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Darabi S, Elliott A, Braxton DR, Zeng J, Hodges K, Poorman K, Swensen J, Shanthappa BU, Hinton JP, Gibney GT, Moser J, Phung T, Atkins MB, In GK, Korn WM, Eisenberg BL, Demeure MJ. Transcriptional Profiling of Malignant Melanoma Reveals Novel and Potentially Targetable Gene Fusions. Cancers (Basel) 2022; 14:cancers14061505. [PMID: 35326655 PMCID: PMC8946593 DOI: 10.3390/cancers14061505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Malignant melanoma is a complex disease that is estimated to claim over 7000 lives in the United States in 2021. Although recent advances in genomic technology have helped with the identification of driver variants, molecular studies and clinical trials have often focused on prevalent alterations, such as the BRAF-V600E mutation. With the inclusion of whole transcriptome sequencing, molecular profiling of melanomas has identified gene fusions and revealed gene expression profiles that are consistent with the activation of signaling pathways by common driver mutations. Patients harboring such fusions may benefit from currently approved targeted therapies and should be considered in the design of future clinical trials to further personalize treatments for patients with malignant melanoma. Abstract Invasive melanoma is the deadliest type of skin cancer, with 101,110 expected cases to be diagnosed in 2021. Recurrent BRAF and NRAS mutations are well documented in melanoma. Biologic implications of gene fusions and the efficacy of therapeutically targeting them remains unknown. Retrospective review of patient samples that underwent next-generation sequencing of the exons of 592 cancer-relevant genes and whole transcriptome sequencing for the detection of gene fusion events and gene expression profiling. Expression of PDL1 and ERK1/2 was assessed by immunohistochemistry (IHC). There were 33 (2.6%) cases with oncogenic fusions (14 novel), involving BRAF, RAF1, PRKCA, TERT, AXL, and FGFR3. MAPK pathway-associated genes were over-expressed in BRAF and RAF1 fusion-positive tumors in absence of other driver alterations. Increased expression in tumors with PRKCA and TERT fusions was concurrent with MAPK pathway alterations. For a subset of samples with available tissue, increased phosphorylation of ERK1/2 was observed in BRAF, RAF1, and PRKCA fusion-positive tumors. Oncogenic gene fusions are associated with transcriptional activation of the MAPK pathway, suggesting they could be therapeutic targets with available inhibitors. Additional analyses to fully characterize the oncogenic effects of these fusions may support biomarker driven clinical trials.
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Affiliation(s)
- Sourat Darabi
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Correspondence:
| | - Andrew Elliott
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - David R. Braxton
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
| | - Jia Zeng
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Kurt Hodges
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Kelsey Poorman
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Jeff Swensen
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Basavaraja U. Shanthappa
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - James P. Hinton
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Geoffrey T. Gibney
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC 20007, USA; (G.T.G.); (M.B.A.)
| | - Justin Moser
- Honor Health Research Institute, Scottsdale, AZ 85258, USA;
| | - Thuy Phung
- Department of Pathology, University of South Alabama, Mobile, AL 36617, USA;
| | - Michael B. Atkins
- Lombardi Comprehensive Cancer Center, MedStar Georgetown University Hospital, Washington, DC 20007, USA; (G.T.G.); (M.B.A.)
| | - Gino K. In
- Division of Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;
| | - Wolfgang M. Korn
- Caris Life Sciences, Phoenix, AZ 85040, USA; (A.E.); (J.Z.); (K.H.); (K.P.); (J.S.); (B.U.S.); (J.P.H.); (W.M.K.)
| | - Burton L. Eisenberg
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Division of Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;
| | - Michael J. Demeure
- Hoag Family Cancer Institute, Newport Beach, CA 92663, USA; (D.R.B.); (B.L.E.); (M.J.D.)
- Translational Genomics Research Institution, Phoenix, AZ 85004, USA
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Contos G, Baca Y, Xiu J, Brown J, Holloway R, Korn WM, Herzog TJ, Jones N, Winer I. Assessment of immune biomarkers and establishing a triple negative phenotype in gynecologic cancers. Gynecol Oncol 2021; 163:312-319. [PMID: 34563366 DOI: 10.1016/j.ygyno.2021.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Immuno-oncology (IO) has rapidly evolved, with many IO therapies either approved or under investigation for multiple malignancies. Biomarkers exist that can predict response to IO therapies including PD-L1 expression, microsatellite instability (MSI), and total mutation burden (TMB). This paper serves to analyze the presence of these biomarkers across gynecologic cancers. METHODS A total of 16,300 gynecologic cancer specimens submitted for molecular profiling to Caris Life Sciences were reviewed. Immunohistochemistry was performed using the SP142 anti-PD-L1 clone and assessed for intensity. Next-generation sequencing, immunohistochemistry, and fragment analysis were used to determine MSI status. TMB was measured by counting all non-synonymous missense mutations found per tumor not previously described as germline alterations. Chi-Square, Fisher Exact, and the Kruskal-Wallis test were used to compare cohorts. RESULTS Of 16,300 specimens, 54.1% were ovarian, 37.2% uterine, 7.2% cervical, 0.3% vulvar, 1.2% vaginal, with 0.1% unspecified. MSI-H was most frequent in uterine cancer (17.7%) and only 1% of ovarian cancers. PD-L1 expression was present in 38.3% of cervical and 62.5% of vulvar cancers, but less than 8% of ovarian and uterine cancers. TMB-H was present in 21.1% cervical, 19.7% uterine, and 5% ovarian cancers. Few specimens exhibited a "triple positive" phenotype - 0.3% ovarian, 1.5% uterine, and 1.5% cervical. Associations were seen between MSI, TMB, and PD-L1 across all cancer types. CONCLUSIONS The frequency of individual biomarkers pertinent to IO therapy varies by cancer type. HPV-driven genital tract cancers have higher frequencies of PD-L1 expression, MSI-H, and TMBH. Endometrial cancers are characterized by MSI-H and TMB, whereas ovarian cancers have a low frequency of MSI-H and modest PD-L1 or TMBH. The incidence of 'triple positive" cases was less than 2%.
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Affiliation(s)
- G Contos
- Wayne State University and Karmanos Cancer Institute, 4100 John R. St., Detroit, MI 48201, United States of America.
| | - Y Baca
- Caris Life Sciences, 4750 S. 44(th) Pl., Phoenix, AZ 85040, United States of America
| | - J Xiu
- Caris Life Sciences, 4750 S. 44(th) Pl., Phoenix, AZ 85040, United States of America
| | - J Brown
- Levine Cancer Institute, 1021 Morehead Medical Dr. #2100, Charlotte, NC 28204, United States of America.
| | - R Holloway
- Advent Health Medical Group, 2501 N. Orange Ave. Suite 786, Orlando, FL 32804, United States of America
| | - W M Korn
- Caris Life Sciences, 4750 S. 44(th) Pl., Phoenix, AZ 85040, United States of America
| | - T J Herzog
- University of Cincinnati Cancer Institute, 3255 Eden Ave. Suite 250B, Cincinnati, OH 45019, United States of America.
| | - N Jones
- University of South Alabama Mitchell Cancer Institute, 1660 Springhill Avenue, Mobile, AL 36604, United States of America.
| | - I Winer
- Wayne State University and Karmanos Cancer Institute, 4100 John R. St., Detroit, MI 48201, United States of America
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Wang JY, Xiu J, Baca Y, Arai H, Battaglin F, Kawanishi N, Soni S, Zhang W, Millstein J, Shields AF, Grothey A, Weinberg BA, Marshall JL, Lou E, Khushman M, Sohal DPS, Hall MJ, Oberley M, Spetzler D, Shen L, Korn WM, Lenz HJ. Distinct genomic landscapes of gastroesophageal adenocarcinoma depending on PD-L1 expression identify mutations in RAS-MAPK pathway and TP53 as potential predictors of immunotherapy efficacy. Ann Oncol 2021; 32:906-916. [PMID: 33798656 DOI: 10.1016/j.annonc.2021.03.203] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/21/2021] [Accepted: 03/28/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The impact of molecular alterations on programmed death-ligand 1 (PD-L1) combined positive score (CPS) is not well studied in gastroesophageal adenocarcinomas (GEAs). We aimed to characterize genomic features of tumors with different CPSs in GEAs. PATIENTS AND METHODS Genomic alterations of 2518 GEAs were compared in three groups (PD-L1 CPS ≥ 10, high; CPS = 1-9, intermediate; CPS < 1, low) using next-generation sequencing. We assessed the impact of gene mutations on the efficacy of immune checkpoint inhibitors (ICIs) and tumor immune environment based on the Memorial Sloan Kettering Cancer Center and The Cancer Genome Atlas databases. RESULTS High, intermediate, and low CPSs were seen in 18%, 54% and 28% of GEAs, respectively. PD-L1 positivity was less prevalent in women and in tissues derived from metastatic sites. PD-L1 CPS was positively associated with mismatch repair deficiency/microsatellite instability-high, but independent of tumor mutation burden distribution. Tumors with mutations in KRAS, TP53, and RAS-mitogen-activated protein kinase (MAPK) pathway were associated with higher PD-L1 CPSs in the mismatch repair proficiency and microsatellite stability (pMMR&MSS) subgroup. Patients with RAS-MAPK pathway alterations had longer overall survival (OS) from ICIs compared to wildtype (WT) patients [27 versus 13 months, hazard ratio (HR) = 0.36, 95% confidence interval (CI): 0.19-0.7, P = 0.016] and a similar trend was observed in the MSS subgroup (P = 0.11). In contrast, patients with TP53 mutations had worse OS from ICIs compared to TP53-WT patients in the MSS subgroup (5 versus 21 months, HR = 2.39, 95% CI: 1.24-4.61, P = 0.016). CONCLUSIONS This is the largest study to investigate the distinct genomic landscapes of GEAs with different PD-L1 CPSs. Our data may provide novel insights for patient selection using mutations in TP53 and RAS-MAPK pathway and for the development of rational combination immunotherapies in GEAs.
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Affiliation(s)
- J Y Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China; Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - J Xiu
- Caris Life Sciences, Phoenix, USA
| | - Y Baca
- Caris Life Sciences, Phoenix, USA
| | - H Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - F Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - N Kawanishi
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - S Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - W Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - J Millstein
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - A F Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, USA
| | - A Grothey
- GI Cancer Research, West Cancer Center and Research Institute, Germantown, USA
| | - B A Weinberg
- Division of Hematology and Oncology, Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, USA
| | - J L Marshall
- Division of Hematology and Oncology, Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, USA
| | - E Lou
- Division of Hematology, Oncology and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, USA
| | - M Khushman
- Department of Interdisciplinary Clinical Oncology, Mitchell Cancer Institute, University of South Alabama, Mobile, USA
| | - D P S Sohal
- Division of Hematology/Oncology, University of Cincinnati, Cincinnati, USA
| | - M J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, USA
| | | | | | - L Shen
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - W M Korn
- Caris Life Sciences, Phoenix, USA
| | - H J Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA.
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Saul M, Poorman K, Tae H, Vanderwalde A, Stafford P, Spetzler D, Korn WM, Gatalica Z, Swensen J. Population bias in somatic measurement of microsatellite instability status. Cancer Med 2020; 9:6452-6460. [PMID: 32644297 PMCID: PMC7476819 DOI: 10.1002/cam4.3294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/23/2022] Open
Abstract
Microsatellite instability (MSI) is a key secondary effect of a defective DNA mismatch repair mechanism resulting in incorrectly replicated microsatellites in many malignant tumors. Historically, MSI detection has been performed by fragment analysis (FA) on a panel of representative genomic markers. More recently, using next-generation sequencing (NGS) to analyze thousands of microsatellites has been shown to improve the robustness and sensitivity of MSI detection. However, NGS-based MSI tests can be prone to population biases if NGS results are aligned to a reference genome instead of patient-matched normal tissue. We observed an increased rate of false positives in patients of African ancestry with an NGS-based diagnostic for MSI status utilizing 7317 microsatellite loci. We then minimized this bias by training a modified calling model that utilized 2011 microsatellite loci. With these adjustments 100% (95% CI: 89.1% to 100%) of African ancestry patients in an independent validation test were called correctly using the updated model. This poses not only a significant technical improvement but also has an important clinical impact on directing immune checkpoint inhibitor therapy.
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Affiliation(s)
| | | | | | - Ari Vanderwalde
- The University of Tennessee Health Science Center and West Cancer CenterMemphisTNUSA
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Jonna S, Feldman RA, Swensen J, Gatalica Z, Korn WM, Borghaei H, Ma PC, Nieva JJ, Spira AI, Vanderwalde AM, Wozniak AJ, Kim ES, Liu SV. Detection of NRG1 Gene Fusions in Solid Tumors. Clin Cancer Res 2019; 25:4966-4972. [PMID: 30988082 PMCID: PMC7470623 DOI: 10.1158/1078-0432.ccr-19-0160] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/04/2019] [Accepted: 04/08/2019] [Indexed: 12/23/2022]
Abstract
PURPOSE NRG1 gene fusions are rare but potentially actionable oncogenic drivers that are present in some solid tumors. Details regarding the incidence of these gene rearrangements are lacking. Here, we assessed the incidence of NRG1 fusions across multiple tumor types and described fusion partners. EXPERIMENTAL DESIGN Tumor specimens submitted for molecular profiling at a Clinical Laboratory Improvement Amendments (CLIA)-certified genomics laboratory and that underwent fusion testing by anchored multiplex PCR for targeted RNA sequencing were retrospectively identified. The overall and tumor-specific incidence was noted, as was the specific fusion partner. RESULTS Out of 21,858 tumor specimens profiled from September 2015 to December 2018, 41 cases (0.2%) harbored an NRG1 fusion. Multiple fusion partners were identified. Fusion events were seen across tumor types. The greatest incidence was in non-small cell lung cancer (NSCLC, 25), though this represented only 0.3% of NSCLC cases tested. Other tumor types harboring an NRG1 fusion included gallbladder cancer, renal cell carcinoma, bladder cancer, ovarian cancer, pancreatic cancer, breast cancer, neuroendocrine tumor, sarcoma, and colorectal cancer. CONCLUSIONS NRG1 fusions can be detected at a low incidence across multiple tumor types with significant heterogeneity in fusion partner.See related commentary by Dimou and Camidge, p. 4865.
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Affiliation(s)
| | | | | | | | | | | | - Patrick C Ma
- WVU Cancer Institute, West Virginia University, Morgantown, West Virginia
| | - Jorge J Nieva
- University of Southern California, Los Angeles, California
| | | | | | | | - Edward S Kim
- Atrium Healthcare, Levine Cancer Institute, Charlotte, North Carolina
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Phuphanich S, Sanai N, Xiu J, Mittal S, Michelhaugh S, Subramaniam DS, Pandey MK, Kesari S, Heimberger AB, Gatalica Z, Korn WM, Sumrall AL. P01.058 Higher immune associated markers (PD-L1, PD-1, TMB, MSI) in gliosarcoma compared to glioblastoma. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy139.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- S Phuphanich
- Barrow Neurological Institute, Phoenix, AZ, United States
| | - N Sanai
- Barrow Neurological Institute, Phoenix, AZ, United States
| | - J Xiu
- Caris Life Sciences, Phoenix, AZ, United States
| | - S Mittal
- Wayne State Univ Karmanos Cancer Inst, Detroit, MI, United States
| | | | - D S Subramaniam
- Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, DC, United States
| | - M K Pandey
- West Cancer Center/University of Tennessee Health Science Center, Memphis, TN, United States
| | - S Kesari
- John Wayne Cancer Institute, Santa Monica, CA, United States
| | - A B Heimberger
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Z Gatalica
- Caris Life Sciences, Phoenix, AZ, United States
| | - W M Korn
- Caris Life Sciences, Phoenix, AZ, United States
| | - A L Sumrall
- Levine Cancer Institute, Charlotte, NC, United States
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Kelley RK, Hwang J, Magbanua MJM, Watt L, Beumer JH, Christner SM, Baruchel S, Wu B, Fong L, Yeh BM, Moore AP, Ko AH, Korn WM, Rajpal S, Park JW, Tempero MA, Venook AP, Bergsland EK. A phase 1 trial of imatinib, bevacizumab, and metronomic cyclophosphamide in advanced colorectal cancer. Br J Cancer 2013; 109:1725-34. [PMID: 24022191 PMCID: PMC3790192 DOI: 10.1038/bjc.2013.553] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 07/14/2013] [Accepted: 08/19/2013] [Indexed: 02/08/2023] Open
Abstract
Background: This phase 1 clinical trial was conducted to determine the safety, maximum-tolerated dose (MTD), and pharmacokinetics of imatinib, bevacizumab, and metronomic cyclophosphamide in patients with advanced colorectal cancer (CRC). Methods: Patients with refractory stage IV CRC were treated with bevacizumab 5 mg kg−1 i.v. every 2 weeks (fixed dose) plus oral cyclophosphamide q.d. and imatinib q.d. or b.i.d. in 28-day cycles with 3+3 dose escalation. Response was assessed every two cycles. Pharmacokinetics of imatinib and cyclophosphamide and circulating tumour, endothelial, and immune cell subsets were measured. Results: Thirty-five patients were enrolled. Maximum-tolerated doses were cyclophosphamide 50 mg q.d., imatinib 400 mg q.d., and bevacizumab 5 mg kg−1 i.v. every 2 weeks. Dose-limiting toxicities (DLTs) included nausea/vomiting, neutropaenia, hyponatraemia, fistula, and haematuria. The DLT window required expansion to 42 days (1.5 cycles) to capture delayed toxicities. Imatinib exposure increased insignificantly after adding cyclophosphamide. Seven patients (20%) experienced stable disease for >6 months. Circulating tumour, endothelial, or immune cells were not associated with progression-free survival. Conclusion: The combination of metronomic cyclophosphamide, imatinib, and bevacizumab is safe and tolerable without significant drug interactions. A subset of patients experienced prolonged stable disease independent of dose level.
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Affiliation(s)
- R K Kelley
- Department of Medicine, University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, 1600 Divisadero Street, Box 1700, San Francisco, CA 94143, USA
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Kelley RK, Nimeiri HS, Munster PN, Vergo MT, Huang Y, Li CM, Hwang J, Mulcahy MF, Yeh BM, Kuhn P, Luttgen MS, Grabowsky JA, Stucky-Marshall L, Korn WM, Ko AH, Bergsland EK, Benson AB, Venook AP. Temsirolimus combined with sorafenib in hepatocellular carcinoma: a phase I dose-finding trial with pharmacokinetic and biomarker correlates. Ann Oncol 2013; 24:1900-1907. [PMID: 23519998 PMCID: PMC3690907 DOI: 10.1093/annonc/mdt109] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/01/2013] [Accepted: 02/05/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Based upon preclinical evidence for improved antitumor activity in combination, this phase I study investigated the maximum-tolerated dose (MTD), safety, activity, pharmacokinetics (PK), and biomarkers of the mammalian target of rapamycin inhibitor, temsirolimus, combined with sorafenib in hepatocellular carcinoma (HCC). PATIENTS AND METHODS Patients with incurable HCC and Child Pugh score ≤B7 were treated with sorafenib plus temsirolimus by 3 + 3 design. The dose-limiting toxicity (DLT) interval was 28 days. The response was assessed every two cycles. PK of temsirolimus was measured in a cohort at MTD. RESULTS Twenty-five patients were enrolled. The MTD was temsirolimus 10 mg weekly plus sorafenib 200 mg twice daily. Among 18 patients at MTD, DLT included grade 3 hand-foot skin reaction (HFSR) and grade 3 thrombocytopenia. Grade 3 or 4 related adverse events at MTD included hypophosphatemia (33%), infection (22%), thrombocytopenia (17%), HFSR (11%), and fatigue (11%). With sorafenib, temsirolimus clearance was more rapid (P < 0.05). Two patients (8%) had a confirmed partial response (PR); 15 (60%) had stable disease (SD). Alpha-fetoprotein (AFP) declined ≥50% in 60% assessable patients. CONCLUSION The MTD of sorafenib plus temsirolimus in HCC was lower than in other tumor types. HCC-specific phase I studies are necessary. The observed efficacy warrants further study.
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Affiliation(s)
- R K Kelley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco.
| | - H S Nimeiri
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago
| | - P N Munster
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco
| | - M T Vergo
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago
| | - Y Huang
- Drug Studies Unit, Department of Bioengineering & Therapeutic Sciences
| | - C-M Li
- Drug Studies Unit, Department of Bioengineering & Therapeutic Sciences
| | - J Hwang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco
| | - M F Mulcahy
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago
| | - B M Yeh
- Department of Radiology, UCSF, San Francisco
| | - P Kuhn
- Department of Cell Biology, The Scripps Research Institute, La Jolla, USA
| | - M S Luttgen
- Department of Cell Biology, The Scripps Research Institute, La Jolla, USA
| | - J A Grabowsky
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco
| | - L Stucky-Marshall
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago
| | - W M Korn
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco
| | - A H Ko
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco
| | - E K Bergsland
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco
| | - A B Benson
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago
| | - A P Venook
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco
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Chien AJ, Illi JA, Ko AH, Korn WM, Fong L, Chen LM, Kashani-Sabet M, Ryan CJ, Rosenberg JE, Dubey S, Small EJ, Jahan TM, Hylton NM, Yeh BM, Huang Y, Koch KM, Moasser MM. A phase I study of a 2-day lapatinib chemosensitization pulse preceding nanoparticle albumin-bound Paclitaxel for advanced solid malignancies. Clin Cancer Res 2009; 15:5569-75. [PMID: 19706807 DOI: 10.1158/1078-0432.ccr-09-0522] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Systemic chemotherapy fails to access much of the tumor burden in patients with advanced cancer, significantly limiting its efficacy. In preclinical studies, brief high doses of tyrosine kinase inhibitors (TKI) targeting the human epidermal growth factor receptor (HER) family can prime tumor vasculature for optimal chemotherapeutic delivery and efficacy. This study investigates the clinical relevance of this approach. EXPERIMENTAL DESIGN A phase I clinical study of escalating doses of the HER TKI lapatinib given as a 2-day pulse before a weekly infusion of nab-paclitaxel (100 mg/m(2)) was conducted in patients with advanced solid tumors. RESULTS Twenty-five patients were treated. Treatment was associated with grade 1 to 2 toxicities including diarrhea, nausea, rash, neutropenia, neuropathy, fatigue, alopecia, and anemia. The two dose-limiting toxicities were grade 3 vomiting and grade 4 neutropenia, and the maximum tolerated dose of lapatinib was defined as 5250 mg/day in divided doses. Lapatinib concentrations increased with increasing dose. Dynamic Contrast Enhanced Magnetic Resonance Imaging studies in a subset of patients confirmed a decrease in tumor vascular permeability immediately following a lapatinib pulse. Sixty-five percent of evaluable patients experienced a partial or stable response on this therapy, 72% of whom were previously taxane-refractory. CONCLUSION A 2-day pulse of high-dose lapatinib given before weekly nab-paclitaxel is a feasible and tolerable clinical regimen, suitable for testing this novel vascular-priming chemosensitization hypothesis developed in preclinical models.
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Affiliation(s)
- Amy J Chien
- Department of Medicine, University of California San Francisco, San Francisco, California 94143-0875, USA
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10
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Abstract
We administered an adenoviral vector, Onyx-015, into the hepatic artery of patients with metastatic colorectal cancer involving the liver. Thirty-five patients enrolled in this multi-institutional phase I/II trial received up to eight arterial infusions of up to 2 × 1012 viral particles. Hepatic toxicity was the primary dose-limiting toxicity observed in preclinical models. However, nearly 200 infusions of this adenoviral vector were administered directly into the hepatic artery without significant toxicity. Therefore, we undertook this analysis to determine the impact of repeated adenoviral exposure on hepatic function. Seventeen patients were treated at our institution, providing a detailed data set on the changes in hepatic function following repeated exposure to adenovirus. No changes in hepatic function occurred with the first treatment of Onyx-015 among these patients. Transient increases in transaminase levels occurred in one patient starting with the second infusion and transient increases in bilirubin was observed in two patients starting with the fifth treatment. These changes occurred too early to be explained by viral-mediated lysis of hepatocytes. In addition, viremia was observed starting 3–5 days after the viral infusion in half of the patient, but was not associated with hepatic toxicity. To further understand the basis for the minimal hepatic toxicity of adenoviral vectors, we evaluated the replication of adenovirus in primary hepatocytes and tumor cells in culture and the expression of the coxsackie-adenoviral receptor (CAR) in normal liver and colon cancer metastatic to the liver. We found that adenovirus replicates poorly in primary hepatocytes but replicates efficiently in tumors including tumors derived from hepatocytes. In addition, we found that CAR is localized at junctions between hepatocytes and is inaccessible to hepatic blood flow. CAR is not expressed on tumor vasculature but is expressed on tumor cells. Spatial restriction of CAR to the intercellular space in normal liver and diminished replication of adenovirus in hepatocytes may explain the minimal toxicity observed following repeated hepatic artery infusions with Onyx-015.
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Affiliation(s)
- T Au
- Palo Alto Veteran's Administration Health Care System and Stanford University, Stanford, CA USA
| | - S Thorne
- Palo Alto Veteran's Administration Health Care System and Stanford University, Stanford, CA USA
| | - W M Korn
- University of California, San Francisco, CA USA
| | - D Sze
- Palo Alto Veteran's Administration Health Care System and Stanford University, Stanford, CA USA
| | - D Kirn
- Oxford University, Jennerex Biotherapeutics, San Francisco, CA USA
| | - T R Reid
- Palo Alto Veteran's Administration Health Care System and Stanford University, Stanford, CA USA
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Korn WM, Macal M, Christian C, Lacher MD, McMillan A, Rauen KA, Warren RS, Ferrell L. Expression of the coxsackievirus- and adenovirus receptor in gastrointestinal cancer correlates with tumor differentiation. Cancer Gene Ther 2006; 13:792-7. [PMID: 16628228 DOI: 10.1038/sj.cgt.7700947] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Modified adenoviruses represent a new approach to treatment of gastrointestinal cancer. However, their uptake by cells in many cases requires the major receptor for adenoviruses, the coxsackievirus and adenovirus receptor (CAR). Thus, lack of CAR expression is a potential cause of intrinsic resistance of tumor cells to this type of treatment. To evaluate this, we studied the localization of CAR protein in normal and malignant gastrointestinal tissues. In normal tissues, CAR was concentrated at sites of cell-cell interaction, in particular at the apico-lateral cellular surface. Expression was particularly strong around bile and pancreatic ducts, which is in agreement with CAR's physiological function as a tight-junction protein. In GI malignancies (esophageal, pancreatic, colorectal and liver cancer), expression of the receptor varied substantially. Loss of CAR expression at cell-cell junction was evident in many samples. A significant correlation between CAR expression and histological grade was found, with moderately to poorly differentiated tumors most frequently demonstrating loss or reduction of CAR expression. These data indicate that CAR expression is frequently altered in gastrointestinal malignancy, potentially reducing the efficacy of adenovirus-based therapies.
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Affiliation(s)
- W M Korn
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
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12
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Abstract
Accumulated knowledge in the molecular processes of tumour development combined with the availability of genetically modified viruses resemble the basis for new promising cancer therapeutics. The main advantages of employing replication-competent viruses are achievement of tumour selective killing and amplification of their oncolytic potential within the tumour mass. In this review, we describe the development of ONYX-015, one of the first and most advanced replication-competent viruses for cancer therapy. We discuss the molecular biology of this therapeutic approach and the interesting results obtained with this virus in clinical trials.
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Affiliation(s)
- S Ries
- MediGene AG, Lochhamer Strasse 11, 82152 Martinsried, Germany
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13
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Affiliation(s)
- W M Korn
- Division of Gastroenterology and Comprehensive Cancer Center, University of California, San Francisco 94143-0128, USA.
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Ries SJ, Brandts CH, Chung AS, Biederer CH, Hann BC, Lipner EM, McCormick F, Korn WM. Loss of p14ARF in tumor cells facilitates replication of the adenovirus mutant dl1520 (ONYX-015). Nat Med 2000; 6:1128-33. [PMID: 11017144 DOI: 10.1038/80466] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The adenovirus mutant dl1520 (ONYX-015) does not express the E1B-55K protein that binds and inactivates p53. This virus replicates in tumor cells with mutant p53, but not in normal cells with functional p53. Although intra-tumoral injection of dl1520 shows promising responses in patients with solid tumors, previous in vitro studies have not established a close correlation between p53 status and dl1520 replication. Here we identify loss of p14ARF as a mechanism that allows dl1520 replication in tumor cells retaining wild-type p53. We demonstrate that the re-introduction of p14ARF into tumor cells with wild-type p53 suppresses replication of dl1520 in a p53-dependent manner. Our study supports the therapeutic use of dl1520 in tumors with lesions within the p53 pathway other than mutation of p53.
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Affiliation(s)
- S J Ries
- Cancer Research Institute, Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94143-0128, USA
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Korn WM, Yasutake T, Kuo WL, Warren RS, Collins C, Tomita M, Gray J, Waldman FM. Chromosome arm 20q gains and other genomic alterations in colorectal cancer metastatic to liver, as analyzed by comparative genomic hybridization and fluorescence in situ hybridization. Genes Chromosomes Cancer 1999; 25:82-90. [PMID: 10337990 DOI: 10.1002/(sici)1098-2264(199906)25:2<82::aid-gcc2>3.0.co;2-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Comprehensive information about the molecular cytogenetic changes in metastases of colorectal cancer is not yet available. To define such changes in metastases, we measured relative DNA sequence copy numbers by comparative genomic hybridization (CGH). Samples from 27 liver metastases and 6 synchronous primary tumors were analyzed. An average of 9.9 aberrations per tumor was found in the metastases. Gains of chromosome arms 20q (85%), 13q (48%), 7p (44%), and 8q (44%) and losses of chromosome arms 18q (89%), 8p (59%), 1p (56%), and 18p (48%) were detected most frequently. Chromosomes 14 and 15 were lost in 26% and 30% of the metastases, respectively. No consistent differences were observed between primary tumors and synchronous metastases. Fluorescence in situ hybridization (FISH) was used for further characterization of gains of chromosome arm 20q. Touch preparations of 13 tumors that had demonstrated 20q gain with CGH were examined with FISH by use of a set of probes mapping to different parts of 20q. A probe for 20p was used as a reference. FISH showed relative gain of at least one 20q locus in 12 of the tumors. High-level gains were detected in 38% of the tumors, preferentially for probes mapping to band 20q13. Our CGH data indicate that colorectal metastases show chromosomal changes similar to those that have been reported for primary tumors. Chromosomal losses were seen at higher frequency, particularly for chromosomes 14 and 15. By FISH, we identified subregions on chromosome arm 20q that are frequently involved in DNA amplifications in colorectal cancer and that may harbor candidate proto-oncogenes.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Chromosome Aberrations/genetics
- Chromosome Disorders
- Chromosomes, Human/genetics
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 14/genetics
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 18/genetics
- Chromosomes, Human, Pair 20/genetics
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 8/genetics
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Female
- Humans
- In Situ Hybridization, Fluorescence/methods
- Liver Neoplasms/genetics
- Liver Neoplasms/secondary
- Male
- Middle Aged
- Neoplasm Staging
- Nucleic Acid Hybridization/methods
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Affiliation(s)
- W M Korn
- Cancer Center, University of California-San Francisco, 94143, USA.
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16
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Becher R, Korn WM, Prescher G. Use of fluorescence in situ hybridization and comparative genomic hybridization in the cytogenetic analysis of testicular germ cell tumors and uveal melanomas. Cancer Genet Cytogenet 1997; 93:22-8. [PMID: 9062576 DOI: 10.1016/s0165-4608(96)00297-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Fluorescence in situ hybridization (FISH) with specific DNA probes and comparative genomic hybridization (CGH) are molecular cytogenetic methods that provide powerful supplementations of classical cancer cytogenetics. We present two examples of successful application of these new techniques in solid tumors in which basic information about specific cytogenetic aberrations had been gained previously by conventional karyotyping. In the first, testicular germ cell tumors (TGCT), FISH analysis allowed further characterization of the i(12p) marker chromosome. By CGH, chromosomal subregions that may harbor genes important for tumorigenesis or progression could be identified. In the second, uveal melanoma, CGH enabled a retrospective study in which monosomy 3 was statistically proved to be a relevant marker for poor prognosis.
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Affiliation(s)
- R Becher
- Innere Klinik und Poliklinik (Tumorforschung), Universitätsklinikum Essen, Germany
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17
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Korn WM, Oide Weghuis DE, Suijkerbuijk RF, Schmidt U, Otto T, du Manoir S, Geurts van Kessel A, Harstrick A, Seeber S, Becher R. Detection of chromosomal DNA gains and losses in testicular germ cell tumors by comparative genomic hybridization. Genes Chromosomes Cancer 1996; 17:78-87. [PMID: 8913724 DOI: 10.1002/(sici)1098-2264(199610)17:2<78::aid-gcc2>3.0.co;2-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
To extend the results of conventional cytogenetic analysis of testicular germ cell tumors (TGCTs), we applied the new molecular cytogenetic method of comparative genomic hybridization (CGH), which enables the detection of chromosomal imbalances without the need for dividing cells. DNA from II TGCTs was studied by CGH. In all tumors examined, gain of 12p, mostly of the whole p arm, could be demonstrated. However, in three tumors, an amplification of 12p material restricted to the chromosomal bands 12p11.2-p12.1 was found. Further fluorescence in situ hybridization (FISH) analysis using a yeast artificial chromosome (YAC) that was previously mapped to that region revealed multiple copies of that chromosomal segment in interphase nuclei of these tumors. This finding is an important clue to the localization of candidate protooncogenes at 12p involved in TGCTs. Gains of small chromosomal regions at 2p, 4q, 6p, and 19p were also detected recurrently. Furthermore, gains of chromosomes 8, 14, 21, and X as well as loss of chromosome 13 were frequent findings. In conclusion, CGH provides new insights into genetic alterations of TGCTs. By using CGH, chromosomal subregions could be identified that may harbor genes involved in the pathogenesis of this malignancy.
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Affiliation(s)
- W M Korn
- West German Cancer Center, University of Essen, Medical School, Federal Republic of Germany
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