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Kaplan HG, Dowdell AK, Berry AB, Shimol RB, Robinson FL, Carney CA, Piening BD. Multi-omic profiling of simultaneous ductal carcinoma in situ and invasive breast cancer. Breast Cancer Res Treat 2024:10.1007/s10549-024-07270-5. [PMID: 38523186 DOI: 10.1007/s10549-024-07270-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/24/2024] [Indexed: 03/26/2024]
Abstract
PURPOSE The progression of ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) in humans is highly variable. To better understand the relationship between them, we performed a multi-omic characterization of co-occurring DCIS and IBC lesions in a cohort of individuals. METHODS Formalin-fixed paraffin-embedded tissue samples from 50 patients with co-occurring DCIS and IBC lesions were subjected to DNA-seq and whole transcriptome RNA-seq. Paired DCIS and IBC multi-omics profiles were then interrogated for DNA mutations, gene expression profiles and pathway analysis. RESULTS Most small variants and copy number variations were shared between co-occurring DCIS and IBC lesions, with IBC exhibiting on average a higher degree of additional mutations. However, 36% of co-occurring lesions shared no common mutations and 49% shared no common copy number variations. The most frequent genomic variants in both DCIS and IBC were PIK3CA, TP53, KMT2C, MAP3K1, GATA3 and SF3B1, with KMT2C being more frequent in DCIS and TP53 and MAP3K1 more frequent in IBC, though the numbers are too small for definitive conclusions. The most frequent copy number variations were seen in MCL1, CKSB1 and ERBB2. ERBB2 changes were not seen in IBC unless present in the corresponding DCIS. Transcriptional profiles were highly distinct between DCIS and IBC, with DCIS exhibiting upregulation of immune-related signatures, while IBC showed significant overexpression in genes and pathways associated with cell division and proliferation. Interestingly, DCIS and IBC exhibited significant differential expression of different components of extracellular matrix (ECM) formation and regulation, with DCIS showing overexpression of ECM-membrane interaction components while IBC showed upregulation of genes associated with fibronectin and invadopodia. CONCLUSION While most co-occurring DCIS and IBC were mutationally similar and suggestive of a common clonal progenitor, transcriptionally the lesions are highly distinct, with IBC expressing key pathways that facilitate invasion and proliferation. These results are suggestive of additional levels of regulation, epigenetic or other, that facilitate the acquisition of invasive properties during tumor evolution.
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Affiliation(s)
- Henry G Kaplan
- Swedish Cancer Institute, 1221 Madison St., Suite 920, Seattle, WA, 98104, USA.
| | - Alexa K Dowdell
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
| | - Anna B Berry
- Swedish Cancer Institute, 1221 Madison St., Suite 920, Seattle, WA, 98104, USA
| | - Racheli Ben Shimol
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
| | - Fred L Robinson
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
| | | | - Brian D Piening
- Earle A. Chiles Research Institute, Providence Health, Portland, OR, 97213, USA
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2
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Medler TR, Blair TC, Alice AF, Dowdell AK, Piening BD, Crittenden MR, Gough MJ. Myeloid MyD88 restricts CD8 + T cell response to radiation therapy in pancreatic cancer. Sci Rep 2023; 13:8634. [PMID: 37244938 PMCID: PMC10224952 DOI: 10.1038/s41598-023-35834-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/24/2023] [Indexed: 05/29/2023] Open
Abstract
Radiation therapy induces immunogenic cell death in cancer cells, whereby released endogenous adjuvants are sensed by immune cells to direct adaptive immune responses. TLRs expressed on several immune subtypes recognize innate adjuvants to direct downstream inflammatory responses in part via the adapter protein MyD88. We generated Myd88 conditional knockout mice to interrogate its contribution to the immune response to radiation therapy in distinct immune populations in pancreatic cancer. Surprisingly, Myd88 deletion in Itgax (CD11c)-expressing dendritic cells had little discernable effects on response to RT in pancreatic cancer and elicited normal T cell responses using a prime/boost vaccination strategy. Myd88 deletion in Lck-expressing T cells resulted in similar or worsened responses to radiation therapy compared to wild-type mice and lacked antigen-specific CD8+ T cell responses from vaccination, similar to observations in Myd88-/- mice. Lyz2-specific loss of Myd88 in myeloid populations rendered tumors more susceptible to radiation therapy and elicited normal CD8+ T cell responses to vaccination. scRNAseq in Lyz2-Cre/Myd88fl/fl mice revealed gene signatures in macrophages and monocytes indicative of enhanced type I and II interferon responses, and improved responses to RT were dependent on CD8+ T cells and IFNAR1. Together, these data implicate MyD88 signaling in myeloid cells as a critical source of immunosuppression that hinders adaptive immune tumor control following radiation therapy.
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Affiliation(s)
- Terry R Medler
- Earle A. Chiles Research Institute, Providence Cancer Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, 4805 NE Glisan Street, Suite 2N100, Portland, OR, 97213, USA
| | - Tiffany C Blair
- Earle A. Chiles Research Institute, Providence Cancer Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, 4805 NE Glisan Street, Suite 2N100, Portland, OR, 97213, USA
| | - Alejandro F Alice
- Earle A. Chiles Research Institute, Providence Cancer Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, 4805 NE Glisan Street, Suite 2N100, Portland, OR, 97213, USA
| | - Alexa K Dowdell
- Earle A. Chiles Research Institute, Providence Cancer Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, 4805 NE Glisan Street, Suite 2N100, Portland, OR, 97213, USA
| | - Brian D Piening
- Earle A. Chiles Research Institute, Providence Cancer Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, 4805 NE Glisan Street, Suite 2N100, Portland, OR, 97213, USA
| | - Marka R Crittenden
- Earle A. Chiles Research Institute, Providence Cancer Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, 4805 NE Glisan Street, Suite 2N100, Portland, OR, 97213, USA
- The Oregon Clinic, Portland, OR, USA
| | - Michael J Gough
- Earle A. Chiles Research Institute, Providence Cancer Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, 4805 NE Glisan Street, Suite 2N100, Portland, OR, 97213, USA.
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3
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Al-Muhanna FA, Dowdell AK, Al Eleq AH, Albaker WI, Brooks AW, Al-Sultan AI, Al-Rubaish AM, Alkharsah KR, Sulaiman RM, Al-Quorain AA, Cyrus C, Alali RA, Vatte C, Robinson FL, Zhou X, Snyder MP, Almuhanna AF, Keating BJ, Piening BD, Al-Ali AK. Gut microbiota analyses of Saudi populations for type 2 diabetes-related phenotypes reveals significant association. BMC Microbiol 2022; 22:301. [PMID: 36510121 PMCID: PMC9746012 DOI: 10.1186/s12866-022-02714-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Large-scale gut microbiome sequencing has revealed key links between microbiome dysfunction and metabolic diseases such as type 2 diabetes (T2D). To date, these efforts have largely focused on Western populations, with few studies assessing T2D microbiota associations in Middle Eastern communities where T2D prevalence is now over 20%. We analyzed the composition of stool 16S rRNA from 461 T2D and 119 non-T2D participants from the Eastern Province of Saudi Arabia. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples based on diabetes status and glucose level. RESULTS In this study we performed the largest microbiome study ever conducted in Saudi Arabia, as well as the first-ever characterization of gut microbiota T2D versus non-T2D in this population. We observed overall positive enrichment within diabetics compared to healthy individuals and amongst diabetic participants; those with high glucose levels exhibited slightly more positive enrichment compared to those at lower risk of fasting hyperglycemia. In particular, the genus Firmicutes was upregulated in diabetic individuals compared to non-diabetic individuals, and T2D was associated with an elevated Firmicutes/Bacteroidetes ratio, consistent with previous findings. CONCLUSION Based on diabetes status and glucose levels of Saudi participants, relatively stable differences in stool composition were perceived by differential abundance and alpha diversity measures. However, community level differences are evident in the Saudi population between T2D and non-T2D individuals, and diversity patterns appear to vary from well-characterized microbiota from Western cohorts. Comparing overlapping and varying patterns in gut microbiota with other studies is critical to assessing novel treatment options in light of a rapidly growing T2D health epidemic in the region. As a rapidly emerging chronic condition in Saudi Arabia and the Middle East, T2D burdens have grown more quickly and affect larger proportions of the population than any other global region, making a regional reference T2D-microbiome dataset critical to understanding the nuances of disease development on a global scale.
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Affiliation(s)
- Fahad A. Al-Muhanna
- grid.411975.f0000 0004 0607 035XDepartment of Internal Medicine, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Alexa K. Dowdell
- grid.240531.10000 0004 0456 863XEarle A Chiles Research Institute, Providence Portland Medical Center, Portland, OR USA
| | - Abdulmohsen H. Al Eleq
- grid.411975.f0000 0004 0607 035XDepartment of Internal Medicine, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Waleed I. Albaker
- grid.411975.f0000 0004 0607 035XDepartment of Internal Medicine, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Andrew W. Brooks
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Ali I. Al-Sultan
- grid.411975.f0000 0004 0607 035XDepartment of Internal Medicine, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Abdullah M. Al-Rubaish
- grid.411975.f0000 0004 0607 035XDepartment of Internal Medicine, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Khaled R. Alkharsah
- grid.411975.f0000 0004 0607 035XDepartment of Microbiology, College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Raed M. Sulaiman
- grid.411975.f0000 0004 0607 035XDepartment of Internal Medicine, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Abdulaziz A. Al-Quorain
- grid.411975.f0000 0004 0607 035XDepartment of Internal Medicine, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Cyril Cyrus
- grid.411975.f0000 0004 0607 035XDepartment of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Rudaynah A. Alali
- grid.411975.f0000 0004 0607 035XDepartment of Internal Medicine, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Chittibabu Vatte
- grid.411975.f0000 0004 0607 035XDepartment of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Fred L. Robinson
- grid.240531.10000 0004 0456 863XEarle A Chiles Research Institute, Providence Portland Medical Center, Portland, OR USA
| | - Xin Zhou
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Michael P. Snyder
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Afnan F. Almuhanna
- grid.411975.f0000 0004 0607 035XDepartment of Radiology, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Brendan J. Keating
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Brian D. Piening
- grid.240531.10000 0004 0456 863XEarle A Chiles Research Institute, Providence Portland Medical Center, Portland, OR USA
| | - Amein K. Al-Ali
- grid.411975.f0000 0004 0607 035XDepartment of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
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Hamilton LT, Koguchi Y, Christie T, Shimada T, Iwamoto N, Fox B, Redmond WL, Piening BD. Durability of B and T cell responses against a spike protein of SARS-CoV2 elicited by mRNA vaccines. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.65.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
The pandemic of SARS-CoV2 had resulted in over 266 million infections and over 5.2 million deaths throughout the world as of early-December 2021. Pfizer and Moderna mRNA vaccines were approved for Emergency Use Authorization by the US FDA. Even though 8.2 billion doses of vaccine have been administered, the world continues to see wide-spread SARS-CoV2 infection. Therefore, it is important to understand the durability of anti-SARS-CoV2 immune responses. Serum and PBMC samples were collected from vaccinated volunteers (N=40, Age 22–67, median age 41, Male/Female = 14/26, Moderna/Pfizer = 37/3) over 8 months (pre-vaccination baseline: TP1, 2 weeks-, 3 months-, and 8 months-post full vaccination: TP2, TP3, and TP4, respectively). First, we found robust induction of anti-S IgG and IgA for all subjects at TP2, which was higher than those from Covid-19 patients. Follow up samples (TP3 and TP4) showed steady decay of antibody levels over 8 months post-vaccination. Next, we evaluated memory B cell response using flow cytometry. We detected S-protein specific B cells by using flag-tagged S-protein. The frequency of S-protein specific B cells varied among donors and was weakly associated with the level of serum anti-S IgG antibody. Lastly, we assessed T cell responses. PBMCs were stimulated with an overlapping 15-mer peptide mix that covers the entire S-protein. Antigen-specific activation of T cells were detected based upon IFN-γ and TNF-α production. We found induction of robust CD4 T cell response at TP2 but a clear reduction at TP3. TP4 showed equivalent levels of T cell responses as TP3. Together, we found that B and T cell responses against the spike protein of SARS-CoV2 induced by mRNA vaccines are not durable.
This study was supported by funding from Shimadzu Corporation.
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Gough MJ, Blair T, Dowdell AK, Bambina S, Kramer G, Piening BD, Crittenden MR. Fluorescence tagging to monitor CD8 T cell recirculation from the tumor to the tumor-draining lymph node: the impact of focal radiation therapy on recirculation. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.118.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
T cells are continuously moving through tissues and recirculating back into the peripheral blood via lymph nodes. In cancer, tumor-specific T cells are enriched in the tumor environment and their presence is associated with improved outcome in patients and in preclinical models. T cells are known to contribute to tumor control following radiotherapy despite evidence indicating that radiation can be directly cytotoxic to lymphocytes. The impact of radiation therapy on recirculation of T cells through the tumor to the tumor draining lymph node (TDLN) and their trafficking to distant sites is unclear. By photoconverting tumor infiltrating cells using focal UV in Kaede mice we can use fluorescence tagging to directly identify T cells in the TDLN that originated in the tumor. We demonstrate that radiation therapy significantly decreases CD8 T cell trafficking from the tumor to the TDLN. Using single cell RNASeq and flow cytometry, we demonstrate that radiation therapy is locally cytotoxic to proliferating effector CD8 T cells within the tumor environment. This results in the loss of this effector population in the TDLN following treatment. Using flow cytometry and direct blockade of T cell entry into the LN, we characterize the CD8 T cells in the TDLN that proliferate following radiation therapy. Our data demonstrate that radiation therapy is locally cytotoxic and restricts CD8 T cell recirculation to the TDLN. Since tumor control following radiation therapy is partially dependent on CD8 T cell responses, these data force us to re-evaluate both the type and location of T cell populations that contribute to tumor control following radiation therapy.
Supported by grants from the NIH (R01CA182311, R01CA244142, R01CA208644)
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Affiliation(s)
- Michael J Gough
- 1Earle A. Chiles Research Institute, Providence Portland Medical Center
| | - Tiffany Blair
- 1Earle A. Chiles Research Institute, Providence Portland Medical Center
| | - Alexa K Dowdell
- 1Earle A. Chiles Research Institute, Providence Portland Medical Center
| | - Shelly Bambina
- 1Earle A. Chiles Research Institute, Providence Portland Medical Center
| | - Gwen Kramer
- 1Earle A. Chiles Research Institute, Providence Portland Medical Center
| | - Brian D Piening
- 1Earle A. Chiles Research Institute, Providence Portland Medical Center
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Blair TC, Bambina S, Kramer GF, Dowdell AK, Alice AF, Baird JR, Lund AW, Piening BD, Crittenden MR, Gough MJ. Fluorescent tracking identifies key migratory dendritic cells in the lymph node after radiotherapy. Life Sci Alliance 2022; 5:5/9/e202101337. [PMID: 35487695 PMCID: PMC9058260 DOI: 10.26508/lsa.202101337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
Radiation therapy impacts all cells within the treatment field. Using novel technology, we track dendritic cells from the tumor to lymph nodes and demonstrate their importance in immune control of tumors. Radiation therapy generates extensive cancer cell death capable of promoting tumor-specific immunity. Within the tumor, conventional dendritic cells (cDCs) are known to carry tumor-associated antigens to the draining lymph node (TdLN) where they initiate T-cell priming. How radiation influences cDC migration is poorly understood. Here, we show that immunological efficacy of radiation therapy is dependent on cDC migration in radioimmunogenic tumors. Using photoconvertible mice, we demonstrate that radiation impairs cDC migration to the TdLN in poorly radioimmunogenic tumors. Comparative transcriptional analysis revealed that cDCs in radioimmunogenic tumors express genes associated with activation of endogenous adjuvant signaling pathways when compared with poorly radioimmunogenic tumors. Moreover, an exogenous adjuvant combined with radiation increased the number of migrating cDCs in these poorly radioimmunogenic tumors. Taken together, our data demonstrate that cDC migration play a critical role in the response to radiation therapy.
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Affiliation(s)
- Tiffany C Blair
- Earle A Chiles Research Institute, Robert W Franz Cancer Center, Providence Portland Medical Center, Portland, OR, USA
| | - Shelly Bambina
- Earle A Chiles Research Institute, Robert W Franz Cancer Center, Providence Portland Medical Center, Portland, OR, USA
| | - Gwen F Kramer
- Earle A Chiles Research Institute, Robert W Franz Cancer Center, Providence Portland Medical Center, Portland, OR, USA
| | - Alexa K Dowdell
- Earle A Chiles Research Institute, Robert W Franz Cancer Center, Providence Portland Medical Center, Portland, OR, USA
| | - Alejandro F Alice
- Earle A Chiles Research Institute, Robert W Franz Cancer Center, Providence Portland Medical Center, Portland, OR, USA
| | - Jason R Baird
- Earle A Chiles Research Institute, Robert W Franz Cancer Center, Providence Portland Medical Center, Portland, OR, USA
| | - Amanda W Lund
- Ronald O Perelman Department of Dermatology, Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Brian D Piening
- Earle A Chiles Research Institute, Robert W Franz Cancer Center, Providence Portland Medical Center, Portland, OR, USA
| | - Marka R Crittenden
- Earle A Chiles Research Institute, Robert W Franz Cancer Center, Providence Portland Medical Center, Portland, OR, USA.,The Oregon Clinic, Portland, OR, USA
| | - Michael J Gough
- Earle A Chiles Research Institute, Robert W Franz Cancer Center, Providence Portland Medical Center, Portland, OR, USA
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Piening BD, Dowdell AK, Zhang M, Loza BL, Walls D, Gao H, Mohebnasab M, Li YR, Elftmann E, Wei E, Gandla D, Lad H, Chaib H, Sweitzer NK, Deng M, Pereira AC, Cadeiras M, Shaked A, Snyder MP, Keating BJ. Whole Transcriptome Profiling of Prospective Endomyocardial Biopsies Reveals Prognostic and Diagnostic Signatures of Cardiac Allograft Rejection. J Heart Lung Transplant 2022; 41:840-848. [DOI: 10.1016/j.healun.2022.01.1377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/26/2022] Open
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8
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Iwamoto N, Koguchi Y, Yokoyama K, Hamada A, Yonezawa A, Piening BD, Tran E, Fox BA, Redmond WL, Shimada T. A rapid and universal liquid chromatograph-mass spectrometry-based platform, refmAb-Q nSMOL, for monitoring monoclonal antibody therapeutics. Analyst 2022; 147:4275-4284. [DOI: 10.1039/d2an01032a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Accurate multiplexed quantitation of unique signature peptides derived from monoclonal antibody therapeutics with a universal reference antibody refmAb-Q using Fab-selective proteolysis nSMOL coupled with LC-MS/MS.
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Affiliation(s)
- Noriko Iwamoto
- Shimadzu Bioscience Research Partnership, Shimadzu Scientific Instruments, 21720 23rd Dr SE, Bothell, WA 98021, USA
| | - Yoshinobu Koguchi
- Earle A. Chiles Research Institute, Providence Cancer Institute, 4805 NE Glisan St., Portland, OR 97213, USA
| | - Kotoko Yokoyama
- Global Application Development Center, Shimadzu Corporation, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center, 5-1-1 Tsukuji, Chuo-ku, Tokyo 104-0045, Japan
| | - Atsushi Yonezawa
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, 54 Kawaharacho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Brian D. Piening
- Earle A. Chiles Research Institute, Providence Cancer Institute, 4805 NE Glisan St., Portland, OR 97213, USA
| | - Eric Tran
- Earle A. Chiles Research Institute, Providence Cancer Institute, 4805 NE Glisan St., Portland, OR 97213, USA
| | - Bernard A. Fox
- Earle A. Chiles Research Institute, Providence Cancer Institute, 4805 NE Glisan St., Portland, OR 97213, USA
| | - William L. Redmond
- Earle A. Chiles Research Institute, Providence Cancer Institute, 4805 NE Glisan St., Portland, OR 97213, USA
| | - Takashi Shimada
- Shimadzu Bioscience Research Partnership, Shimadzu Scientific Instruments, 21720 23rd Dr SE, Bothell, WA 98021, USA
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Koguchi Y, Iwamoto N, Shimada T, Chang SC, Cha J, Curti BD, Urba WJ, Piening BD, Redmond WL. Trough levels of ipilimumab in serum as a potential biomarker of clinical outcomes for patients with advanced melanoma after treatment with ipilimumab. J Immunother Cancer 2021; 9:jitc-2021-002663. [PMID: 34620702 PMCID: PMC8499328 DOI: 10.1136/jitc-2021-002663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 12/29/2022] Open
Abstract
Background Immune checkpoint blockade (ICB) using anti-CTLA-4 and anti-PD-1/PD-L1 has revolutionized the treatment of advanced cancer. However, ICB is effective for only a small fraction of patients, and biomarkers such as expression of PD-L1 in tumor or serum levels of CXCL11 have suboptimal sensitivity and specificity. Exposure–response (E-R) relationships have been observed with other therapeutic monoclonal antibodies. There are many factors influencing E-R relationships, yet several studies have shown that trough levels of anti-PD-1/PD-L1 correlated with clinical outcomes. However, the potential utility of anti-CTLA-4 levels as a biomarker remains unknown. Methods Serum was obtained at trough levels at weeks 7 and 12 (after doses 2 and 4) from patients with advanced melanoma who received ipilimumab alone (3 mg/kg every 3 weeks for four treatments) via an expanded access program (NCT00495066). We have successfully established a proteomics assay to measure the concentration of ipilimumab in serum using an liquid chromatography with tandem mass spectrometry-based nanosurface and molecular-orientation limited proteolysis (nSMOL) approach. Serum samples from 38 patients were assessed for trough levels of ipilimumab by the nSMOL assay. Results We found that trough levels of ipilimumab were higher in patients who developed immune-related adverse events but did not differ based on the presence or absence of disease progression. We found that patients with higher trough levels of ipilimumab had better overall survival when grouped based on ipilimumab trough levels. Trough levels of ipilimumab were inversely associated with pretreatment serum levels of CXCL11, a predictive biomarker we previously identified, and soluble CD25 (sCD25), a prognostic biomarker for advanced melanoma, as well as C reactive protein (CRP) and interleukin (IL)-6 levels at week 7. Conclusions Our results suggest that trough levels of ipilimumab may be a useful biomarker for the long-term survival of patients with advanced melanoma treated with ipilimumab. The association of ipilimumab trough levels with pretreatment serum levels of CXCL11 and sCD25 is suggestive of a baseline-driven E-R relationship, and the association of ipilimumab trough levels with on-treatment levels of CRP and IL-6 is suggestive of response-driven E-R relationship. Our findings highlight the potential utility of trough levels of ipilimumab as a biomarker. Trial registration number NCT00495066.
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Affiliation(s)
- Yoshinobu Koguchi
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Noriko Iwamoto
- Shimadzu Bioscience Research Partnership, Shimadzu Scientific Instruments, Bothell, Washington, USA
| | - Takashi Shimada
- Shimadzu Bioscience Research Partnership, Shimadzu Scientific Instruments, Bothell, Washington, USA
| | - Shu-Ching Chang
- Medical Data Research Center, Providence St Joseph Health, Portland, Oregon, USA
| | - John Cha
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Brendan D Curti
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Walter J Urba
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Brian D Piening
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - William L Redmond
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
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Sato Y, Passerini L, Piening BD, Uyeda MJ, Goodwin M, Gregori S, Snyder MP, Bertaina A, Roncarolo M, Bacchetta R. Human-engineered Treg-like cells suppress FOXP3-deficient T cells but preserve adaptive immune responses in vivo. Clin Transl Immunology 2020; 9:e1214. [PMID: 33304583 PMCID: PMC7688376 DOI: 10.1002/cti2.1214] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/12/2020] [Accepted: 10/25/2020] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Genetic or acquired defects in FOXP3+ regulatory T cells (Tregs) play a key role in many immune-mediated diseases including immune dysregulation polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome. Previously, we demonstrated CD4+ T cells from healthy donors and IPEX patients can be converted into functional Treg-like cells by lentiviral transfer of FOXP3 (CD4LVFOXP3). These CD4LVFOXP3 cells have potent regulatory function, suggesting their potential as an innovative therapeutic. Here, we present molecular and preclinical in vivo data supporting CD4LVFOXP3 cell clinical progression. METHODS The molecular characterisation of CD4LVFOXP3 cells included flow cytometry, qPCR, RNA-seq and TCR-seq. The in vivo suppressive function of CD4LVFOXP3 cells was assessed in xenograft-versus-host disease (xeno-GvHD) and FOXP3-deficient IPEX-like humanised mouse models. The safety of CD4LVFOXP3 cells was evaluated using peripheral blood (PB) humanised (hu)- mice testing their impact on immune response against pathogens, and immune surveillance against tumor antigens. RESULTS We demonstrate that the conversion of CD4+ T cells to CD4LVFOXP3 cells leads to specific transcriptional changes as compared to CD4+ T-cell transduction in the absence of FOXP3, including upregulation of Treg-related genes. Furthermore, we observe specific preservation of a polyclonal TCR repertoire during in vitro cell production. Both allogeneic and autologous CD4LVFOXP3 cells protect from xeno-GvHD after two sequential infusions of effector T cells. CD4LVFOXP3 cells prevent hyper-proliferation of CD4+ memory T cells in the FOXP3-deficient IPEX-like hu-mice. CD4LVFOXP3 cells do not impede in vivo expansion of antigen-primed T cells or tumor clearance in the PB hu-mice. CONCLUSION These data support the clinical readiness of CD4LVFOXP3 cells to treat IPEX syndrome and other immune-mediated diseases caused by insufficient or dysfunctional FOXP3+ Tregs.
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Affiliation(s)
- Yohei Sato
- Department of PediatricsDivision of Hematology, OncologyStem Cell Transplantation and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
| | - Laura Passerini
- Mechanisms of Peripheral Tolerance UnitSan Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS San Raffaele Scientific InstituteMilanItaly
| | - Brian D Piening
- Earle A Chiles Research InstituteProvidence Portland Medical CenterPortlandORUSA
| | - Molly Javier Uyeda
- Department of PediatricsDivision of Hematology, OncologyStem Cell Transplantation and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
- Institute for Stem Cell Biology and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
| | - Marianne Goodwin
- Department of PediatricsDivision of Hematology, OncologyStem Cell Transplantation and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
| | - Silvia Gregori
- Mechanisms of Peripheral Tolerance UnitSan Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS San Raffaele Scientific InstituteMilanItaly
| | - Michael P Snyder
- Department of GeneticsStanford University School of MedicineStanfordCAUSA
| | - Alice Bertaina
- Department of PediatricsDivision of Hematology, OncologyStem Cell Transplantation and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
| | - Maria‐Grazia Roncarolo
- Department of PediatricsDivision of Hematology, OncologyStem Cell Transplantation and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
- Institute for Stem Cell Biology and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
- Center for Definitive and Curative Medicine (CDCM)Stanford University School of MedicineStanfordCAUSA
| | - Rosa Bacchetta
- Department of PediatricsDivision of Hematology, OncologyStem Cell Transplantation and Regenerative MedicineStanford University School of MedicineStanfordCAUSA
- Center for Definitive and Curative Medicine (CDCM)Stanford University School of MedicineStanfordCAUSA
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11
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Khachatoorian Y, Khachadourian V, Chang E, Sernas ER, Reed EF, Deng M, Piening BD, Pereira AC, Keating B, Cadeiras M. Noninvasive biomarkers for prediction and diagnosis of heart transplantation rejection. Transplant Rev (Orlando) 2020; 35:100590. [PMID: 33401139 DOI: 10.1016/j.trre.2020.100590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 07/19/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/12/2023]
Abstract
For most patients with end-stage heart failure, heart transplantation is the treatment of choice. Allograft rejection is one of the major post-transplantation complications affecting graft outcome and survival. Recent advancements in science and technology offer an opportunity to integrate genomic and other omics-based biomarkers into clinical practice, facilitating noninvasive evaluation of allograft for diagnostic and prognostic purposes. Omics, including gene expression profiling (GEP) of blood immune cell components and donor-derived cell-free DNA (dd-cfDNA) are of special interest to researchers. Several studies have investigated levels of dd-cfDNA and miroRNAs in blood as potential markers for early detection of allograft rejection. One of the achievements in the field of transcriptomics is AlloMap, GEP of peripheral blood mononuclear cells (PBMC), which can identify 11 differentially expressed genes and help with detection of moderate and severe acute cellular rejection in stable heart transplant recipients. In recent years, the utilization of GEP of PBMC for identifying differentially expressed genes to diagnose acute antibody-mediated rejection and cardiac allograft vasculopathy has yielded promising results. Advancements in the field of metabolomics and proteomics as well as their potential implications have been further discussed in this paper.
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Affiliation(s)
- Yeraz Khachatoorian
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.
| | - Vahe Khachadourian
- Turpanjian School of Public Health, American University of Armenia, Yerevan, Armenia
| | - Eleanor Chang
- Division of Cardiology, David Geffen School of Medicine, Los Angeles, CA, United States of America
| | - Erick R Sernas
- Division of Cardiovascular Medicine, University of California Davis, Davis, CA, United States of America
| | - Elaine F Reed
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, United States of America
| | - Mario Deng
- Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, United States of America
| | - Brian D Piening
- Earle A Chiles Research Institute, Providence Health and Services, Portland, OR, United States of America
| | | | - Brendan Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Martin Cadeiras
- Division of Cardiovascular Medicine, University of California Davis, Davis, CA, United States of America
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12
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Piening BD, Lovejoy J, Earls JC. Ageotypes: Distinct Biomolecular Trajectories in Human Aging. Trends Pharmacol Sci 2020; 41:299-301. [PMID: 32192755 DOI: 10.1016/j.tips.2020.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 11/18/2022]
Abstract
Many studies have demonstrated that biological age (BA) varies significantly among individuals of similar chronological age. A recent study by Ahadi et al. used longitudinal and deep multi-omic profiling to identify individuals with distinct BA phenotypes or 'ageotypes'. These ageotypes open new avenues to creating diagnostic and treatment strategies that may slow the aging process based on the unique biochemistry of each individual.
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Affiliation(s)
- Brian D Piening
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA.
| | | | - John C Earls
- Institute for Systems Biology, Seattle, WA, USA; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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13
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Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science 2019; 364:364/6436/eaau8650. [PMID: 30975860 DOI: 10.1126/science.aau8650] [Citation(s) in RCA: 399] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
To understand the health impact of long-duration spaceflight, one identical twin astronaut was monitored before, during, and after a 1-year mission onboard the International Space Station; his twin served as a genetically matched ground control. Longitudinal assessments identified spaceflight-specific changes, including decreased body mass, telomere elongation, genome instability, carotid artery distension and increased intima-media thickness, altered ocular structure, transcriptional and metabolic changes, DNA methylation changes in immune and oxidative stress-related pathways, gastrointestinal microbiota alterations, and some cognitive decline postflight. Although average telomere length, global gene expression, and microbiome changes returned to near preflight levels within 6 months after return to Earth, increased numbers of short telomeres were observed and expression of some genes was still disrupted. These multiomic, molecular, physiological, and behavioral datasets provide a valuable roadmap of the putative health risks for future human spaceflight.
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Affiliation(s)
- Francine E Garrett-Bakelman
- Weill Cornell Medicine, New York, NY, USA.,University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Manjula Darshi
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Ruben C Gur
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ling Lin
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Jad Nasrini
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health, San Antonio, TX, USA
| | | | - Lynn Taylor
- Colorado State University, Fort Collins, CO, USA
| | | | | | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sara Ahadi
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Aditya Ambati
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Songjie Chen
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Marisa Covington
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | - Brian E Crucian
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | - David F Dinges
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | - Ryan P Hillary
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Peng Jiang
- Northwestern University, Evanston, IL, USA
| | | | | | | | | | | | | | | | - Tyler M Moore
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Hemal H Patel
- University of California, San Diego, La Jolla, CA, USA
| | | | - Varsha Rao
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Rintaro Saito
- University of California, San Diego, La Jolla, CA, USA
| | - Denis N Salins
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Michael B Stenger
- National Aeronautics and Space Administration (NASA), Houston, TX, USA
| | | | | | | | | | - Jing Zhang
- Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Sara R Zwart
- University of Texas Medical Branch, Galveston, TX, USA
| | - John B Charles
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
| | - Craig E Kundrot
- Space Life and Physical Sciences Division, NASA Headquarters, Washington, DC, USA.
| | - Graham B I Scott
- National Space Biomedical Research Institute, Baylor College of Medicine, Houston, TX, USA.
| | | | - Mathias Basner
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | | | | | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA. .,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.,The Feil Family Brain and Mind Research Institute, New York, NY, USA.,The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | | | - Brinda K Rana
- University of California, San Diego, La Jolla, CA, USA.
| | - Scott M Smith
- National Aeronautics and Space Administration (NASA), Houston, TX, USA.
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14
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Mardinoglu A, Wu H, Bjornson E, Zhang C, Hakkarainen A, Räsänen SM, Lee S, Mancina RM, Bergentall M, Pietiläinen KH, Söderlund S, Matikainen N, Ståhlman M, Bergh PO, Adiels M, Piening BD, Granér M, Lundbom N, Williams KJ, Romeo S, Nielsen J, Snyder M, Uhlén M, Bergström G, Perkins R, Marschall HU, Bäckhed F, Taskinen MR, Borén J. An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans. Cell Metab 2018; 27:559-571.e5. [PMID: 29456073 PMCID: PMC6706084 DOI: 10.1016/j.cmet.2018.01.005] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/06/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023]
Abstract
A carbohydrate-restricted diet is a widely recommended intervention for non-alcoholic fatty liver disease (NAFLD), but a systematic perspective on the multiple benefits of this diet is lacking. Here, we performed a short-term intervention with an isocaloric low-carbohydrate diet with increased protein content in obese subjects with NAFLD and characterized the resulting alterations in metabolism and the gut microbiota using a multi-omics approach. We observed rapid and dramatic reductions of liver fat and other cardiometabolic risk factors paralleled by (1) marked decreases in hepatic de novo lipogenesis; (2) large increases in serum β-hydroxybutyrate concentrations, reflecting increased mitochondrial β-oxidation; and (3) rapid increases in folate-producing Streptococcus and serum folate concentrations. Liver transcriptomic analysis on biopsy samples from a second cohort revealed downregulation of the fatty acid synthesis pathway and upregulation of folate-mediated one-carbon metabolism and fatty acid oxidation pathways. Our results highlight the potential of exploring diet-microbiota interactions for treating NAFLD.
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Affiliation(s)
- Adil Mardinoglu
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Hao Wu
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Elias Bjornson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Antti Hakkarainen
- HUS Medical Imaging Center, Radiology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Sari M Räsänen
- Research Programs Unit, Diabetes and Obesity, University of Helsinki and Department of Internal Medicine, Helsinki University Hospital, Helsinki, Finland
| | - Sunjae Lee
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rosellina M Mancina
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mattias Bergentall
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Kirsi H Pietiläinen
- Research Programs Unit, Diabetes and Obesity, University of Helsinki and Department of Internal Medicine, Helsinki University Hospital, Helsinki, Finland; Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - Sanni Söderlund
- Research Programs Unit, Diabetes and Obesity, University of Helsinki and Department of Internal Medicine, Helsinki University Hospital, Helsinki, Finland
| | - Niina Matikainen
- Research Programs Unit, Diabetes and Obesity, University of Helsinki and Department of Internal Medicine, Helsinki University Hospital, Helsinki, Finland; Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - Marcus Ståhlman
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per-Olof Bergh
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Martin Adiels
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Brian D Piening
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Marit Granér
- Research Programs Unit, Diabetes and Obesity, University of Helsinki and Department of Internal Medicine, Helsinki University Hospital, Helsinki, Finland
| | - Nina Lundbom
- HUS Medical Imaging Center, Radiology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Kevin J Williams
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Stefano Romeo
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Mathias Uhlén
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Rosie Perkins
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden.
| | - Marja-Riitta Taskinen
- Research Programs Unit, Diabetes and Obesity, University of Helsinki and Department of Internal Medicine, Helsinki University Hospital, Helsinki, Finland
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg, and Sahlgrenska University Hospital, Gothenburg, Sweden.
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15
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Keating BJ, Pereira AC, Snyder M, Piening BD. Applying genomics in heart transplantation. Transpl Int 2018; 31:278-290. [PMID: 29363220 PMCID: PMC5990370 DOI: 10.1111/tri.13119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/18/2017] [Accepted: 01/17/2018] [Indexed: 12/13/2022]
Abstract
While advances in patient care and immunosuppressive pharmacotherapies have increased the lifespan of heart allograft recipients, there are still significant comorbidities post-transplantation and 5-year survival rates are still significant, at approximately 70%. The last decade has seen massive strides in genomics and other omics fields, including transcriptomics, with many of these advances now starting to impact heart transplant clinical care. This review summarizes a number of the key advances in genomics which are relevant for heart transplant outcomes, and we highlight the translational potential that such knowledge may bring to patient care within the next decade.
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Affiliation(s)
- Brendan J. Keating
- Division of Transplantation, Department of Surgery, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandre C. Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School Hospital, São Paulo, Brazil
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA
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16
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Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP. Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. Cell Syst 2018; 6:157-170.e8. [PMID: 29361466 PMCID: PMC6021558 DOI: 10.1016/j.cels.2017.12.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/09/2017] [Accepted: 12/14/2017] [Indexed: 12/16/2022]
Abstract
Advances in omics technologies now allow an unprecedented level of phenotyping for human diseases, including obesity, in which individual responses to excess weight are heterogeneous and unpredictable. To aid the development of better understanding of these phenotypes, we performed a controlled longitudinal weight perturbation study combining multiple omics strategies (genomics, transcriptomics, multiple proteomics assays, metabolomics, and microbiomics) during periods of weight gain and loss in humans. Results demonstrated that: (1) weight gain is associated with the activation of strong inflammatory and hypertrophic cardiomyopathy signatures in blood; (2) although weight loss reverses some changes, a number of signatures persist, indicative of long-term physiologic changes; (3) we observed omics signatures associated with insulin resistance that may serve as novel diagnostics; (4) specific biomolecules were highly individualized and stable in response to perturbations, potentially representing stable personalized markers. Most data are available open access and serve as a valuable resource for the community.
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Affiliation(s)
- Brian D Piening
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hannes Röst
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gucci Jijuan Gu Urban
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tejaswini Mishra
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Blake M Hanson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Christine Y Yeh
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Canary Center at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA; Biomedical Informatics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Imon Banerjee
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cynthia Chen
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kimberly Kukurba
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dalia Perelman
- Division of Endocrinology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Colleen Craig
- Division of Endocrinology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elizabeth Colbert
- Division of Endocrinology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Denis Salins
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shannon Rego
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sunjae Lee
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jessica Wheeler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - M Reza Sailani
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liang Liang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles Abbott
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ulf Smith
- Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel L Rubin
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sharon Pitteri
- Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Canary Center at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Tracey L McLaughlin
- Division of Endocrinology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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17
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Affiliation(s)
- Brian D Piening
- Molecular Genomics Laboratory, Providence Portland Medical Center, Portland, OR
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Research Center, Providence Portland Cancer Center, Portland, OR
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18
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Lee S, Zhang C, Liu Z, Klevstig M, Mukhopadhyay B, Bergentall M, Cinar R, Ståhlman M, Sikanic N, Park JK, Deshmukh S, Harzandi AM, Kuijpers T, Grøtli M, Elsässer SJ, Piening BD, Snyder M, Smith U, Nielsen J, Bäckhed F, Kunos G, Uhlen M, Boren J, Mardinoglu A. Network analyses identify liver-specific targets for treating liver diseases. Mol Syst Biol 2017; 13:938. [PMID: 28827398 PMCID: PMC5572395 DOI: 10.15252/msb.20177703] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 01/02/2023] Open
Abstract
We performed integrative network analyses to identify targets that can be used for effectively treating liver diseases with minimal side effects. We first generated co-expression networks (CNs) for 46 human tissues and liver cancer to explore the functional relationships between genes and examined the overlap between functional and physical interactions. Since increased de novo lipogenesis is a characteristic of nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC), we investigated the liver-specific genes co-expressed with fatty acid synthase (FASN). CN analyses predicted that inhibition of these liver-specific genes decreases FASN expression. Experiments in human cancer cell lines, mouse liver samples, and primary human hepatocytes validated our predictions by demonstrating functional relationships between these liver genes, and showing that their inhibition decreases cell growth and liver fat content. In conclusion, we identified liver-specific genes linked to NAFLD pathogenesis, such as pyruvate kinase liver and red blood cell (PKLR), or to HCC pathogenesis, such as PKLR, patatin-like phospholipase domain containing 3 (PNPLA3), and proprotein convertase subtilisin/kexin type 9 (PCSK9), all of which are potential targets for drug development.
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Affiliation(s)
- Sunjae Lee
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Zhengtao Liu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Martina Klevstig
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bani Mukhopadhyay
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Mattias Bergentall
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Resat Cinar
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Marcus Ståhlman
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Natasha Sikanic
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Joshua K Park
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Sumit Deshmukh
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Azadeh M Harzandi
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Tim Kuijpers
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Simon J Elsässer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Brian D Piening
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ulf Smith
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jens Nielsen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - George Kunos
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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19
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Murakami-Sekimata A, Huang D, Piening BD, Bangur C, Paulovich AG. The Saccharomyces cerevisiae RAD9, RAD17 and RAD24 genes are required for suppression of mutagenic post-replicative repair during chronic DNA damage. DNA Repair (Amst) 2010; 9:824-34. [PMID: 20472512 DOI: 10.1016/j.dnarep.2010.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/25/2010] [Accepted: 04/16/2010] [Indexed: 12/31/2022]
Abstract
In Saccharomyces cerevisiae, a DNA damage checkpoint in the S-phase is responsible for delaying DNA replication in response to genotoxic stress. This pathway is partially regulated by the checkpoint proteins Rad9, Rad17 and Rad24. Here, we describe a novel hypermutable phenotype for rad9Delta, rad17Delta and rad24Delta cells in response to a chronic 0.01% dose of the DNA alkylating agent MMS. We report that this hypermutability results from DNA damage introduction during the S-phase and is dependent on a functional translesion synthesis pathway. In addition, we performed a genetic screen for interactions with rad9Delta that confer sensitivity to 0.01% MMS. We report and quantify 25 genetic interactions with rad9Delta, many of which involve the post-replication repair machinery. From these data, we conclude that defects in S-phase checkpoint regulation lead to increased reliance on mutagenic translesion synthesis, and we describe a novel role for members of the S-phase DNA damage checkpoint in suppressing mutagenic post-replicative repair in response to sublethal MMS treatment.
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20
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Piening BD, Wang P, Subramanian A, Paulovich AG. A radiation-derived gene expression signature predicts clinical outcome for breast cancer patients. Radiat Res 2009; 171:141-54. [PMID: 19267539 DOI: 10.1667/rr1223.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Activation of the DNA damage response pathway is a hallmark for early tumorigenesis, while loss of pathway activity is associated with disease progression. Thus we hypothesized that a gene expression signature associated with the DNA damage response may serve as a prognostic signature for outcome in cancer patients. We identified ionizing radiation-responsive transcripts in human lymphoblast cells derived from 12 individuals and used this signature to screen a panel of cancer data sets for the ability to predict long-term survival of cancer patients. We demonstrate that gene sets induced or repressed by ionizing radiation can predict clinical outcome in two independent breast cancer data sets, and we compare the radiation signature to previously described gene expression-based outcome predictors. While genes repressed in response to radiation likely represent the well-characterized proliferation signature predictive of breast cancer outcome, genes induced by radiation likely encode additional information representing other deregulated biological properties of tumors such as checkpoint or apoptotic responses.
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Affiliation(s)
- Brian D Piening
- Fred Hutchinson Cancer Research Center, Seattle Washington, USA
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21
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Whiteaker JR, Zhang H, Zhao L, Wang P, Kelly-Spratt KS, Ivey RG, Piening BD, Feng LC, Kasarda E, Gurley KE, Eng JK, Chodosh LA, Kemp CJ, McIntosh MW, Paulovich AG. Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res 2007; 6:3962-75. [PMID: 17711321 DOI: 10.1021/pr070202v] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Despite their potential to impact diagnosis and treatment of cancer, few protein biomarkers are in clinical use. Biomarker discovery is plagued with difficulties ranging from technological (inability to globally interrogate proteomes) to biological (genetic and environmental differences among patients and their tumors). We urgently need paradigms for biomarker discovery. To minimize biological variation and facilitate testing of proteomic approaches, we employed a mouse model of breast cancer. Specifically, we performed LC-MS/MS of tumor and normal mammary tissue from a conditional HER2/Neu-driven mouse model of breast cancer, identifying 6758 peptides representing >700 proteins. We developed a novel statistical approach (SASPECT) for prioritizing proteins differentially represented in LC-MS/MS datasets and identified proteins over- or under-represented in tumors. Using a combination of antibody-based approaches and multiple reaction monitoring-mass spectrometry (MRM-MS), we confirmed the overproduction of multiple proteins at the tissue level, identified fibulin-2 as a plasma biomarker, and extensively characterized osteopontin as a plasma biomarker capable of early disease detection in the mouse. Our results show that a staged pipeline employing shotgun-based comparative proteomics for biomarker discovery and multiple reaction monitoring for confirmation of biomarker candidates is capable of finding novel tissue and plasma biomarkers in a mouse model of breast cancer. Furthermore, the approach can be extended to find biomarkers relevant to human disease.
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22
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Whiteaker JR, Zhang H, Eng JK, Fang R, Piening BD, Feng LC, Lorentzen TD, Schoenherr RM, Keane JF, Holzman T, Fitzgibbon M, Lin C, Zhang H, Cooke K, Liu T, Camp DG, Anderson L, Watts J, Smith RD, McIntosh MW, Paulovich AG. Head-to-Head Comparison of Serum Fractionation Techniques. J Proteome Res 2007; 6:828-36. [PMID: 17269739 DOI: 10.1021/pr0604920] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multiple approaches for simplifying the serum proteome have been described. These techniques are generally developed across different laboratories, samples, mass spectrometry platforms, and analysis tools. Hence, comparing the available schemes is impossible from the existing literature because of confounding variables. We describe a head-to-head comparison of several serum fractionation schemes, including N-linked glycopeptide enrichment, cysteinyl-peptide enrichment, magnetic bead separation (C3, C8, and WCX), size fractionation, protein A/G depletion, and immunoaffinity column depletion of abundant serum proteins. Each technique was compared to results obtained from unfractionated human serum. The results show immunoaffinity subtraction is the most effective means for simplifying the serum proteome while maintaining reasonable sample throughput. The reported dataset is publicly available and provides a standard against which emergent technologies can be compared and evaluated for their contribution to serum-based biomarker discovery.
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Affiliation(s)
- Jeffrey R Whiteaker
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109-1024, USA
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23
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Whiteaker JR, Zhao L, Zhang HY, Feng LC, Piening BD, Anderson L, Paulovich AG. Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Anal Biochem 2006; 362:44-54. [PMID: 17241609 PMCID: PMC1852426 DOI: 10.1016/j.ab.2006.12.023] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 12/05/2006] [Accepted: 12/12/2006] [Indexed: 12/17/2022]
Abstract
A major bottleneck for validation of new clinical diagnostics is the development of highly sensitive and specific assays for quantifying proteins. We previously described a method, stable isotope standards with capture by antipeptide antibodies, wherein a specific tryptic peptide is selected as a stoichiometric representative of the protein from which it is cleaved, is enriched from biological samples using immobilized antibodies, and is quantitated using mass spectrometry against a spiked internal standard to yield a measure of protein concentration. In this study, we optimized a magnetic-bead-based platform amenable to high-throughput peptide capture and demonstrated that antibody capture followed by mass spectrometry can achieve ion signal enhancements on the order of 10(3), with precision (CVs <10%) and accuracy (relative error approximately 20%) sufficient for quantifying biomarkers in the physiologically relevant ng/mL range. These methods are generally applicable to any protein or biological fluid of interest and hold great potential for providing a desperately needed bridging technology between biomarker discovery and clinical application.
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Affiliation(s)
- Jeffrey R Whiteaker
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., PO Box 19024, Seattle, WA 98109-1024, USA
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24
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Piening BD, Wang P, Bangur CS, Whiteaker J, Zhang H, Feng LC, Keane JF, Eng JK, Tang H, Prakash A, McIntosh MW, Paulovich A. Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles. J Proteome Res 2006; 5:1527-34. [PMID: 16823959 DOI: 10.1021/pr050436j] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantitative proteomic profiling using liquid chromatography-mass spectrometry is emerging as an important tool for biomarker discovery, prompting development of algorithms for high-throughput peptide feature detection in complex samples. However, neither annotated standard data sets nor quality control metrics currently exist for assessing the validity of feature detection algorithms. We propose a quality control metric, Mass Deviance, for assessing the accuracy of feature detection tools. Because the Mass Deviance metric is derived from the natural distribution of peptide masses, it is machine- and proteome-independent and enables assessment of feature detection tools in the absence of completely annotated data sets. We validate the use of Mass Deviance with a second, independent metric that is based on isotopic distributions, demonstrating that we can use Mass Deviance to identify aberrant features with high accuracy. We then demonstrate the use of independent metrics in tandem as a robust way to evaluate the performance of peptide feature detection algorithms. This work is done on complex LC-MS profiles of Saccharomyces cerevisiae which present a significant challenge to peptide feature detection algorithms.
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Affiliation(s)
- Brian D Piening
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, Washington, 98109, USA
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Hakim AH, Piening BD, McCormick NJ. Near-asymptotic angle dependence of ocean optical radiance. Appl Opt 2004; 43:5825-5831. [PMID: 15540440 DOI: 10.1364/ao.43.005825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The approach of ocean optical radiance to an approximate asymptotic dependence with increasing depth in spatially uniform waters is numerically examined for a variety of sea surface illumination conditions.
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Affiliation(s)
- Ammar H Hakim
- Department of Mechanical Engineering, University of Washington, Seattle, Washington 98195-2600, USA.
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26
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Abstract
The depth dependence for which the downward diffuse attenuation coefficient, the upward-to-downward plane irradiance ratio, the vertically upward radiance-to-downward plane irradiance ratio, and the mean cosine of the radiance depend negligibly on the surface incident illumination have been examined. The depths at which these coefficients approach to within a specified percent of their asymptotic values depends significantly on the characteristics of the incident illumination and on the inherent optical properties of the water. This information is useful when solving inverse ocean optics problems with a method for which the radiance is assumed to be approximately in the asymptotic regime.
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Affiliation(s)
- Brian D Piening
- Department of Mechanical Engineering, University of Washington, Seattle, Washington 98195-2600, USA
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