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Hwang WL, Su J, Shiau C, Wang PL, Guo JA, Lester NA, Barth JL, Hoffman HI, Aguirre A, Hong TS, Wo JY, Ting D, Zheng L, Mino-Kenudson M, Jacks T. Molecular Mechanisms of Intratumoral Nerve Recruitment and Perineural Invasion Elucidated with Spatial Transcriptomics and CRISPR Activation. Int J Radiat Oncol Biol Phys 2023; 117:S21. [PMID: 37784453 DOI: 10.1016/j.ijrobp.2023.06.244] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Perineural invasion (PNI) is an aggressive manifestation of tumor-nerve interactions associated with postoperative recurrence, metastasis, pain, and decreased survival. Hence, PNI is included in the staging criteria of several malignancies and often an indication for treatment intensification using adjuvant radiotherapy. However, the diverse molecular mechanisms underlying tumor-nerve crosstalk remain largely unknown-hindering the development of new therapies targeting this key pathological process. Moreover, prior studies were limited by a lack of cell-type information, spatial context, and/or a fragmented focus on a small number of pathways. MATERIALS/METHODS Using pancreatic ductal adenocarcinoma (PDAC) as an exemplar given the exceptionally high frequency of PNI in this malignancy, we performed the first comprehensive, cell-type specific, and spatially resolved whole-transcriptome analysis of human PDAC to identify molecular mediators of tumor-nerve crosstalk and PNI. We constructed 12 custom tissue microarrays (TMAs) derived from matched malignant regions with and without tumor-nerve proximity (n = 288 cores). We performed whole-transcriptome digital spatial profiling (DSP) to independently determine mRNA abundance from the malignant, fibroblast, and nerve compartments through optical sectioning. RESULTS We mapped malignant subtypes we previously identified onto the spatial data and found strong (p<0.0001) positive nerve associations with the mesenchymal, basaloid, and neural-like progenitor subtypes and a negative nerve association with the classical subtype. Numerous genes expressed by malignant cells were enriched (e.g., MMP2, PLXND1, NRP1) or depleted (e.g., SEMA3B) in association with radial distance from nerves, including recapitulation of prior literature. To functionally explore these candidate mediators of tumor-nerve crosstalk, we derived genetically-engineered murine organoids (KrasLSL-G12D/+; Trp53FL/FL; Rosa26-dCas9-VPR) and transduced them with guide RNAs to overexpress subtype-specific transcription factors or candidate genes from the spatial analysis. We quantified (1) cancer cell invasion through extracellular matrix using cultured dorsal root ganglia (DRG) sensory neurons as the chemoattractant, and (2) the role of cancer-intrinsic signaling on nerve recruitment/outgrowth by applying conditioned media or exogenous proteins to cultured DRG sensory neurons and tracking their growth with live imaging. CONCLUSION Our results suggest that the mechanisms enabling cancer cells to recruit nerves into the tumor microenvironment are distinct from those facilitating perineural invasion. This study has transformed our understanding of how cancer cells and the peripheral nervous system collaborate to promote tumor growth, survival, and dissemination, and is now guiding prioritization of therapeutic strategies that synergize with adjuvant radiotherapy in the burgeoning field of cancer neuroscience.
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Affiliation(s)
- W L Hwang
- Harvard Medical School / Massachusetts General Hospital, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA
| | - J Su
- Massachusetts General Hospital, BOSTON, MA
| | - C Shiau
- Massachusetts General Hospital, Boston, MA
| | - P L Wang
- Massaschusetts General Hospital, Boston, MA
| | - J A Guo
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - N A Lester
- Massaschusetts General Hospital, Boston, MA
| | - J L Barth
- Massaschusetts General Hospital, Boston, MA
| | | | - A Aguirre
- Dana-Farber Cancer Institute, Boston, MA
| | - T S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - J Y Wo
- Newton-Wellesley Hospital, Newton, MA
| | - D Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - L Zheng
- Department of Medical Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - T Jacks
- Massachusetts Institute of Technology, Cambridge, MA
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2
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Shiau C, Cao J, Gregory MT, Gong D, Yin X, Cho JW, Wang PL, Su J, Wang S, Reeves JW, Kim TK, Kim Y, Guo JA, Lester NA, Schurman N, Barth JL, Weissleder R, Jacks T, Qadan M, Hong TS, Wo JY, Roberts H, Beechem JM, Castillo CFD, Mino-Kenudson M, Ting DT, Hemberg M, Hwang WL. Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis. bioRxiv 2023:2023.06.28.546848. [PMID: 37425692 PMCID: PMC10327107 DOI: 10.1101/2023.06.28.546848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In combination with cell intrinsic properties, interactions in the tumor microenvironment modulate therapeutic response. We leveraged high-plex single-cell spatial transcriptomics to dissect the remodeling of multicellular neighborhoods and cell-cell interactions in human pancreatic cancer associated with specific malignant subtypes and neoadjuvant chemotherapy/radiotherapy. We developed Spatially Constrained Optimal Transport Interaction Analysis (SCOTIA), an optimal transport model with a cost function that includes both spatial distance and ligand-receptor gene expression. Our results uncovered a marked change in ligand-receptor interactions between cancer-associated fibroblasts and malignant cells in response to treatment, which was supported by orthogonal datasets, including an ex vivo tumoroid co-culture system. Overall, this study demonstrates that characterization of the tumor microenvironment using high-plex single-cell spatial transcriptomics allows for identification of molecular interactions that may play a role in the emergence of chemoresistance and establishes a translational spatial biology paradigm that can be broadly applied to other malignancies, diseases, and treatments.
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Affiliation(s)
- Carina Shiau
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jingyi Cao
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Dennis Gong
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard-MIT Health Sciences and Technology Program, Cambridge, MA, USA
| | - Xunqin Yin
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jae-Won Cho
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter L Wang
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jennifer Su
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven Wang
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | - Jimmy A Guo
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Nicole A Lester
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jamie L Barth
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Motaz Qadan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer Y Wo
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hannah Roberts
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin Hemberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - William L Hwang
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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3
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Hwang WL, Su J, Shiau C, Wang PL, Guo JA, Lester NA, Barth JL, Hoffman HI, Divakar P, Reeves JW, Miller E, Beechem JM, Aguirre AJ, Zheng L, Ting DT, Mino-Kenudson M, Jacks T. Abstract 2513: Distinct cancer-intrinsic mechanisms mediate nerve recruitment/outgrowth versus perineural invasion. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2513] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) features abundant perineural invasion (PNI). Intra-tumoral nerves play critical roles in cancer initiation, progression, recurrence, treatment-resistance, metastasis, and mortality for many malignancies but the diverse molecular mechanisms underlying tumor-nerve crosstalk remain largely unknown—hindering the development of therapies targeting this key pathological process. To address this gap, we performed whole transcriptome digital spatial profiling on twelve custom tissue microarrays (n=288 cores) derived from intratumorally-matched regions with and without PNI in primary PDAC specimens (n=31 patients) and independently measured gene expression from cancer cells, fibroblasts, and nerves. We undertook a differential gene expression analysis comparing malignant cells in PNI-present and -absent regions. We quantified the growth kinetics of dorsal root ganglia (DRG) sensory neurons cultured with exogenous candidate proteins, which validated that some candidates augment (e.g., Lgals1) and others inhibit (e.g., Sema3b) neurite outgrowth. Next, we mapped our previously discovered malignant cell programs onto the epithelial segments and observed a significant enrichment of the mesenchymal, basal-like, and neural-like progenitor (NRP) programs versus depletion of the classical program in PNI-present regions. To determine the effects of malignant subtype on nerve outgrowth, we engineered isogenic KrasG12D/+;Trp53FL/FL;Rosa26-dCas9-VPR (KP;dCas9-VPR) organoids to overexpress the master transcription factors (TFs) for each malignant subtype (e.g., Gata6 for classical, Glis3 for NRP). We then performed the DRG neuronal outgrowth assay using conditioned media from each subtype-specific organoid line versus an off-target control and observed that the classical line suppressed neurite outgrowth, the mesenchymal and basal-like lines were neutral, and the NRP line enhanced neurite outgrowth dynamics comparable to the Ngf positive control. Taken together, our findings suggest that the mechanisms underlying nerve recruitment/outgrowth and perineural invasion may be partly decoupled. To further test this hypothesis, we are performing transwell invasion assays comparing KP;dCas9-VPR cancer cell lines that overexpress each of the candidate PNI-associated genes and malignant subtype TFs. We anticipate that this study will transform our understanding of how cancer cells and the peripheral nervous system collaborate and guide prioritization for therapeutic intervention in the burgeoning cancer neuroscience field.
Citation Format: William L. Hwang, Jennifer Su, Carina Shiau, Peter L. Wang, Jimmy A. Guo, Nicole A. Lester, Jaimie L. Barth, Hannah I. Hoffman, Prajan Divakar, Jason W. Reeves, Eric Miller, Joseph M. Beechem, Andrew J. Aguirre, Lei Zheng, David T. Ting, Mari Mino-Kenudson, Tyler Jacks. Distinct cancer-intrinsic mechanisms mediate nerve recruitment/outgrowth versus perineural invasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2513.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Lei Zheng
- 5Johns Hopkins University, Baltimore, MD
| | | | | | - Tyler Jacks
- 6Massachusetts Institute of Technology, Cambridge, MA
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4
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Christie KA, Guo JA, Silverstein RA, Doll RM, Mabuchi M, Stutzman HE, Lin J, Ma L, Walton RT, Pinello L, Robb GB, Kleinstiver BP. Precise DNA cleavage using CRISPR-SpRYgests. Nat Biotechnol 2023; 41:409-416. [PMID: 36203014 PMCID: PMC10023266 DOI: 10.1038/s41587-022-01492-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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] [Received: 11/17/2021] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Methods for in vitro DNA cleavage and molecular cloning remain unable to precisely cleave DNA directly adjacent to bases of interest. Restriction enzymes (REs) must bind specific motifs, whereas wild-type CRISPR-Cas9 or CRISPR-Cas12 nucleases require protospacer adjacent motifs (PAMs). Here we explore the utility of our previously reported near-PAMless SpCas9 variant, named SpRY, to serve as a universal DNA cleavage tool for various cloning applications. By performing SpRY DNA digests (SpRYgests) using more than 130 guide RNAs (gRNAs) sampling a wide diversity of PAMs, we discovered that SpRY is PAMless in vitro and can cleave DNA at practically any sequence, including sites refractory to cleavage with wild-type SpCas9. We illustrate the versatility and effectiveness of SpRYgests to improve the precision of several cloning workflows, including those not possible with REs or canonical CRISPR nucleases. We also optimize a rapid and simple one-pot gRNA synthesis protocol to streamline SpRYgest implementation. Together, SpRYgests can improve various DNA engineering applications that benefit from precise DNA breaks.
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Affiliation(s)
- Kathleen A Christie
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jimmy A Guo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Rachel A Silverstein
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Roman M Doll
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Molecular Biosciences/Cancer Biology Program, Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hannah E Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Jiecong Lin
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Molecular Pathology Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital Charlestown, Boston, MA, USA
| | - Linyuan Ma
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Russell T Walton
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luca Pinello
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Molecular Pathology Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital Charlestown, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
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5
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Guo JA, Su J, Jambhale A, Dilly J, Hennessey CJ, Shiau C, Yu P, Wang S, Wang J, Abbassi L, Neiswender J, Bertea T, Yang A, Yu Q, Westcott P, Schenkel J, Kim DY, Hoffman HI, Jaramillo GC, Uribe GA, Wu WW, Mehta A, Ting D, Pacheco JA, Deik A, Clish C, Vazquez F, Wolpin B, Regev A, Freed-Pastor WA, Mancias JD, Jacks T, Hwang WL, Aguirre AJ. Abstract A052: Systematic dissection of transcriptional states in pancreatic cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-a052] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract
Transcriptional states in pancreatic cancer can stratify patients by response to chemotherapy and clinical outcomes. These include the classical and basal-like states as well as a newly identified neural-like progenitor (NRP) state, which we have previously found to be enriched in primary patient tumors treated with neoadjuvant chemotherapy and radiotherapy. While several transcription factor drivers of classical and basal-like identity have been described, key regulators of the NRP state are unknown. Through in silico approaches, we identified candidate transcription factors of the NRP state, including GLIS3, a Krüppel-like zinc finger protein that mediates neuroendocrine fate during pancreatic development and differentiation of human embryonic stem cells into posterior neural progenitor cells. Our understanding of biologic and clinically-relevant attributes of transcriptional cell states remains limited by state-specific biases in various preclinical models. Existing human cell lines maintained as two-dimensional cultures tend to preferentially represent the basal-like state, whereas human three-dimensional organoid models grown in standard culture conditions best reflect the classical state. These phenotypes are therefore impacted by culture conditions as well as underlying genetic features. Furthermore, most murine pancreatic cancer models do not fully reflect the classical vs. basal-like state heterogeneity observed in humans. To enable systematic study of the classical, basal-like and NRP phenotypes, we developed isogenic KP (KrasG12D/+;Trp53FL/FL) murine organoids with a germline dCas9-VPR system to enable facile overexpression of state-specific transcription factors through CRISPR activation approaches. Quantitative PCR, RNA-sequencing, and proteomics confirmed Gata6, deltaN Trp63, and Glis3 as drivers of classical, basal-like, and NRP identity, respectively. DeltaN Trp63 organoids were further differentiated by loss of luminal morphology. Pairwise comparisons of global transcriptional alterations suggest the greatest similarities between the Gata6- and Glis3-overexpressed models, which is consistent with enhanced associations between classical and NRP states in patient tumors. Finally, although basal-like and NRP states are associated with poorer response to multi-agent chemotherapy, state-specific therapeutic sensitivities to other treatments remain incompletely defined. We therefore performed drug sensitivity assays with a panel of targeted therapies and unveiled state-specific sensitivities. These data were corroborated by drug sensitivity profiling of human patient-derived organoids and cell lines. Taken together, these results suggest a framework for defining cell state-specific vulnerabilities that may aid in stratifying and treating pancreatic cancer patients with new therapies.
Citation Format: Jimmy A. Guo, Jennifer Su, Ananya Jambhale, Julien Dilly, Connor J. Hennessey, Carina Shiau, Patrick Yu, Steven Wang, Junning Wang, Laleh Abbassi, James Neiswender, Tate Bertea, Annan Yang, Qijia Yu, Peter Westcott, Jason Schenkel, Daniel Y. Kim, Hannah I. Hoffman, Grissel Cervantes Jaramillo, Giselle A. Uribe, Westley W. Wu, Arnav Mehta, David Ting, Julian A. Pacheco, Amy Deik, Clary Clish, Francisca Vazquez, Brian Wolpin, Aviv Regev, William A. Freed-Pastor, Joseph D. Mancias, Tyler Jacks, William L. Hwang, Andrew J. Aguirre. Systematic dissection of transcriptional states in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A052.
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Affiliation(s)
- Jimmy A. Guo
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | - Carina Shiau
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Patrick Yu
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Steven Wang
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | - Tate Bertea
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Annan Yang
- 3Dana Farber Cancer Institute, Boston, MA,
| | - Qijia Yu
- 3Dana Farber Cancer Institute, Boston, MA,
| | | | | | | | | | | | | | | | - Arnav Mehta
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - David Ting
- 6Massachusetts General Hospital, Boston, MA,
| | | | - Amy Deik
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Clary Clish
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
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6
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Hwang WL, Su J, Guo JA, Shiau C, Barth JL, Hoffman HI, Divakar P, Reeves JW, Miller E, Cervantes-Jaramillo G, Freed-Pastor W, Funes V, Wo JY, Hong TS, Castillo CFD, Zheng L, Aguirre AJ, Ting DT, Mino-Kenudson M, Jacks T. Abstract C052: Identifying mediators of perineural invasion in pancreatic cancer using spatial transcriptomics. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-c052] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract
Intratumoral nerves play important and versatile roles in cancer initiation, progression, recurrence, treatment-resistance, metastasis, morbidity, and mortality for many malignancies but the diverse molecular mechanisms underlying tumor-nerve crosstalk remain largely unknown. One of the differentiating hallmarks of pancreatic ductal adenocarcinoma (PDAC) is an exceptionally high frequency of perineural invasion (PNI), a histopathologic manifestation of tumor-nerve crosstalk whereby cancer cells recruit, migrate towards, and envelop or invade peripheral nerves. Evidence for some neurochemicals/neurotrophins involved in PNI have been uncovered, but most of the underlying work was limited by a lack of cell-type specificity, spatial context, and fragmented focus on individual pathways. To address these shortcomings, we set out to comprehensively identify cell-type specific genes spatially linked to PNI in patient tumors and then dissect the functional roles of these genes through live imaging of dorsal root ganglia (DRG) sensory neurons incubated in conditioned media from cancer cell organoids overexpressing candidate genes via CRISPR activation (CRISPRa). First, we performed whole transcriptome digital spatial profiling (NanoString GeoMx) on twelve custom tissue microarrays (n=288 cores) derived from intratumorally-matched malignant regions with and without PNI in primary resected PDAC specimens (n=31 patients). Differential gene expression (DE) analysis (FDR < 0.001) for PNI demonstrated that for malignant cells there were 271 enriched and 65 depleted genes, and for fibroblasts there were 16 enriched and 27 depleted genes. We further evaluated associations between PNI and expression of malignant subtypes previously identified from single-nucleus RNA-seq applied to 43 primary resected PDAC specimens. We found that malignant cells engaged in PNI were enriched in the mesenchymal, basaloid and neural-like progenitor (NRP) subtypes and depleted in the classical subtype. To test these associations functionally, we generated isogenic murine organoid lines (KrasG12D/+;Trp53FL/FL;R26-dCas9-VPR) overexpressing subtype-driving transcription factors and collected conditioned media. DRG sensory neurons demonstrate enhanced and suppressed growth kinetics when grown in NRP and classical conditioned media, respectively; mesenchymal and basal-like conditioned media do not appear to influence growth kinetics. These results suggest that while mesenchymal, basaloid, and NRP cells likely all play a role in cancer cell invasion of nerves, NRP cells may have an additional role in tumor-nerve tropism. Additional experiments exploring the functional effects of the top enriched and depleted genes from the DE analysis are ongoing. We anticipate that this study will provide a high-resolution understanding of critical intercellular interactions in the PDAC tumor microenvironment that facilitate PNI and tumor-nerve crosstalk more broadly to guide novel therapeutic strategies.
Citation Format: William L. Hwang, Jennifer Su, Jimmy A. Guo, Carina Shiau, Jaimie L. Barth, Hannah I. Hoffman, Prajan Divakar, Jason W. Reeves, Eric Miller, Grissel Cervantes-Jaramillo, William Freed-Pastor, Vanessa Funes, Jennifer Y. Wo, Theodore S. Hong, Carlos Fernandez-del Castillo, Lei Zheng, Andrew J. Aguirre, David T. Ting, Mari Mino-Kenudson, Tyler Jacks. Identifying mediators of perineural invasion in pancreatic cancer using spatial transcriptomics [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C052.
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Affiliation(s)
| | - Jennifer Su
- 2Massachusetts Institute of Technology, Cambridge, MA,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lei Zheng
- 6Johns Hopkins University, Baltimore, MD,
| | | | | | | | - Tyler Jacks
- 2Massachusetts Institute of Technology, Cambridge, MA,
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7
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Shiau C, Su J, Guo JA, Hong TS, Wo JY, Jagadeesh KA, Hwang WL. Treatment-associated remodeling of the pancreatic cancer endothelium at single-cell resolution. Front Oncol 2022; 12:929950. [PMID: 36185212 PMCID: PMC9524152 DOI: 10.3389/fonc.2022.929950] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 04/27/2022] [Accepted: 08/19/2022] [Indexed: 11/14/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most treatment refractory and lethal malignancies. The diversity of endothelial cell (EC) lineages in the tumor microenvironment (TME) impacts the efficacy of antineoplastic therapies, which in turn remodel EC states and distributions. Here, we present a single-cell resolution framework of diverse EC lineages in the PDAC TME in the context of neoadjuvant chemotherapy, radiotherapy, and losartan. We analyzed a custom single-nucleus RNA-seq dataset derived from 37 primary PDAC specimens (18 untreated, 14 neoadjuvant FOLFIRINOX + chemoradiotherapy, 5 neoadjuvant FOLFIRINOX + chemoradiotherapy + losartan). A single-nucleus transcriptome analysis of 15,185 EC profiles revealed two state programs (ribosomal, cycling), four lineage programs (capillary, arterial, venous, lymphatic), and one program that did not overlap significantly with prior signatures but was enriched in pathways involved in vasculogenesis, stem-like state, response to wounding and hypoxia, and endothelial-to-mesenchymal transition (reactive EndMT). A bulk transcriptome analysis of two independent cohorts (n = 269 patients) revealed that the lymphatic and reactive EndMT lineage programs were significantly associated with poor clinical outcomes. While losartan and proton therapy were associated with reduced lymphatic ECs, these therapies also correlated with an increase in reactive EndMT. Thus, the development and inclusion of EndMT-inhibiting drugs (e.g., nintedanib) to a neoadjuvant chemoradiotherapy regimen featuring losartan and/or proton therapy may be most effective in depleting both lymphatic and reactive EndMT populations and potentially improving patient outcomes.
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Affiliation(s)
- Carina Shiau
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
| | - Jennifer Su
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
| | - Jimmy A. Guo
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, United States
| | - Theodore S. Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Jennifer Y. Wo
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Karthik A. Jagadeesh
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
- *Correspondence: William L. Hwang, ; Karthik A. Jagadeesh,
| | - William L. Hwang
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
- *Correspondence: William L. Hwang, ; Karthik A. Jagadeesh,
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8
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Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Yadollahpour P, Reeves JW, Mohan R, Drokhlyansky E, Van Wittenberghe N, Ashenberg O, Farhi SL, Schapiro D, Divakar P, Miller E, Zollinger DR, Eng G, Schenkel JM, Su J, Shiau C, Yu P, Freed-Pastor WA, Abbondanza D, Mehta A, Gould J, Lambden C, Porter CBM, Tsankov A, Dionne D, Waldman J, Cuoco MS, Nguyen L, Delorey T, Phillips D, Barth JL, Kem M, Rodrigues C, Ciprani D, Roldan J, Zelga P, Jorgji V, Chen JH, Ely Z, Zhao D, Fuhrman K, Fropf R, Beechem JM, Loeffler JS, Ryan DP, Weekes CD, Ferrone CR, Qadan M, Aryee MJ, Jain RK, Neuberg DS, Wo JY, Hong TS, Xavier R, Aguirre AJ, Rozenblatt-Rosen O, Mino-Kenudson M, Castillo CFD, Liss AS, Ting DT, Jacks T, Regev A. Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment. Nat Genet 2022; 54:1178-1191. [PMID: 35902743 DOI: 10.1038/s41588-022-01134-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 06/16/2022] [Indexed: 12/24/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here, we construct a high-resolution molecular landscape of the cellular subtypes and spatial communities that compose PDAC using single-nucleus RNA sequencing and whole-transcriptome digital spatial profiling (DSP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment naive. We uncovered recurrent expression programs across malignant cells and fibroblasts, including a newly identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities with distinct contributions from malignant, fibroblast and immune subtypes: classical, squamoid-basaloid and treatment enriched. Our refined molecular and cellular taxonomy can provide a framework for stratification in clinical trials and serve as a roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.
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Affiliation(s)
- William L Hwang
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karthik A Jagadeesh
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jimmy A Guo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA, USA
| | - Hannah I Hoffman
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT MD/PhD and Health Sciences and Technology Program, Harvard Medical School, Boston, MA, USA
| | - Payman Yadollahpour
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Rahul Mohan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Denis Schapiro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Institute for Computational Biomedicine and Institute of Pathology, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
| | | | | | | | - George Eng
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason M Schenkel
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer Su
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carina Shiau
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William A Freed-Pastor
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Arnav Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Joshua Gould
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | - Julia Waldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Toni Delorey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Devan Phillips
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marina Kem
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clifton Rodrigues
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Debora Ciprani
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jorge Roldan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Piotr Zelga
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vjola Jorgji
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zackery Ely
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | | | - Jay S Loeffler
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David P Ryan
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Colin D Weekes
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Motaz Qadan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rakesh K Jain
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Edwin L. Steele Laboratory for Tumor Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jennifer Y Wo
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theodore S Hong
- Center for Systems Biology and Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genentech, South San Francisco, CA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Andrew S Liss
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Genentech, South San Francisco, CA, USA.
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9
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Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Shiau C, Su J, Yadollahpour P, Reeves JW, Kim Y, Kim S, Gregory M, Divakar P, Miller E, Rhodes M, Warren S, Rueckert E, Fuhrman K, Zollinger DR, Fropf R, Beechem JM, Mehta A, Delorey T, McCabe C, Barth JL, Zelga P, Ferrone CR, Qadan M, Lillemoe KD, Jain RK, Wo JY, Hong TS, Xavier R, Rozenblatt-Rosen O, Aguirre AJ, Castillo CFD, Liss AS, Mino-Kenudson M, Ting DT, Jacks T, Regev A. Abstract SY12-04: Multicellular spatial community featuring a novel neuronal-like malignant phenotype is enriched in pancreatic cancer after neoadjuvant chemotherapy and radiotherapy. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-sy12-04] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is projected to be the second leading cause of cancer mortality in the United States by 2030. Given that resistance to cytotoxic therapy is pervasive, there is a critical need to elucidate salient gene expression programs and spatial relationships among malignant and stromal cells in the tumor microenvironment (TME), particularly in residual disease. We developed and applied a single-nucleus RNA-seq (snRNA-seq) technique to 43 banked frozen primary PDAC specimens that either received neoadjuvant therapy (n=25) or were treatment-naïve (n=18). We discovered expression programs across malignant cell and fibroblast profiles that formed the basis for a refined molecular taxonomy, including a novel neural-like progenitor (NRP) malignant program enriched with neoadjuvant treatment in tumors and organoids, and associated with the worst prognosis in bulk profiles from independent cohorts.
To elucidate how neoadjuvant treatment and cancer cell- and fibroblast-intrinsic programs modulate the composition of multicellular neighborhoods, we performed spatial profiling with the GeoMx[1] platform (NanoString) on 21 formalin-fixed paraffin-embedded sections using the human whole transcriptome atlas (WTA). Each tumor showed intra-tumoral heterogeneity in tissue architecture and regions of interest (ROIs) with diverse patterns of neoplastic cells, cancer-associated fibroblasts (CAFs), and immune cells were selected for profiling. We deconvolved the WTA data with our snRNA-seq cell type signatures and mapped expression programs onto the tumor architecture to reveal three distinct multicellular neighborhoods, which we annotated as classical, squamoid-basaloid, and treatment-enriched. The observed enrichment in post-treatment residual disease of multiple spatially-defined receptor-ligand interactions and a neighborhood featuring the NRP program, neurotropic CAF program, and CD8+ T cells may open new therapeutic opportunities.
Next, we mapped malignant/CAF programs and immune cell subsets at single-cell spatial resolution by performing spatial molecular imaging (SMI[2]; NanoString CosMx) using a panel of 960 RNA targets on a subset of seven tumors (2 untreated, 5 treated) and captured over 200,000 cells with an average of more than 450 transcripts detected per cell. Correlating ROIs from whole-transcriptome DSP to matched fields of view in kiloplex SMI enabled further dissection of PDAC architecture and treatment-associated remodeling of cell type distributions and receptor-ligand interactions.
Ongoing functional studies have begun to elucidate the key regulatory elements underlying the distinct treatment-associated NRP malignant program and its interactions with the TME. Overall, the complementary combination of snRNA-seq, whole-transcriptome DSP, and kiloplex SMI provides a high-resolution molecular framework that can be harnessed to augment precision oncology efforts in pancreatic cancer.
[1] GeoMx DSP is for Research Use Only and not for use in diagnostic procedures. [2] CosMx SMI is for Research Use Only and not for use in diagnostic procedures.
Citation Format: William L. Hwang, Karthik A. Jagadeesh, Jimmy A. Guo, Hannah I. Hoffman, Carina Shiau, Jennifer Su, Payman Yadollahpour, Jason W. Reeves, Youngmi Kim, Sean Kim, Mark Gregory, Prajan Divakar, Eric Miller, Michael Rhodes, Sarah Warren, Erroll Rueckert, Kit Fuhrman, Daniel R. Zollinger, Robin Fropf, Joseph M. Beechem, Arnav Mehta, Toni Delorey, Cristin McCabe, Jaimie L. Barth, Piotr Zelga, Cristina R. Ferrone, Motaz Qadan, Keith D. Lillemoe, Rakesh K. Jain, Jennifer Y. Wo, Theodore S. Hong, Ramnik Xavier, Orit Rozenblatt-Rosen, Andrew J. Aguirre, Carlos Fernandez-Del Castillo, Andrew S. Liss, Mari Mino-Kenudson, David T. Ting, Tyler Jacks, Aviv Regev. Multicellular spatial community featuring a novel neuronal-like malignant phenotype is enriched in pancreatic cancer after neoadjuvant chemotherapy and radiotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr SY12-04.
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Affiliation(s)
| | | | | | | | | | - Jennifer Su
- 4Massachusetts Institute of Technology, Cambridge, MA
| | | | | | | | - Sean Kim
- 5NanoString Technologies, Seattle, WA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tyler Jacks
- 4Massachusetts Institute of Technology, Cambridge, MA
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10
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Abstract
This genetic association study examines the tumor genomic profiles by race in a large, diverse patient cohort using next-generation sequencing (NGS) data in the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange.
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Affiliation(s)
- Neha Goel
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Jimmy A. Guo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Daniel Zhao
- Department of Human Genetics, University of California, Los Angeles, Los Angeles
| | - Brandon A. Mahal
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Mohammed Alshalalfa
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
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11
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Shi DD, Guo JA, Hoffman HI, Su J, Mino-Kenudson M, Barth JL, Schenkel JM, Loeffler JS, Shih HA, Hong TS, Wo JY, Aguirre AJ, Jacks T, Zheng L, Wen PY, Wang TC, Hwang WL. Therapeutic avenues for cancer neuroscience: translational frontiers and clinical opportunities. Lancet Oncol 2022; 23:e62-e74. [PMID: 35114133 PMCID: PMC9516432 DOI: 10.1016/s1470-2045(21)00596-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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] [Received: 06/22/2021] [Revised: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 02/03/2023]
Abstract
With increasing attention on the essential roles of the tumour microenvironment in recent years, the nervous system has emerged as a novel and crucial facilitator of cancer growth. In this Review, we describe the foundational, translational, and clinical advances illustrating how nerves contribute to tumour proliferation, stress adaptation, immunomodulation, metastasis, electrical hyperactivity and seizures, and neuropathic pain. Collectively, this expanding knowledge base reveals multiple therapeutic avenues for cancer neuroscience that warrant further exploration in clinical studies. We discuss the available clinical data, including ongoing trials investigating novel agents targeting the tumour-nerve axis, and the therapeutic potential for repurposing existing neuroactive drugs as an anti-cancer approach, particularly in combination with established treatment regimens. Lastly, we discuss the clinical challenges of these treatment strategies and highlight unanswered questions and future directions in the burgeoning field of cancer neuroscience.
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Affiliation(s)
- Diana D Shi
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Jimmy A Guo
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA; School of Medicine, University of California, San Francisco, San Francisco, CA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hannah I Hoffman
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Health Sciences and Technology Program, Harvard Medical School, Boston, MA, USA
| | - Jennifer Su
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jaimie L Barth
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason M Schenkel
- Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jay S Loeffler
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Helen A Shih
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Jennifer Y Wo
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tyler Jacks
- Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lei Zheng
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Timothy C Wang
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, USA
| | - William L Hwang
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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12
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Guo JA, Alshalalfa M, Kim DY, Hoffman HI, Shiau C, Su J, Hwang WL, Mahal BA. DNA repair and immune checkpoint blockade response. Cancer Genet 2022; 264-265:1-4. [DOI: 10.1016/j.cancergen.2022.02.007] [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: 08/17/2021] [Revised: 01/18/2022] [Accepted: 02/17/2022] [Indexed: 11/02/2022]
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13
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Guo JA, Zhao D, Ginebaugh SP, Wang S, Jambhale AD, Yu PZ, Wu WW, Chen P, Zhao M, Lowder KE, Kapner KS, Hoffman HI, Cheng SW, Kim DY, Boiarsky R, Aguet F, Paolella B, Krill-Burger JM, McFarland JM, Oni T, Jacks T, Regev A, Getz G, Hwang WL, Singh H, Aguirre AJ. Abstract PR-006: Integrative genomic characterization of therapeutic targets for pancreatic cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.panca21-pr-006] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Targeted therapies for molecularly-defined subtypes have led to immense clinical benefit for many cancer types but have generally not been successful for pancreatic cancer. Given that the mainstay of treatment remains multi-agent chemotherapy with FOLFIRINOX or gemcitabine/nab-paclitaxel, there remains an urgent need to identify novel actionable vulnerabilities for subsets of PDAC patients. Toward this end, we conducted an integrative, genome-scale examination of genetic dependencies and cell surface targets for PDAC by leveraging CRISPR and RNAi screening data from The Cancer Dependency Map Project, genomic data of bulk patient tumors from The Cancer Genome Atlas, and custom single-nucleus RNA-seq of a 43-patient cohort comprised of untreated and treated specimens. Our results re-affirm the prominence of Ras/MAPK signaling and a synthetically-lethal interaction between VPS4A/B, but also reveal recurrent susceptibilities to genes within the fatty acid metabolism, vesicular transport and exocytosis, and nucleobase synthesis pathways that otherwise have minor to moderate depleting effects on the majority of cell lines. Aberrations in frequent tumor suppressor genes and chromosomal arm-level variations appear to modify the strength of dependencies, including that of KRAS, CCND1, and GPX4, and may serve as predictive biomarkers of response. In addition, we leveraged mRNA profiling of bulk primary tumors as well as metastatic organoid models to conduct a genome-wide search for cell surface targets that are highly-expressed in tumors while lowly or not expressed in other toxicity-prone, non-malignant tissues. These putative drug targets do not need to be cancer dependencies and can be compatible with antibody-based therapeutic strategies that leverage alternative modes of cellular toxicity. Our approach identifies MSLN, NECTIN4, TROP2, and other antigens which have previously been shown to be largely tumor-specific but also reveals the expression of multiple putative targets within the CEACAM, claudin, and tetraspanin families. Finally, molecular subtyping efforts over the past decade have yielded classical and basal-like as consensus subtypes with variations therein, but genetic dependencies and cell surface expression patterns unique to either are insufficiently understood. We identified CLDN18, CEACAM5, and CEACAM6 as cell surface antigens for the classical subtype and MSLN, AQP5, and SLC6A14 for basal-like. Dependency on TLK2 and CCND1 is associated with the basal-like and classical subtype, respectively. Taken together, our integrative genomic approach may provide a precision medicine blueprint for stratifying and targeting pancreatic cancer.
Citation Format: Jimmy A. Guo, Daniel Zhao, Scott P. Ginebaugh, Steven Wang, Ananya D. Jambhale, Patrick Z. Yu, Westley W. Wu, Peter Chen, Maryann Zhao, Kristen E. Lowder, Kevin S. Kapner, Hannah I. Hoffman, Stephanie W. Cheng, Daniel Y. Kim, Rebecca Boiarsky, Francois Aguet, Brenton Paolella, John M. Krill-Burger, James M. McFarland, Tobiloba Oni, Tyler Jacks, Aviv Regev, Gad Getz, William L. Hwang, Harshabad Singh, Andrew J. Aguirre. Integrative genomic characterization of therapeutic targets for pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PR-006.
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Affiliation(s)
- Jimmy A. Guo
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | | | | | - Peter Chen
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Maryann Zhao
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gad Getz
- 1Broad Institute of MIT and Harvard, Cambridge, MA,
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14
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Swami N, Hwang WL, Guo JA, Hoffman H, Abramowitz MC, Elbakouny Z, Beltran H, Chipidza F, Choueiri T, Pra AD, Huang F, Kaochar S, Kantoff P, Kim DW, Kishan AU, Kobetz E, Marinac C, Mucci LA, Muralidhar V, Pollack A, Sanford NN, Schaeffer EM, Spratt DE, Zhao SG, Rebbeck TR, Nguyen PL, Feng FY, Mahal BA, Alshalalfa M. Novel genomic signature predictive of response to immune checkpoint blockade: A pan-cancer analysis from project Genomics Evidence Neo-plasia Information Exchange (GENIE). Cancer Genet 2021; 258-259:61-68. [PMID: 34551377 DOI: 10.1016/j.cancergen.2021.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/09/2021] [Revised: 06/07/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND High tumor mutation burden (TMB) and total mutation count (TMC) can be predictive of better response to immune checkpoint blockade (ICB). Nevertheless, TMB and TMC are limited by variation across cancers and inconsistent definitions due to different profiling methods (targeted vs whole genome sequencing). Our objective was to identify genomic alterations (GAs) associated with ICB response and builds a novel genomic signature predictive of ICB response, independent of TMB/TMC. METHODS This was a pan-cancer next generation sequencing (NGS)-association study using January 2014-May 2016 data from AACR Project Genomics Evidence Neo-plasia Information Exchange (GENIE). Participants included 6619 patients with metastatic or un-resectable cancer across 9 cancer types (including 1572 ICB-treated patients). GA data was collected using next-generation sequencing (NGS) assays and downloaded from cbioportal.org. Predictive analyses for ICB response were performed to develop the signature (ImmGA). RESULTS GAs in 16 genes were associated with improved OS in ICB-treated patients (p < 0.005). 13 GAs were associated with an OS benefit in ICB-treated patients (Pinteraction < 0.05); these genes composed the ImmGA signature. High ImmGA score (≥2 alterations out of 13 predictive GAs) was associated with better OS in ICB-treated patients (AHR:0.67, 95%CI [0.6-0.75], p = 1.4e-12), even after accounting for TMC (Pinteraction = 8e-16). High ImmGA was associated with better OS in ICB-treated patients across most cancers and across different ICB treatment modalities. CONCLUSION A novel signature predictive of ICB response (ImmGA) was developed from 13 GAs. Further investigation of the utility of ImmGA for treatment and trial selection is warranted.
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Affiliation(s)
- Nishwant Swami
- University of Massachusetts Medical School, Worcester, MA, USA
| | - William L Hwang
- Massachusetts General Hospital, Boston, MA, USA; Broad Institute, Cambridge MA, USA
| | - Jimmy A Guo
- Massachusetts General Hospital, Boston, MA, USA; Broad Institute, Cambridge MA, USA; University of California at San Francisco, San Francisco, CA, USA
| | | | - Matthew C Abramowitz
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, USA
| | - Ziad Elbakouny
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Himisha Beltran
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Fallon Chipidza
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Toni Choueiri
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Alan Dal Pra
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, USA
| | - Franklin Huang
- University of California at San Francisco, San Francisco, CA, USA
| | | | - Philip Kantoff
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel W Kim
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Amar U Kishan
- University of California Los Angeles, Los Angeles, CA, USA
| | - Erin Kobetz
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, USA
| | - Catherine Marinac
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | | | - Vinayak Muralidhar
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Alan Pollack
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, USA
| | - Nina N Sanford
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | | | - Timothy R Rebbeck
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA; Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Paul L Nguyen
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Felix Y Feng
- University of California at San Francisco, San Francisco, CA, USA
| | - Brandon A Mahal
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, USA.
| | - Mohammed Alshalalfa
- University of California at San Francisco, San Francisco, CA, USA; Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA.
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15
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Zhao D, Kim DY, Chen P, Yu P, Ho S, Cheng SW, Zhao C, Guo JA, Li YR. Pan-Cancer Survival Classification With Clinicopathological and Targeted Gene Expression Features. Cancer Inform 2021; 20:11769351211035137. [PMID: 34376966 PMCID: PMC8330450 DOI: 10.1177/11769351211035137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/05/2021] [Indexed: 11/15/2022] Open
Abstract
Prognostication for patients with cancer is important for clinical planning and management, but remains challenging given the large number of factors that can influence outcomes. As such, there is a need to identify features that can robustly predict patient outcomes. We evaluated 8608 patient tumor samples across 16 cancer types from The Cancer Genome Atlas and generated distinct survival classifiers for each using clinical and histopathological data accessible to standard oncology workflows. For cancers that had poor model performance, we deployed a random-forest-embedded sequential forward selection approach that began with an initial subset of the 15 most predictive clinicopathological features before sequentially appending the next most informative gene as an additional feature. With classifiers derived from clinical and histopathological features alone, we observed cancer-type-dependent model performance and an area under the receiver operating curve (AUROC) range of 0.65 to 0.91 across all 16 cancer types for 1- and 3-year survival prediction, with some classifiers consistently outperforming those for others. As such, for cancers that had poor model performance, we posited that the addition of more complex biomolecular features could enhance our ability to prognose patients where clinicopathological features were insufficient. With the inclusion of gene expression data, model performance for 3 select cancers (glioblastoma, stomach/gastric adenocarcinoma, ovarian serous carcinoma) markedly increased from initial AUROC scores of 0.66, 0.69, and 0.67 to 0.76, 0.77, and 0.77, respectively. As a whole, this study provides a thorough examination of the relative contributions of clinical, pathological, and gene expression data in predicting overall survival and reveals cancer types for which clinical features are already strong predictors and those where additional biomolecular information is needed.
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Affiliation(s)
- Daniel Zhao
- School of Medicine, New York Medical College, Valhalla, NY, USA
| | - Daniel Y Kim
- Molecular Pathology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Peter Chen
- Raytheon Technologies, Brooklyn, NY, USA
| | - Patrick Yu
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,College of Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Sophia Ho
- Northeastern University, Boston, MA, USA
| | | | - Cindy Zhao
- Northeastern University, Boston, MA, USA
| | - Jimmy A Guo
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.,School of Medicine, UCSF, San Francisco, CA, USA
| | - Yun R Li
- Department of Radiation Oncology, UCSF, San Francisco, CA, USA
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16
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Guo JA, Hoffman HI, Weekes CD, Zheng L, Ting DT, Hwang WL. Refining the Molecular Framework for Pancreatic Cancer with Single-cell and Spatial Technologies. Clin Cancer Res 2021; 27:3825-3833. [PMID: 33653818 PMCID: PMC8282742 DOI: 10.1158/1078-0432.ccr-20-4712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Received: 12/04/2020] [Revised: 01/18/2021] [Accepted: 02/12/2021] [Indexed: 12/27/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a treatment-refractory malignancy in urgent need of a molecular framework for guiding therapeutic strategies. Bulk transcriptomic efforts over the past decade have yielded two broad consensus subtypes: classical pancreatic/epithelial versus basal-like/squamous/quasi-mesenchymal. Although this binary classification enables prognostic stratification, it does not currently inform the administration of treatments uniquely sensitive to either subtype. Furthermore, bulk mRNA studies are challenged by distinguishing contributions from the neoplastic compartment versus other cell types in the microenvironment, which is accentuated in PDAC given that neoplastic cellularity can be low. The application of single-cell transcriptomics to pancreatic tumors has generally lagged behind other cancer types due in part to the difficulty of extracting high-quality RNA from enzymatically degradative tissue, but emerging studies have and will continue to shed light on intratumoral heterogeneity, malignant-stromal interactions, and subtle transcriptional programs previously obscured at the bulk level. In conjunction with insights provided by single-cell/nucleus dissociative techniques, spatially resolved technologies should also facilitate the contextualization of gene programs and inferred cell-cell interactions within the tumor architecture. Finally, given that patients often receive neoadjuvant chemotherapy and/or chemoradiotherapy even in resectable disease, deciphering the gene programs enriched in or induced by cytotoxic therapy will be crucial for developing insights into complementary treatments aimed at eradicating residual cancer cells. Taken together, single-cell and spatial technologies provide an unprecedented opportunity to refine the foundations laid by prior bulk molecular studies and significantly augment precision oncology efforts in pancreatic cancer.
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Affiliation(s)
- Jimmy A Guo
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Biological and Biomedical Sciences Program, Harvard University, Boston, Massachusetts
- School of Medicine, University of California, San Francisco, San Francisco, California
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Hannah I Hoffman
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Colin D Weekes
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Lei Zheng
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David T Ting
- Division of Hematology and Oncology, Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - William L Hwang
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
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17
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Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Yadollahpour P, Reeves J, Drokhlyansky E, Van Wittenberghe N, Farhi S, Schapiro D, Eng G, Schenkel JM, Freed-Pastor WA, Ashenberg O, Rodrigues C, Abbondanza D, Delorey T, Phillips D, Roldan J, Ciprani D, Kern M, Barth JL, Zollinger DR, Fuhrman K, Fropf R, Beechem J, Weekes C, Ferrone CR, Wo JY, Hong TS, Rozenblatt-Rosen O, Aguirre AJ, Mino-Kenudson M, Fernandez-del- Castillo C, Liss AS, Ting DT, Jacks T, Regev A. Abstract 94: Multi-compartment reprogramming and spatially-resolved interactions in frozen pancreatic cancer with and without neoadjuvant chemotherapy and radiotherapy at single-cell resolution. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-94] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A molecular classification of pancreatic ductal adenocarcinoma (PDAC) that informs clinical management remains elusive. Previously identified bulk expression subtypes in the untreated setting were influenced by contaminating stroma whereas single cell RNA-seq (scRNA-seq) of fresh tumors under-represented key cell types. Two consensus subtypes have arisen from these prior efforts: (1) classical-like, and (2) basal-like. Basal-like tumors were associated with worse survival in the metastatic setting but attempts to refine this binary classification have failed to further stratify patient survival. Here, we developed a robust single-nucleus RNA-seq (snRNA-seq) technique for banked frozen PDAC specimens and studied a cohort of untreated resected primary tumors (n ~ 20). Gene expression programs learned across malignant cell and cancer-associated fibroblast (CAF) profiles uncovered a clinically-relevant molecular taxonomy with improved prognostic stratification compared to prior classifications. Digital spatial profiling revealed an association between malignant cells expressing basal-like programs and greater immune infiltration with relatively fewer macrophages, whereas those exhibiting classical-like programs were linked to inflammatory CAFs and macrophage-predominant microniches. Recent clinical trials have supported the increasing adoption of neoadjuvant therapy to aggressively address the risk of micro-metastatic spread and to circumvent concerns of treatment tolerance in the postoperative setting. There is an urgent need to understand how preoperative treatment impacts residual tumor cells and their interactions with other cell types in the tumor microenvironment to identify additional therapeutic vulnerabilities that can be exploited. Towards this end, we performed snRNA-seq on an unmatched cohort of neoadjuvant-treated resected primary tumors (n ~ 25) with most cases involving FOLFIRINOX chemotherapy followed by chemoradiation. Remarkably, the quality of single-nucleus mRNA profiles was comparable between heavily pre-treated and untreated specimens. We identified differentially expressed genes between treated and untreated samples to infer cell-type specific reprogramming in the residual tumor. This analysis revealed that in the neoadjuvant treatment context, there was lower expression of classical-like phenotypes in malignant cells in favor of basal-like phenotypes associated with TNF-NFkB and interferon signaling as well as the presence of novel acinar and neuroendocrine classical-like states. Our refined molecular taxonomy and spatial resolution may help advance precision oncology in PDAC through informative stratification in clinical trials and insights into compartment-specific therapies.
Citation Format: William L. Hwang, Karthik A. Jagadeesh, Jimmy A. Guo, Hannah I. Hoffman, Payman Yadollahpour, Jason Reeves, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Samouil Farhi, Denis Schapiro, George Eng, Jason M. Schenkel, William A. Freed-Pastor, Orr Ashenberg, Clifton Rodrigues, Domenic Abbondanza, Toni Delorey, Devan Phillips, Jorge Roldan, Debora Ciprani, Marina Kern, Jaimie L. Barth, Daniel R. Zollinger, Kit Fuhrman, Robin Fropf, Joseph Beechem, Colin Weekes, Cristina R. Ferrone, Jennifer Y. Wo, Theodore S. Hong, Orit Rozenblatt-Rosen, Andrew J. Aguirre, Mari Mino-Kenudson, Carlos Fernandez-del- Castillo, Andrew S. Liss, David T. Ting, Tyler Jacks, Aviv Regev. Multi-compartment reprogramming and spatially-resolved interactions in frozen pancreatic cancer with and without neoadjuvant chemotherapy and radiotherapy at single-cell resolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 94.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - George Eng
- 1Massachusetts General Hospital, Boston, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tyler Jacks
- 3Massachusetts Institute of Technology, Cambridge, MA
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18
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Garrood WT, Kranjc N, Petri K, Kim DY, Guo JA, Hammond AM, Morianou I, Pattanayak V, Joung JK, Crisanti A, Simoni A. Analysis of off-target effects in CRISPR-based gene drives in the human malaria mosquito. Proc Natl Acad Sci U S A 2021; 118:e2004838117. [PMID: 34050017 PMCID: PMC8179207 DOI: 10.1073/pnas.2004838117] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 04/15/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 nuclease-based gene drives have been developed toward the aim of control of the human malaria vector Anopheles gambiae Gene drives are based on an active source of Cas9 nuclease in the germline that promotes super-Mendelian inheritance of the transgene by homology-directed repair ("homing"). Understanding whether CRISPR-induced off-target mutations are generated in Anopheles mosquitoes is an important aspect of risk assessment before any potential field release of this technology. We compared the frequencies and the propensity of off-target events to occur in four different gene-drive strains, including a deliberately promiscuous set-up, using a nongermline restricted promoter for SpCas9 and a guide RNA with many closely related sites (two or more mismatches) across the mosquito genome. Under this scenario we observed off-target mutations at frequencies no greater than 1.42%. We witnessed no evidence that CRISPR-induced off-target mutations were able to accumulate (or drive) in a mosquito population, despite multiple generations' exposure to the CRISPR-Cas9 nuclease construct. Furthermore, judicious design of the guide RNA used for homing of the CRISPR construct, combined with tight temporal constriction of Cas9 expression to the germline, rendered off-target mutations undetectable. The findings of this study represent an important milestone for the understanding and managing of CRISPR-Cas9 specificity in mosquitoes, and demonstrates that CRISPR off-target editing in the context of a mosquito gene drive can be reduced to minimal levels.
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Affiliation(s)
- William T Garrood
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Karl Petri
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Daniel Y Kim
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Jimmy A Guo
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Andrew M Hammond
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins University, Baltimore, MD 21205
| | - Ioanna Morianou
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Vikram Pattanayak
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom;
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Alekos Simoni
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom;
- Polo d'Innovazione Genomica, Genetica, e Biologia, 05100 Terni, Italy
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19
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Guo JA, Hoffman HI, Shroff SG, Chen P, Hwang PG, Kim DY, Kim DW, Cheng SW, Zhao D, Mahal BA, Alshalalfa M, Niemierko A, Wo JY, Loeffler JS, Fernandez-Del Castillo C, Jacks T, Aguirre AJ, Hong TS, Mino-Kenudson M, Hwang WL. Pan-cancer Transcriptomic Predictors of Perineural Invasion Improve Occult Histopathologic Detection. Clin Cancer Res 2021; 27:2807-2815. [PMID: 33632928 DOI: 10.1158/1078-0432.ccr-20-4382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/16/2021] [Accepted: 02/19/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Perineural invasion (PNI) is associated with aggressive tumor behavior, recurrence, and metastasis, and can influence the administration of adjuvant treatment. However, standard histopathologic examination has limited sensitivity in detecting PNI and does not provide insights into its mechanistic underpinnings. EXPERIMENTAL DESIGN A multivariate Cox regression was performed to validate associations between PNI and survival in 2,029 patients across 12 cancer types. Differential expression and gene set enrichment analysis were used to learn PNI-associated programs. Machine learning models were applied to build a PNI gene expression classifier. A blinded re-review of hematoxylin and eosin (H&E) slides by a board-certified pathologist helped determine whether the classifier could improve occult histopathologic detection of PNI. RESULTS PNI associated with both poor overall survival [HR, 1.73; 95% confidence interval (CI), 1.27-2.36; P < 0.001] and disease-free survival (HR, 1.79; 95% CI, 1.38-2.32; P < 0.001). Neural-like, prosurvival, and invasive programs were enriched in PNI-positive tumors (P adj < 0.001). Although PNI-associated features likely reflect in part the increased presence of nerves, many differentially expressed genes mapped specifically to malignant cells from single-cell atlases. A PNI gene expression classifier was derived using random forest and evaluated as a tool for occult histopathologic detection. On a blinded H&E re-review of sections initially described as PNI negative, more specimens were reannotated as PNI positive in the high classifier score cohort compared with the low-scoring cohort (P = 0.03, Fisher exact test). CONCLUSIONS This study provides salient biological insights regarding PNI and demonstrates a role for gene expression classifiers to augment detection of histopathologic features.
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Affiliation(s)
- Jimmy A Guo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts.,School of Medicine, University of California, San Francisco, San Francisco, California.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hannah I Hoffman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Stuti G Shroff
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Peter Chen
- Raytheon Technologies, Brooklyn, New York
| | - Peter G Hwang
- Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Daniel Y Kim
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts
| | - Daniel W Kim
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Daniel Zhao
- New York Medical College, Valhalla, New York
| | - Brandon A Mahal
- Department of Radiation Oncology, Miller School of Medicine, Miami, Florida
| | - Mohammed Alshalalfa
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Andrzej Niemierko
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jennifer Y Wo
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jay S Loeffler
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Tyler Jacks
- Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - William L Hwang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. .,Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
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20
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Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Drokhlyansky E, Van Wittenberghe N, Farhi S, Schapiro D, Reeves J, Zollinger DR, Eng G, Schenkel JM, Freed-Pastor WA, Rodrigues C, Abbondanza D, Ciprani D, Wo JY, Hong TS, Aguirre AJ, Rozenblatt-Rosen O, Mino-Kenudson M, Fernandez-del Castillo C, Liss AS, Jacks TE, Regev A. Abstract PR-007: Single-nucleus and spatial transcriptomics of archival pancreatic ductal adenocarcinoma reveals multi-compartment reprogramming after neoadjuvant treatment. Cancer Res 2020. [DOI: 10.1158/1538-7445.panca20-pr-007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Molecular subtyping of pancreatic ductal adenocarcinoma (PDAC) remains in its nascent stages and does not currently inform clinical management or therapeutic development. Previously identified bulk expression subtypes in the untreated setting were influenced by contaminating stroma whereas single cell RNA-seq (scRNA-seq) of fresh tumors under-represented key cell types. Two consensus subtypes have arisen from these prior efforts: (1) classical-pancreatic, encompassing a spectrum of pancreatic lineage precursors, and (2) basal-like/squamous/quasi-mesenchymal, characterized by loss of endodermal identity and aberrations in chromatin modifiers. Basal-like tumors were associated with poorer responses to chemotherapy and worse survival in the metastatic setting but attempts to refine this binary classification have failed to further stratify patient survival. Recent clinical trials have supported the increasing adoption of neoadjuvant therapy to aggressively address the risk of micro-metastatic spread and to circumvent concerns of treatment tolerance in the postoperative setting. There is an urgent need to understand how preoperative treatment reprograms residual tumor cells to identify additional therapeutic vulnerabilities that can be exploited in combination with neoadjuvant CRT. Here, we developed a robust single-nucleus RNA-seq (snRNA-seq) technique for frozen archival PDAC specimens and used it to study both untreated tumors (n = 15) and those that received neoadjuvant CRT (n = 11). Gene expression programs learned across malignant cell and fibroblast profiles uncovered a clinically relevant molecular taxonomy with improved prognostic stratification (median survival: 11.2 months in highest risk group to 44.7 months in lowest risk group) compared to prior classifications. Moreover, in the neoadjuvant treatment context, there was lower expression of classical-like phenotypes in malignant cells in favor of basal-like phenotypes associated with TNF-NFkB and interferon signaling as well as the presence of novel acinar and neuroendocrine classical-like states, which may be more resilient to cytotoxic treatment. These results suggest that differentiated endodermal phenotypes are only prevalent enough to be detected under treatment selection pressure and when observed in treatment-naïve bulk studies, may reflect normal cell contamination. Spatially-resolved transcriptomics revealed an association between malignant cells expressing basal-like programs and higher immune infiltration with increased lymphocytic content, whereas those exhibiting classical-like programs were linked to sparser macrophage-predominant microniches, perhaps pointing to distinct therapeutic susceptibilities. Our refined molecular taxonomy and spatial resolution may help advance precision oncology in PDAC through informative stratification in clinical trials and insights into differential therapeutic targeting leveraging the immune system.
Citation Format: William L. Hwang, Karthik A. Jagadeesh, Jimmy A. Guo, Hannah I. Hoffman, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Samouil Farhi, Denis Schapiro, Jason Reeves, Daniel R. Zollinger, George Eng, Jason M. Schenkel, William A. Freed-Pastor, Clifton Rodrigues, Domenic Abbondanza, Debora Ciprani, Jennifer Y. Wo, Theodore S. Hong, Andrew J. Aguirre, Orit Rozenblatt-Rosen, Mari Mino-Kenudson, Carlos Fernandez-del Castillo, Andrew S. Liss, Tyler E. Jacks, Aviv Regev. Single-nucleus and spatial transcriptomics of archival pancreatic ductal adenocarcinoma reveals multi-compartment reprogramming after neoadjuvant treatment [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PR-007.
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Affiliation(s)
- William L. Hwang
- 1Massachusetts General Hospital/Broad Institute/Koch Institute, Boston, MA, USA,
| | | | | | | | | | | | | | | | | | | | - George Eng
- 5Massachusetts General Hospital, Boston, MA, USA,
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21
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Hoffman HI, Guo JA, Hawkins MA, Bridgewater JA, Wo JY, Hong TS, Hwang WL. Silver Linings: An Opportunity to Improve Clinical Paradigms After the COVID-19 Pandemic. JCO Oncol Pract 2020; 16:532-534. [DOI: 10.1200/op.20.00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Lee K, Zhang Y, Kleinstiver BP, Guo JA, Aryee MJ, Miller J, Malzahn A, Zarecor S, Lawrence‐Dill CJ, Joung JK, Qi Y, Wang K. Activities and specificities of CRISPR/Cas9 and Cas12a nucleases for targeted mutagenesis in maize. Plant Biotechnol J 2019; 17:362-372. [PMID: 29972722 PMCID: PMC6320322 DOI: 10.1111/pbi.12982] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/14/2018] [Accepted: 06/27/2018] [Indexed: 05/11/2023]
Abstract
CRISPR/Cas9 and Cas12a (Cpf1) nucleases are two of the most powerful genome editing tools in plants. In this work, we compared their activities by targeting maize glossy2 gene coding region that has overlapping sequences recognized by both nucleases. We introduced constructs carrying SpCas9-guide RNA (gRNA) and LbCas12a-CRISPR RNA (crRNA) into maize inbred B104 embryos using Agrobacterium-mediated transformation. On-target mutation analysis showed that 90%-100% of the Cas9-edited T0 plants carried indel mutations and 63%-77% of them were homozygous or biallelic mutants. In contrast, 0%-60% of Cas12a-edited T0 plants had on-target mutations. We then conducted CIRCLE-seq analysis to identify genome-wide potential off-target sites for Cas9. A total of 18 and 67 potential off-targets were identified for the two gRNAs, respectively, with an average of five mismatches compared to the target sites. Sequencing analysis of a selected subset of the off-target sites revealed no detectable level of mutations in the T1 plants, which constitutively express Cas9 nuclease and gRNAs. In conclusion, our results suggest that the CRISPR/Cas9 system used in this study is highly efficient and specific for genome editing in maize, while CRISPR/Cas12a needs further optimization for improved editing efficiency.
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Affiliation(s)
- Keunsub Lee
- Crop Bioengineering CenterIowa State UniversityAmesIAUSA
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Yingxiao Zhang
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
| | - Benjamin P. Kleinstiver
- Molecular Pathology UnitCenter for Cancer Research, and Center for Computational and Integrative BiologyMassachusetts General HospitalCharlestownMAUSA
- Department of PathologyHarvard Medical SchoolBostonMAUSA
| | - Jimmy A. Guo
- Molecular Pathology UnitCenter for Cancer Research, and Center for Computational and Integrative BiologyMassachusetts General HospitalCharlestownMAUSA
| | - Martin J. Aryee
- Department of PathologyHarvard Medical SchoolBostonMAUSA
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Jonah Miller
- Crop Bioengineering CenterIowa State UniversityAmesIAUSA
| | - Aimee Malzahn
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
| | - Scott Zarecor
- Crop Bioengineering CenterIowa State UniversityAmesIAUSA
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
| | - Carolyn J. Lawrence‐Dill
- Crop Bioengineering CenterIowa State UniversityAmesIAUSA
- Department of AgronomyIowa State UniversityAmesIAUSA
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Bioinformatics and Computational Biology ProgramIowa State UniversityAmesIAUSA
| | - J. Keith Joung
- Molecular Pathology UnitCenter for Cancer Research, and Center for Computational and Integrative BiologyMassachusetts General HospitalCharlestownMAUSA
- Department of PathologyHarvard Medical SchoolBostonMAUSA
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMDUSA
| | - Kan Wang
- Crop Bioengineering CenterIowa State UniversityAmesIAUSA
- Department of AgronomyIowa State UniversityAmesIAUSA
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23
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Abstract
Circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq) is a sensitive and unbiased method for defining the genome-wide activity (on-target and off-target) of CRISPR-Cas9 nucleases by selective sequencing of nuclease-cleaved genomic DNA (gDNA). Here, we describe a detailed experimental and analytical protocol for CIRCLE-seq. The principle of our method is to generate a library of circularized gDNA with minimized numbers of free ends. Highly purified gDNA circles are treated with CRISPR-Cas9 ribonucleoprotein complexes, and nuclease-linearized DNA fragments are then ligated to adapters for high-throughput sequencing. The primary advantages of CIRCLE-seq as compared with other in vitro methods for defining genome-wide genome editing activity are (i) high enrichment for sequencing nuclease-cleaved gDNA/low background, enabling sensitive detection with low sequencing depth requirements; and (ii) the fact that paired-end reads can contain complete information on individual nuclease cleavage sites, enabling use of CIRCLE-seq in species without high-quality reference genomes. The entire protocol can be completed in 2 weeks, including time for gRNA cloning, sequence verification, in vitro transcription, library preparation, and sequencing.
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Affiliation(s)
- Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nhu T Nguyen
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xing Tang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jose Malagon-Lopez
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jimmy A Guo
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Martin J Aryee
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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24
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Akcakaya P, Bobbin ML, Guo JA, Malagon-Lopez J, Clement K, Garcia SP, Fellows MD, Porritt MJ, Firth MA, Carreras A, Baccega T, Seeliger F, Bjursell M, Tsai SQ, Nguyen NT, Nitsch R, Mayr LM, Pinello L, Bohlooly-Y M, Aryee MJ, Maresca M, Joung JK. In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature 2018; 561:416-419. [PMID: 30209390 PMCID: PMC6194229 DOI: 10.1038/s41586-018-0500-9] [Citation(s) in RCA: 223] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Pinar Akcakaya
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Maggie L Bobbin
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jimmy A Guo
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Jose Malagon-Lopez
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Kendell Clement
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Sara P Garcia
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Mick D Fellows
- Advanced Medicines Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Michelle J Porritt
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike A Firth
- Quantitative Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Alba Carreras
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.,Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Tania Baccega
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.,San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Frank Seeliger
- Pathology Science, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Mikael Bjursell
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Shengdar Q Tsai
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA.,Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nhu T Nguyen
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Roberto Nitsch
- Advanced Medicines Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Lorenz M Mayr
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.,GE Healthcare Life Sciences, The Grove Centre, Amersham, UK
| | - Luca Pinello
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Mohammad Bohlooly-Y
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Martin J Aryee
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Marcello Maresca
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.
| | - J Keith Joung
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA. .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA. .,Department of Pathology, Harvard Medical School, Boston, MA, USA.
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25
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Guo JA, Wang XY, Dai LM. [Pharmacokinetics of sodium selenite in human body at different levels of selenium]. Zhongguo Yao Li Xue Bao 1991; 12:226-8. [PMID: 1664167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Twelve health adults (6 M, 6 F) from the endemic area of Keshan disease and Kaschin-Beck's disease and 12 adults from nonaffected area were administered a single oral dose of 4 mg sodium selenite. Selenium in whole blood was determined by fluorescence spectrometry. Their basic levels of blood selenium were 64 +/- 16 and 220 +/- 20 ng.ml-1, respectively. The concentration-time data were treated by a computer with program 3P87, which revealed 2-compartment models with first order absorption and lag time. The pharmacokinetic parameters of low-Se group were T1/2g 1.8 +/- 0.6h, T1/2g 72 +/- 18 h, T1/2ka 3.2 +/- 1.8h, AUC 3,100 +/- 500 ng.h.ml-1, CL 32 +/- 7 ml.kg-1.h-1, Vc 1.45 +/- 0.19 L.kg-1, Tp 6.1 +/- 2.0 h, Cp 36 +/- 4 ng.ml-1, AUMC (S1) 130 +/- 26, VRT 174 +/- 17 h, MRT 55 +/- 4 h, and of normal-Se group were T1/2 3.4 +/- 0.7h, T1/2g 14 +/- 3 h. T1/2ka 2.3 +/- 0.6, AUC 1,420 +/- 210 ng.h.ml-1, Cl 57 +/- 7 ml.kg-1. h-1, Vc 0.54 +/- 0.09 L.kg-1, Tp 4.6 +/- 0.9h, Cp 75 +/- 5 ng.ml-1, AUMC (S1) 25 +/- 5, VRT 16 +/- 3 h, MRT 16.1 +/- 1.5 h.
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Affiliation(s)
- J A Guo
- Institute of Basic Medical Sciences of Liaoning Province, Shenyang, China
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26
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Wang XY, Li L, Han J, Cui GA, Guo JA. [Pharmacokinetic study of sodium selenite in low-selenium rabbits]. Zhongguo Yao Li Xue Bao 1990; 11:184-7. [PMID: 2177311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sodium selenite has been used for prevention and treatment of Keshan disease and Kaschin-Beck's disease. The efficacious dosage regimens of sodium selenite in low-Se human body have not been clear. A single iv or ig of sodium selenite 2.0 mg/kg was given to rabbits. Selenium in whole blood was determined fluorophotomerically. The concentration-time curve following a single iv of sodium selenite in rabbits was found to be of 3-compartment open model. The pharmacokinetic parameters were: T1/2 x 0.11 +/- 0.03 h, T1/2 alpha 6.8 +/- 2.8 h, T1/2 beta 215 +/- 35 h, Vc 0.50 +/- 0.07 L/kg, Cl 19 +/- 5 ml/(kg.h), AUC 146 +/- 26 mg.h/L. The concentration-time curve following a single ig of sodium selenite showed a pattern of 2-compartment open model. The parameters were: T1/2 kappa a 13 +/- 6 h, T1/2 alpha 3.6 +/- 1.9 h, T1/2 beta 338 +/- 107 h, Vc 2.9 +/- 1.3 L/kg, AUC 78 +/- 29 mg.h/L, Cl 27 +/- 11 ml/(kg.h). In low-Se rabbits the distribution in body was more rapid and more extensive, and the bioavailability was higher than that in normal-Se rabbits. Therefore, attention should be paid to the different levels of selenium during therapy with sodium selenite.
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Affiliation(s)
- X Y Wang
- Institute of Basic Medical Sciences of Liaoning Province, Shenyang, China
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27
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Guo JA, Mo PS, Li GX. Immobilization of glucose oxidase and peroxidase and their application in flow-injection analysis for glucose in serum. Appl Biochem Biotechnol 1990; 23:15-24. [PMID: 2105696 DOI: 10.1007/bf02942049] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [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: 12/30/2022]
Abstract
Glucose oxidase (GOD) and Horseradish peroxidase (HRP) were covalently coupled to alkylamine controlled pore glass by means of glutaraldehyde. About 700-800 U/g of immobilized GOD and 300-400 U/g of immobilized HRP were obtained. Some factors of affecting enzyme immobilization were discussed. The immobilized enzymes were packed into a plastic tube and used in flow-injection analysis (FIA) for glucose in serum. A good linearity range was observed for this immobilized enzyme system at 20 mg/mL to 1000 mg/dL D-glucose, the recovery was 95.4-103.5%, the within-batch imprecision was 0.8-2.2%, and the between-batch imprecision was 2.2-4.2%. More than 100 samples were measured within an hour. One enzyme column with five units of immobilized GOD and HRP, applied for 50 assays/d, has been used for more than 2 mo.
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Affiliation(s)
- J A Guo
- National Center for Clinical Laboratory, Beijing, People's Republic of China
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28
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Tang FZ, Guo JA, Zhao WG, Tang SY, Xie YJ, Li GM. [Anti-arrhythmic effects of sodium selenite]. Zhongguo Yao Li Xue Bao 1983; 4:244-7. [PMID: 6230868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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29
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Guo JA, Tang FZ, Li GM, Zhao WG. [Influence of sodium selenite on cardiac myodynamic effects (author's transl)]. Zhongguo Yao Li Xue Bao 1982; 3:25-9. [PMID: 6211898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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30
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Guo JA, Li GM, Zhao WG, Tang FZ, Zhang X, Zhang CY. [Cardiovascular effects of sodium selenite (author's transl)]. Zhongguo Yao Li Xue Bao 1981; 2:93-7. [PMID: 6461221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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