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Zhang W, Dhondalay GK, Liu TA, Kaushik A, Hoh R, Kwok S, Kambham N, Fernandez‐Becker NQ, Andorf S, Desai M, Galli SJ, Boyd SD, Nadeau KC, Manohar M, DeKruyff RH, Chinthrajah RS. Gastrointestinal γδ T cells reveal differentially expressed transcripts and enriched pathways during peanut oral immunotherapy. Allergy 2022; 77:1606-1610. [PMID: 35143054 PMCID: PMC9581524 DOI: 10.1111/all.15250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Wenming Zhang
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
| | - Gopal Krishna Dhondalay
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
| | - Taryn Audrey Liu
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
| | - Abhinav Kaushik
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
| | - Ramona Hoh
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
- Department of Pathology Stanford University School of Medicine Stanford California USA
| | - Shirley Kwok
- Department of Pathology Stanford University School of Medicine Stanford California USA
| | - Neeraja Kambham
- Department of Pathology Stanford University School of Medicine Stanford California USA
| | - Nielsen Q Fernandez‐Becker
- Department of Medicine Division of Gastroenterology and Hepatology Stanford University School of Medicine Stanford California USA
| | - Sandra Andorf
- Department of Pediatrics University of Cincinnati College of Medicine Cincinnati Ohio USA
- Divisions of Biomedical Informatics and Allergy & Immunology Cincinnati Children’s Hospital Medical Center Cincinnati Ohio USA
| | - Manisha Desai
- Department of Biomedical Data Science Stanford University Stanford California USA
| | - Stephen J. Galli
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
- Department of Pathology Stanford University School of Medicine Stanford California USA
- Department of Microbiology and Immunology Stanford University School of Medicine Stanford California USA
| | - Scott D. Boyd
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
- Department of Pathology Stanford University School of Medicine Stanford California USA
| | - Kari C. Nadeau
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
| | - Monali Manohar
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
| | - Rosemarie H. DeKruyff
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
| | - R. Sharon Chinthrajah
- Department of Medicine Sean N. Parker Center for Allergy and Asthma Research Stanford University School of Medicine Stanford California USA
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Dhondalay GK, Rael E, Acharya S, Zhang W, Sampath V, Galli SJ, Tibshirani R, Boyd SD, Maecker H, Nadeau KC, Andorf S. Food allergy and omics. J Allergy Clin Immunol 2019; 141:20-29. [PMID: 29307411 DOI: 10.1016/j.jaci.2017.11.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 01/06/2023]
Abstract
Food allergy (FA) prevalence has been increasing over the last few decades and is now a global health concern. Current diagnostic methods for FA result in a high number of false-positive results, and the standard of care is either allergen avoidance or use of epinephrine on accidental exposure, although currently with no other approved treatments. The increasing prevalence of FA, lack of robust biomarkers, and inadequate treatments warrants further research into the mechanism underlying food allergies. Recent technological advances have made it possible to move beyond traditional biological techniques to more sophisticated high-throughput approaches. These technologies have created the burgeoning field of omics sciences, which permit a more systematic investigation of biological problems. Omics sciences, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, and exposomics, have enabled the construction of regulatory networks and biological pathway models. Parallel advances in bioinformatics and computational techniques have enabled the integration, analysis, and interpretation of these exponentially growing data sets and opens the possibility of personalized or precision medicine for FA.
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Affiliation(s)
- Gopal Krishna Dhondalay
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Efren Rael
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Swati Acharya
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Wenming Zhang
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Stephen J Galli
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif
| | - Robert Tibshirani
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, Calif
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Holden Maecker
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Kari Christine Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif.
| | - Sandra Andorf
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
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Eswarachary V, Mohammed IG, Jayanna PK, Patilokaly GV, Nargund AR, Dhondalay GK, Prabhudesai S, Sahoo R. HER2/ neu Testing In 432 Consecutive Breast Cancer Cases using FISH and IHC - A Comparative Study. J Clin Diagn Res 2017; 11:EC01-EC05. [PMID: 28571140 PMCID: PMC5449786 DOI: 10.7860/jcdr/2017/25625.9521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/20/2017] [Indexed: 11/24/2022]
Abstract
INTRODUCTION The development of trastuzumab, a HER-2/neu targeted monoclonal antibody resulted in significant improvements in clinical response and survival in HER-2/neu gene amplified group of patients. Thus, accurate assessment of HER-2/neu status becomes critical. Fluorescence In Situ Hybridization (FISH) and Immunohistochemistry (IHC) are the most commonly used methods for this purpose and specific recommendations exist with regard to the concordance to be observed between the two tests. AIM Here, we report and evaluate the concordance rate between FISH and IHC for HER-2/neu status in breast cancer specimens. MATERIALS AND METHODS Archival paraffin blocks of tumour tissue from 450 patients of breast cancer were analyzed for Her-2/neu status using FISH and IHC. RESULTS There was a highly significant concordance between the results of FISH and IHC assays in HER-2/neu status assessment in invasive breast cancer cases. There were inverse associations between the expression of Oestrogen Receptors/Progesterone Receptors (ER/PR) and HER-2/neu amplification. CONCLUSION Although, IHC gave significant concordant results with FISH in determining HER-2/neu status, its subjective grading system precludes its use as a gold standard. FISH should always be used to determine true gene amplification when the IHC results are equivocal.
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Affiliation(s)
- Venkataswamy Eswarachary
- Senior Scientist, Department of Triesta Reference Laboratory, HealthCare Global Enterprise Ltd (HCG), Bengaluru, Karnataka, India
| | - Imran Gorur Mohammed
- Consultant Pathologist, Department of Triesta Reference Laboratory, HealthCare Global Enterprise Ltd (HCG), Bengaluru, Karnataka, India
| | - Prashanth K Jayanna
- Scientist, Department of Triesta Reference Laboratory, HealthCare Global Enterprise Ltd (HCG), Bengaluru, Karnataka, India
| | - Geeta V Patilokaly
- Consultant Pathologist, Department of Triesta Reference Laboratory, HealthCare Global Enterprise Ltd (HCG), Bengaluru, Karnataka, India
| | - Ashwini R Nargund
- Consultant Pathologist, Department of Triesta Reference Laboratory, HealthCare Global Enterprise Ltd (HCG), Bengaluru, Karnataka, India
| | - Gopal Krishna Dhondalay
- Scientist, Department of Triesta Reference Laboratory, HealthCare Global Enterprise Ltd (HCG), Bengaluru, Karnataka, India
| | - Shilpa Prabhudesai
- Consultant Pathologist, Department of Triesta Reference Laboratory, HealthCare Global Enterprise Ltd (HCG), Bengaluru, Karnataka, India
| | - Rashmita Sahoo
- Senior Scientist, Department of Triesta Reference Laboratory, HealthCare Global Enterprise Ltd (HCG), Bengaluru, Karnataka, India
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