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Wallen ZD, Ko H, Nesline MK, Hastings SB, Strickland KC, Previs RA, Zhang S, Pabla S, Conroy J, Jackson JB, Saini KS, Jensen TJ, Eisenberg M, Caveney B, Sathyan P, Severson EA, Ramkissoon SH. Real-world comprehensive genomic and immune profiling reveals distinct age- and sex-based genomic and immune landscapes in tumors of patients with non-small cell lung cancer. Front Immunol 2024; 15:1413956. [PMID: 38975340 PMCID: PMC11224431 DOI: 10.3389/fimmu.2024.1413956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/07/2024] [Indexed: 07/09/2024] Open
Abstract
Introduction Younger patients with non-small cell lung cancer (NSCLC) (<50 years) represent a significant patient population with distinct clinicopathological features and enriched targetable genomic alterations compared to older patients. However, previous studies of younger NSCLC suffer from inconsistent findings, few studies have incorporated sex into their analyses, and studies targeting age-related differences in the tumor immune microenvironment are lacking. Methods We performed a retrospective analysis of 8,230 patients with NSCLC, comparing genomic alterations and immunogenic markers of younger and older patients while also considering differences between male and female patients. We defined older patients as those ≥65 years and used a 5-year sliding threshold from <45 to <65 years to define various groups of younger patients. Additionally, in an independent cohort of patients with NSCLC, we use our observations to inform testing of the combinatorial effect of age and sex on survival of patients given immunotherapy with or without chemotherapy. Results We observed distinct genomic and immune microenvironment profiles for tumors of younger patients compared to tumors of older patients. Younger patient tumors were enriched in clinically relevant genomic alterations and had gene expression patterns indicative of reduced immune system activation, which was most evident when analyzing male patients. Further, we found younger male patients treated with immunotherapy alone had significantly worse survival compared to male patients ≥65 years, while the addition of chemotherapy reduced this disparity. Contrarily, we found younger female patients had significantly better survival compared to female patients ≥65 years when treated with immunotherapy plus chemotherapy, while treatment with immunotherapy alone resulted in similar outcomes. Discussion These results show the value of comprehensive genomic and immune profiling (CGIP) for informing clinical treatment of younger patients with NSCLC and provides support for broader coverage of CGIP for younger patients with advanced NSCLC.
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Affiliation(s)
| | - Heidi Ko
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | - Mary K. Nesline
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | | | - Kyle C. Strickland
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
- Duke University Medical Center, Duke Cancer Institute, Department of Pathology, Durham, NC, United States
| | - Rebecca A. Previs
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
- Duke University Medical Center, Duke Cancer Institute, Department of Obstetrics and Gynecology, Durham, NC, United States
| | - Shengle Zhang
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | - Sarabjot Pabla
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | - Jeffrey Conroy
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
| | | | - Kamal S. Saini
- Fortrea Inc, Medical Oncology, Durham, NC, United States
| | | | - Marcia Eisenberg
- Labcorp, Early Development Laboratories, Burlington, NC, United States
| | - Brian Caveney
- Labcorp, Early Development Laboratories, Burlington, NC, United States
| | | | | | - Shakti H. Ramkissoon
- Labcorp Oncology, Medical Oncology, Durham, NC, United States
- Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Department of Pathology, Winston-Salem, NC, United States
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Kalvapudi S, Pachimatla AG, Seager RJ, Conroy J, Pabla S, Mukherjee S. Cancer/testis antigen expression and co-expression patterns in Gastroesophageal Adenocarcinoma. RESEARCH SQUARE 2024:rs.3.rs-4499622. [PMID: 38947068 PMCID: PMC11213187 DOI: 10.21203/rs.3.rs-4499622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Gastroesophageal adenocarcinoma (GEAC) poses a significant challenge due to its poor prognosis and limited treatment options. Recently, Cancer/testis antigens (CTAs) have emerged as potential therapy targets due to their high expression in tumor cells and their immunogenic nature. We aimed to explore the expression and co-expression of CTAs in GEAC. We analyzed 63 GEAC patients initially and validated our findings in 329 patients from The Cancer Genome Atlas (TCGA) database. CTA expression was measured after RNA sequencing, while clinical information, including survival outcomes and treatment details, was collected from an institutional database. Co-expression patterns among CTAs were determined using Pearson correlation analysis. The majority of the study cohort were male (87%), Caucasian (94%), and had stage IV disease (64%). CTAs were highly prevalent, ranging from 58-19%. The MAGE gene family showed the highest expression, consistent across both cohorts. The correlation matrix revealed a distinct cluster of significantly co-expressed genes, including MAGEA3, NY-ESO-1, and others (0.27 ≤ r ≤ 0.73). Survival analysis revealed that individual CTAs were associated with poorer survival outcomes in patients not receiving immunotherapy while showing potential for improved survival in those undergoing immunotherapy, although these findings lacked robust reliability. Our study provides a comprehensive characterization of CTA expression and co-expression in GEAC. The strong correlation among CTAs like MAGE, NY-ESO-1, and GAGE suggests a potential for therapies targeting multiple CTAs simultaneously. Further research, including prospective trials, is warranted to assess the prognostic value of CTAs and their suitability as therapeutic targets.
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El-Sayed MM, Bianco JR, Li Y, Fabian Z. Tumor-Agnostic Therapy-The Final Step Forward in the Cure for Human Neoplasms? Cells 2024; 13:1071. [PMID: 38920700 PMCID: PMC11201516 DOI: 10.3390/cells13121071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer accounted for 10 million deaths in 2020, nearly one in every six deaths annually. Despite advancements, the contemporary clinical management of human neoplasms faces a number of challenges. Surgical removal of tumor tissues is often not possible technically, while radiation and chemotherapy pose the risk of damaging healthy cells, tissues, and organs, presenting complex clinical challenges. These require a paradigm shift in developing new therapeutic modalities moving towards a more personalized and targeted approach. The tumor-agnostic philosophy, one of these new modalities, focuses on characteristic molecular signatures of transformed cells independently of their traditional histopathological classification. These include commonly occurring DNA aberrations in cancer cells, shared metabolic features of their homeostasis or immune evasion measures of the tumor tissues. The first dedicated, FDA-approved tumor-agnostic agent's profound progression-free survival of 78% in mismatch repair-deficient colorectal cancer paved the way for the accelerated FDA approvals of novel tumor-agnostic therapeutic compounds. Here, we review the historical background, current status, and future perspectives of this new era of clinical oncology.
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Affiliation(s)
| | | | | | - Zsolt Fabian
- School of Medicine and Dentistry, Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK; (M.M.E.-S.); (J.R.B.); (Y.L.)
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Satgunaseelan L, Lee M, Iannuzzi S, Hallal S, Deang K, Stanceski K, Wei H, Mason S, Shivalingam B, Sim HW, Buckland ME, Alexander KL. 'The Reports of My Death Are Greatly Exaggerated'-Evaluating the Effect of Necrosis on MGMT Promoter Methylation Testing in High-Grade Glioma. Cancers (Basel) 2024; 16:1906. [PMID: 38791984 PMCID: PMC11120496 DOI: 10.3390/cancers16101906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
(1) Background: MGMT (O-6-methylguanine-DNA methyltransferase) promoter methylation remains an important predictive biomarker in high-grade gliomas (HGGs). The influence of necrosis on the fidelity of MGMT promoter (MGMTp) hypermethylation testing is currently unknown. Therefore, our study aims to evaluate the effect of varying degrees of necrosis on MGMTp status, as determined by pyrosequencing, in a series of primary and recurrent HGGs; (2) Methods: Within each case, the most viable blocks (assigned as 'true' MGMTp status) and the most necrotic block were determined by histopathology review. MGMTp status was determined by pyrosequencing. Comparisons of MGMTp status were made between the most viable and most necrotic blocks. (3) Results: 163 samples from 64 patients with HGGs were analyzed. MGMTp status was maintained in 84.6% of primary and 78.3% of recurrent HGGs between the most viable and necrotic blocks. A threshold of ≥60% tumor cellularity was established at which MGMTp status was unaltered, irrespective of the degree of necrosis. (4) Conclusions: MGMTp methylation status, as determined by pyrosequencing, does not appear to be influenced by necrosis in the majority of cases at a cellularity of at least 60%. Further investigation into the role of intratumoral heterogeneity on MGMTp status will increase our understanding of this predictive marker.
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Affiliation(s)
- Laveniya Satgunaseelan
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (M.L.); (S.I.); (S.H.); (K.S.); (H.W.); (M.E.B.); (K.L.A.)
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
| | - Maggie Lee
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (M.L.); (S.I.); (S.H.); (K.S.); (H.W.); (M.E.B.); (K.L.A.)
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
| | - Sebastian Iannuzzi
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (M.L.); (S.I.); (S.H.); (K.S.); (H.W.); (M.E.B.); (K.L.A.)
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
| | - Susannah Hallal
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (M.L.); (S.I.); (S.H.); (K.S.); (H.W.); (M.E.B.); (K.L.A.)
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
- Department of Neurosurgery, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia
| | - Kristine Deang
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
- Department of Neurosurgery, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia
| | - Kristian Stanceski
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (M.L.); (S.I.); (S.H.); (K.S.); (H.W.); (M.E.B.); (K.L.A.)
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
| | - Heng Wei
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (M.L.); (S.I.); (S.H.); (K.S.); (H.W.); (M.E.B.); (K.L.A.)
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
| | - Sofia Mason
- Department of Medical Oncology, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia; (S.M.); (H.-W.S.)
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Brindha Shivalingam
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
- Department of Neurosurgery, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia
- Department of Neurosurgery, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Hao-Wen Sim
- Department of Medical Oncology, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia; (S.M.); (H.-W.S.)
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, NSW 2050, Australia
- Department of Medical Oncology, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Michael E. Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (M.L.); (S.I.); (S.H.); (K.S.); (H.W.); (M.E.B.); (K.L.A.)
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
| | - Kimberley L. Alexander
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (M.L.); (S.I.); (S.H.); (K.S.); (H.W.); (M.E.B.); (K.L.A.)
- Faculty of Medicine and Health, School of Medicine, University of Sydney, Camperdown Campus, Sydney, NSW 2000, Australia; (K.D.); (B.S.)
- Department of Neurosurgery, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia
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Seager RJ, Ko H, Pabla S, Senosain MF, Kalinski P, Van Roey E, Gao S, Strickland KC, Previs RA, Nesline MK, Hastings S, Zhang S, Conroy JM, Jensen TJ, Eisenberg M, Caveney B, Severson EA, Ramkissoon S, Gandhi S. Immunologic Factors Associated with Differential Response to Neoadjuvant Chemoimmunotherapy in Triple-Negative Breast Cancer. J Pers Med 2024; 14:481. [PMID: 38793063 PMCID: PMC11122407 DOI: 10.3390/jpm14050481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/17/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Background: KEYNOTE-522 resulted in FDA approval of the immune checkpoint inhibitor pembrolizumab in combination with neoadjuvant chemotherapy for patients with early-stage, high-risk, triple-negative breast cancer (TNBC). Unfortunately, pembrolizumab is associated with several immune-related adverse events (irAEs). We aimed to identify potential tumor microenvironment (TME) biomarkers which could predict patients who may attain pathological complete response (pCR) with chemotherapy alone and be spared the use of anti-PD-1 immunotherapy. Methods: Comprehensive immune profiling, including RNA-seq gene expression assessment of 395 immune genes, was performed on matched FFPE tumor samples from 22 stage I-III TNBC patients (14 patients treated with neoadjuvant chemotherapy alone (NAC) and 8 treated with neoadjuvant chemotherapy combined with pembrolizumab (NAC+I)). Results: Differential gene expression analysis revealed that in the NAC group, IL12B and IL13 were both significantly associated with pCR. In the NAC+I group, LCK and TP63 were significantly associated with pCR. Patients in both treatment groups exhibiting pCR tended to have greater tumor inflammation than non-pCR patients. In the NAC+I group, patients with pCR tended to have greater cell proliferation and higher PD-L1 expression, while in the NAC group, patients with pCR tended to have lower cancer testis antigen expression. Additionally, the NAC+I group trended toward a lower relative dose intensity averaged across all chemotherapy drugs, suggesting that more dose reductions or treatment delays occurred in the NAC+I group than the NAC group. Conclusions: A comprehensive understanding of immunologic factors could potentially predict pCR to chemotherapy alone, enabling the avoidance of the unnecessary treatment of these patients with checkpoint inhibitors.
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Affiliation(s)
- Robert J. Seager
- Labcorp Oncology, Buffalo, NY 14263, USA; (S.P.); (M.-F.S.); (E.V.R.); (S.G.); (S.Z.); (J.M.C.)
| | - Heidi Ko
- Labcorp Oncology, Durham, NC 27710, USA; (H.K.); (K.C.S.); (R.A.P.); (M.K.N.); (S.H.); (T.J.J.); (E.A.S.); (S.R.)
| | - Sarabjot Pabla
- Labcorp Oncology, Buffalo, NY 14263, USA; (S.P.); (M.-F.S.); (E.V.R.); (S.G.); (S.Z.); (J.M.C.)
| | - Maria-Fernanda Senosain
- Labcorp Oncology, Buffalo, NY 14263, USA; (S.P.); (M.-F.S.); (E.V.R.); (S.G.); (S.Z.); (J.M.C.)
| | - Pawel Kalinski
- Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Erik Van Roey
- Labcorp Oncology, Buffalo, NY 14263, USA; (S.P.); (M.-F.S.); (E.V.R.); (S.G.); (S.Z.); (J.M.C.)
| | - Shuang Gao
- Labcorp Oncology, Buffalo, NY 14263, USA; (S.P.); (M.-F.S.); (E.V.R.); (S.G.); (S.Z.); (J.M.C.)
| | - Kyle C. Strickland
- Labcorp Oncology, Durham, NC 27710, USA; (H.K.); (K.C.S.); (R.A.P.); (M.K.N.); (S.H.); (T.J.J.); (E.A.S.); (S.R.)
- Department of Pathology, Duke University Medical Center, Duke Cancer Institute, Durham, NC 27710, USA
| | - Rebecca Ann Previs
- Labcorp Oncology, Durham, NC 27710, USA; (H.K.); (K.C.S.); (R.A.P.); (M.K.N.); (S.H.); (T.J.J.); (E.A.S.); (S.R.)
- Department of Obstetrics & Gynecology, Duke University Medical Center, Duke Cancer Institute, Division of Gynecologic Oncology, Durham, NC 27710, USA
| | - Mary K. Nesline
- Labcorp Oncology, Durham, NC 27710, USA; (H.K.); (K.C.S.); (R.A.P.); (M.K.N.); (S.H.); (T.J.J.); (E.A.S.); (S.R.)
| | - Stephanie Hastings
- Labcorp Oncology, Durham, NC 27710, USA; (H.K.); (K.C.S.); (R.A.P.); (M.K.N.); (S.H.); (T.J.J.); (E.A.S.); (S.R.)
| | - Shengle Zhang
- Labcorp Oncology, Buffalo, NY 14263, USA; (S.P.); (M.-F.S.); (E.V.R.); (S.G.); (S.Z.); (J.M.C.)
| | - Jeffrey M. Conroy
- Labcorp Oncology, Buffalo, NY 14263, USA; (S.P.); (M.-F.S.); (E.V.R.); (S.G.); (S.Z.); (J.M.C.)
| | - Taylor J. Jensen
- Labcorp Oncology, Durham, NC 27710, USA; (H.K.); (K.C.S.); (R.A.P.); (M.K.N.); (S.H.); (T.J.J.); (E.A.S.); (S.R.)
| | | | | | - Eric A. Severson
- Labcorp Oncology, Durham, NC 27710, USA; (H.K.); (K.C.S.); (R.A.P.); (M.K.N.); (S.H.); (T.J.J.); (E.A.S.); (S.R.)
| | - Shakti Ramkissoon
- Labcorp Oncology, Durham, NC 27710, USA; (H.K.); (K.C.S.); (R.A.P.); (M.K.N.); (S.H.); (T.J.J.); (E.A.S.); (S.R.)
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC 27710, USA
| | - Shipra Gandhi
- Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
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Shreenivas A, Nishizaki D, Lee S, Pabla S, Nesline M, Conroy JM, DePietro P, Kato S, Kurzrock R. Clinical and Biologic Correlates of ADORA2A Transcriptomic Expression in Cancer. Int J Mol Sci 2024; 25:4742. [PMID: 38731962 PMCID: PMC11083822 DOI: 10.3390/ijms25094742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
ADORA2A (adenosine A2a receptor) and ADORA2B propagate immunoregulatory signals, including restricting both innate and adaptive immunity, though recent data also suggest a tumor suppressor effect in certain settings. We evaluated the RNA expression from 514 tumors in a clinical-grade laboratory; 489 patients with advanced/metastatic disease had clinical outcome correlates. Transcript expression was standardized to internal housekeeping genes and ranked (0-100 scale) relative to 735 specimens from 35 different cancer types. Transcript abundance rank values were defined as "low/moderate" (0-74) or "high" (75-100) percentile RNA expression ranks. Overall, 20.8% of tumors had high ADORA2A (≥75 percentile RNA rank). The greatest proportion of high ADORA2A expressors was found in neuroendocrine and breast cancers and sarcomas, whereas the lowest was found in colorectal and ovarian cancers, albeit with patient-to-patient variability. In multivariable logistic regression analysis, there was a significant positive correlation between high ADORA2A RNA expression and a high expression of the immune checkpoint-related molecules PD-1 (p = 0.015), VISTA (p ≤ 0.001), CD38 (p = 0.031), and CD39 (p ≤ 0.001). In 217 immunotherapy-treated patients, high ADORA2A did not correlate significantly with progression-free (p = 0.51) or overall survival (OS) (p = 0.09) from the initiation of the checkpoint blockade. However, high versus not-high ADORA2A transcript expression correlated with longer OS from the time of advanced/metastatic disease (N = 489 patients; (HR 0.69 (95% CI 0.51-0.95) (p = 0.02)). Therefore, high ADORA2A transcript levels may be a favorable prognostic factor, unrelated to immunotherapy. Importantly, ascertaining co-expression patterns of ADORA2A with PD-1 and VISTA in individual tumors as a basis for the precision co-targeting of ADORA2A and these other checkpoint-related molecules warrants investigation in clinical trials.
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Affiliation(s)
- Aditya Shreenivas
- Department of Oncology, Medical College of Wisconsin Cancer Center, Milwaukee, WI 53226, USA
| | - Daisuke Nishizaki
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA 92037, USA
| | - Suzanna Lee
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA 92037, USA
| | | | | | | | | | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA 92037, USA
| | - Razelle Kurzrock
- Department of Oncology, Medical College of Wisconsin Cancer Center, Milwaukee, WI 53226, USA
- WIN Consortium, 24, rue Albert Thuret, 94550 Chevilly-Larue, France
- Department of Medical Oncology, University of Nebraska, Omaha, NE 68105, USA
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Dakal TC, George N, Xu C, Suravajhala P, Kumar A. Predictive and Prognostic Relevance of Tumor-Infiltrating Immune Cells: Tailoring Personalized Treatments against Different Cancer Types. Cancers (Basel) 2024; 16:1626. [PMID: 38730579 PMCID: PMC11082991 DOI: 10.3390/cancers16091626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024] Open
Abstract
TIICs are critical components of the TME and are used to estimate prognostic and treatment responses in many malignancies. TIICs in the tumor microenvironment are assessed and quantified by categorizing immune cells into three subtypes: CD66b+ tumor-associated neutrophils (TANs), FoxP3+ regulatory T cells (Tregs), and CD163+ tumor-associated macrophages (TAMs). In addition, many cancers have tumor-infiltrating M1 and M2 macrophages, neutrophils (Neu), CD4+ T cells (T-helper), CD8+ T cells (T-cytotoxic), eosinophils, and mast cells. A variety of clinical treatments have linked tumor immune cell infiltration (ICI) to immunotherapy receptivity and prognosis. To improve the therapeutic effectiveness of immune-modulating drugs in a wider cancer patient population, immune cells and their interactions in the TME must be better understood. This study examines the clinicopathological effects of TIICs in overcoming tumor-mediated immunosuppression to boost antitumor immune responses and improve cancer prognosis. We successfully analyzed the predictive and prognostic usefulness of TIICs alongside TMB and ICI scores to identify cancer's varied immune landscapes. Traditionally, immune cell infiltration was quantified using flow cytometry, immunohistochemistry, gene set enrichment analysis (GSEA), CIBERSORT, ESTIMATE, and other platforms that use integrated immune gene sets from previously published studies. We have also thoroughly examined traditional limitations and newly created unsupervised clustering and deconvolution techniques (SpatialVizScore and ProTICS). These methods predict patient outcomes and treatment responses better. These models may also identify individuals who may benefit more from adjuvant or neoadjuvant treatment. Overall, we think that the significant contribution of TIICs in cancer will greatly benefit postoperative follow-up, therapy, interventions, and informed choices on customized cancer medicines.
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Affiliation(s)
- Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur 313001, Rajasthan, India
| | - Nancy George
- Department of Biotechnology, Chandigarh University, Mohali 140413, Punjab, India;
| | - Caiming Xu
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of the City of Hope, Monrovia, CA 91010, USA;
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana P.O. 690525, Kerala, India;
| | - Abhishek Kumar
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
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Fujiwara Y, Kato S, Nishizaki D, Miyashita H, Lee S, Nesline MK, Conroy JM, DePietro P, Pabla S, Lippman SM, Kurzrock R. High indoleamine 2,3-dioxygenase transcript levels predict better outcome after front-line cancer immunotherapy. iScience 2024; 27:109632. [PMID: 38632994 PMCID: PMC11022045 DOI: 10.1016/j.isci.2024.109632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/07/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1), which catabolizes tryptophan, is a potential target to unlock the immunosuppressive tumor microenvironment. Correlations between IDO1 and immune checkpoint inhibitor (ICI) efficacy remain unclear. Herein, we investigated IDO1 transcript expression across cancers and clinical outcome correlations. High IDO1 transcripts were more frequent in uterine (54.2%) and ovarian cancer (37.2%) but varied between and within malignancies. High IDO1 RNA expression was associated with high expression of PD-L1 (immune checkpoint ligand), CXCL10 (an effector T cell recruitment chemokine), and STAT1 (a component of the JAK-STAT pathway) (all multivariable p < 0.05). PIK3CA and CTCF alterations were more frequent in the high IDO1 group. High IDO1 expression was an independent predictor of progression-free survival (adjusted HR = 0.44, 95% CI 0.20-0.99, p = 0.049) and overall survival (adjusted HR = 0.31, 95% CI 0.11-0.87, p = 0.026) after front-line ICIs. IDO1 expression warrants further exploration as a predictive biomarker for immunotherapy. Moreover, co-expressed immunoregulatory molecules merit exploration for co-targeting.
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Affiliation(s)
- Yu Fujiwara
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, Mount Sinai Beth Israel, New York, NY 10003, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy, University of California, San Diego, Moores Cancer Center, La Jolla, CA 92093, USA
| | - Daisuke Nishizaki
- Center for Personalized Cancer Therapy, University of California, San Diego, Moores Cancer Center, La Jolla, CA 92093, USA
| | - Hirotaka Miyashita
- Division of Hematology and Oncology, Dartmouth Cancer Center. One Medical Center Drive, Lebanon, NH 03766, USA
| | - Suzanna Lee
- Center for Personalized Cancer Therapy, University of California, San Diego, Moores Cancer Center, La Jolla, CA 92093, USA
| | | | | | | | | | - Scott M. Lippman
- Center for Personalized Cancer Therapy, University of California, San Diego, Moores Cancer Center, La Jolla, CA 92093, USA
| | - Razelle Kurzrock
- MCW Cancer Center and Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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9
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Nishizaki D, Kurzrock R, Miyashita H, Adashek JJ, Lee S, Nikanjam M, Eskander RN, Patel H, Botta GP, Nesline MK, Pabla S, Conroy JM, DePietro P, Sicklick JK, Kato S. Viewing the immune checkpoint VISTA: landscape and outcomes across cancers. ESMO Open 2024; 9:102942. [PMID: 38503143 PMCID: PMC10966162 DOI: 10.1016/j.esmoop.2024.102942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/18/2023] [Accepted: 02/16/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Optimizing immune checkpoint inhibitor (ICI) therapy may require identification of co-targetable checkpoint pathways via immune profiling. Herein, we analyzed the transcriptomic expression and clinical correlates of V-domain immunoglobulin suppressor of T-cell activation (VISTA), a promising targetable checkpoint. PATIENTS AND METHODS RNA sequencing was carried out on 514 tissues reflecting diverse advanced/metastatic cancers. Expression of eight immune checkpoint markers [lymphocyte-activation gene 3 (LAG-3), tumor necrosis factor receptor superfamily 14 (TNFRSF14), programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), programmed death-ligand 2 (PD-L2), B- and T-lymphocyte attenuator (BTLA), T-cell immunoglobulin and mucin domain-containing protein 3 (TIM-3), cytotoxic T-lymphocyte antigen 4 (CTLA-4)], in addition to VISTA, was analyzed, along with clinical outcomes. RESULTS High VISTA RNA expression was observed in 32% of tumors (66/514) and was the most common highly expressed checkpoint among the nine assessed. High VISTA expression was independently correlated with high BTLA, TIM-3, and TNFRSF14, and with a diagnosis of pancreatic, small intestine, and stomach cancer. VISTA transcript levels did not correlate with overall survival (OS) from metastatic/advanced disease in the pan-cancer cohort or with immunotherapy outcome (progression-free survival and OS from the start of ICI) in 217 ICI-treated patients. However, in ICI-treated pancreatic cancer patients (n = 16), median OS was significantly shorter (from immunotherapy initiation) for the high- versus not-high-VISTA groups (0.28 versus 1.21 years) (P = 0.047); in contrast, VISTA levels were not correlated with OS in 36 pancreatic cancer patients who did not receive ICI. CONCLUSION High VISTA expression correlates with high BTLA, TIM-3, and TNFRSF14 checkpoint-related molecules and with poorer post-immunotherapy survival in pancreatic cancer, consistent with prior literature indicating that VISTA is prominently expressed on CD68+ macrophages in pancreatic cancers and requiring validation in larger prospective studies. Immunomic analysis may be important for individualized precision immunotherapy.
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Affiliation(s)
- D Nishizaki
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, La Jolla.
| | - R Kurzrock
- MCW Cancer Center and Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, USA; WIN Consortium, Paris, France
| | - H Miyashita
- Dartmouth Cancer Center, Hematology and Medical Oncology, Lebanon
| | - J J Adashek
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Hospital, Baltimore
| | - S Lee
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, La Jolla
| | - M Nikanjam
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, La Jolla
| | - R N Eskander
- Center for Personalized Cancer Therapy and Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, Moores Cancer Center, La Jolla
| | - H Patel
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, La Jolla
| | - G P Botta
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, La Jolla
| | | | | | | | | | - J K Sicklick
- Division of Surgical Oncology, Department of Surgery, Center for Personalized Cancer Therapy, University of California San Diego, La Jolla, USA
| | - S Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego, Moores Cancer Center, La Jolla.
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10
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Seager RJ, Senosain MF, Van Roey E, Gao S, DePietro P, Nesline MK, Dash DP, Zhang S, Ko H, Hastings SB, Strickland KC, Previs RA, Jensen TJ, Eisenberg M, Caveney BJ, Severson EA, Ramkissoon S, Conroy JM, Pabla S. Cancer testis antigen burden (CTAB): a novel biomarker of tumor-associated antigens in lung cancer. J Transl Med 2024; 22:141. [PMID: 38326843 PMCID: PMC10851610 DOI: 10.1186/s12967-024-04918-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/21/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Cancer-testis antigens (CTAs) are tumor antigens that are normally expressed in the testes but are aberrantly expressed in several cancers. CTA overexpression drives the metastasis and progression of lung cancer, and is associated with poor prognosis. To improve lung cancer diagnosis, prognostic prediction, and drug discovery, robust CTA identification and quantitation is needed. In this study, we examined and quantified the co-expression of CTAs in lung cancer to derive cancer testis antigen burden (CTAB), a novel biomarker of immunotherapy response. METHODS Formalin fixed paraffin embedded (FFPE) tumor samples in discovery cohort (n = 5250) and immunotherapy and combination therapy treated non-small cell lung cancer (NSCLC) retrospective (n = 250) cohorts were tested by comprehensive genomic and immune profiling (CGIP), including tumor mutational burden (TMB) and the mRNA expression of 17 CTAs. PD-L1 expression was evaluated by IHC. CTA expression was summed to derive the CTAB score. The median CTAB score for the discovery cohort of 170 was applied to the retrospective cohort as cutoff for CTAB "high" and "low". Biomarker and gene expression correlation was measured by Spearman correlation. Kaplan-Meier survival analyses were used to detect overall survival (OS) differences, and objective response rate (ORR) based on RECIST criteria was compared using Fisher's exact test. RESULTS The CTAs were highly co-expressed (p < 0.05) in the discovery cohort. There was no correlation between CTAB and PD-L1 expression (R = 0.011, p = 0.45) but some correlation with TMB (R = 0.11, p = 9.2 × 10-14). Kaplan-Meier survival analysis of the immunotherapy-treated NSCLC cohort revealed better OS for the pembrolizumab monotherapy treated patients with high CTAB (p = 0.027). The combination group demonstrated improved OS compared to pembrolizumab monotherapy group (p = 0.04). The pembrolizumab monotherapy patients with high CTAB had a greater ORR than the combination therapy group (p = 0.02). CONCLUSIONS CTA co-expression can be reliably measured using CGIP in solid tumors. As a biomarker, CTAB appears to be independent from PD-L1 expression, suggesting that CTAB represents aspects of tumor immunogenicity not measured by current standard of care testing. Improved OS and ORR for high CTAB NSCLC patients treated with pembrolizumab monotherapy suggests a unique underlying aspect of immune response to these tumor antigens that needs further investigation.
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Affiliation(s)
- R J Seager
- OmniSeq (Labcorp Oncology), Buffalo, NY, USA
| | | | | | - Shuang Gao
- OmniSeq (Labcorp Oncology), Buffalo, NY, USA
| | | | | | | | | | - Heidi Ko
- Labcorp Oncology, Durham, NC, USA
| | | | - Kyle C Strickland
- Labcorp Oncology, Durham, NC, USA
- Duke University Medical Center, Duke Cancer Institute, Durham, NC, USA
| | - Rebecca A Previs
- Labcorp Oncology, Durham, NC, USA
- Duke University Medical Center, Duke Cancer Institute, Durham, NC, USA
| | | | | | | | | | - Shakti Ramkissoon
- Labcorp Oncology, Durham, NC, USA
- Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA
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11
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Jou J, Kato S, Miyashita H, Thangathurai K, Pabla S, DePietro P, Nesline MK, Conroy JM, Rubin E, Eskander RN, Kurzrock R. Cancer-Immunity Marker RNA Expression Levels across Gynecologic Cancers: Implications for Immunotherapy. Mol Cancer Ther 2023; 22:1352-1362. [PMID: 37619986 DOI: 10.1158/1535-7163.mct-23-0270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/25/2023] [Accepted: 08/22/2023] [Indexed: 08/26/2023]
Abstract
Our objective was to characterize cancer-immunity marker expression in gynecologic cancers and compare immune landscapes between gynecologic tumor subtypes and with nongynecologic solid tumors. RNA expression levels of 51 cancer-immunity markers were analyzed in patients with gynecologic cancers versus nongynecologic cancers, and normalized to a reference population of 735 control cancers, ranked from 0 to 100, and categorized as low (0-24), moderate (25-74), or high (75-100) percentile rank. Of the 72 patients studied, 43 (60%) had ovarian, 24 (33%) uterine, and 5 (7%) cervical cancer. No two immune profiles were identical according to expression rank (0-100) or rank level (low, moderate, or high). Patients with cervical cancer had significantly higher expression level ranks of immune activating, proinflammatory, tumor-infiltrating lymphocyte markers, and checkpoints than patients with uterine or ovarian cancer (P < 0.001 for all comparisons). However, there were no significant differences in immune marker expression between uterine and ovarian cancers. Tumors with PD-L1 tumor proportional score (TPS) ≥1% versus 0% had significantly higher expression levels of proinflammatory markers (58 vs. 49%, P = 0.0004). Compared to patients with nongynecologic cancers, more patients with gynecologic cancers express high levels of IDO-1 (44 vs. 13%, P < 0.001), LAG3 (35 vs. 21%, P = 0.008), and IL10 (31 vs. 15%, P = 0.002.) Patients with gynecologic cancers have complex and heterogeneous immune landscapes that are distinct from patient to patient and from other solid tumors. High levels of IDO1 and LAG3 suggest that clinical trials with IDO1 inhibitors or LAG3 inhibitors, respectively, may be warranted in gynecologic cancers.
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Affiliation(s)
- Jessica Jou
- Division of Gynecologic Oncology, Oregon Health and Sciences University, Knight Cancer Institute, Portland, Oregon
| | - Shumei Kato
- Division of Hematology & Oncology and Center for Personalized Cancer Therapy, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Hirotaka Miyashita
- Department of Hematology & Oncology, Dartmouth Cancer Center, Lebanon, New Hampshire
| | | | | | - Paul DePietro
- OmniSeq, Inc. (a Labcorp subsidiary), Buffalo, New York
| | | | | | - Eitan Rubin
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ramez N Eskander
- Division of Gynecologic Oncology, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- WIN Consortium and Medical College of Wisconsin Cancer Center, Milwaukee, Wisconsin
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12
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Nesline MK, Previs RA, Dy GK, Deng L, Lee YH, DePietro P, Zhang S, Meyers N, Severson E, Ramkissoon S, Pabla S, Conroy JM. PD-L1 Expression by RNA-Sequencing in Non-Small Cell Lung Cancer: Concordance with Immunohistochemistry and Associations with Pembrolizumab Treatment Outcomes. Cancers (Basel) 2023; 15:4789. [PMID: 37835483 PMCID: PMC10571724 DOI: 10.3390/cancers15194789] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Programmed cell death ligand (PD-L1) expression by immunohistochemistry (IHC) lacks sensitivity for pembrolizumab immunotherapy selection in non-small cell lung cancer (NSCLC), particularly for tumors with low expression. We retrospectively evaluated transcriptomic PD-L1 by mRNA next-generation sequencing (RNA-seq). In an unselected NSCLC patient cohort (n = 3168) tested during standard care (2017-2021), PD-L1 IHC and RNA-seq demonstrated moderate concordance, with 80% agreement overall. Most discordant cases were either low or negative for PD-L1 expression by IHC but high by RNA-seq. RNA-seq accurately discriminated PD-L1 IHC high from low tumors by receiver operator curve (ROC) analysis but could not distinguish PD-L1 IHC low from negative tumors. In a separate pembrolizumab monotherapy cohort (n = 102), NSCLC tumors classified as PD-L1 high versus not high by RNA-seq had significantly improved response, progression-free survival, and overall survival as an individual measure and in combination with IHC high or low status. PD-L1 IHC status (high or low) trended toward but had no significant associations with improved outcomes. Conventional PD-L1 IHC testing has inherent limitations, making it an imperfect reference standard for evaluating novel testing technologies. RNA-seq offers an objective PD-L1 measure that could represent a complementary method to IHC to improve NSCLC patient selection for immunotherapy.
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Affiliation(s)
- Mary K. Nesline
- Labcorp Oncology, Durham, NC 27560, USA; (R.A.P.); (E.S.); (S.R.)
| | - Rebecca A. Previs
- Labcorp Oncology, Durham, NC 27560, USA; (R.A.P.); (E.S.); (S.R.)
- Division of Gynecologic Oncology, Duke Cancer Institute, Durham, NC 27710, USA
| | - Grace K. Dy
- Division of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Lei Deng
- Fred Hutchinson Cancer Center, Seattle, WA 98109, USA;
| | - Yong Hee Lee
- Mantech International, Virginia Beach, VA 23452, USA
| | - Paul DePietro
- OmniSeq, Inc., Buffalo, NY 14203, USA; (P.D.); (S.Z.); (N.M.); (S.P.); (J.M.C.)
| | - Shengle Zhang
- OmniSeq, Inc., Buffalo, NY 14203, USA; (P.D.); (S.Z.); (N.M.); (S.P.); (J.M.C.)
| | - Nathan Meyers
- OmniSeq, Inc., Buffalo, NY 14203, USA; (P.D.); (S.Z.); (N.M.); (S.P.); (J.M.C.)
| | - Eric Severson
- Labcorp Oncology, Durham, NC 27560, USA; (R.A.P.); (E.S.); (S.R.)
| | - Shakti Ramkissoon
- Labcorp Oncology, Durham, NC 27560, USA; (R.A.P.); (E.S.); (S.R.)
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157, USA
| | - Sarabjot Pabla
- OmniSeq, Inc., Buffalo, NY 14203, USA; (P.D.); (S.Z.); (N.M.); (S.P.); (J.M.C.)
| | - Jeffrey M. Conroy
- OmniSeq, Inc., Buffalo, NY 14203, USA; (P.D.); (S.Z.); (N.M.); (S.P.); (J.M.C.)
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13
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Miyashita H, Kurzrock R, Bevins NJ, Thangathurai K, Lee S, Pabla S, Nesline M, Glenn ST, Conroy JM, DePietro P, Rubin E, Sicklick JK, Kato S. T-cell priming transcriptomic markers: implications of immunome heterogeneity for precision immunotherapy. NPJ Genom Med 2023; 8:19. [PMID: 37553332 PMCID: PMC10409760 DOI: 10.1038/s41525-023-00359-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/14/2023] [Indexed: 08/10/2023] Open
Abstract
Immune checkpoint blockade is effective for only a subset of cancers. Targeting T-cell priming markers (TPMs) may enhance activity, but proper application of these agents in the clinic is challenging due to immune complexity and heterogeneity. We interrogated transcriptomics of 15 TPMs (CD137, CD27, CD28, CD80, CD86, CD40, CD40LG, GITR, ICOS, ICOSLG, OX40, OX40LG, GZMB, IFNG, and TBX21) in a pan-cancer cohort (N = 514 patients, 30 types of cancer). TPM expression was analyzed for correlation with histological type, microsatellite instability high (MSI-H), tumor mutational burden (TMB), and programmed death-ligand 1 (PD-L1) expression. Among 514 patients, the most common histological types were colorectal (27%), pancreatic (11%), and breast cancer (10%). No statistically significant association between histological type and TPM expression was seen. In contrast, expression of GZMB (granzyme B, a serine protease stored in activated T and NK cells that induces cancer cell apoptosis) and IFNG (activates cytotoxic T cells) were significantly higher in tumors with MSI-H, TMB ≥ 10 mutations/mb and PD-L1 ≥ 1%. PD-L1 ≥ 1% was also associated with significantly higher CD137, GITR, and ICOS expression. Patients' tumors were classified into "Hot", "Mixed", or "Cold" clusters based on TPM expression using hierarchical clustering. The cold cluster showed a significantly lower proportion of tumors with PD-L1 ≥ 1%. Overall, 502 patients (98%) had individually distinct patterns of TPM expression. Diverse expression patterns of TPMs independent of histological type but correlating with other immunotherapy biomarkers (PD-L1 ≥ 1%, MSI-H and TMB ≥ 10 mutations/mb) were observed. Individualized selection of patients based on TPM immunomic profiles may potentially help with immunotherapy optimization.
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Affiliation(s)
- Hirotaka Miyashita
- Department of Hematology and Oncology, Dartmouth Cancer Center, Lebanon, NH, USA.
| | - Razelle Kurzrock
- Worldwide Innovative Network (WIN) for Personalized Cancer Therapy, Paris, France
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nicholas J Bevins
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Kartheeswaran Thangathurai
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Department of Physical Science, University of Vavuniya, Vavuniya, Sri Lanka
| | - Suzanna Lee
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC, San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | | | - Sean T Glenn
- Roswell Park Comprehensive Cancer Center, Center for Personalized Medicine, Buffalo, NY, USA
| | | | | | - Eitan Rubin
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jason K Sicklick
- Division of Surgical Oncology, Department of Surgery, and Center for Personalized Cancer Therapy, University of California, San Diego, La Jolla, CA, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC, San Diego Moores Cancer Center, La Jolla, CA, USA.
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14
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Severson E, Achyut BR, Nesline M, Pabla S, Previs RA, Kannan G, Chenn A, Zhang S, Klein R, Conroy J, Sausen M, Sathyan P, Saini KS, Ghosh A, Jensen TJ, Reddy P, Ramkissoon SH. RNA Sequencing Identifies Novel NRG1 Fusions in Solid Tumors that Lack Co-Occurring Oncogenic Drivers. J Mol Diagn 2023; 25:454-466. [PMID: 37164276 DOI: 10.1016/j.jmoldx.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/02/2023] [Accepted: 03/30/2023] [Indexed: 05/12/2023] Open
Abstract
NRG1 gene fusions are rare, therapeutically relevant, oncogenic drivers that occur across solid tumor types. To understand the landscape of NRG1 gene fusions, 4397 solid tumor formalin-fixed, paraffin-embedded samples consecutively tested by comprehensive genomic and immune profiling during standard care were analyzed. Nineteen NRG1 fusions were found in 17 unique patients, across multiple tumor types, including non-small-cell lung (n = 7), breast (n = 2), colorectal (n = 3), esophageal (n = 2), ovarian (n = 1), pancreatic (n = 1), and unknown primary (n = 1) carcinomas, with a cumulative incidence of 0.38%. Fusions were identified with breakpoints across four NRG1 introns spanning 1.4 megabases, with a mixture of known (n = 8) and previously unreported (n = 11) fusion partners. Co-occurring driver alterations in tumors with NRG1 fusions were uncommon, except colorectal carcinoma, where concurrent alterations in APC, BRAF, and ERBB2 were present in a subset of cases. The overall lack of co-occurring drivers highlights the importance of identifying NRG1 gene fusions, as these patients are unlikely to harbor other targetable alterations. In addition, RNA sequencing is important to identify NRG1 gene fusions given the variety of fusion partners and large genomic areas where breakpoints can occur.
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Affiliation(s)
- Eric Severson
- Enterprise Oncology, Labcorp, Durham, North Carolina.
| | | | | | | | - Rebecca A Previs
- Enterprise Oncology, Labcorp, Durham, North Carolina; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | | | - Anjen Chenn
- Enterprise Oncology, Labcorp, Durham, North Carolina
| | | | | | | | - Mark Sausen
- Personal Genome Diagnostics, Baltimore, Maryland
| | | | - Kamal S Saini
- Enterprise Oncology, Labcorp, Durham, North Carolina
| | | | | | | | - Shakti H Ramkissoon
- Enterprise Oncology, Labcorp, Durham, North Carolina; Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina
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15
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Teuwen LA, Roets E, D’Hoore P, Pauwels P, Prenen H. Comprehensive Genomic Profiling and Therapeutic Implications for Patients with Advanced Cancers: The Experience of an Academic Hospital. Diagnostics (Basel) 2023; 13:1619. [PMID: 37175010 PMCID: PMC10177779 DOI: 10.3390/diagnostics13091619] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Next-generation sequencing (NGS) can be used to detect tumor-specific genomic alterations. This retrospective single-center study aims to assess the application of an extensive NGS panel to identify actionable alterations and initiate matched targeted treatment for patients with advanced cancer. We analyzed genomic alterations in solid tumor biopsies from 464 patients with advanced cancer with the Foundation Medicine assay (FoundationOne®CDx). Therapeutic implications were determined using the Memorial Sloan Kettering Precision Oncology Knowledge Base (OncoKB) classification. The FoundationOne®CDx was successfully applied in 464/521 patients (89%). The most common altered genes were TP53 (61%), KRAS (20%), CDKN2A (20%), TERT (16%), and APC (16%). Among the 419 patients with successfully analyzed tumor mutational burden (TMB), 43 patients presented with a high TMB (≥10 mutations/megabase). Out of the 126 patients with an actionable target, 40 patients received matched treatment (32%) of which 17 were within a clinical trial. This study shows that the application of NGS is feasible in an academic center and increases the detection of actionable alterations and identification of patients eligible for targeted treatment or immunotherapy regardless of tumor histology. Strategies such as early referral for NGS, inclusion in clinical (basket) trials, and the development of new targeted drugs are necessary to improve the matched treatment rate.
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Affiliation(s)
- Laure-Anne Teuwen
- Department of Oncology, Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium; (L.-A.T.); (E.R.); (P.D.)
| | - Evelyne Roets
- Department of Oncology, Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium; (L.-A.T.); (E.R.); (P.D.)
| | - Pieter D’Hoore
- Department of Oncology, Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium; (L.-A.T.); (E.R.); (P.D.)
| | - Patrick Pauwels
- Department of Pathology, Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium;
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Hans Prenen
- Department of Oncology, Antwerp University Hospital, Drie Eikenstraat 655, 2650 Edegem, Belgium; (L.-A.T.); (E.R.); (P.D.)
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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16
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Vathiotis IA, Salichos L, Martinez-Morilla S, Gavrielatou N, Aung TN, Shafi S, Wong PF, Jessel S, Kluger HM, Syrigos KN, Warren S, Gerstein M, Rimm DL. Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade. NPJ Precis Oncol 2022; 6:92. [PMID: 36522538 PMCID: PMC9755314 DOI: 10.1038/s41698-022-00330-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022] Open
Abstract
Treatment with immune checkpoint inhibitors has altered the course of malignant melanoma, with approximately half of the patients with advanced disease surviving for more than 5 years after diagnosis. Currently, there are no biomarker methods for predicting outcome from immunotherapy. Here, we obtained transcriptomic information from a total of 105 baseline tumor samples comprising two cohorts of patients with advanced melanoma treated with programmed cell death protein 1 (PD-1)-based immunotherapies. Gene expression profiles were correlated with progression-free survival (PFS) within consecutive clinical benefit intervals (i.e., 6, 12, 18, and 24 months). Elastic net binomial regression models with cross validation were utilized to compare the predictive value of distinct genes across time. Lasso regression was used to generate a signature predicting long-term benefit (LTB), defined as patients who remain alive and free of disease progression at 24 months post treatment initiation. We show that baseline gene expression profiles were consistently able to predict long-term immunotherapy outcomes with high accuracy. The predictive value of different genes fluctuated across consecutive clinical benefit intervals, with a distinct set of genes defining benefit at 24 months compared to earlier outcomes. A 12-gene signature was able to predict LTB following anti-PD-1 therapy with an area under the curve (AUC) equal to 0.92 and 0.74 in the training and validation set, respectively. Evaluation of LTB, via a unique signature may complement objective response classification and characterize the logistics of sustained antitumor immune responses.
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Affiliation(s)
- Ioannis A Vathiotis
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
| | - Leonidas Salichos
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, USA
| | - Sandra Martinez-Morilla
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Niki Gavrielatou
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Thazin Nwe Aung
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Saba Shafi
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Pok Fai Wong
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Shlomit Jessel
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Harriet M Kluger
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Konstantinos N Syrigos
- Department of Internal Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
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17
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Fujiwara Y, Kato S, Nesline MK, Conroy JM, DePietro P, Pabla S, Kurzrock R. Indoleamine 2,3-dioxygenase (IDO) inhibitors and cancer immunotherapy. Cancer Treat Rev 2022; 110:102461. [DOI: 10.1016/j.ctrv.2022.102461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 11/02/2022]
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18
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Brown LC, Zhu J, Desai K, Kinsey E, Kao C, Lee YH, Pabla S, Labriola MK, Tran J, Dragnev KH, Tafe LJ, Dayyani F, Gupta RT, McCall S, George DJ, Glenn ST, Nesline MK, George S, Zibelman M, Morrison C, Ornstein MC, Zhang T. Evaluation of tumor microenvironment and biomarkers of immune checkpoint inhibitor response in metastatic renal cell carcinoma. J Immunother Cancer 2022; 10:jitc-2022-005249. [PMID: 36252996 PMCID: PMC9577926 DOI: 10.1136/jitc-2022-005249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Immunotherapy combinations including ipilimumab and nivolumab are now the standard of care for untreated metastatic renal cell carcinoma (mRCC). Biomarkers of response are lacking to predict patients who will have a favorable or unfavorable response to immunotherapy. This study aimed to use the OmniSeq transcriptome-based platform to develop biomarkers of response to immunotherapy. METHODS Two cohorts of patients were retrospectively collected. These included an investigational cohort of patients with mRCC treated with immune checkpoint inhibitor therapy from five institutions, and a subsequent validation cohort of patients with mRCC treated with combination ipilimumab and nivolumab from two institutions (Duke Cancer Institute and Cleveland Clinic Taussig Cancer Center). Tissue-based RNA sequencing was performed using the OmniSeq Immune Report Card on banked specimens to identify gene signatures and immune checkpoints associated with differential clinical outcomes. A 5-gene expression panel was developed based on the investigational cohort and was subsequently evaluated in the validation cohort. Clinical outcomes including progression-free survival (PFS) and overall survival (OS) were extracted by retrospective chart review. Objective response rate (ORR) was assessed by Response Evaluation Criteria in Solid Tumors (RECIST) V.1.1. RESULTS The initial investigation cohort identified 86 patients with mRCC who received nivolumab (80%, 69/86), ipilimumab/nivolumab (14%, 12/86), or pembrolizumab (6%, 5/86). A gene expression score was created using the top five genes found in responders versus non-responders (FOXP3, CCR4, KLRK1, ITK, TIGIT). The ORR in patients with high gene expression (GEhigh) on the 5-gene panel was 29% (14/48), compared with low gene expression (GElow) 3% (1/38, χ2 p=0.001). The validation cohort was comprised of 62 patients who received ipilimumab/nivolumab. There was no difference between GEhigh and GElow in terms of ORR (44% vs 38.5%), PFS (HR 1.5, 95% CI 0.58 to 3.89), or OS (HR 0.96, 95% CI 0.51 to 1.83). Similarly, no differences in ORR, PFS or OS were observed when patients were stratified by tumor mutational burden (high=top 20%), PD-L1 (programmed death-ligand 1) expression by immunohistochemistry or RNA expression, or CTLA-4 (cytotoxic T-lymphocytes-associated protein 4) RNA expression. The International Metastatic RCC Database Consortium (IMDC) risk score was prognostic for OS but not PFS. CONCLUSION A 5-gene panel that was associated with improved ORR in a predominantly nivolumab monotherapy population of patients with mRCC was not predictive for radiographic response, PFS, or OS among patients with mRCC treated with ipilimumab and nivolumab.
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Affiliation(s)
- Landon C Brown
- Levine Cancer Institute, Charlotte, North Carolina, USA,Department of Medicine, Duke Cancer Institute, Durham, North Carolina, USA
| | - Jason Zhu
- Levine Cancer Institute, Charlotte, North Carolina, USA,Department of Medicine, Duke Cancer Institute, Durham, North Carolina, USA
| | - Kunal Desai
- Department of Internal Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Emily Kinsey
- Department of Medicine, Duke Cancer Institute, Durham, North Carolina, USA
| | - Chester Kao
- Department of Medicine, Duke Cancer Institute, Durham, North Carolina, USA
| | | | | | - Matthew K Labriola
- Department of Medicine, Duke Cancer Institute, Durham, North Carolina, USA
| | - Jennifer Tran
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland, Ohio, USA
| | | | - Laura J Tafe
- Department of Medicine, Dartmouth Cancer Center, Lebanon, Pennsylvania, USA
| | - Farshid Dayyani
- Department of Medicine, University of California-Irvine Health, Orange, California, USA
| | - Rajan T Gupta
- Department of Medicine, Duke Cancer Institute, Durham, North Carolina, USA
| | - Shannon McCall
- Department of Medicine, Duke Cancer Institute, Durham, North Carolina, USA
| | - Daniel J George
- Department of Medicine, Duke Cancer Institute, Durham, North Carolina, USA
| | - Sean T Glenn
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York, USA,OmniSeq, Inc, Buffalo, New York, USA
| | | | - Saby George
- Department of Medicine, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Matthew Zibelman
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | | | - Moshe C Ornstein
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland, Ohio, USA
| | - Tian Zhang
- Department of Medicine, Duke Cancer Institute, Durham, North Carolina, USA,Hematology and Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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19
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Visceral Obesity in Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14143450. [PMID: 35884508 PMCID: PMC9315749 DOI: 10.3390/cancers14143450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
While obesity measured by body mass index (BMI) has been paradoxically associated with reduced risk and better outcome for lung cancer, recent studies suggest that the harm of obesity becomes apparent when measured as visceral adiposity. However, the prevalence of visceral obesity and its associations with demographic and tumor features are not established. We therefore conducted an observational study of visceral obesity in 994 non-small cell lung cancer (NSCLC) patients treated during 2008-2020 at our institution. Routine computerized tomography (CT) images of the patients, obtained within a year of tumor resection or biopsy, were used to measure cross-sectional abdominal fat areas. Important aspects of the measurement approach such as inter-observer variability and time stability were examined. Visceral obesity was semi-quantified as visceral fat index (VFI), the fraction of fat area that was visceral. VFI was found to be higher in males compared to females, and in former compared to current or never smokers. There was no association of VFI with tumor histology or stage. A gene expression-based measure of tumor immunogenicity was negatively associated with VFI but had no bearing with BMI. Visceral obesity is appraisable in routine CT and can be an important correlate in lung cancer studies.
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20
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Yao H, Shen N, Ji G, Huang J, Sun J, Wang G, Tang Z, Chen X. Cisplatin Nanoparticles Promote Intratumoral CD8 + T Cell Priming via Antigen Presentation and T Cell Receptor Crosstalk. NANO LETTERS 2022; 22:3328-3339. [PMID: 35404605 DOI: 10.1021/acs.nanolett.2c00478] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanomedicines are highly promising for cancer therapy due to their minimal side effects. However, little is known regarding their host immune response, which may limit their clinical efficacy and applications. Here, we find that cisplatin (CDDP)-loaded poly(l-glutamic acid)-graft-methoxy poly(ethylene glycol) complex nanoparticles (CDDP-NPs) elicit a strong antitumor CD8+ T cell-mediated immune response in a tumor-bearing mouse model compared to free CDDP. Mechanistically, the sustained retention of CDDP-NPs results in persistent tumor MHC-I overexpression, which promotes the formation of MHC-I-antigen peptide complex (pMHC-I), enhances the interaction between pMHC-I and T cell receptor (TCR), and leads to the activation of TCR signaling pathway and CD8+ T cell-mediated immune response. Furthermore, CDDP-NPs upregulate the costimulatory OX40 on intratumoral CD8+ T cells, and synergize with the agonistic OX40 antibody (aOX40) to suppress tumor growth by 89.2%. Our study provides a basis for the efficacy advantage of CDDP-based nanomedicines and immunotherapy.
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Affiliation(s)
- Haochen Yao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun 130021, P.R. China
| | - Na Shen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Guofeng Ji
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Juanjuan Huang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun 130021, P.R. China
| | - Jiali Sun
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- School of Applied Chemistry and Engineering, University of Sciences and Technology of China, Hefei 230026, China
| | - Guoqing Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun 130021, P.R. China
| | - Zhaohui Tang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- School of Applied Chemistry and Engineering, University of Sciences and Technology of China, Hefei 230026, China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
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21
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Devereaux KA, Souers RJ, Graham RP, Portier BP, Surrey LF, Yemelyanova A, Vasalos P, Trembath DG, Moncur JT. Neoplastic Cellularity Assessment in Molecular Testing. Arch Pathol Lab Med 2022; 146:1062-1071. [PMID: 35089997 DOI: 10.5858/arpa.2021-0166-cp] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Neoplastic cellularity assessment has become an essential component of molecular oncology testing; however, there are currently no best practice recommendations or guidelines for this potentially variable step in the testing process. OBJECTIVE.— To describe the domestic and international practices of neoplastic cellularity assessment and to determine how variations in laboratory practices affect neoplastic cellularity assessment accuracy. DESIGN.— Data were derived from 57 US and international laboratories that participated in the 2019 College of American Pathologists Neoplastic Cellularity Proficiency Testing Survey (NEO-B 2019). NEO-B 2019 included 29 laboratory practice questions and 5 images exhibiting challenging histologic features. Participants assessed the neoplastic cellularity of hematoxylin-eosin-stained digital images, and results were compared to a criterion standard derived from a manual cell count. RESULTS.— The survey responses showed variations in the laboratory practices for the assessment of neoplastic cellularity, including the definition of neoplastic cellularity, assessment methodology, counting practices, and quality assurance practices. In some instances, variation in laboratory practice affected neoplastic cellularity assessment performance. CONCLUSIONS.— The results highlight the need for a consensus definition and improved standardization of the assessment of neoplastic cellularity. We put forth an initial set of best practice recommendations to begin the process of standardizing neoplastic cellularity assessment.
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Affiliation(s)
- Kelly A Devereaux
- From the Department of Pathology, Stanford University School of Medicine, Stanford, California (Devereaux).,Devereaux is currently with the Department of Pathology, NYU Grossman School of Medicine, New York, New York
| | - Rhona J Souers
- The Biostatistics Department (Souers), College of American Pathologists, Northfield, Illinois
| | - Rondell P Graham
- The Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Graham)
| | - Bryce P Portier
- the Medical Affairs Department, Agilent Technologies Inc, Santa Clara, California (Portier)
| | - Lea F Surrey
- The Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (Surrey)
| | - Anna Yemelyanova
- The Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York (Yemelyanova)
| | - Patricia Vasalos
- Proficiency Testing (Vasalos), College of American Pathologists, Northfield, Illinois
| | - Dimitri G Trembath
- The Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill (Trembath)
| | - Joel T Moncur
- The Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Moncur)
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22
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Patnaik SK, Petrucci C, Barbi J, Seager RJ, Pabla S, Yendamuri S. Obesity-Specific Association of Statin Use and Reduced Risk of Recurrence of Early Stage NSCLC. JTO Clin Res Rep 2021; 2:100254. [PMID: 34877556 PMCID: PMC8633682 DOI: 10.1016/j.jtocrr.2021.100254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 02/03/2023] Open
Abstract
Introduction Statins, used for their lipid-lowering activity, have anti-inflammatory and anticancer properties as well. We evaluated this potential benefit of statin use in patients with NSCLC. Methods All 613 patients with pathologic stage 1 or 2 NSCLC who had lobectomy without neoadjuvant therapy at our institution during 2008 to 2015 were included. Association between presurgery statin use and overall survival and recurrence-free survival (RFS) was analyzed using Cox proportional hazards regression. Association of statin use with tumor transcriptome was evaluated in another 350 lung cancer cases. Results Univariable analyses did not reveal a statistically significant association of statin use with either overall survival or RFS, with hazard ratio equals to 1.19 and 0.70 (Wald p = 0.28 and 0.09), respectively. In subgroup analyses, significantly improved RFS was found in statin users, but only in overweight/obese patients (body mass index [BMI] > 25; n = 422), with univariable and multivariable hazard ratio of 0.49 and 0.46 (p = 0.005 and 0.002), respectively, but not in patients with BMI less than or equal to 25 (n = 191; univariable p = 0.21). Transcriptomes of tumor statin users had high expression of tumoricidal genes such as granzyme A and interferon-γ compared with those of nonusers among high- but not low-BMI patients with lung cancer. Conclusions Our study suggests that statins may improve the outcome of early stage NSCLC but only in overweight or obese patients. This benefit may stem from a favorable reprogramming of the antitumor immune response that statins perpetrate specifically in the obese.
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Affiliation(s)
- Santosh K Patnaik
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Cara Petrucci
- Department of Health Behavior, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Joseph Barbi
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | | | - Sai Yendamuri
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, New York
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23
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Mukherjee S, Seager RJ, Lee YH, Conroy JM, Kalinski P, Pabla S. Tumor Inflammation, Obesity, and Proliferative Status as Biomarkers in Gastroesophageal Adenocarcinoma. J Pers Med 2021; 11:1324. [PMID: 34945796 PMCID: PMC8708257 DOI: 10.3390/jpm11121324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 11/21/2022] Open
Abstract
Recent epidemiological studies have shown that obesity, typically measured by increased body mass index (BMI), is associated with an increased risk of gastroesophageal adenocarcinoma (GEAC), but the contributing molecular and immune mechanisms remain unknown. Since obesity is known to promote chronic inflammation, we hypothesized that obesity leads to inflammation-related immune dysfunction, which can be reversed by immune-modulating therapy. To test our hypothesis, we examined the clinical and molecular data from advanced GEAC patients. To this end, 46 GEAC tumors were evaluated for biomarkers representing tumor inflammation, cell proliferation, and PD-L1 expression. A CoxPH regression model with potential co-variates, followed by pairwise post hoc analysis, revealed that inflammation in the GEAC tumor microenvironment is associated with improved overall survival, regardless of BMI. We also observed a significant association between cell proliferation and progression-free survival in overweight individuals who received immune-modulating therapy. In conclusion, our data confirm the role of the immune system in the natural course of GEAC and its responses to immunotherapies, but do not support the role of BMI as an independent clinically relevant biomarker in this group of patients.
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Affiliation(s)
- Sarbajit Mukherjee
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, New York, NY 14206, USA
| | - R. J. Seager
- Bioinformatics, OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY 14203, USA; (R.J.S.); (Y.H.L.); (S.P.)
| | - Yong Hee Lee
- Bioinformatics, OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY 14203, USA; (R.J.S.); (Y.H.L.); (S.P.)
| | - Jeffrey M. Conroy
- Roswell Park Comprehensive Cancer Center, Center for Personalized Medicine, Elm and Carlton Streets, New York, NY 14206, USA;
- Research and Development, OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Pawel Kalinski
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, New York, NY 14206, USA;
| | - Sarabjot Pabla
- Bioinformatics, OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY 14203, USA; (R.J.S.); (Y.H.L.); (S.P.)
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24
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Conroy JM, Pabla S, Glenn ST, Seager RJ, Van Roey E, Gao S, Burgher B, Andreas J, Giamo V, Mallon M, Lee YH, DePietro P, Nesline M, Wang Y, Lenzo FL, Klein R, Zhang S. A scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors. PLoS One 2021; 16:e0260089. [PMID: 34855780 PMCID: PMC8639101 DOI: 10.1371/journal.pone.0260089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
Timely and accurate identification of molecular alterations in solid tumors is essential for proper management of patients with advanced cancers. This has created a need for rapid, scalable comprehensive genomic profiling (CGP) systems that detect an increasing number of therapeutically-relevant variant types and molecular signatures. In this study, we assessed the analytical performance of the TruSight Oncology 500 High-Throughput assay for detection of somatic alterations from formalin-fixed paraffin-embedded tissue specimens. In parallel, we developed supporting software and automated sample preparation systems designed to process up to 70 clinical samples in a single NovaSeq 6000TM sequencing run with a turnaround time of <7 days from specimen receipt to report. The results demonstrate that the scalable assay accurately and reproducibly detects small variants, copy number alterations, microsatellite instability (MSI) and tumor mutational burden (TMB) from 40ng DNA, and multiple gene fusions, including known and unknown partners and splice variants from 20ng RNA. 717 tumor samples and reference materials with previously known alterations in 96 cancer-related genes were sequenced to evaluate assay performance. All variant classes were reliably detected at consistent and reportable variant allele percentages with >99% overall accuracy and precision. Our results demonstrate that the high-throughput CGP assay is a reliable method for accurate detection of molecular alterations in support of precision therapeutics in oncology. The supporting systems and scalable workflow allow for efficient interpretation and prompt reporting of hundreds of patient cancer genomes per week with excellent analytical performance.
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Affiliation(s)
- Jeffrey M. Conroy
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
- Research Support Services, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Sarabjot Pabla
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Sean T. Glenn
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
- Laboratory Operations, OmniSeq Inc., Buffalo, New York, United States of America
- HemePath Molecular, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - R. J. Seager
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Erik Van Roey
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Shuang Gao
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Blake Burgher
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Jonathan Andreas
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Vincent Giamo
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Melissa Mallon
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Yong Hee Lee
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Paul DePietro
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Mary Nesline
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Yirong Wang
- Information Technology, OmniSeq Inc., Buffalo, New York, United States of America
| | - Felicia L. Lenzo
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Roger Klein
- Medical Affairs, OmniSeq Inc., Buffalo, New York, United States of America
| | - Shengle Zhang
- Laboratory Operations, OmniSeq Inc., Buffalo, New York, United States of America
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25
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Tomlins SA, Hovelson DH, Harms P, Drewery S, Falkner J, Fischer A, Hipp J, Kwiatkowski K, Lazo de la Vega L, Mitchell K, Reeder T, Siddiqui J, Vakil H, Johnson DB, Rhodes DR. Development and Validation of StrataNGS, a Multiplex PCR, Semiconductor Sequencing-Based Comprehensive Genomic Profiling Test. J Mol Diagn 2021; 23:1515-1533. [PMID: 34454112 DOI: 10.1016/j.jmoldx.2021.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 07/09/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
Despite widespread use in targeted tumor testing, multiplex PCR/semiconductor (Ion Torrent) sequencing-based assessment of all comprehensive genomic profiling (CGP) variant classes has been limited. Herein, we describe the development and validation of StrataNGS, a 429-gene, multiplex PCR/semiconductor sequencing-based CGP laboratory-developed test performed on co-isolated DNA and RNA from formalin-fixed, paraffin-embedded tumor specimens with ≥2 mm2 tumor surface area. Validation was performed in accordance with MolDX CGP validation guidelines using 1986 clinical formalin-fixed, paraffin-embedded samples and an in-house developed optimized bioinformatics pipeline. Across CGP variant classes, accuracy ranged from 0.945 for tumor mutational burden (TMB) status to >0.999 for mutations and gene fusions, positive predictive value ranged from 0.915 for TMB status to 1.00 for gene fusions, and reproducibility ranged from 0.998 for copy number alterations to 1.00 for splice variants and insertions/deletions. StrataNGS TMB estimates were highly correlated to those from whole exome- or FoundationOne CDx-determined TMB (Pearson r = 0.998 and 0.960, respectively); TMB reproducibility was 0.996 (concordance correlation coefficient). Limit of detection for all variant classes was <20% tumor content. Together, we demonstrate that multiplex PCR/semiconductor sequencing-based tumor tissue CGP is feasible using optimized bioinformatic approaches described herein.
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Affiliation(s)
| | | | - Paul Harms
- Departments of Pathology and Dermatology, University of Michigan, Ann Arbor, Michigan
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26
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Wang C, Shi M, Zhang L, Ji J, Xie R, Wu C, Guo X, Yang Y, Zhou W, Peng C, Zhang H, Yuan F, Zhang J. Identification of KRAS G12V associated clonal neoantigens and immune microenvironment in long-term survival of pancreatic adenocarcinoma. Cancer Immunol Immunother 2021; 71:491-504. [PMID: 34255132 PMCID: PMC8783870 DOI: 10.1007/s00262-021-03012-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/06/2021] [Indexed: 11/06/2022]
Abstract
Objective To investigate the molecular characteristics in tumor immune microenvironment that affect long-term survival of patients with pancreatic adenocarcinoma (PAAD). Methods The tumor related genetic features of a female PAAD patient (over 13-year survival) who suffered from multiple recurrences and metastases, and six operations over one decade were investigated deeply. Genomic features and immune microenvironment signatures of her primary lesion as well as six metastatic tumors at different time-points were characterized. Results High-frequency clonal neoantigenic mutations identified in these specimens revealed the significant associations between clonal neoantigens with her prognosis after each surgery. Meanwhile, the TCGA and ICGC databases were employed to analyse the function of KRAS G12V in pancreatic cancer. Conclusions The genomic analysis of clonal neoantigens combined with tumor immune microenvironment could promote the understandings of personalized prognostic evaluation and the stratification of resected PAAD individuals with better outcome. Supplementary Information The online version contains supplementary material available at 10.1007/s00262-021-03012-4.
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Affiliation(s)
- Chao Wang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, 200032, China
| | - Min Shi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Lei Zhang
- Genecast Biotechnology Co., Ltd, Wuxi City, 214104, Jiangsu, China
| | - Jun Ji
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Ruyan Xie
- VIP Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Chao Wu
- VIP Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Xianchao Guo
- Genecast Biotechnology Co., Ltd, Wuxi City, 214104, Jiangsu, China
| | - Ying Yang
- Genecast Biotechnology Co., Ltd, Wuxi City, 214104, Jiangsu, China
| | - Wei Zhou
- Genecast Biotechnology Co., Ltd, Wuxi City, 214104, Jiangsu, China
| | - Chenhong Peng
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China
| | - Henghui Zhang
- Genecast Biotechnology Co., Ltd, Wuxi City, 214104, Jiangsu, China
| | - Fei Yuan
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China.
| | - Jun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin er Road, Shanghai, 200025, China. .,State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, 200032, China.
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27
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Pabla S, Seager RJ, Van Roey E, Gao S, Hoefer C, Nesline MK, DePietro P, Burgher B, Andreas J, Giamo V, Wang Y, Lenzo FL, Schoenborn M, Zhang S, Klein R, Glenn ST, Conroy JM. Integration of tumor inflammation, cell proliferation, and traditional biomarkers improves prediction of immunotherapy resistance and response. Biomark Res 2021; 9:56. [PMID: 34233760 PMCID: PMC8265007 DOI: 10.1186/s40364-021-00308-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/14/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Contemporary to the rapidly evolving landscape of cancer immunotherapy is the equally changing understanding of immune tumor microenvironments (TMEs) which is crucial to the success of these therapies. Their reliance on a robust host immune response necessitates clinical grade measurements of immune TMEs at diagnosis. In this study, we describe a stable tumor immunogenic profile describing immune TMEs in multiple tumor types with ability to predict clinical benefit from immune checkpoint inhibitors (ICIs). METHODS A tumor immunogenic signature (TIGS) was derived from targeted RNA-sequencing (RNA-seq) and gene expression analysis of 1323 clinical solid tumor cases spanning 35 histologies using unsupervised analysis. TIGS correlation with ICI response and survival was assessed in a retrospective cohort of NSCLC, melanoma and RCC tumor blocks, alone and combined with TMB, PD-L1 IHC and cell proliferation biomarkers. RESULTS Unsupervised clustering of RNA-seq profiles uncovered a 161 gene signature where T cell and B cell activation, IFNg, chemokine, cytokine and interleukin pathways are over-represented. Mean expression of these genes produced three distinct TIGS score categories: strong (n = 384/1323; 29.02%), moderate (n = 354/1323; 26.76%), and weak (n = 585/1323; 44.22%). Strong TIGS tumors presented an improved ICI response rate of 37% (30/81); with highest response rate advantage occurring in NSCLC (ORR = 36.6%; 16/44; p = 0.051). Similarly, overall survival for strong TIGS tumors trended upward (median = 25 months; p = 0.19). Integrating the TIGS score categories with neoplastic influence quantified via cell proliferation showed highly proliferative and strong TIGS tumors correlate with significantly higher ICI ORR than poorly proliferative and weak TIGS tumors [14.28%; p = 0.0006]. Importantly, we noted that strong TIGS and highly [median = not achieved; p = 0.025] or moderately [median = 16.2 months; p = 0.025] proliferative tumors had significantly better survival compared to weak TIGS, highly proliferative tumors [median = 7.03 months]. Importantly, TIGS discriminates subpopulations of potential ICI responders that were considered negative for response by TMB and PD-L1. CONCLUSIONS TIGS is a comprehensive and informative measurement of immune TME that effectively characterizes host immune response to ICIs in multiple tumors. The results indicate that when combined with PD-L1, TMB and cell proliferation, TIGS provides greater context of both immune and neoplastic influences on the TME for implementation into clinical practice.
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Affiliation(s)
- Sarabjot Pabla
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - R J Seager
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Erik Van Roey
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Shuang Gao
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Carrie Hoefer
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Mary K Nesline
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Paul DePietro
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Blake Burgher
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | | | - Vincent Giamo
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Yirong Wang
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | | | | | - Shengle Zhang
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Roger Klein
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Sean T Glenn
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | - Jeffrey M Conroy
- OmniSeq, Inc, 700 Ellicott Street, Buffalo, NY, 14203, USA.
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA.
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28
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Models that combine transcriptomic with spatial protein information exceed the predictive value for either single modality. NPJ Precis Oncol 2021; 5:45. [PMID: 34050252 PMCID: PMC8163775 DOI: 10.1038/s41698-021-00184-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/16/2021] [Indexed: 01/10/2023] Open
Abstract
Immunotherapy has reshaped the field of cancer therapeutics but the population that benefits are small in many tumor types, warranting a companion diagnostic test. While immunohistochemistry (IHC) for programmed death-ligand 1 (PD-L1) or mismatch repair (MMR) and polymerase chain reaction (PCR) for microsatellite instability (MSI) are the only approved companion diagnostics others are under consideration. An optimal companion diagnostic test might combine the spatial information of IHC with the quantitative information from RNA expression profiling. Here, we show proof of concept for combination of spatially resolved protein information acquired by the NanoString GeoMx® Digital Spatial Profiler (DSP) with transcriptomic information from bulk mRNA gene expression acquired using NanoString nCounter® PanCancer IO 360™ panel on the same cohort of immunotherapy treated melanoma patients to create predictive models associated with clinical outcomes. We show that the combination of mRNA and spatially defined protein information can predict clinical outcomes more accurately (AUC 0.97) than either of these factors alone.
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29
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Visceral Obesity Promotes Lung Cancer Progression-Toward Resolution of the Obesity Paradox in Lung Cancer. J Thorac Oncol 2021; 16:1333-1348. [PMID: 34144926 DOI: 10.1016/j.jtho.2021.04.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/12/2021] [Accepted: 04/26/2021] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Although obesity is associated with adverse cancer outcomes in general, most retrospective clinical studies suggest a beneficial effect of obesity in NSCLC. METHODS Hypothesizing that this "obesity paradox" arises partly from the limitations of using body mass index (BMI) to measure obesity, we quantified adiposity using preoperative computed tomography images. This allowed the specific determination of central obesity as abdominal visceral fat area normalized to total fat area (visceral fat index [VFI]). In addition, owing to the previously reported salutary effect of metformin on high-BMI patients with lung cancer, metformin users were excluded. We then explored associations between visceral obesity and outcomes after surgical resection of stage I and II NSCLC. We also explored potential immunologic underpinnings of such association using complimentary analyses of tumor gene expression data from NSCLC tumors and the tumor transcriptome and immune microenvironment in an immunocompetent model of lung cancer with diet-induced obesity. RESULTS We found that in 513 patients with stage I and II NSCLC undergoing lobectomy, a high VFI is associated with decreased recurrence-free and overall survival. VFI was also inversely related to an inflammatory transcriptomic signature in NSCLC tumors, consistent with observations made in immunocompetent murine models wherein diet-induced obesity promoted cancer progression while exacerbating elements of immune suppression in the tumor niche. CONCLUSIONS In all, this study uses multiple lines of evidence to reveal the adverse effects of visceral obesity in patients with NSCLC, which align with those found in animal models. Thus, the obesity paradox may, at least in part, be secondary to the use of BMI as a measure of obesity and the confounding effects of metformin use.
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Abstract
The past 30 years have borne witness to a gradual evolution in the treatment landscape of advanced renal cell carcinoma (aRCC). Early immunotherapy approaches such as interferon-α and high-dose interleukin-2 (IL-2) therapy in this immunogenic tumor provided durable responses in only a minority of patients and came with toxic side effects. A growing understanding of the tumor biology elucidated pathways of tumorigenesis, which in turn revealed novel targets amenable to targeted therapies. Inhibition of angiogenesis and cell signaling emerged as cornerstones of treatment with the approval of bevacizumab and several pan-kinase and tyrosine kinase inhibitors. Though effective, their use has been limited by low rates of durable response, resistance, and side effects. The immunotherapy revolution of the past decade has led to immunotherapy-based combination regimens such as ipilimumab plus nivolumab, pembrolizumab plus axitinib, and avelumab plus axitinib, displacing single agent anti-angiogenic therapy in the first-line setting by demonstrating durable responses and improved survival over sunitinib. These immunotherapy-based combinations define first-line standard of care for aRCC today. The pipeline of second-line agents for consideration in patients who have disease progression despite immunotherapy regimens is robust but still in early stages of development.
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Affiliation(s)
- Landon C Brown
- Division of Medical Oncology, Department of Medicine, Duke University, DUMC 103861, Durham, NC, 27710, USA
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC, USA
| | - Kunal Desai
- Department of Internal Medicine, Cleveland Clinic, 9500 Euclid Avenue, NA10, Cleveland, OH, 44195, USA
| | - Tian Zhang
- Division of Medical Oncology, Department of Medicine, Duke University, DUMC 103861, Durham, NC, 27710, USA
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC, USA
| | - Moshe C Ornstein
- Department of Hematology and Medical Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA.
- Genitourinary Oncology, Cleveland Clinic Taussig Cancer Institute, 9500 Euclid Ave, CA-60, Cleveland, OH, 44195, USA.
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31
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Yamauchi T, Hoki T, Oba T, Jain V, Chen H, Attwood K, Battaglia S, George S, Chatta G, Puzanov I, Morrison C, Odunsi K, Segal BH, Dy GK, Ernstoff MS, Ito F. T-cell CX3CR1 expression as a dynamic blood-based biomarker of response to immune checkpoint inhibitors. Nat Commun 2021; 12:1402. [PMID: 33658501 PMCID: PMC7930182 DOI: 10.1038/s41467-021-21619-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
Immune checkpoint inhibitors (ICI) have revolutionized treatment for various cancers; however, durable response is limited to only a subset of patients. Discovery of blood-based biomarkers that reflect dynamic change of the tumor microenvironment, and predict response to ICI, will markedly improve current treatment regimens. Here, we investigate CX3C chemokine receptor 1 (CX3CR1), a marker of T-cell differentiation, as a predictive correlate of response to ICI therapy. Successful treatment of tumor-bearing mice with ICI increases the frequency and T-cell receptor clonality of the peripheral CX3CR1+CD8+ T-cell subset that includes an enriched repertoire of tumor-specific and tumor-infiltrating CD8+ T cells. Furthermore, an increase in the frequency of the CX3CR1+ subset in circulating CD8+ T cells early after initiation of anti-PD-1 therapy correlates with response and survival in patients with non-small cell lung cancer. Collectively, these data support T-cell CX3CR1 expression as a blood-based dynamic early on-treatment predictor of response to ICI therapy.
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MESH Headings
- Aged
- Aged, 80 and over
- Animals
- Antibodies, Monoclonal, Humanized/pharmacology
- Biomarkers, Pharmacological/blood
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/physiology
- CX3C Chemokine Receptor 1/blood
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/mortality
- Cell Line, Tumor
- Female
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Ki-67 Antigen/blood
- Lung Neoplasms/drug therapy
- Lung Neoplasms/immunology
- Lung Neoplasms/mortality
- Lymphocytes, Tumor-Infiltrating/drug effects
- Male
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Middle Aged
- Neoplasms, Experimental/blood supply
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/immunology
- Nivolumab/pharmacology
- Receptors, Antigen, T-Cell/metabolism
- Survival Rate
- Treatment Outcome
- Mice
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Affiliation(s)
- Takayoshi Yamauchi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Toshifumi Hoki
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Merck Sharp & Dohme, Tokyo, Japan
| | - Takaaki Oba
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Vaibhav Jain
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Hongbin Chen
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Medicine, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA
| | - Kristopher Attwood
- Department of Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Sebastiano Battaglia
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Saby George
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Medicine, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA
| | - Gurkamal Chatta
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Carl Morrison
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Kunle Odunsi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | - Brahm H Segal
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Medicine, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Grace K Dy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Marc S Ernstoff
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Medicine, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA
- Division of Cancer Treatment and Diagnosis, Developmental Therapeutics Program, National Cancer Institute, Bethesda, MD, USA
| | - Fumito Ito
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA.
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Mirizio E, Liu C, Yan Q, Waltermire J, Mandel R, Schollaert KL, Konnikova L, Wang X, Chen W, Torok KS. Genetic Signatures From RNA Sequencing of Pediatric Localized Scleroderma Skin. Front Pediatr 2021; 9:669116. [PMID: 34164359 PMCID: PMC8215272 DOI: 10.3389/fped.2021.669116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/12/2021] [Indexed: 01/02/2023] Open
Abstract
The purpose of this study was to explore the skin transcriptional profile in pediatric localized scleroderma (LS) to provide a better understanding of the altered immune and fibrotic pathways promoting disease. LS is a progressive disease of the skin and underlying tissue that causes significant functional disability and disfigurement, especially in developing children. RNA sequencing (RNAseq) technology allows for improved understanding of relevant cellular expression through transcriptome analysis of phases during LS disease progression (more active/inflammatory vs. inactive/fibrotic) and also permits the use of RNA extracted from existing paraffin-embedded skin tissue, which is important in pediatrics. A strong correlation was observed between the comparison of genes expressed between fresh (RNAlater) and paraffinized skin in healthy and LS subjects, supporting the use of paraffinized tissue. LS gene signatures compared to healthy controls showed a distinct expression of an inflammatory response gene signature (IRGS) composed of IFNγ-, IFNα-, and TNFα-associated genes. GSEA© enrichment analysis showed that the IRGS, including interferon-inducible chemokines such as CXCL9, CXCL10, CXCL11, and IFNγ itself, was more highly expressed in LS patients with more inflammatory lesions. The use of paraffinized skin for sequencing was proven to be an effective substitute for fresh skin by comparing gene expression profiles. The prevalence of the IFNγ signature in the lesion biopsies of active LS patients indicates that these genes reflect clinical activity parameters and may be the promoters of early, inflammatory disease.
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Affiliation(s)
- Emily Mirizio
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Christopher Liu
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Qi Yan
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Julia Waltermire
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Roosha Mandel
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kaila L Schollaert
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Liza Konnikova
- Division of Neonatal Medicine, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Xinjun Wang
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Wei Chen
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kathryn S Torok
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States.,Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, United States
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Lenzo FL, Kato S, Pabla S, DePietro P, Nesline MK, Conroy JM, Burgher B, Glenn ST, Kuvshinoff B, Kurzrock R, Morrison C. Immune profiling and immunotherapeutic targets in pancreatic cancer. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:119. [PMID: 33569421 PMCID: PMC7867882 DOI: 10.21037/atm-20-1076] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Immunotherapeutic approaches for pancreatic ductal adenocarcinoma (PDAC) are less successful as compared to many other tumor types. In this study, comprehensive immune profiling was performed in order to identify novel, potentially actionable targets for immunotherapy. Methods Formalin-fixed paraffin embedded (FFPE) specimens from 68 patients were evaluated for expression of 395 immune-related markers (RNA-seq), mutational burden by complete exon sequencing of 409 genes, PD-L1 expression by immunohistochemistry (IHC), pattern of tumor infiltrating lymphocytes (TILs) infiltration by CD8 IHC, and PD-L1/L2 copy number by fluorescent in situ hybridization (FISH). Results The seven classes of actionable genes capturing myeloid immunosuppression, metabolic immunosuppression, alternative checkpoint blockade, CTLA-4 immune checkpoint, immune infiltrate, and programmed cell death 1 (PD-1) axis immune checkpoint, discerned 5 unique clinically relevant immunosuppression expression profiles (from most to least common): (I) combined myeloid and metabolic immunosuppression [affecting 25 of 68 patients (36.8%)], (II) multiple immunosuppressive mechanisms (29.4%), (III) PD-L1 positive (20.6%), (IV) highly inflamed PD-L1 negative (10.3%); and (V) immune desert (2.9%). The Wilcoxon rank-sum test was used to compare the PDAC cohort with a comparison cohort (n=1,416 patients) for the mean expressions of the 409 genes evaluated. Multiple genes including TIM3, VISTA, CCL2, CCR2, TGFB1, CD73, and CD39 had significantly higher mean expression versus the comparison cohort, while three genes (LAG3, GITR, CD38) had significantly lower mean expression. Conclusions This study demonstrates that a clinically relevant unique profile of immune markers can be identified in PDAC and be used as a roadmap for personalized immunotherapeutic decision-making strategies.
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Affiliation(s)
| | - Shumei Kato
- Center for Personalized Cancer Therapy, Moores Cancer Center, La Jolla, CA, USA
| | | | | | | | - Jeffrey M Conroy
- OmniSeq, Inc., Buffalo, NY, USA.,Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | | | - Sean T Glenn
- OmniSeq, Inc., Buffalo, NY, USA.,Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Boris Kuvshinoff
- Department of Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, Moores Cancer Center, La Jolla, CA, USA
| | - Carl Morrison
- OmniSeq, Inc., Buffalo, NY, USA.,Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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34
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Buechler SA, Stephens MT, Hummon AB, Ludwig K, Cannon E, Carter TC, Resnick J, Gökmen-Polar Y, Badve SS. ColoType: a forty gene signature for consensus molecular subtyping of colorectal cancer tumors using whole-genome assay or targeted RNA-sequencing. Sci Rep 2020; 10:12123. [PMID: 32694712 PMCID: PMC7374173 DOI: 10.1038/s41598-020-69083-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/03/2020] [Indexed: 01/02/2023] Open
Abstract
Colorectal cancer (CRC) tumors can be partitioned into four biologically distinct consensus molecular subtypes (CMS1-4) using gene expression. Evidence is accumulating that tumors in different subtypes are likely to respond differently to treatments. However, to date, there is no clinical diagnostic test for CMS subtyping. In this study, we used novel methodology in a multi-cohort training domain (n = 1,214) to develop the ColoType scores and classifier to predict CMS1-4 based on expression of 40 genes. In three validation cohorts (n = 1,744, in total) representing three distinct gene-expression measurement technologies, ColoType predicted gold-standard CMS subtypes with accuracies 0.90, 0.91, 0.88, respectively. To accommodate for potential intratumoral heterogeneity and tumors of mixed subtypes, ColoType was designed to report continuous scores measuring the prevalence of each of CMS1-4 in a tumor, in addition to specifying the most prevalent subtype. For analysis of clinical specimens, ColoType was also implemented with targeted RNA-sequencing (Illumina AmpliSeq). In a series of formalin-fixed, paraffin-embedded CRC samples (n = 49), ColoType by targeted RNA-sequencing agreed with subtypes predicted by two independent methods with accuracies 0.92, 0.82, respectively. With further validation, ColoType by targeted RNA-sequencing, may enable clinical application of CMS subtyping with widely-available and cost-effective technology.
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Affiliation(s)
- Steven A Buechler
- Department of Applied and Computational Mathematics and Statistics, Harper Cancer Research Institute, University of Notre Dame, 102B Crowley Hall, Notre Dame, IN, 46556, USA.
| | - Melissa T Stephens
- Genomics and Bioinformatics Core Facility, University of Notre Dame, Notre Dame, IN, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Katelyn Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Emily Cannon
- Department of Applied and Computational Mathematics and Statistics, Harper Cancer Research Institute, University of Notre Dame, 102B Crowley Hall, Notre Dame, IN, 46556, USA
| | - Tonia C Carter
- Center for Precision Medicine Research, Marshfield Clinic, Marshfield, WI, USA
| | - Jeffrey Resnick
- Department of Pathology, Marshfield Clinic, Marshfield, WI, USA
| | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
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35
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Immunogenomic Analysis of Exceptional Responder to ALT-803 (IL-15 Analogue) in BCG Unresponsive Nonmuscle Invasive Bladder Cancer: A Case Series and Review of the Literature. J Immunother 2020; 42:354-358. [PMID: 31107371 DOI: 10.1097/cji.0000000000000269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The clinical validity and utility of complex biomarkers have not been extensively studied in bladder cancer. Three patients with nonmuscle invasive bladder cancer [1 patient with an exceptional response; complete response (CR) for 30 months] who failed intravesical BCG were evaluated using an NYS CLEP approved assay, Immune Report Card, which measures programmed death-ligand 1 expression, CD8 T-cell infiltration pattern, mutational burden, and gene expression of 51 immune-related transcripts using RNA-Seq. Patients were tested before being treated under our expanded access protocol for intravesical BCG with ALT-803. Subject 1 had failed his fourth line of therapy, subject 2 had failed only his first line of therapy, and subject 3 had failed his seventh line of therapy. Surprisingly, subject 1 had an unusually prolonged CR which lasted 30 months; subject 2 had the persistent and recurrent disease until 12 months when he then developed a CR; subject 3 had disease recurrence at 3 months, along with progression noted at 6 months. Immunomutational status was extensively evaluated to identify potential alterations that might play a role as predictive markers for subject 1, who had an exceptional response. Compared with subject 3, tumor in subject 1 demonstrated a high level of expression for CTLA4 (immunosuppression) and CD39 (immunosuppressive). Together, an immunosuppressive tumor environment in nonmuscle invasive bladder cancer that have failed prior BCG may respond better to interleukin-15 immunotherapy compared with tumors without an immunosuppressive environment.
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36
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Zhang T, Pabla S, Lenzo FL, Conroy JM, Nesline MK, Glenn ST, Papanicolau-Sengos A, Burgher B, Giamo V, Andreas J, Wang Y, Bshara W, Madden KG, Shirai K, Dragnev K, Tafe LJ, Gupta R, Zhu J, Labriola M, McCall S, George DJ, Ghatalia P, Dayyani F, Edwards R, Park MS, Singh R, Jacob R, George S, Xu B, Zibelman M, Kurzrock R, Morrison C. Proliferative potential and response to nivolumab in clear cell renal cell carcinoma patients. Oncoimmunology 2020; 9:1773200. [PMID: 32923131 PMCID: PMC7458647 DOI: 10.1080/2162402x.2020.1773200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background Biomarkers predicting immunotherapy response in metastatic renal cell cancer (mRCC) are lacking. PD-L1 immunohistochemistry is a complementary diagnostic for immune checkpoint inhibitors (ICIs) in mRCC, but has shown minimal clinical utility and is not used in routine clinical practice. Methods Tumor specimens from 56 patients with mRCC who received nivolumab were evaluated for PD-L1, cell proliferation (targeted RNA-seq), and outcome. Results For 56 patients treated with nivolumab as a standard of care, there were 2 complete responses and 8 partial responses for a response rate of 17.9%. Dividing cell proliferation into tertiles, derived from the mean expression of 10 proliferation-associated genes in a reference set of tumors, poorly proliferative tumors (62.5%) were more common than moderately (30.4%) or highly proliferative (8.9%) counterparts. Moderately proliferative tumors were enriched for PD-L1 positive (41.2%), compared to poorly proliferative counterparts (11.4%). Objective response for moderately proliferative (29.4%) tumors was higher than that of poorly (11.4%) proliferative counterparts, but not statistically significant (p = .11). When cell proliferation and negative PD-L1 tumor proportion scores were combined statistically significant results were achieved (p = .048), showing that patients with poorly proliferative and PD-L1 negative tumors have a very low response rate (6.5%) compared to moderately proliferative PD-L1 negative tumors (30%). Conclusions Cell proliferation has value in predicting response to nivolumab in clear cell mRCC patients, especially when combined with PD-L1 expression. Further studies which include the addition of progression-free survival (PFS) along with sufficiently powered subgroups are required to further support these findings.
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Affiliation(s)
- Tian Zhang
- Department of Medicine, Duke University, Durham, NC, USA
| | | | | | - Jeffrey M Conroy
- R&D, OmniSeq, Inc, Buffalo, NY, USA.,Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | | | - Sean T Glenn
- R&D, OmniSeq, Inc, Buffalo, NY, USA.,Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | | | | | | | | | | | | | - Katherine G Madden
- Department of Hematology/Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Keisuke Shirai
- Department of Hematology/Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Konstantin Dragnev
- Department of Hematology/Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Laura J Tafe
- Department of Hematology/Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Rajan Gupta
- Department of Medicine, Duke University, Durham, NC, USA
| | - Jason Zhu
- Department of Medicine, Duke University, Durham, NC, USA
| | | | - Shannon McCall
- Department of Medicine, Duke University, Durham, NC, USA
| | | | - Pooja Ghatalia
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - Farshid Dayyani
- Department of Medicine, University of California, Irvine, CA, USA
| | - Robert Edwards
- Department of Medicine, University of California, Irvine, CA, USA
| | - Michelle S Park
- Department of Medicine, University of California, Irvine, CA, USA
| | - Rajbir Singh
- Department of Medicine, Meharry Medical College, Nashville, TN, US
| | - Robin Jacob
- Department of Medicine, Meharry Medical College, Nashville, TN, US
| | - Saby George
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Bo Xu
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Matthew Zibelman
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, Moores Cancer Center, La Jolla, CA, USA
| | - Carl Morrison
- R&D, OmniSeq, Inc, Buffalo, NY, USA.,Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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Talla SB, Rempel E, Endris V, Jenzer M, Allgäuer M, Schwab C, Kazdal D, Stögbauer F, Volckmar AL, Kocsmar I, Neumann O, Schirmacher P, Zschäbitz S, Duensing S, Budczies J, Stenzinger A, Kirchner M. Immuno-oncology gene expression profiling of formalin-fixed and paraffin-embedded clear cell renal cell carcinoma: Performance comparison of the NanoString nCounter technology with targeted RNA sequencing. Genes Chromosomes Cancer 2020; 59:406-416. [PMID: 32212351 DOI: 10.1002/gcc.22843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 01/05/2023] Open
Abstract
Inflammatory gene signatures are currently being explored as predictive biomarkers for immune checkpoint blockade, and particularly for the treatment of renal cell cancers. From a diagnostic point of view, the nCounter analysis platform and targeted RNA sequencing are emerging alternatives to microarrays and comprehensive transcriptome sequencing in assessing formalin-fixed and paraffin-embedded (FFPE) cancer samples. So far, no systematic study has analyzed and compared the technical performance metrics of these two approaches. Filling this gap, we performed a head-to-head comparison of two commercially available immune gene expression assays, using clear cell renal cell cancer FFPE specimens. We compared the nCounter system that utilizes a direct hybridization technology without amplification with an NGS assay that is based on targeted RNA-sequencing with preamplification. We found that both platforms displayed high technical reproducibility and accuracy (Pearson coefficient: ≥0.96, concordance correlation coefficient [CCC]: ≥0.93). A density plot for normalized expression of shared genes on both platforms showed a comparable bi-modal distribution and dynamic range. RNA-Seq demonstrated relatively larger signaling intensity whereas the nCounter system displayed higher inter-sample variability. Estimated fold changes for all shared genes showed high correlation (Spearman coefficient: 0.73). This agreement is even better when only significantly differentially expressed genes were compared. Composite gene expression profiles, such as an interferon gamma (IFNg) signature, can be reliably inferred by both assays. In summary, our study demonstrates that focused transcript read-outs can reliably be achieved by both technologies and that both approaches achieve comparable results despite their intrinsic technical differences.
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Affiliation(s)
- Suranand B Talla
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Eugen Rempel
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg Partner Site, Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Maximilian Jenzer
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Michael Allgäuer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Constantin Schwab
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Fabian Stögbauer
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ildiko Kocsmar
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg Partner Site, Heidelberg, Germany
| | - Stefanie Zschäbitz
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg Partner Site, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg Partner Site, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg Partner Site, Heidelberg, Germany
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Shimazawa R, Ikeda M. Regulatory perspectives on next-generation sequencing and complementary diagnostics in Japan. Expert Rev Mol Diagn 2020; 20:601-610. [DOI: 10.1080/14737159.2020.1728256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rumiko Shimazawa
- Department of Clinical Pharmacology, Tokai University School of Medicine, Isehara, Japan
| | - Masayuki Ikeda
- Department of Medical Informatics, Kagawa University Hospital, Takamatsu, Japan
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39
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Kato S, Okamura R, Kumaki Y, Ikeda S, Nikanjam M, Eskander R, Goodman A, Lee S, Glenn ST, Dressman D, Papanicolau-Sengos A, Lenzo FL, Morrison C, Kurzrock R. Expression of TIM3/VISTA checkpoints and the CD68 macrophage-associated marker correlates with anti-PD1/PDL1 resistance: implications of immunogram heterogeneity. Oncoimmunology 2020; 9:1708065. [PMID: 32117584 PMCID: PMC7028323 DOI: 10.1080/2162402x.2019.1708065] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/11/2019] [Accepted: 11/01/2019] [Indexed: 01/26/2023] Open
Abstract
Although immunotherapies have achieved remarkable salutary effects among subgroups of advanced cancers, most patients do not respond. We comprehensively evaluated biomarkers associated with the "cancer-immunity cycle" in the pan-cancer setting in order to understand the immune landscape of metastatic malignancies as well as anti-PD-1/PD-L1 inhibitor resistance mechanisms. Interrogation of 51 markers of the cancer-immunity cycle was performed in 101 patients with diverse malignancies using a clinical-grade RNA sequencing assay. Overall, the immune phenotypes demonstrated overexpression of multiple checkpoints including VISTA (15.8% of 101 patients), PD-L2 (10.9%), TIM3 (9.9%), LAG3 (8.9%), PD-L1 (6.9%) and CTLA4 (3.0%). Additionally, aberrant expression of macrophage-associated markers (e.g. CD68 and CSF1R; 11-23%), metabolic immune escape markers (e.g. ADORA2A and IDO1; 9-16%) and T-cell priming markers (e.g. CD40, GITR, ICOS and OX40; 4-31%) were observed. Most tumors (87.1%, 88/101) expressed distinct immune portfolios, with a median of six theoretically actionable biomarkers (pharmacologically tractable by Food and Drug Administration approved agents [on- or off-label] or with agents in clinical development). Overexpression of TIM-3, VISTA and CD68 were significantly associated with shorter progression-free survival (PFS) after anti-PD-1/PD-L1-based therapies (among 39 treated patients) (all P < .01). In conclusion, cancer-immunity cycle biomarker evaluation was feasible in diverse solid tumors. High expression of alternative checkpoints TIM-3 and VISTA and of the macrophage-associated markers CD68 were associated with significantly worse PFS after anti-PD-1/PD-L1-based therapies. Most patients had distinct and complex immune expression profiles suggesting the need for customized combinations of immunotherapy.
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Affiliation(s)
- Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Yuichi Kumaki
- Cancer Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sadakatsu Ikeda
- Cancer Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Mina Nikanjam
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Ramez Eskander
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Aaron Goodman
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Suzanna Lee
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Sean T. Glenn
- OmniSeq Inc., Buffalo, NY, USA
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | | | | | - Carl Morrison
- OmniSeq Inc., Buffalo, NY, USA
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
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40
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Analytical Performance of an Immunoprofiling Assay Based on RNA Models. J Mol Diagn 2020; 22:555-570. [PMID: 32036085 DOI: 10.1016/j.jmoldx.2020.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/03/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
As immuno-oncology drugs grow more popular in the treatment of cancer, better methods are needed to quantify the tumor immune cell component to determine which patients are most likely to benefit from treatment. Methods such as flow cytometry can accurately assess the composition of infiltrating immune cells; however, they show limited use in formalin-fixed, paraffin-embedded (FFPE) specimens. This article describes a novel hybrid-capture RNA sequencing assay, ImmunoPrism, that estimates the relative percentage abundance of eight immune cell types in FFPE solid tumors. Immune health expression models were generated using machine learning methods and used to uniquely identify each immune cell type using the most discriminatively expressed genes. The analytical performance of the assay was assessed using 101 libraries from 40 FFPE and 32 fresh-frozen samples. With defined samples, ImmunoPrism had a precision of ±2.72%, a total error of 2.75%, and a strong correlation (r2 = 0.81; P < 0.001) to flow cytometry. ImmunoPrism had similar performance in dissociated tumor cell samples (total error of 8.12%) and correlated strongly with immunohistochemistry (CD8: r2 = 0.83; P < 0.001) in FFPE samples. Other performance metrics were determined, including limit of detection, reportable range, and reproducibility. The approach used for analytical validation is shared here so that it may serve as a helpful framework for other laboratories when validating future complex RNA-based assays.
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41
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Jiang J, Wu L, Yuan F, Ji J, Lin X, Yang W, Wu J, Shi M, Yang H, Ma Y, Song X, Zhu Z, Zhang H, Zhang J. Characterization of the immune microenvironment in brain metastases from different solid tumors. Cancer Med 2020; 9:2299-2308. [PMID: 32017467 PMCID: PMC7131856 DOI: 10.1002/cam4.2905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/19/2020] [Accepted: 01/21/2020] [Indexed: 12/26/2022] Open
Abstract
Background Brain metastases are one of the most common intracranial neoplasms. Increasing evidence have indicated that systemic immunotherapy may provide long‐term benefits for brain metastases. Herein, we presented the results of an immune oncology panel RNA sequencing platform for patients with brain metastases from different primary sites. Methods We investigated 25 samples of human brain metastases from lung cancer (n = 12), breast cancer (n = 6), and colorectal cancer (n = 7). Besides, 13 paired samples of adjacent noncancerous brain tissue (10 from patients with lung cancer and 3 from patients with breast cancer) were collected as controls. By comparing the brain metastases and paired samples of adjacent noncancerous brain tissue from 13 patients, we detected three upregulated and six downregulated genes, representing the malignant properties of cancer cells and increased immune infiltration in the microenvironment. Next, we profiled the immune‐related genes in brain metastases from three primary cancer types. Results A group of genes were significantly overexpressed in the microenvironment of brain metastases from lung cancer, covering the checkpoint pathways, lymphocyte infiltration, and TCR‐coexpression. Especially, immune checkpoint molecules, PD‐L1, PD‐L2, and IDO1 were expressed at higher levels in brain metastases from lung cancer than those from the other two cancer types. Conclusions This study presents an immune landscape of brain metastases from different cancer types. With high RNA expression levels of PD‐1/PD‐L1 axis and immune infiltration in brain metastases, it would be worthwhile to explore the efficacy of immune checkpoint blockade for lung cancer patients with intracranial metastases.
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Affiliation(s)
- Jinling Jiang
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lihong Wu
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Fei Yuan
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jun Ji
- Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaojing Lin
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Wanning Yang
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Junwei Wu
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Min Shi
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hui Yang
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yanna Ma
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Xue Song
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Zhenggang Zhu
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Henghui Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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42
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Cui Y, Yu S, Zhu M, Cheng X, Yu Y, Tang Z, Wang X, Hou J, Hou Y, Ren D, Mao B, Khalid R, Liu T. Identifying Predictive Factors of Recurrence after Radical Resection in Gastric Cancer by RNA Immune-oncology Panel. J Cancer 2020; 11:638-647. [PMID: 31942187 PMCID: PMC6959033 DOI: 10.7150/jca.38536] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/30/2019] [Indexed: 01/28/2023] Open
Abstract
Aiming to identify novel immunotargets for gastric cancer (GC), we retrospectively analyzed the formalin-fixed paraffin embedded (FFPE) samples of gastric cancer tissues from postoperative patients who relapsed or metastasized within (early recurrence, n=25) or after two years (late recurrence, n=23). RNA immune-oncology panel (RIOP) including 398 immune-related genes was used to detect the RNA expression level. Disease free survival (DFS) time in early and late recurrent group was 7.52±0.72 and 28.49±0.81 months, respectively. 18 genes were significantly different between the early and late recurrent groups, and the expression of ITK, EBI3, CX3CL1, MYC, EOMES, CA4, TAGAP, MMP2, HAVCR2, FCGR1 and SNAI2 were verified to be associated with the DFS time. We also found that 18 genes were differentially expressed in diffusal type and non-diffusal type of GC. Leukocyte-inhibition, Leukocyte-migration, and Lymphocyte-infiltrate signal/functional pathways were activated in diffusal type of GC by cluster analysis. Our data uncovered the gene set consisted of ITK, EBI3, and CX3CL1 as a potential tool for prediction of early recurrence or poor prognosis in GC, which could be used as novel immunotargets and prognostic markers for the management of GC.
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Affiliation(s)
- Yuehong Cui
- Department of medical oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shan Yu
- Department of medical oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengxuan Zhu
- Department of medical oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xi Cheng
- Department of medical oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiyi Yu
- Department of medical oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhaoqing Tang
- Department of general surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xuefei Wang
- Department of general surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jun Hou
- Department of pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yingyong Hou
- Department of pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dandan Ren
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Beibei Mao
- Genecast Precision Medicine Technology Institute, Beijing, China
| | - Rashid Khalid
- Department of medical oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tianshu Liu
- Department of medical oncology, Zhongshan Hospital, Fudan University, Shanghai, China
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43
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Chen Y, Chen H, Mao B, Zhou Y, Shi X, Tang L, Jiang H, Wang G, Zhuang W. Transcriptional Characterization Of The Tumor Immune Microenvironment And Its Prognostic Value For Locally Advanced Lung Adenocarcinoma In A Chinese Population. Cancer Manag Res 2019; 11:9165-9173. [PMID: 31802941 PMCID: PMC6827523 DOI: 10.2147/cmar.s209571] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 10/12/2019] [Indexed: 12/25/2022] Open
Abstract
Objective We investigated the relationship of the transcriptional tumor immune microenvironment with prognosis of patients with locally advanced lung adenocarcinoma (LUAD). Materials and methods A targeted RNA-Seq approach was used to measure the abundance of 395 immune-related transcripts of 24 formalin-fixed paraffin embedded (FFPE) tumor specimens from our institution and transcription data of 85 matched LUAD samples from The Cancer Genome Atlas (TCGA). Gene set variation analysis (GSVA) was used to identify gene sets related to prognosis, and the microenvironment cell-population (MCP)-counter method was used to quantify infiltrated immune cells. Survival analysis with the log rank test was used to determine the relationships of different immune-related transcripts with prognosis. Cox proportional hazards models were also used to identify risk factors associated with poor prognosis. Results Among our patients, GSVA and the log rank test demonstrated that enrichment of the antigen processing pathway (P = 0.01) correlated with a favorable prognosis. MCP-counter and survival analysis demonstrated that greater CD8 T cell infiltration correlated with a favorable prognosis (P = 0.05), but greater infiltration of neutrophils (P = 0.014) and NK cells (P = 0.015) correlated with poor prognoses. Cox hazard analysis showed that greater infiltration of neutrophils was an independent risk factor for poor prognosis. These results were consistent with LUAD data from TCGA. Conclusion When integrated with computational bioinformatics methods, targeted RNA-Seq from FFPE specimens provides profiles of the tumor immune microenvironment that have prognostic value for patients with locally advanced LUAD.
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Affiliation(s)
- Yuqiao Chen
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Huan Chen
- Beijing Genecast Biotechnology Co., Beijing 100000, People's Republic of China
| | - Beibei Mao
- Beijing Genecast Biotechnology Co., Beijing 100000, People's Republic of China
| | - Yuan Zhou
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Xinying Shi
- Beijing Genecast Biotechnology Co., Beijing 100000, People's Republic of China
| | - Lu Tang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Guo Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Wei Zhuang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
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44
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Yendamuri S, Barbi J, Pabla S, Petrucci C, Punnanitinont A, Nesline M, Glenn ST, Depietro P, Papanicalou-Sengos A, Morrison C, Dy GK, Elkin PL. Body Mass Index Influences the Salutary Effects of Metformin on Survival After Lobectomy for Stage I NSCLC. J Thorac Oncol 2019; 14:2181-2187. [PMID: 31398539 DOI: 10.1016/j.jtho.2019.07.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Metformin, a common medication used in the treatment of diabetes mellitus is known to have anticancer effects. We hypothesized that the salutary effect of metformin on the survival of patients with stage I NSCLC is influenced by body mass index (BMI). METHODS Patients undergoing lobectomy for stage I NSCLC without neoadjuvant therapy were included. Univariate and multivariate survival analyses to examine the association between metformin use and overall survival (OS), disease-specific survival (DSS), and recurrence-free survival were performed, stratified by BMI (>25 kg/m2 and ≤25 kg/m2). Expression of immune checkpoints in patients on metformin and not was performed in a separate cohort of 205 patients with advanced disease. RESULTS Four hundred thirty-four stage I patients (including 74 metformin users) were deemed eligible for analysis. Univariate and multivariate analysis revealed an association between metformin use and OS (hazard ratio [HR] = 0.52; p = 0.04) as well as DSS (HR = 0.21; p = 0.04) but not recurrence-free survival (HR = 0.67; p = 0.33) in high-BMI patients only. In a separate cohort of 205 patients with tumors of all stages (including 35 metformin users), downregulation of immune checkpoint gene expression (programmed cell death 1, cytotoxic T-lymphocyte associated protein 4, B and T lymphocyte associated, CD27 molecule, lymphocyte activating 3, and inducible T cell costimulator) in metformin users was seen only in high-BMI patients, with upregulation of these genes seen in low-BMI patients with metformin use. CONCLUSIONS Metformin use may be associated with better OS and DSS only in high-BMI patients. This hypothesis is supported by gene expression data of immune checkpoint genes in metformin users using a separate cohort of advanced-stage tumors. Further studies examining the interaction of BMI with metformin in NSCLC are worthwhile.
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Affiliation(s)
- Sai Yendamuri
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
| | - Joseph Barbi
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | - Cara Petrucci
- Department of Health Behavior, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | | | - Sean T Glenn
- Omniseq Inc., Buffalo, New York; Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | | | - Carl Morrison
- Omniseq Inc., Buffalo, New York; Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Grace K Dy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Peter L Elkin
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York; Department of Veterans Affairs, Buffalo, New York
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Haynes BC, Blidner RA, Cardwell RD, Zeigler R, Gokul S, Thibert JR, Chen L, Fujimoto J, Papadimitrakopoulou VA, Wistuba II, Latham GJ. An Integrated Next-Generation Sequencing System for Analyzing DNA Mutations, Gene Fusions, and RNA Expression in Lung Cancer. Transl Oncol 2019; 12:836-845. [PMID: 30981944 PMCID: PMC6463765 DOI: 10.1016/j.tranon.2019.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
We developed and characterized a next-generation sequencing (NGS) technology for streamlined analysis of DNA and RNA using low-input, low-quality cancer specimens. A single-workflow, targeted NGS panel for non-small cell lung cancer (NSCLC) was designed covering 135 RNA and 55 DNA disease-relevant targets. This multiomic panel was used to assess 219 formalin-fixed paraffin-embedded NSCLC surgical resections and core needle biopsies. Mutations and expression phenotypes were identified consistent with previous large-scale genomic studies, including mutually exclusive DNA and RNA oncogenic driver events. Evaluation of a second cohort of low cell count fine-needle aspirate smears from the BATTLE-2 trial yielded 97% agreement with an independent, validated NGS panel that was used with matched surgical specimens. Collectively, our data indicate that broad, clinically actionable insights that previously required independent assays, workflows, and analyses to assess both DNA and RNA can be conjoined in a first-tier, highly multiplexed NGS test, thereby providing faster, simpler, and more economical results.
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Affiliation(s)
| | | | | | | | | | | | | | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vassiliki A Papadimitrakopoulou
- Department of Thoracic/Head and Neck Medical Oncology, Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Jones W, Greytak S, Odeh H, Guan P, Powers J, Bavarva J, Moore HM. Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles. Sci Rep 2019; 9:6980. [PMID: 31061401 PMCID: PMC6502812 DOI: 10.1038/s41598-019-43282-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/08/2019] [Indexed: 11/09/2022] Open
Abstract
The National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine the effects of formalin fixation and delay to fixation (DTF) on the analysis of nucleic acids. By performing whole transcriptome sequencing and small RNA profiling on matched snap-frozen and FFPE specimens exposed to different delays to fixation, this study aimed to determine acceptable delays to fixation and proper workflow for accurate and reliable Next-Generation Sequencing (NGS) analysis of FFPE specimens. In comparison to snap-freezing, formalin fixation changed the relative proportions of intronic/exonic/untranslated RNA captured by RNA-seq for most genes. The effects of DTF on NGS analysis were negligible. In 80% of specimens, a subset of RNAs was found to differ between snap-frozen and FFPE specimens in a consistent manner across tissue groups; this subset was unaffected in the remaining 20% of specimens. In contrast, miRNA expression was generally stable across various formalin fixation protocols, but displayed increased variability following a 12 h delay to fixation.
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Affiliation(s)
| | | | - Hana Odeh
- National Cancer Institute, Bethesda, MD, USA
| | - Ping Guan
- National Cancer Institute, Bethesda, MD, USA
| | - Jason Powers
- Q2 Solutions - EA Genomics, Morrisville, NC, USA
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Papanicolau-Sengos A, Yang Y, Pabla S, Lenzo FL, Kato S, Kurzrock R, DePietro P, Nesline M, Conroy J, Glenn S, Chatta G, Morrison C. Identification of targets for prostate cancer immunotherapy. Prostate 2019; 79:498-505. [PMID: 30614027 DOI: 10.1002/pros.23756] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND We performed profiling of the immune microenvironment of castration-resistant (CRPC) and castration-sensitive (CSPC) prostate cancer (PC) in order to identify novel targets for immunotherapy. METHODS PD-L1 and CD3/CD8 immunohistochemistry, PD-L1/2 fluorescent in situ hybridization, tumor mutation burden, microsatellite instability, and RNA-seq of 395 immune-related genes were performed in 19 CRPC and CSPC. Targeted genomic sequencing and fusion analysis were performed in 17 of these specimens. RESULTS CD276, PVR, and NECTIN2 were highly expressed in PC. Comparison of CRPC versus CSPC and primary versus metastatic tissue revealed the differential expression of immunostimulatory, immunosuppressive, and epithelial-to-mesenchymal transition (EMT)-related genes. Unsupervised clustering of differentially expressed genes yielded two final clusters best segregated by CRPC and CSPC status. CONCLUSION CD276 and the alternative checkpoint inhibition PVR/NECTIN2/CD226/TIGIT pathway emerged as relevant to PC checkpoint inhibition target development.
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Affiliation(s)
| | - Yuanquan Yang
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | | | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California
| | | | | | - Jeffrey Conroy
- OmniSeq, Inc., Buffalo, New York
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Sean Glenn
- OmniSeq, Inc., Buffalo, New York
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | - Carl Morrison
- OmniSeq, Inc., Buffalo, New York
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
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48
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Pabla S, Conroy JM, Nesline MK, Glenn ST, Papanicolau-Sengos A, Burgher B, Hagen J, Giamo V, Andreas J, Lenzo FL, Yirong W, Dy GK, Yau E, Early A, Chen H, Bshara W, Madden KG, Shirai K, Dragnev K, Tafe LJ, Marin D, Zhu J, Clarke J, Labriola M, McCall S, Zhang T, Zibelman M, Ghatalia P, Araujo-Fernandez I, Singavi A, George B, MacKinnon AC, Thompson J, Singh R, Jacob R, Dressler L, Steciuk M, Binns O, Kasuganti D, Shah N, Ernstoff M, Odunsi K, Kurzrock R, Gardner M, Galluzzi L, Morrison C. Proliferative potential and resistance to immune checkpoint blockade in lung cancer patients. J Immunother Cancer 2019; 7:27. [PMID: 30709424 PMCID: PMC6359802 DOI: 10.1186/s40425-019-0506-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/13/2019] [Indexed: 02/04/2023] Open
Abstract
Background Resistance to immune checkpoint inhibitors (ICIs) has been linked to local immunosuppression independent of major ICI targets (e.g., PD-1). Clinical experience with response prediction based on PD-L1 expression suggests that other factors influence sensitivity to ICIs in non-small cell lung cancer (NSCLC) patients. Methods Tumor specimens from 120 NSCLC patients from 10 institutions were evaluated for PD-L1 expression by immunohistochemistry, and global proliferative profile by targeted RNA-seq. Results Cell proliferation, derived from the mean expression of 10 proliferation-associated genes (namely BUB1, CCNB2, CDK1, CDKN3, FOXM1, KIAA0101, MAD2L1, MELK, MKI67, and TOP2A), was identified as a marker of response to ICIs in NSCLC. Poorly, moderately, and highly proliferative tumors were somewhat equally represented in NSCLC, with tumors with the highest PD-L1 expression being more frequently moderately proliferative as compared to lesser levels of PD-L1 expression. Proliferation status had an impact on survival in patients with both PD-L1 positive and negative tumors. There was a significant survival advantage for moderately proliferative tumors compared to their combined highly/poorly counterparts (p = 0.021). Moderately proliferative PD-L1 positive tumors had a median survival of 14.6 months that was almost twice that of PD-L1 negative highly/poorly proliferative at 7.6 months (p = 0.028). Median survival in moderately proliferative PD-L1 negative tumors at 12.6 months was comparable to that of highly/poorly proliferative PD-L1 positive tumors at 11.5 months, but in both instances less than that of moderately proliferative PD-L1 positive tumors. Similar to survival, proliferation status has impact on disease control (DC) in patients with both PD-L1 positive and negative tumors. Patients with moderately versus those with poorly or highly proliferative tumors have a superior DC rate when combined with any classification schema used to score PD-L1 as a positive result (i.e., TPS ≥ 50% or ≥ 1%), and best displayed by a DC rate for moderately proliferative tumors of no less than 40% for any classification of PD-L1 as a negative result. While there is an over representation of moderately proliferative tumors as PD-L1 expression increases this does not account for the improved survival or higher disease control rates seen in PD-L1 negative tumors. Conclusions Cell proliferation is potentially a new biomarker of response to ICIs in NSCLC and is applicable to PD-L1 negative tumors. Electronic supplementary material The online version of this article (10.1186/s40425-019-0506-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarabjot Pabla
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Jeffrey M Conroy
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA.,Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | - Mary K Nesline
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Sean T Glenn
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA.,Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | | | - Blake Burgher
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Jacob Hagen
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Vincent Giamo
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | | | | | - Wang Yirong
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Grace K Dy
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | - Edwin Yau
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | - Amy Early
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | - Hongbin Chen
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | - Wiam Bshara
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | | | - Keisuke Shirai
- Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | | | - Laura J Tafe
- Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | | | - Jason Zhu
- Duke University, Durham, NC, 27708, USA
| | | | | | | | | | | | | | | | - Arun Singavi
- Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Ben George
- Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | | | | | - Rajbir Singh
- Meharry Medical College, Nashville, TN, 37208, USA
| | - Robin Jacob
- Meharry Medical College, Nashville, TN, 37208, USA
| | | | - Mark Steciuk
- Mission Health System, Asheville, NC, 28801, USA
| | - Oliver Binns
- Mission Health System, Asheville, NC, 28801, USA
| | | | - Neel Shah
- Community Hospital, Munster, IN, 46321, USA
| | - Marc Ernstoff
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | - Kunle Odunsi
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Mark Gardner
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, 10065, USA.,Sandra and Edward Meyer Cancer Center, New York, NY, 10065, USA.,Université Paris Descartes/Paris V, 75006, Paris, France
| | - Carl Morrison
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA. .,Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14206, USA.
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49
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Conroy JM, Pabla S, Nesline MK, Glenn ST, Papanicolau-Sengos A, Burgher B, Andreas J, Giamo V, Wang Y, Lenzo FL, Bshara W, Khalil M, Dy GK, Madden KG, Shirai K, Dragnev K, Tafe LJ, Zhu J, Labriola M, Marin D, McCall SJ, Clarke J, George DJ, Zhang T, Zibelman M, Ghatalia P, Araujo-Fernandez I, de la Cruz-Merino L, Singavi A, George B, MacKinnon AC, Thompson J, Singh R, Jacob R, Kasuganti D, Shah N, Day R, Galluzzi L, Gardner M, Morrison C. Next generation sequencing of PD-L1 for predicting response to immune checkpoint inhibitors. J Immunother Cancer 2019; 7:18. [PMID: 30678715 PMCID: PMC6346512 DOI: 10.1186/s40425-018-0489-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/19/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND PD-L1 immunohistochemistry (IHC) has been traditionally used for predicting clinical responses to immune checkpoint inhibitors (ICIs). However, there are at least 4 different assays and antibodies used for PD-L1 IHC, each developed with a different ICI. We set to test if next generation RNA sequencing (RNA-seq) is a robust method to determine PD-L1 mRNA expression levels and furthermore, efficacy of predicting response to ICIs as compared to routinely used, standardized IHC procedures. METHODS A total of 209 cancer patients treated on-label by FDA-approved ICIs, with evaluable responses were assessed for PD-L1 expression by RNA-seq and IHC, based on tumor proportion score (TPS) and immune cell staining (ICS). A subset of serially diluted cases was evaluated for RNA-seq assay performance across a broad range of PD-L1 expression levels. RESULTS Assessment of PD-L1 mRNA levels by RNA-seq demonstrated robust linearity across high and low expression ranges. PD-L1 mRNA levels assessed by RNA-seq and IHC (TPS and ICS) were highly correlated (p < 2e-16). Sub-analyses showed sustained correlation when IHC results were classified as high or low by clinically accepted cut-offs (p < 0.01), and results did not differ by tumor type or anti-PD-L1 antibody used. Overall, a combined positive PD-L1 result (≥1% IHC TPS and high PD-L1 expression by RNA-Seq) was associated with a 2-to-5-fold higher overall response rate (ORR) compared to a double negative result. Standard assessments of sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) showed that a PD-L1 positive assessment for melanoma samples by RNA-seq had the lowest sensitivity (25%) but the highest PPV (72.7%). Among the three tumor types analyzed in this study, the only non-overlapping confidence interval for predicting response was for "RNA-seq low vs high" in melanoma. CONCLUSIONS Measurement of PD-L1 mRNA expression by RNA-seq is comparable to PD-L1 expression by IHC both analytically and clinically in predicting ICI response. RNA-seq has the added advantages of being amenable to standardization and avoidance of interpretation bias. PD-L1 by RNA-seq needs to be validated in future prospective ICI clinical studies across multiple histologies.
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Affiliation(s)
- Jeffrey M Conroy
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Sarabjot Pabla
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Mary K Nesline
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Sean T Glenn
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | | | - Blake Burgher
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | | | - Vincent Giamo
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Yirong Wang
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | | | - Wiam Bshara
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Maya Khalil
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Grace K Dy
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | | | - Keisuke Shirai
- Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | | | - Laura J Tafe
- Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Jason Zhu
- Duke University Medical Center, 905 S. Lasalle Street, Durham, NC, 27710, USA
| | - Matthew Labriola
- Duke University Medical Center, 905 S. Lasalle Street, Durham, NC, 27710, USA
| | - Daniele Marin
- Duke University Medical Center, 905 S. Lasalle Street, Durham, NC, 27710, USA
| | - Shannon J McCall
- Duke University Medical Center, 905 S. Lasalle Street, Durham, NC, 27710, USA
| | - Jeffrey Clarke
- Duke University Medical Center, 905 S. Lasalle Street, Durham, NC, 27710, USA
| | - Daniel J George
- Duke University Medical Center, 905 S. Lasalle Street, Durham, NC, 27710, USA
| | - Tian Zhang
- Duke University Medical Center, 905 S. Lasalle Street, Durham, NC, 27710, USA
| | - Matthew Zibelman
- Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA
| | - Pooja Ghatalia
- Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA
| | | | | | - Arun Singavi
- Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, WI, 53226, USA
| | - Ben George
- Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, WI, 53226, USA
| | | | - Jonathan Thompson
- Medical College of Wisconsin, 8701 W Watertown Plank Rd, Milwaukee, WI, 53226, USA
| | - Rajbir Singh
- Meharry Medical College, 1005 Dr DB Todd Jr Blvd, Nashville, TN, 37208, USA
| | - Robin Jacob
- Meharry Medical College, 1005 Dr DB Todd Jr Blvd, Nashville, TN, 37208, USA
| | | | - Neel Shah
- Community Hospital, Munster, IN, 46321, USA
| | - Roger Day
- University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, 10065, USA
- Université Paris Descartes/Paris V, 75006, Paris, France
| | - Mark Gardner
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Carl Morrison
- OmniSeq, Inc., 700 Ellicott Street, Buffalo, NY, 14203, USA.
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA.
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50
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Nagahashi M, Shimada Y, Ichikawa H, Kameyama H, Takabe K, Okuda S, Wakai T. Next generation sequencing-based gene panel tests for the management of solid tumors. Cancer Sci 2019; 110:6-15. [PMID: 30338623 PMCID: PMC6317963 DOI: 10.1111/cas.13837] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Abstract
Next generation sequencing (NGS) has been an invaluable tool to put genomic sequencing into clinical practice. The incorporation of clinically relevant target sequences into NGS-based gene panel tests has generated practical diagnostic tools that enable individualized cancer-patient care. The clinical utility of gene panel testing includes investigation of the genetic basis for an individual's response to therapy, such as signaling pathways associated with a response to specific therapies, microsatellite instability and a hypermutated phenotype, and deficiency in the DNA double-strand break repair pathway. In this review, we describe the concept of precision cancer medicine using target sequences in gene panel tests as well as the importance of the control of sample quality in routine NGS-based genomic testing. We describe geographic and ethnic differences in cancer genomes, and discuss issues that need to be addressed in the future based on our experiences in Japan.
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Affiliation(s)
- Masayuki Nagahashi
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Yoshifumi Shimada
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Hiroshi Ichikawa
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Hitoshi Kameyama
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Kazuaki Takabe
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
- Breast SurgeryRoswell Park Cancer InstituteBuffaloNew York
- Department of SurgeryThe State University of New York Jacobs School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNew York
| | - Shujiro Okuda
- Division of BioinformaticsGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Toshifumi Wakai
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
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