperglycemia at 70 mg (21/28 schedule). The pharmacokinetic profile was dose-proportional. Phosphorylated serine-473 AKT levels were suppressed by ≥90% in platelet-rich plasma within 4 hours at the MTD (50 mg). Pharmacodynamic decreases in fluorodeoxyglucose positron emission tomography uptake of >25% occurred in 66% (21/32) of patients dosed at 40 mg once daily. Evidence of single-agent activity included 10 RECIST partial responses (PR; confirmed for peritoneal mesothelioma, PIK3CA mutant head-and-neck cancer, and three pleural mesotheliomas). CONCLUSIONS Apitolisib exhibited dose-proportional pharmacokinetics with target modulation at doses ≥16 mg. The RP2D was 40 mg once-daily 28/28 schedule; severe on-target toxicities were apparent at ≥40 mg, particularly pneumonitis. Apitolisib was reasonably tolerated at 30 mg, the selected dose for pleural mesothelioma patients given limited respiratory reserve. Modest but durable antitumor activity was demonstrated. Clin Cancer Res; 22(12); 2874-84. ©2016 AACR.
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Affiliation(s)
- Saoirse O Dolly
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Sutton, Surrey, United Kingdom
| | - Andrew J Wagner
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Johanna C Bendell
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
| | - Hedy L Kindler
- The Gastrointestinal Oncology and Mesothelioma Programs, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Lee M Krug
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, New York
| | - Tanguy Y Seiwert
- The Gastrointestinal Oncology and Mesothelioma Programs, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois
| | - Marjorie G Zauderer
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, New York
| | - Martijn P Lolkema
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Sutton, Surrey, United Kingdom. Department of Medical Oncology, Cancer Institute Rotterdam, Erasmus MC, Rotterdam, the Netherlands
| | - Doris Apt
- Genentech, Inc., South San Francisco, California
| | - Ru-Fang Yeh
- Genentech, Inc., South San Francisco, California
| | | | | | | | | | | | - Howard A Burris
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
| | - Johann S de Bono
- The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust, Sutton, Surrey, United Kingdom.
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15
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Markou A, Farkona S, Schiza C, Efstathiou T, Kounelis S, Malamos N, Georgoulias V, Lianidou E. PIK3CA mutational status in circulating tumor cells can change during disease recurrence or progression in patients with breast cancer. Clin Cancer Res 2015; 20:5823-34. [PMID: 25398847 DOI: 10.1158/1078-0432.ccr-14-0149] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Molecular characterization of circulating tumor cells (CTC) is crucial for the investigation of molecular-targeted therapies while PIK3CA somatic mutations play a crucial role in therapy response. We investigated the presence of PIK3CA mutations in CTC and whether this is associated with clinical outcome. EXPERIMENTAL DESIGN We developed and validated an ultrasensitive methodology for the detection of PIK3CA mutations that is based on a combination of allele-specific, asymmetric rapid PCR and melting analysis. We analyzed PIK3CA hotspot mutations in: (i) a training group consisting of EpCAM-positive CTC fraction from 37 patients with clinically confirmed metastasis, and 26 healthy female volunteers and 15 primary breast tumor tissues and (ii) an independent group consisting of EpCAM-positive CTC fraction from 57 metastatic and 118 operable breast cancer patients and 76 corresponding primary tumors. RESULTS The assay could detect 0.05% of mutated dsDNA in the presence of 99.95% wtDNA for both exons (9 and 20) and was highly specific (0/26 healthy donors). PIK3CA mutations were identified in EpCAM-positive CTC in 20 of 57(35.1%) and in 23 of 118 (19.5%) patients with metastatic and operable breast cancer, and in 45 of 76(59.2%) corresponding FFPEs. Our data indicate that PIK3CA mutational status in CTCs can change during disease progression and is associated with worse survival (P = 0.047). CONCLUSIONS PIK3CA hotspot mutations are present at a relatively high frequency in CTCs and their presence is associated with worse survival in patients with breast cancer with metastasis. Evaluation of PIK3CA mutational status in CTCs is a strategy with potential clinical application.
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Affiliation(s)
- Athina Markou
- Analysis of Circulating Tumor Cells, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Sofia Farkona
- Analysis of Circulating Tumor Cells, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Christina Schiza
- Analysis of Circulating Tumor Cells, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Tonia Efstathiou
- Analysis of Circulating Tumor Cells, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Sophia Kounelis
- Oncology Unit and Pathology Department, Helena Venizelou Hospital, Athens, Greece
| | - Nikos Malamos
- Oncology Unit and Pathology Department, Helena Venizelou Hospital, Athens, Greece
| | - Vassilis Georgoulias
- Laboratory of Tumor Cell Biology, Medical School, University of Crete, Heraklion, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells, Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece.
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16
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Zhang L, Chen L, Sah S, Latham GJ, Patel R, Song Q, Koeppen H, Tam R, Schleifman E, Mashhedi H, Chalasani S, Fu L, Sumiyoshi T, Raja R, Forrest W, Hampton GM, Lackner MR, Hegde P, Jia S. Profiling cancer gene mutations in clinical formalin-fixed, paraffin-embedded colorectal tumor specimens using targeted next-generation sequencing. Oncologist 2014; 19:336-43. [PMID: 24664487 DOI: 10.1634/theoncologist.2013-0180] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The success of precision oncology relies on accurate and sensitive molecular profiling. The Ion AmpliSeq Cancer Panel, a targeted enrichment method for next-generation sequencing (NGS) using the Ion Torrent platform, provides a fast, easy, and cost-effective sequencing workflow for detecting genomic "hotspot" regions that are frequently mutated in human cancer genes. Most recently, the U.K. has launched the AmpliSeq sequencing test in its National Health Service. This study aimed to evaluate the clinical application of the AmpliSeq methodology. METHODS We used 10 ng of genomic DNA from formalin-fixed, paraffin-embedded human colorectal cancer (CRC) tumor specimens to sequence 46 cancer genes using the AmpliSeq platform. In a validation study, we developed an orthogonal NGS-based resequencing approach (SimpliSeq) to assess the AmpliSeq variant calls. RESULTS Validated mutational analyses revealed that AmpliSeq was effective in profiling gene mutations, and that the method correctly pinpointed "true-positive" gene mutations with variant frequency >5% and demonstrated high-level molecular heterogeneity in CRC. However, AmpliSeq enrichment and NGS also produced several recurrent "false-positive" calls in clinically druggable oncogenes such as PIK3CA. CONCLUSION AmpliSeq provided highly sensitive and quantitative mutation detection for most of the genes on its cancer panel using limited DNA quantities from formalin-fixed, paraffin-embedded samples. For those genes with recurrent "false-positive" variant calls, caution should be used in data interpretation, and orthogonal verification of mutations is recommended for clinical decision making.
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Affiliation(s)
- Liangxuan Zhang
- Departments of Oncology Biomarker Development, Biostatistics, and Pathology, Genentech Inc., South San Francisco, California, USA; Technology Development, Asuragen Inc., Austin, Texas, USA
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17
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Schleifman EB, Tam R, Patel R, Tsan A, Sumiyoshi T, Fu L, Desai R, Schoenbrunner N, Myers TW, Bauer K, Smith E, Raja R. Next generation MUT-MAP, a high-sensitivity high-throughput microfluidics chip-based mutation analysis panel. PLoS One 2014; 9:e90761. [PMID: 24658394 PMCID: PMC3962342 DOI: 10.1371/journal.pone.0090761] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/03/2014] [Indexed: 11/19/2022] Open
Abstract
Molecular profiling of tumor tissue to detect alterations, such as oncogenic mutations, plays a vital role in determining treatment options in oncology. Hence, there is an increasing need for a robust and high-throughput technology to detect oncogenic hotspot mutations. Although commercial assays are available to detect genetic alterations in single genes, only a limited amount of tissue is often available from patients, requiring multiplexing to allow for simultaneous detection of mutations in many genes using low DNA input. Even though next-generation sequencing (NGS) platforms provide powerful tools for this purpose, they face challenges such as high cost, large DNA input requirement, complex data analysis, and long turnaround times, limiting their use in clinical settings. We report the development of the next generation mutation multi-analyte panel (MUT-MAP), a high-throughput microfluidic, panel for detecting 120 somatic mutations across eleven genes of therapeutic interest (AKT1, BRAF, EGFR, FGFR3, FLT3, HRAS, KIT, KRAS, MET, NRAS, and PIK3CA) using allele-specific PCR (AS-PCR) and Taqman technology. This mutation panel requires as little as 2 ng of high quality DNA from fresh frozen or 100 ng of DNA from formalin-fixed paraffin-embedded (FFPE) tissues. Mutation calls, including an automated data analysis process, have been implemented to run 88 samples per day. Validation of this platform using plasmids showed robust signal and low cross-reactivity in all of the newly added assays and mutation calls in cell line samples were found to be consistent with the Catalogue of Somatic Mutations in Cancer (COSMIC) database allowing for direct comparison of our platform to Sanger sequencing. High correlation with NGS when compared to the SuraSeq500 panel run on the Ion Torrent platform in a FFPE dilution experiment showed assay sensitivity down to 0.45%. This multiplexed mutation panel is a valuable tool for high-throughput biomarker discovery in personalized medicine and cancer drug development.
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Affiliation(s)
- Erica B. Schleifman
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Rachel Tam
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Rajesh Patel
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Alison Tsan
- Chemistry and Innovation Technology, Pleasanton, California, United States of America
| | - Teiko Sumiyoshi
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Ling Fu
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Rupal Desai
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
| | - Nancy Schoenbrunner
- Chemistry and Innovation Technology, Pleasanton, California, United States of America
| | - Thomas W. Myers
- Program in Core Research, Roche Molecular Systems Inc., Pleasanton, California, United States of America
| | - Keith Bauer
- Program in Core Research, Roche Molecular Systems Inc., Pleasanton, California, United States of America
| | - Edward Smith
- Program in Core Research, Roche Molecular Systems Inc., Pleasanton, California, United States of America
| | - Rajiv Raja
- Oncology Biomarker Development, Genentech Inc., South San Francisco, California, United States of America
- * E-mail:
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18
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Bourgon R, Lu S, Yan Y, Lackner MR, Wang W, Weigman V, Wang D, Guan Y, Ryner L, Koeppen H, Patel R, Hampton GM, Amler LC, Wang Y. High-throughput detection of clinically relevant mutations in archived tumor samples by multiplexed PCR and next-generation sequencing. Clin Cancer Res 2014; 20:2080-91. [PMID: 24573554 DOI: 10.1158/1078-0432.ccr-13-3114] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Tailoring cancer treatment to tumor molecular characteristics promises to make personalized medicine a reality. However, reliable genetic profiling of archived clinical specimens has been hindered by limited sensitivity and high false-positive rates. Here, we describe a novel methodology, MMP-seq, which enables sensitive and specific high-throughput, high-content genetic profiling in archived clinical samples. EXPERIMENTAL DESIGN We first validated the technical performance of MMP-seq in 66 cancer cell lines and a Latin square cross-dilution of known somatic mutations. We next characterized the performance of MMP-seq in 17 formalin-fixed paraffin-embedded (FFPE) clinical samples using matched fresh-frozen tissue from the same tumors as benchmarks. To demonstrate the potential clinical utility of our methodology, we profiled FFPE tumor samples from 73 patients with endometrial cancer. RESULTS We demonstrated that MMP-seq enabled rapid and simultaneous profiling of a panel of 88 cancer genes in 48 samples, and detected variants at frequencies as low as 0.4%. We identified DNA degradation and deamination as the main error sources and developed practical and robust strategies for mitigating these issues, and dramatically reduced the false-positive rate. Applying MMP-seq to a cohort of endometrial tumor samples identified extensive, potentially actionable alterations in the PI3K (phosphoinositide 3-kinase) and RAS pathways, including novel PIK3R1 hotspot mutations that may disrupt negative regulation of PIK3CA. CONCLUSIONS MMP-seq provides a robust solution for comprehensive, reliable, and high-throughput genetic profiling of clinical tumor samples, paving the way for the incorporation of genomic-based testing into clinical investigation and practice.
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Affiliation(s)
- Richard Bourgon
- Authors' Affiliations: Departments of Oncology Biomarker Development, Bioinformatics, Structural Biology, and Pathology, Genentech, Inc.; Fluidigm Inc., South San Francisco, California; and Expression Analysis, Durham, North Carolina
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Targeted biomarker profiling of matched primary and metastatic estrogen receptor positive breast cancers. PLoS One 2014; 9:e88401. [PMID: 24520381 PMCID: PMC3919784 DOI: 10.1371/journal.pone.0088401] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/06/2014] [Indexed: 11/26/2022] Open
Abstract
Patients with newly diagnosed, early stage estrogen receptor positive (ER+) breast cancer often show disease free survival in excess of five years following surgery and systemic adjuvant therapy. An important question is whether diagnostic tumor tissue from the primary lesion offers an accurate molecular portrait of the cancer post recurrence and thus may be used for predictive diagnostic purposes for patients with relapsed, metastatic disease. As the class I phosphatidylinositol 3' kinase (PI3K) pathway is frequently activated in ER+ breast cancer and has been linked to acquired resistance to hormonal therapy, we hypothesized pathway status could evolve over time and treatment. Biomarker analyses were conducted on matched, asynchronous primary and metastatic tumors from 77 patients with ER+ breast cancer. We examined whether PIK3CA and AKT1 alterations or PTEN and Ki67 levels showed differences between primary and metastatic samples. We also sought to look more broadly at gene expression markers reflective of proliferation, molecular subtype, and key receptors and signaling pathways using an mRNA analysis platform developed on the Fluidigm BioMark™ microfluidics system to measure the relative expression of 90 breast cancer related genes in formalin-fixed paraffin-embedded (FFPE) tissue. Application of this panel of biomarker assays to matched tumor pairs showed a high concordance between primary and metastatic tissue, with generally few changes in mutation status, proliferative markers, or gene expression between matched samples. The collection of assays described here has been optimized for FFPE tissue and may have utility in exploratory analyses to identify patient subsets responsive to targeted therapies.
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20
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Shames DS, Wistuba II. The evolving genomic classification of lung cancer. J Pathol 2014; 232:121-33. [PMID: 24114583 PMCID: PMC4285848 DOI: 10.1002/path.4275] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 09/17/2013] [Accepted: 09/21/2013] [Indexed: 01/02/2023]
Abstract
EGFR gene mutations and ALK gene fusions are well-characterized molecular targets in NSCLC. Activating alterations in a variety of potential oncogenic driver genes have also been identified in NSCLC, including ROS1, RET, MET, HER2, and BRAF. Together with EGFR and ALK, these mutations account for ∼20% of NSCLCs. The identification of these oncogenic drivers has led to the design of rationally targeted therapies that have produced superior clinical outcomes in tumours harbouring these mutations. Many patients, however, have de novo or acquired resistance to these therapies. In addition, most NSCLCs are genetically complex tumours harbouring multiple potential activating events. For these patients, disease subsets are likely to be defined by combination strategies involving a number of targeted agents. These targets include FGFR1, PTEN, MET, MEK, PD-1/PD-L1, and NaPi2b. In light of the myriad new biomarkers and targeted agents, multiplex testing strategies will be invaluable in identifying the appropriate patients for each therapy and enabling targeted agents to be channelled to the patients most likely to gain benefit. The challenge now is how best to interpret the results of these genomic tests, in the context of other clinical data, to optimize treatment choices in NSCLC.
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Affiliation(s)
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer CenterHouston, Texas, USA
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21
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Acquired PIK3CA amplification causes resistance to selective phosphoinositide 3-kinase inhibitors in breast cancer. Oncogenesis 2013; 2:e83. [PMID: 24366379 PMCID: PMC3940863 DOI: 10.1038/oncsis.2013.46] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/21/2013] [Accepted: 10/29/2013] [Indexed: 12/11/2022] Open
Abstract
Agents targeting the PI3K/mTOR signaling axis have shown promise in early-phase clinical trials and are currently being studied in later stages of clinical development in multiple indications. Experience with other targeted agents suggests that clinical responses may be short-lived because of acquired resistance to therapy. Here, we report preclinical modeling of acquired resistance in a HER2-positive, PIK3CA mutant breast cancer cell line, KPL-4. We identified a heretofore-unreported mechanism of resistance, specifically high-level amplification of the mutant allele of PIK3CA, which resulted in a marked upregulation of PI3K signaling, enabling resistant cells to regain proliferative capacity at clinically relevant concentrations of the PI3K inhibitor, GDC-0941. We show that knockdown of the amplified PIK3CA mutant allele in these cells by small interfering RNA restored pathway signaling and sensitivity to PI3K inhibition at levels comparable to parental cells. These novel preclinical findings suggest that, in addition to assessment of other previously reported mechanisms of resistance, evaluation of PI3K copy number variation should be integrated into the exploratory analysis of biopsies obtained at disease progression.
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Yan Y, Serra V, Prudkin L, Scaltriti M, Murli S, Rodríguez O, Guzman M, Sampath D, Nannini M, Xiao Y, Wagle MC, Wu JQ, Wongchenko M, Hampton G, Ramakrishnan V, Lackner MR, Saura C, Roda D, Cervantes A, Tabernero J, Patel P, Baselga J. Evaluation and clinical analyses of downstream targets of the Akt inhibitor GDC-0068. Clin Cancer Res 2013; 19:6976-86. [PMID: 24141624 DOI: 10.1158/1078-0432.ccr-13-0978] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The oncogenic PI3K/Akt/mTOR pathway is an attractive therapeutic target in cancer. However, it is unknown whether the pathway blockade required for tumor growth inhibition is clinically achievable. Therefore, we conducted pharmacodynamic studies with GDC-0068, an ATP competitive, selective Akt1/2/3 inhibitor, in preclinical models and in patients treated with this compound. EXPERIMENTAL DESIGN We used a reverse phase protein array (RPPA) platform to identify a biomarker set indicative of Akt inhibition in cell lines and human-tumor xenografts, and correlated the degree of pathway inhibition with antitumor activity. Akt pathway activity was measured using this biomarker set in pre- and post-dose tumor biopsies from patients treated with GDC-0068 in the dose escalation clinical trial. RESULTS The set of biomarkers of Akt inhibition is composed of 10 phosphoproteins, including Akt and PRAS40, and is modulated in a dose-dependent fashion, both in vitro and in vivo. In human-tumor xenografts, this dose dependency significantly correlated with tumor growth inhibition. Tumor biopsies from patients treated with GDC-0068 at clinically achievable doses attained a degree of biomarker inhibition that correlated with tumor growth inhibition in preclinical models. In these clinical samples, compensatory feedback activation of ERK and HER3 was observed, consistent with preclinical observations. CONCLUSION This study identified a set of biomarkers of Akt inhibition that can be used in the clinical setting to assess target engagement. Here, it was used to show that robust Akt inhibition in tumors from patients treated with GDC-0068 is achievable, supporting the clinical development of this compound in defined patient populations.
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Affiliation(s)
- Yibing Yan
- Authors' Affiliations: Oncology Biomarker Development, Portfolio Management and Operations, Translational Oncology, Biostatistics, and Exploratory Clinical Development, Genentech Inc., DNA Way, South San Francisco, California; Experimental Therapeutics, Molecular Pathology, Breast Cancer and Melanoma, Gastrointestinal and Endocrine Tumors Groups, and Medical Oncology Service, Vall d'Hebron Institute of Oncology, Barcelona; Department of Hematology and Medical Oncology, Institute of Health Research INCLIVA, University of Valencia, Valencia, Spain; and Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
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