87 results on '"Sasikanth Manne"'
Search Results
2. 579-C Reinvigoration of progenitor-exhausted CD8 T cells by anti-CTLA-4 contributes to the sustained activity of combination checkpoint blockade
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Xiaowei Xu, Wei Xu, Alexander Huang, Jeffrey Weber, Andy Minn, Kevin Wang, Tara Mitchell, Sasikanth Manne, Divij Mathew, E John Wherry, Daniel Tenney, Paulina Coutifaris, David Brocks, Sabrina Solis, Nicholas Han, Evgeny Kiner, Chirag Sachar, Sangeeth George, Patrick Yan, Melanie W Kiner, Amy I Laughlin, Shawn Kothari, Josephine R Giles, Rheem Ghinnagow, Cecile Alanio, Ahron Flowers, Ravi K Amaravadi, Giorgos C Karakousis, Lynn M Schuchter, Marcus Buggert, and Ramin S Herati
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Published
- 2023
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3. Signaling Through FcγRIIA and the C5a-C5aR Pathway Mediate Platelet Hyperactivation in COVID-19
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Sokratis A. Apostolidis, Amrita Sarkar, Heather M. Giannini, Rishi R. Goel, Divij Mathew, Aae Suzuki, Amy E. Baxter, Allison R. Greenplate, Cécile Alanio, Mohamed Abdel-Hakeem, Derek A. Oldridge, Josephine R. Giles, Jennifer E. Wu, Zeyu Chen, Yinghui Jane Huang, Jonathan Belman, Ajinkya Pattekar, Sasikanth Manne, Oliva Kuthuru, Jeanette Dougherty, Brittany Weiderhold, Ariel R. Weisman, Caroline A. G. Ittner, Sigrid Gouma, Debora Dunbar, Ian Frank, Alexander C. Huang, Laura A. Vella, The UPenn COVID Processing Unit, John P. Reilly, Scott E. Hensley, Lubica Rauova, Liang Zhao, Nuala J. Meyer, Mortimer Poncz, Charles S. Abrams, E. John Wherry, Sharon Adamski, Zahidul Alam, Mary M. Addison, Katelyn T. Byrne, Aditi Chandra, Hélène C. Descamps, Nicholas Han, Yaroslav Kaminskiy, Shane C. Kammerman, Justin Kim, Jacob T. Hamilton, Nune Markosyan, Julia Han Noll, Dalia K. Omran, Eric Perkey, Elizabeth M. Prager, Dana Pueschl, Austin Rennels, Jennifer B. Shah, Jake S. Shilan, Nils Wilhausen, and Ashley N. Vanderbeck
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platelet ,COVID - 19 ,FcγRIIa ,complement ,fostamatinib ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Patients with COVID-19 present with a wide variety of clinical manifestations. Thromboembolic events constitute a significant cause of morbidity and mortality in patients infected with SARS-CoV-2. Severe COVID-19 has been associated with hyperinflammation and pre-existing cardiovascular disease. Platelets are important mediators and sensors of inflammation and are directly affected by cardiovascular stressors. In this report, we found that platelets from severely ill, hospitalized COVID-19 patients exhibited higher basal levels of activation measured by P-selectin surface expression and had poor functional reserve upon in vitro stimulation. To investigate this question in more detail, we developed an assay to assess the capacity of plasma from COVID-19 patients to activate platelets from healthy donors. Platelet activation was a common feature of plasma from COVID-19 patients and correlated with key measures of clinical outcome including kidney and liver injury, and APACHEIII scores. Further, we identified ferritin as a pivotal clinical marker associated with platelet hyperactivation. The COVID-19 plasma-mediated effect on control platelets was highest for patients that subsequently developed inpatient thrombotic events. Proteomic analysis of plasma from COVID-19 patients identified key mediators of inflammation and cardiovascular disease that positively correlated with in vitro platelet activation. Mechanistically, blocking the signaling of the FcγRIIa-Syk and C5a-C5aR pathways on platelets, using antibody-mediated neutralization, IgG depletion or the Syk inhibitor fostamatinib, reversed this hyperactivity driven by COVID-19 plasma and prevented platelet aggregation in endothelial microfluidic chamber conditions. These data identified these potentially actionable pathways as central for platelet activation and/or vascular complications and clinical outcomes in COVID-19 patients. In conclusion, we reveal a key role of platelet-mediated immunothrombosis in COVID-19 and identify distinct, clinically relevant, targetable signaling pathways that mediate this effect.
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- 2022
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4. 253 PD1 and LAG3 converge to limit polyfunctionality and systemic immunity
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Dario Vignali, Creg Workman, Sasikanth Manne, Lawrence Andrews, and E John Wherry
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Published
- 2021
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5. 310 T cell intrinsic DNA damage and repair response as a novel marker associated with clinical response to PD-1 blockade
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Alexander Huang, Claire Friedman, Yuki Muroyama, Sasikanth Manne, Divij Mathew, Lakshmi Chilukuri, Allison Greenplate, Ramin Herati, E John Wherry, Derek Oldridge, Caiyue Xu, and Dimitriy Zamarin
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Published
- 2021
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6. Vaccine-induced ICOS+CD38+ circulating Tfh are sensitive biosensors of age-related changes in inflammatory pathways
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Ramin Sedaghat Herati, Luisa Victoria Silva, Laura A. Vella, Alexander Muselman, Cecile Alanio, Bertram Bengsch, Raj K. Kurupati, Senthil Kannan, Sasikanth Manne, Andrew V. Kossenkov, David H. Canaday, Susan A. Doyle, Hildegund C.J. Ertl, Kenneth E. Schmader, and E. John Wherry
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T follicular helper ,vaccine ,NF-kB ,aging ,cellular biosensors ,CD4 ,Medicine (General) ,R5-920 - Abstract
Summary: Humoral immune responses are dysregulated with aging, but the cellular and molecular pathways involved remain incompletely understood. In particular, little is known about the effects of aging on T follicular helper (Tfh) CD4 cells, the key cells that provide help to B cells for effective humoral immunity. We performed transcriptional profiling and cellular analysis on circulating Tfh before and after influenza vaccination in young and elderly adults. First, whole-blood transcriptional profiling shows that ICOS+CD38+ cTfh following vaccination preferentially enriches in gene sets associated with youth versus aging compared to other circulating T cell types. Second, vaccine-induced ICOS+CD38+ cTfh from the elderly had increased the expression of genes associated with inflammation, including tumor necrosis factor-nuclear factor κB (TNF-NF-κB) pathway activation. Finally, vaccine-induced ICOS+CD38+ cTfh display strong enrichment for signatures of underlying age-associated biological changes. These data highlight the ability to use vaccine-induced cTfh as cellular “biosensors” of underlying inflammatory and/or overall immune health.
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- 2021
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7. 186 Distinct immune signatures predicting clinical response to PD-1 blockade therapy in gynecological cancers revealed by high-dimensional immune profiling
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Dmitriy Zamarin, Claire Friedman, Yuki Muroyama, Sasikanth Manne, Alexandar Huang, Divij Mathew, Lakshmi Chilukuri, Allison Greenplate, Takuya Ohtani, and John Wherry
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Published
- 2020
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8. Genomic Circuitry Underlying Immunological Response to Pediatric Acute Respiratory Infection
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Sarah E. Henrickson, Sasikanth Manne, Douglas V. Dolfi, Kathleen D. Mansfield, Kaela Parkhouse, Rakesh D. Mistry, Elizabeth R. Alpern, Scott E. Hensley, Kathleen E. Sullivan, Susan E. Coffin, and E. John Wherry
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Biology (General) ,QH301-705.5 - Abstract
Summary: Acute respiratory tract viral infections (ARTIs) cause significant morbidity and mortality. CD8 T cells are fundamental to host responses, but transcriptional alterations underlying anti-viral mechanisms and links to clinical characteristics remain unclear. CD8 T cell transcriptional circuitry in acutely ill pediatric patients with influenza-like illness was distinct for different viral pathogens. Although changes included expected upregulation of interferon-stimulated genes (ISGs), transcriptional downregulation was prominent upon exposure to innate immune signals in early IFV infection. Network analysis linked changes to severity of infection, asthma, sex, and age. An influenza pediatric signature (IPS) distinguished acute influenza from other ARTIs and outperformed other influenza prediction gene lists. The IPS allowed a deeper investigation of the connection between transcriptional alterations and clinical characteristics of acute illness, including age-based differences in circuits connecting the STAT1/2 pathway to ISGs. A CD8 T cell-focused systems immunology approach in pediatrics identified age-based alterations in ARTI host response pathways. : Henrickson et al. measure transcriptional alterations in blood CD8 T cells from pediatric patients with acute respiratory tract infections and correlate gene modules with clinical characteristics. This approach defines an influenza prediction signature that is effective across ages, revealing age-based alterations in genetic circuitry underlying host responses to influenza. Keywords: influenza, gene expression, rhinovirus, human immunology, CD8 T cell
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- 2018
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9. Notch transactivates Rheb to maintain the multipotency of TSC-null cells
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Jun-Hung Cho, Bhaumik Patel, Santosh Bonala, Sasikanth Manne, Yan Zhou, Surya K. Vadrevu, Jalpa Patel, Marco Peronaci, Shanawaz Ghouse, Elizabeth P. Henske, Fabrice Roegiers, Krinio Giannikou, David J. Kwiatkowski, Hossein Mansouri, Maciej M. Markiewski, Brandon White, and Magdalena Karbowniczek
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Science - Abstract
Tuberous sclerosis complex (TSC) is a rare genetic condition causing tumours with differentiation abnormalities; however the molecular mechanisms causing these defects are unclear. Here the authors show that Notch cooperates with Rheb to block cell differentiation forming a regulatory loop that could underlie TSC tumorigenesis.
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- 2017
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10. miR-150 Regulates Memory CD8 T Cell Differentiation via c-Myb
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Zeyu Chen, Erietta Stelekati, Makoto Kurachi, Sixiang Yu, Zhangying Cai, Sasikanth Manne, Omar Khan, Xiaolu Yang, and E. John Wherry
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CD8 T cell ,T cell memory ,viral infection ,miR-150 ,c-Myb ,Bcl-2 ,Bcl-xl ,immune memory ,T cell differentiation ,Biology (General) ,QH301-705.5 - Abstract
MicroRNAs play an important role in T cell responses. However, how microRNAs regulate CD8 T cell memory remains poorly defined. Here, we found that miR-150 negatively regulates CD8 T cell memory in vivo. Genetic deletion of miR-150 disrupted the balance between memory precursor and terminal effector CD8 T cells following acute viral infection. Moreover, miR-150-deficient memory CD8 T cells were more protective upon rechallenge. A key circuit whereby miR-150 repressed memory CD8 T cell development through the transcription factor c-Myb was identified. Without miR-150, c-Myb was upregulated and anti-apoptotic targets of c-Myb, such as Bcl-2 and Bcl-xL, were also increased, suggesting a miR-150-c-Myb survival circuit during memory CD8 T cell development. Indeed, overexpression of non-repressible c-Myb rescued the memory CD8 T cell defects caused by overexpression of miR-150. Overall, these results identify a key role for miR-150 in memory CD8 T cells through a c-Myb-controlled enhanced survival circuit.
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- 2017
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11. Shared and distinct biological circuits in effector, memory and exhausted CD8+ T cells revealed by temporal single-cell transcriptomics and epigenetics
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Josephine R. Giles, Shin Foong Ngiow, Sasikanth Manne, Amy E. Baxter, Omar Khan, Ping Wang, Ryan Staupe, Mohamed S. Abdel-Hakeem, Hua Huang, Divij Mathew, Mark M. Painter, Jennifer E. Wu, Yinghui Jane Huang, Rishi R. Goel, Patrick K. Yan, Giorgos C. Karakousis, Xiaowei Xu, Tara C. Mitchell, Alexander C. Huang, and E. John Wherry
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Immunology ,Immunology and Allergy - Published
- 2022
12. PD-1 directed immunotherapy alters Tfh and humoral immune responses to seasonal influenza vaccine
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Ramin Sedaghat Herati, David A. Knorr, Laura A. Vella, Luisa Victoria Silva, Lakshmi Chilukuri, Sokratis A. Apostolidis, Alexander C. Huang, Alexander Muselman, Sasikanth Manne, Oliva Kuthuru, Ryan P. Staupe, Sharon A. Adamski, Senthil Kannan, Raj K. Kurupati, Hildegund C. J. Ertl, Jeffrey L. Wong, Stylianos Bournazos, Suzanne McGettigan, Lynn M. Schuchter, Ritesh R. Kotecha, Samuel A. Funt, Martin H. Voss, Robert J. Motzer, Chung-Han Lee, Dean F. Bajorin, Tara C. Mitchell, Jeffrey V. Ravetch, and E. John Wherry
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Adult ,Influenza Vaccines ,Vaccination ,Immunology ,Humans ,Immunology and Allergy ,Seasons ,T-Lymphocytes, Helper-Inducer ,Immunity, Humoral - Abstract
Anti-programmed death-1 (anti-PD-1) immunotherapy reinvigorates CD8 T cell responses in patients with cancer but PD-1 is also expressed by other immune cells, including follicular helper CD4 T cells (Tfh) which are involved in germinal centre responses. Little is known, however, about the effects of anti-PD-1 immunotherapy on noncancer immune responses in humans. To investigate this question, we examined the impact of anti-PD-1 immunotherapy on the Tfh-B cell axis responding to unrelated viral antigens. Following influenza vaccination, a subset of adults receiving anti-PD-1 had more robust circulating Tfh responses than adults not receiving immunotherapy. PD-1 pathway blockade resulted in transcriptional signatures of increased cellular proliferation in circulating Tfh and responding B cells compared with controls. These latter observations suggest an underlying change in the Tfh-B cell and germinal centre axis in a subset of immunotherapy patients. Together, these results demonstrate dynamic effects of anti-PD-1 therapy on influenza vaccine responses and highlight analytical vaccination as an approach that may reveal underlying immune predisposition to adverse events.
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- 2022
13. In Vitro Modeling of CD8 T Cell Exhaustion Enables CRISPR Screening to Reveal a Role for BHLHE40
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Jennifer E. Wu, Sasikanth Manne, Shin Foong Ngiow, Amy E. Baxter, Hua Huang, Elizabeth Freilich, Megan L. Clark, Joanna H. Lee, Zeyu Chen, Omar Khan, Ryan P. Staupe, Yinghui J. Huang, Junwei Shi, Josephine R. Giles, and E. John Wherry
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Article - Abstract
Identifying novel molecular mechanisms of exhausted CD8 T cells (Tex) is a key goal of improving immunotherapy of cancer and other diseases. However, high-throughput interrogation ofin vivoTexcan be costly and inefficient.In vitromodels of Texare easily customizable and quickly generate high cellular yield, offering an opportunity to perform CRISPR screening and other high-throughput assays. We established anin vitromodel of chronic stimulation and benchmarked key phenotypic, functional, transcriptional, and epigenetic features against bona fidein vivoTex. We leveraged this model ofin vitrochronic stimulation in combination with pooled CRISPR screening to uncover transcriptional regulators of T cell exhaustion. This approach identified several transcription factors, including BHLHE40.In vitroandin vivovalidation defined a role for BHLHE40 in regulating a key differentiation checkpoint between progenitor and intermediate subsets of Tex. By developing and benchmarking anin vitromodel of Tex, we demonstrate the utility of mechanistically annotatedin vitromodels of Tex, in combination with high-throughput approaches, as a discovery pipeline to uncover novel Texbiology.
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- 2023
14. Data from The Codon 72 TP53 Polymorphism Contributes to TSC Tumorigenesis through the Notch–Nodal Axis
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Magdalena Karbowniczek, Maciej M. Markiewski, David J. Kwiatkowski, Elizabeth P. Henske, Aristotelis Astrinidis, Maureen E. Murphy, Che-Pei Kung, Shanawaz Ghouse, Surya Kumari Vadrevu, Sasikanth Manne, Hossein Mansouri, Santosh Bonala, Bhaumik Patel, and Jun-Hung Cho
- Abstract
We discovered that 90.3% of patients with angiomyolipomas, lymphangioleiomyomatosis (LAM), and tuberous sclerosis complex (TSC) carry the arginine variant of codon 72 (R72) of TP53 and that R72 increases the risk for angiomyolipoma. R72 transactivates NOTCH1 and NODAL better than the proline variant of codon 72 (P72); therefore, the expression of NOTCH1 and NODAL is increased in angiomyolipoma cells that carry R72. The loss of Tp53 and Tsc1 within nestin-expressing cells in mice resulted in the development of renal cell carcinomas (RCC) with high Notch1 and Nodal expression, suggesting that similar downstream mechanisms contribute to tumorigenesis as a result of p53 loss in mice and p53 polymorphism in humans. The loss of murine Tp53 or expression of human R72 contributes to tumorigenesis via enhancing epithelial-to-mesenchymal transition and motility of tumor cells through the Notch and Nodal pathways.Implications:This work revealed unexpected contributions of the p53 polymorphism to the pathogenesis of TSC and established signaling alterations caused by this polymorphism as a target for therapy. We found that the codon 72 TP53 polymorphism contributes to TSC-associated tumorigenesis via Notch and Nodal signaling.
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- 2023
15. Supplementary Figure, Figure Legends, Tables and Material and Methods from The Codon 72 TP53 Polymorphism Contributes to TSC Tumorigenesis through the Notch–Nodal Axis
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Magdalena Karbowniczek, Maciej M. Markiewski, David J. Kwiatkowski, Elizabeth P. Henske, Aristotelis Astrinidis, Maureen E. Murphy, Che-Pei Kung, Shanawaz Ghouse, Surya Kumari Vadrevu, Sasikanth Manne, Hossein Mansouri, Santosh Bonala, Bhaumik Patel, and Jun-Hung Cho
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S1. Expression of hamartin and p53 in mice. S2. CRISPR-Cas9 mediated editing of TP53 codon 72 in angiomyolipoma cells and the impact of R72 on Notch/Nodal axis. S3. Overexpression of Nodal in LAM. S4. Overexpression of Nodal in TSC-associated renal tumors. S5. R72 increases migration of angiomyolipoma cells. Supplementary Table S1. The frequency of TP53 codon 72 germline polymorphism in TSC and LAM patients. Supplementary Table S2. The frequency of TP53 R72 codon polymorphism in TSC and sporadic angiomyolipoma and TSC-associated RCC. Supplementary Table S3. The number of experimental mice used in study.
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- 2023
16. Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3
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Stephanie Grebinoski, Qianxia Zhang, Anthony R. Cillo, Sasikanth Manne, Hanxi Xiao, Erin A. Brunazzi, Tracy Tabib, Carly Cardello, Christine G. Lian, George F. Murphy, Robert Lafyatis, E. John Wherry, Jishnu Das, Creg J. Workman, and Dario A. A. Vignali
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Immunology ,Immunology and Allergy - Published
- 2022
17. Supplementary Materials and Methods from Complement C5a Receptor Facilitates Cancer Metastasis by Altering T-Cell Responses in the Metastatic Niche
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Maciej M. Markiewski, Magdalena Karbowniczek, Othon Almanza, Wojciech Gorczyca, David P. Fairlie, Sasikanth Manne, Linley Riediger, Clayton Cleveland, Priya Sharma, Sharad K. Sharma, Navin K. Chintala, and Surya Kumari Vadrevu
- Abstract
PDF file - 209KB
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- 2023
18. Supplementary Figure Legends from Complement C5a Receptor Facilitates Cancer Metastasis by Altering T-Cell Responses in the Metastatic Niche
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Maciej M. Markiewski, Magdalena Karbowniczek, Othon Almanza, Wojciech Gorczyca, David P. Fairlie, Sasikanth Manne, Linley Riediger, Clayton Cleveland, Priya Sharma, Sharad K. Sharma, Navin K. Chintala, and Surya Kumari Vadrevu
- Abstract
PDF file - 85KB
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- 2023
19. Supplementary Figures 1 - 5 from Complement C5a Receptor Facilitates Cancer Metastasis by Altering T-Cell Responses in the Metastatic Niche
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Maciej M. Markiewski, Magdalena Karbowniczek, Othon Almanza, Wojciech Gorczyca, David P. Fairlie, Sasikanth Manne, Linley Riediger, Clayton Cleveland, Priya Sharma, Sharad K. Sharma, Navin K. Chintala, and Surya Kumari Vadrevu
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PDF file - 981KB, Liver metastasis, C5aR expression on myeloid, 4T1 and T cells, infiltration of CD8+ T cells and MDSCs in livers of breast tumor-bearing mice (S1). MDSCs infiltrate lungs of breast tumor bearing mice prior to metastases (S2). Complement production and activation in tumor bearing mice and C5aR expression in lymph nodes of breast cancer patients (S3). Gating for regulatory T (Treg) cells (S4). Gating for cytokine producing myeloid cells (S5).
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- 2023
20. Enhanced STAT5a activation rewires exhausted CD8 T cells during chronic stimulation to acquire a hybrid durable effector like state
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Jean-Christophe Beltra, Mohamed S. Abdel-Hakeem, Sasikanth Manne, Zhen Zhang, Hua Huang, Makoto Kurachi, Leon Su, Lora Picton, Yuki Muroyama, Valentina Casella, Yinghui J. Huang, Josephine R. Giles, Divij Mathew, Jonathan Belman, Max Klapholz, Hélène Decaluwe, Alexander C. Huang, Shelley L. Berger, K. Christopher Garcia, and E. John Wherry
- Abstract
Rewiring exhausted CD8 T cells (TEX) towards more functional states is a major goal of cancer immunotherapy but has proven challenging due to the epigenetic stability of TEX. Indeed, TEX are epigenetically programmed by the transcription factor Tox. However, epigenetic changes continue to occur as TEX transition from progenitor (TEXprog), to intermediate (TEXint) and terminal (TEXterm) subsets, suggesting potential developmental flexibility in mature TEX subsets. By examining the transition of TEXprog into TEXint cells, we discovered a reciprocally antagonistic circuit between Stat5a and Tox in TEX cells. Stat5-activity controlled TEXint development, antagonized Tox, and instigated partial effector biology. Stat5 was also essential for TEX reinvigoration by PD-1 blockade. Indeed, temporal induction of Stat5-activity in TEX using an orthogonal IL-2/IL2Rβ-pair fostered TEXint cell accumulation and synergized with PD-L1 blockade. Constitutive Stat5a activity (STAT5CA) antagonized Tox-dependent TEX epigenetic programming to generate a durable hybrid effector/NK-like population with enhanced tumor control. Finally, enforcing Stat5-signals in established TEXprog partially rewired the TEX epigenetic landscape towards the effector/memory lineage. Together, these data highlight therapeutic opportunities of manipulating Stat5 to rewire TEX towards a durably protective hybrid program.
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- 2022
21. Distinct Heterogeneity in the Naive T cell Compartments of Children and Adults
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Claire E. Gustafson, Zachary Thomson, Ziyuan He, Elliott Swanson, Katherine Henderson, Mark-Phillip Pebworth, Lauren Y. Okada, Alexander T. Heubeck, Charles R. Roll, Veronica Hernandez, Morgan Weiss, Palak C. Genge, Julian Reading, Josephine R. Giles, Sasikanth Manne, Jeanette Dougherty, CJ Jasen, Allison R. Greenplate, Lynne A. Becker, Lucas T. Graybuck, Suhas V. Vasaikar, Gregory L. Szeto, Adam K. Savage, Cate Speake, Jane H. Buckner, Xiao-jun Li, Troy R. Torgerson, E. John Wherry, Thomas F. Bumol, Laura A. Vella, Sarah E. Henrickson, and Peter J. Skene
- Abstract
The naive T cell compartment undergoes multiple changes across age that associate with altered susceptibility to infection and autoimmunity. In addition to the acquisition of naive-like memory T cell subsets, mouse studies describe substantial molecular reprogramming of the naive compartment in adults compared with adolescents. However, these alterations are not well delineated in human aging. Using a new trimodal single cell technology (TEA-seq), we discovered that the composition and transcriptional and epigenetic programming of the naive T cell compartment in children (11-13 yrs) is distinct from that of older adults (55-65 yrs). Naive CD4 T cells, previously considered relatively resistant to aging, exhibited far more pronounced molecular reprogramming than naive CD8 T cells, in which alterations are preferentially driven by shifts in naive-like memory subsets. These data reveal the complex nature of the naive T cell compartment that may contribute to differential immune responses across the spectrum of human age.One Sentence Summary:The naive CD8 and CD4 T cell compartments in humans are heterogeneous and impacted differently with age, in which naive CD8 T cell subsets dramatically shift in composition and true naive CD4 T cells display significant molecular re-programming.
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- 2022
22. Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation
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Mohamed S. Abdel-Hakeem, Mohammed-Alkhatim Ali, Allison R. Greenplate, Sasikanth Manne, Golnaz Vahedi, Zeyu Chen, Jean-Christophe Beltra, E. John Wherry, Josephine R. Giles, Divij Mathew, Erietta Stelekati, Kito Nzingha, and John L. Johnson
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epigenetic landscape of exhausted T cells ,Transcription, Genetic ,T cell ,Immunology ,Mice, Transgenic ,CD8-Positive T-Lymphocytes ,Lymphocytic Choriomeningitis ,Biology ,Article ,Cell Line ,Epigenesis, Genetic ,Mice ,Immune system ,Antigen ,Cricetinae ,Chlorocebus aethiops ,medicine ,Animals ,Lymphocytic choriomeningitis virus ,Immunology and Allergy ,Cytotoxic T cell ,Hepatocyte Nuclear Factor 1-alpha ,Epigenetics ,recall capacity ,Antigens, Viral ,Vero Cells ,Epigenomics ,T cell exhaustion ,Cell Differentiation ,Acquired immune system ,Chromatin ,Cell biology ,Mice, Inbred C57BL ,medicine.anatomical_structure ,immunological recovery ,Female ,Immunologic Memory - Abstract
Exhausted CD8 T cells (TEX) are a distinct state of T cell differentiation associated with failure to clear chronic viruses and cancer. Immunotherapies such as PD-1 blockade can reinvigorate TEX cells, but reinvigoration is not durable. A major unanswered question is whether TEX cells differentiate into functional durable memory T cells (TMEM) upon antigen clearance. Here, using a mouse model, we found that upon eliminating chronic antigenic stimulation, TEX cells partially (re)acquire phenotypic and transcriptional features of TMEM cells. These ‘recovering’ TEX cells originated from the T cell factor (TCF-1+) TEX progenitor subset. Nevertheless, the recall capacity of these recovering TEX cells remained compromised as compared to TMEM cells. Chromatin-accessibility profiling revealed a failure to recover core memory epigenetic circuits and maintenance of a largely exhausted open chromatin landscape. Thus, despite some phenotypic and transcriptional recovery upon antigen clearance, exhaustion leaves durable epigenetic scars constraining future immune responses. These results support epigenetic remodeling interventions for TEX cell–targeted immunotherapies. Wherry and colleagues examine whether exhausted T cells (TEX) can differentiate into functional memory T cells (TMEM) when chronic antigen is withdrawn. Using the chronic LCMV infection mouse model, they show that ‘recovering’ TEX cells (REC-TEX) only partially recover immunophenotypic and functional characteristics of TMEM cells. The epigenomic status of REC-TEX cells more closely resembles that of TEX cells, and, upon rechallenge, the REC-TEX cells were still compromised in their ability to respond to virus.
- Published
- 2021
23. MicroRNA-29a attenuates CD8 T cell exhaustion and induces memory-like CD8 T cells during chronic infection
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Erietta Stelekati, Zhangying Cai, Sasikanth Manne, Zeyu Chen, Jean-Christophe Beltra, Lance Alec Buchness, Xuebing Leng, Svetlana Ristin, Kito Nzingha, Viktoriya Ekshyyan, Christina Niavi, Mohamed S. Abdel-Hakeem, Mohammed-Alkhatim Ali, Sydney Drury, Chi Wai Lau, Zhen Gao, Yuguang Ban, Simon K. Zhou, K. Mark Ansel, Makoto Kurachi, Martha S. Jordan, Alejandro V. Villarino, Shin Foong Ngiow, and E. John Wherry
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MicroRNAs ,Multidisciplinary ,Neoplasms ,Humans ,Persistent Infection ,Immunotherapy ,CD8-Positive T-Lymphocytes - Abstract
Significance CD8 T cell exhaustion is a key underlying factor limiting immunity in chronic infections and cancer. Persistent antigen exposure antagonizes formation of functional memory CD8 T cells that provide long-term protection and, instead, drives the development of exhausted CD8 T cells (T EX ). Improving T EX persistence and function is a major goal for reinvigorating immune responses against chronic infections and tumors. Here, we identify miR-29a as a molecule that attenuates exhaustion and enhances persistence and function of T EX . Enforced expression of miR-29a alters T EX transcriptome, resulting in robust changes in molecular pathways governed by fundamental transcription factors and epigenetic modulators. Thus, enforced miR-29a expression enhances T EX responses, attenuates exhaustion, and represents a target for improving the outcome of immunotherapy.
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- 2022
24. Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates
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Josephine R. Giles, Shin Foong Ngiow, Sasikanth Manne, Amy E. Baxter, Omar Khan, Ping Wang, Ryan Staupe, Mohamed S. Abdel-Hakeem, Hua Huang, Divij Mathew, Mark M. Painter, Jennifer E. Wu, Yinghui Jane Huang, Rishi Goel, and E. John Wherry
- Abstract
Naïve CD8 T cells can differentiate into effector (TEFF), memory (TMEM), or exhausted (TEX) CD8 T cells. These developmental pathways are associated with distinct transcriptional and epigenetic changes that endow cells with different functional capacities and therefore therapeutic potential. The molecular circuitry underlying these developmental trajectories and the extent of heterogeneity within TEFF, TMEM, TEX populations remain poorly understood. Here, we used the lymphocytic choriomeningitis virus model of acutely-resolved and chronic infection and addressed these gaps by applying longitudinal scRNA-seq and scATAC-seq analysis. These analyses uncovered new subsets, including a subpopulation of TEX expressing NK cell-associated genes, as well as multiple distinct TCF1+ stem/progenitor-like subsets in acute and chronic infection. These data also revealed insights into the reshaping of TEX subsets following PD1 pathway blockade and identified a key role for the cell stress regulator, Btg1, in TEX differentiation. Finally, these results highlighted how the same biological circuits such as cytotoxicity or stem/progenitor pathways can be used by CD8 T cells with highly divergent underlying chromatin landscapes. Thus, this transcriptional and chromatin accessibility landscape map elucidates developmental biology and underlying mechanisms governing TEFF, TMEM, and TEX differentiation.
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- 2022
25. Autoreactive CD8
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Stephanie, Grebinoski, Qianxia, Zhang, Anthony R, Cillo, Sasikanth, Manne, Hanxi, Xiao, Erin A, Brunazzi, Tracy, Tabib, Carly, Cardello, Christine G, Lian, George F, Murphy, Robert, Lafyatis, E John, Wherry, Jishnu, Das, Creg J, Workman, and Dario A A, Vignali
- Subjects
Phenotype ,Neoplasms ,Humans ,Autoimmunity ,CD8-Positive T-Lymphocytes - Abstract
Impaired chronic viral and tumor clearance has been attributed to CD8
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- 2022
26. Neuropilin-1 is a T cell memory checkpoint limiting long-term antitumor immunity
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Robert L. Ferris, E. John Wherry, Andrea L. Szymczak-Workman, Ellen N. Scott, Evan J. Lipson, Creg J. Workman, Sasikanth Manne, Dario A. A. Vignali, Ashwin Somasundaram, Angela M. Gocher, Daniel P. Normolle, Tullia C. Bruno, Kate M. Vignali, and Chang Liu
- Subjects
0301 basic medicine ,T cell ,medicine.medical_treatment ,Immunology ,T-cell receptor ,Immunotherapy ,Biology ,Immune checkpoint ,Immune tolerance ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,Immune system ,Memory cell ,medicine ,Cancer research ,Immunology and Allergy ,CD8 ,030215 immunology - Abstract
Robust CD8+ T cell memory is essential for long-term protective immunity but is often compromised in cancer, where T cell exhaustion leads to loss of memory precursors. Immunotherapy via checkpoint blockade may not effectively reverse this defect, potentially underlying disease relapse. Here we report that mice with a CD8+ T cell–restricted neuropilin-1 (NRP1) deletion exhibited substantially enhanced protection from tumor rechallenge and sensitivity to anti-PD1 immunotherapy, despite unchanged primary tumor growth. Mechanistically, NRP1 cell-intrinsically limited the self-renewal of the CD44+PD1+TCF1+TIM3− progenitor exhausted T cells, which was associated with their reduced ability to induce c-Jun/AP-1 expression on T cell receptor restimulation, a mechanism that may contribute to terminal T cell exhaustion at the cost of memory differentiation in wild-type tumor-bearing hosts. These data indicate that blockade of NRP1, a unique ‘immune memory checkpoint’, may promote the development of long-lived tumor-specific Tmem that are essential for durable antitumor immunity. T cell exhaustion limits antitumor immune responses. Vignali and colleagues identify neuropilin-1 as a novel immune checkpoint that cell-intrinsically operates to limit memory cell formation and can be targeted to enhance antitumor responses.
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- 2020
27. Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers
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Josephine R. Giles, Sasikanth Manne, Elizabeth Freilich, Derek A. Oldridge, Amy E. Baxter, Sangeeth George, Zeyu Chen, Hua Huang, Lakshmi Chilukuri, Mary Carberry, Lydia Giles, Nan-Ping P. Weng, Regina M. Young, Carl H. June, Lynn M. Schuchter, Ravi K. Amaravadi, Xiaowei Xu, Giorgos C. Karakousis, Tara C. Mitchell, Alexander C. Huang, Junwei Shi, and E. John Wherry
- Subjects
Epigenomics ,Infectious Diseases ,Immunology ,Immunology and Allergy ,Humans ,Cell Differentiation ,CD8-Positive T-Lymphocytes ,Lymphocyte Activation ,Chromatin ,Article ,Epigenesis, Genetic - Abstract
The clinical benefit of T cell immunotherapies remains limited by incomplete understanding of T cell differentiation and dysfunction. We generated an epigenetic and transcriptional atlas of T cell differentiation from healthy humans that included exhausted CD8 T cells and applied this resource in three ways. First, we identified modules of gene expression and chromatin accessibility, revealing molecular coordination of differentiation after activation and between central memory and effector memory. Second, we applied this healthy molecular framework to three settings - a neoadjuvant anti-PD1 melanoma trial, a basal cell carcinoma scATAC-seq data set, and autoimmune disease-associated SNPs - yielding insights into disease-specific biology. Third, we predicted genome-wide cis-regulatory elements and validated this approach for key effector genes using CRISPR interference, providing functional annotation and demonstrating the ability to identify targets for non-coding cellular engineering. These studies define epigenetic and transcriptional regulation of human T cells and illustrate the utility of interrogating disease in the context of a healthy T cell atlas.
- Published
- 2021
28. Signaling through FcγRIIA and the C5a-C5aR pathway mediates platelet hyperactivation in COVID-19
- Author
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Jeanette Dougherty, Sasikanth Manne, Amy E. Baxter, Josephine R. Giles, Yinghui Jane Huang, Ajinkya Pattekar, Oliva Kuthuru, Jennifer E. Wu, Aae Suzuki, Nuala J. Meyer, Debora Dunbar, Zeyu Chen, Alexander C. Huang, Ariel R. Weisman, Allison R. Greenplate, Mortimer Poncz, Charles S. Abrams, Ian Frank, Liang Zhao, Caroline A. G. Ittner, Mohamed S. Abdel-Hakeem, Amrita Sarkar, Rishi R. Goel, Sigrid Gouma, Divij Mathew, Sokratis A. Apostolidis, John P. Reilly, Derek A. Oldridge, Cécile Alanio, Scott E. Hensley, Laura A. Vella, E. John Wherry, Heather M. Giannini, Lubica Rauova, and Brittany Weiderhold
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Adult ,Blood Platelets ,Male ,Morpholines ,Immunology ,Aminopyridines ,Syk ,Complement C5a ,Inflammation ,Fostamatinib ,Severity of Illness Index ,Article ,Thromboembolism ,medicine ,Humans ,Syk Kinase ,Immunology and Allergy ,Platelet ,Platelet activation ,Receptor, Anaphylatoxin C5a ,Cells, Cultured ,biology ,Hyperactivation ,SARS-CoV-2 ,business.industry ,Receptors, IgG ,COVID-19 ,Platelet Activation ,Hospitalization ,Ferritin ,Pyrimidines ,biology.protein ,Female ,medicine.symptom ,Signal transduction ,business ,Signal Transduction ,medicine.drug - Abstract
Patients with COVID-19 present with a wide variety of clinical manifestations. Thromboembolic events constitute a significant cause of morbidity and mortality in patients infected with SARS-CoV-2. Severe COVID-19 has been associated with hyperinflammation and pre-existing cardiovascular disease. Platelets are important mediators and sensors of inflammation and are directly affected by cardiovascular stressors. In this report, we found that platelets from severely ill, hospitalized COVID-19 patients exhibit higher basal levels of activation measured by P-selectin surface expression, and have a poor functional reserve upon in vitro stimulation. Correlating clinical features to the ability of plasma from COVID-19 patients to stimulate control platelets identified ferritin as a pivotal clinical marker associated with platelet hyperactivation. The COVID-19 plasma-mediated effect on control platelets was highest for patients that subsequently developed inpatient thrombotic events. Proteomic analysis of plasma from COVID-19 patients identified key mediators of inflammation and cardiovascular disease that positively correlated with in vitro platelet activation. Mechanistically, blocking the signaling of the FcγRIIa-Syk and C5a-C5aR pathways on platelets, using antibody-mediated neutralization, IgG depletion or the Syk inhibitor fostamatinib, reversed this hyperactivity driven by COVID-19 plasma and prevented platelet aggregation in endothelial microfluidic chamber conditions, thus identifying these potentially actionable pathways as central for platelet activation and/or vascular complications in COVID-19 patients. In conclusion, we reveal a key role of platelet-mediated immunothrombosis in COVID-19 and identify distinct, clinically relevant, targetable signaling pathways that mediate this effect. These studies have implications for the role of platelet hyperactivation in complications associated with SARS-CoV-2 infection., Cover illustration, One-sentence summary: The FcγRIIA and C5a-C5aR pathways mediate platelet hyperactivation in COVID-19
- Published
- 2021
29. The Codon 72 TP53 Polymorphism Contributes to TSC Tumorigenesis through the Notch–Nodal Axis
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Elizabeth P. Henske, David J. Kwiatkowski, Shanawaz M. Ghouse, Santosh Bonala, Aristotelis Astrinidis, Maciej M. Markiewski, Hossein Mansouri, Magdalena Karbowniczek, Surya Kumari Vadrevu, Maureen E. Murphy, Che-Pei Kung, Sasikanth Manne, Jun-Hung Cho, and Bhaumik Patel
- Subjects
0301 basic medicine ,Regulation of gene expression ,Cancer Research ,Angiomyolipoma ,Nodal signaling ,Biology ,medicine.disease_cause ,medicine.disease ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,Oncology ,030220 oncology & carcinogenesis ,Lymphangioleiomyomatosis ,Cancer research ,medicine ,Epithelial–mesenchymal transition ,TSC1 ,Carcinogenesis ,NODAL ,neoplasms ,Molecular Biology - Abstract
We discovered that 90.3% of patients with angiomyolipomas, lymphangioleiomyomatosis (LAM), and tuberous sclerosis complex (TSC) carry the arginine variant of codon 72 (R72) of TP53 and that R72 increases the risk for angiomyolipoma. R72 transactivates NOTCH1 and NODAL better than the proline variant of codon 72 (P72); therefore, the expression of NOTCH1 and NODAL is increased in angiomyolipoma cells that carry R72. The loss of Tp53 and Tsc1 within nestin-expressing cells in mice resulted in the development of renal cell carcinomas (RCC) with high Notch1 and Nodal expression, suggesting that similar downstream mechanisms contribute to tumorigenesis as a result of p53 loss in mice and p53 polymorphism in humans. The loss of murine Tp53 or expression of human R72 contributes to tumorigenesis via enhancing epithelial-to-mesenchymal transition and motility of tumor cells through the Notch and Nodal pathways. Implications: This work revealed unexpected contributions of the p53 polymorphism to the pathogenesis of TSC and established signaling alterations caused by this polymorphism as a target for therapy. We found that the codon 72 TP53 polymorphism contributes to TSC-associated tumorigenesis via Notch and Nodal signaling.
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- 2019
30. T follicular helper cells in human efferent lymph retain lymphoid characteristics
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Marcus Buggert, Irene Bukh Brody, Hagop Kaprielian, Laura A. Vella, Terri M. Laufer, Ali Naji, Vitaly V. Ganusov, Son Nguyen, E. John Wherry, Jack P. Antel, Ismail Sayin, Maxim Itkin, Michael R. Betts, Yoav Dori, Leticia Kuri-Cervantes, Josephine R. Giles, Amit Bar-Or, Ramin S. Herati, David H. Canaday, Sasikanth Manne, Kaitlin C. O'Boyle, Matthew E. Johnson, Andrew D. Wells, and Alexander Muselman
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0301 basic medicine ,education.field_of_study ,T-cell receptor ,Population ,Germinal center ,General Medicine ,Biology ,Phenotype ,CXCR5 ,03 medical and health sciences ,Chemokine receptor ,030104 developmental biology ,0302 clinical medicine ,Lymphatic system ,030220 oncology & carcinogenesis ,Immunology ,Epigenetics ,education - Abstract
T follicular helper cells (Tfh), a subset of CD4+ T cells, provide requisite help to B cells in the germinal centers (GC) of lymphoid tissue. GC Tfh are identified by high expression of the chemokine receptor CXCR5 and the inhibitory molecule PD-1. Although more accessible, blood contains lower frequencies of CXCR5+ and PD-1+ cells that have been termed circulating Tfh (cTfh). However, it remains unclear whether GC Tfh exit lymphoid tissues and populate this cTfh pool. To examine exiting cells, we assessed the phenotype of Tfh present within the major conduit of efferent lymph from lymphoid tissues into blood, the human thoracic duct. Unlike what was found in blood, we consistently identified a CXCR5-bright PD-1-bright (CXCR5BrPD-1Br) Tfh population in thoracic duct lymph (TDL). These CXCR5BrPD-1Br TDL Tfh shared phenotypic and transcriptional similarities with GC Tfh. Moreover, components of the epigenetic profile of GC Tfh could be detected in CXCR5BrPD-1Br TDL Tfh and the transcriptional imprint of this epigenetic signature was enriched in an activated cTfh subset known to contain vaccine-responding cells. Together with data showing shared TCR sequences between the CXCR5BrPD-1Br TDL Tfh and cTfh, these studies identify a population in TDL as a circulatory intermediate connecting the biology of Tfh in blood to Tfh in lymphoid tissue.
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- 2019
31. TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion
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Michael T. Werner, Jennifer E. Wu, Wei Xu, Patrick Yan, Giorgos C. Karakousis, Bertram Bengsch, Kunal P. Patel, Alexander C. Huang, Jonathan Kaye, Shelley L. Berger, Sasikanth Manne, Tara C. Mitchell, Omar Khan, Ryan P. Staupe, John Attanasio, Sierra McDonald, Xiaowei Xu, Sangeeth M. George, Shin Foong Ngiow, Josephine R. Giles, Ravi K. Amaravadi, Lynn M. Schuchter, E. John Wherry, Katherine A. Alexander, and Greg Donahue
- Subjects
0301 basic medicine ,Male ,Genotype ,Transcription, Genetic ,Cell ,Biology ,CD8-Positive T-Lymphocytes ,Article ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Immune system ,fluids and secretions ,medicine ,Cytotoxic T cell ,Animals ,Epigenetics ,Calcium Signaling ,Transcription factor ,Feedback, Physiological ,Homeodomain Proteins ,Mice, Inbred BALB C ,Multidisciplinary ,NFATC Transcription Factors ,Effector ,Calcineurin ,Epistasis, Genetic ,3. Good health ,Chromatin ,Cell biology ,Mice, Inbred C57BL ,030104 developmental biology ,medicine.anatomical_structure ,Gene Expression Regulation ,bacteria ,Female ,Tumor Escape ,Immunologic Memory ,CD8 ,030215 immunology - Abstract
Exhausted CD8+ T (Tex) cells in chronic infections and cancer have limited effector function, high co-expression of inhibitory receptors and extensive transcriptional changes compared with effector (Teff) or memory (Tmem) CD8+ T cells. Tex cells are important clinical targets of checkpoint blockade and other immunotherapies. Epigenetically, Tex cells are a distinct immune subset, with a unique chromatin landscape compared with Teff and Tmem cells. However, the mechanisms that govern the transcriptional and epigenetic development of Tex cells remain unknown. Here we identify the HMG-box transcription factor TOX as a central regulator of Tex cells in mice. TOX is largely dispensable for the formation of Teff and Tmem cells, but it is critical for exhaustion: in the absence of TOX, Tex cells do not form. TOX is induced by calcineurin and NFAT2, and operates in a feed-forward loop in which it becomes calcineurin-independent and sustained in Tex cells. Robust expression of TOX therefore results in commitment to Tex cells by translating persistent stimulation into a distinct Tex cell transcriptional and epigenetic developmental program.
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- 2019
32. A single dose of neoadjuvant PD-1 blockade predicts clinical outcomes in resectable melanoma
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Felix Quagliarello, Michael D. Farwell, Lydia Giles, Lakshmi Chilukuri, Qing Zhao, Sangeeth M. George, Melanie W. Kier, Shujing Liu, Patrick Yan, Lakshmanan Annamalai, Kurt D'Andrea, Suzanne McGettigan, Kristin Kreider, Wendy M. Blumenschein, Lynn M. Schuchter, Andrew Kozlov, Robin Mogg, Robert J. Orlowski, E. John Wherry, Bradley Wubbenhorst, Bertram Bengsch, Katherine L. Nathanson, Jennifer H. Yearley, Rosemarie Mick, Sasikanth Manne, Ramin S. Herati, Xiaowei Xu, Brandon Wenz, Tara C. Mitchell, Gerald P. Linette, Liza Dorfman, Alexander C. Huang, Adam A. Kraya, Ravi K. Amaravadi, Giorgos C. Karakousis, Wei Xu, and Mary Carberry
- Subjects
Adult ,Male ,0301 basic medicine ,Oncology ,medicine.medical_specialty ,Skin Neoplasms ,medicine.medical_treatment ,Dermatologic Surgical Procedures ,Kaplan-Meier Estimate ,CD8-Positive T-Lymphocytes ,Antibodies, Monoclonal, Humanized ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Antineoplastic Agents, Immunological ,0302 clinical medicine ,Immune system ,Internal medicine ,medicine ,Humans ,Melanoma ,Neoadjuvant therapy ,Aged ,Neoplasm Staging ,Proportional Hazards Models ,Aged, 80 and over ,Tumor microenvironment ,business.industry ,Gene Expression Profiling ,General Medicine ,Immunotherapy ,Middle Aged ,medicine.disease ,Neoadjuvant Therapy ,3. Good health ,Blockade ,030104 developmental biology ,Chemotherapy, Adjuvant ,030220 oncology & carcinogenesis ,Monoclonal ,Female ,Tumor Escape ,Transcriptome ,business ,Adjuvant - Abstract
Immunologic responses to anti-PD-1 therapy in melanoma patients occur rapidly with pharmacodynamic T cell responses detectable in blood by 3 weeks. It is unclear, however, whether these early blood-based observations translate to the tumor microenvironment. We conducted a study of neoadjuvant/adjuvant anti-PD-1 therapy in stage III/IV melanoma. We hypothesized that immune reinvigoration in the tumor would be detectable at 3 weeks and that this response would correlate with disease-free survival. We identified a rapid and potent anti-tumor response, with 8 of 27 patients experiencing a complete or major pathological response after a single dose of anti-PD-1, all of whom remain disease free. These rapid pathologic and clinical responses were associated with accumulation of exhausted CD8 T cells in the tumor at 3 weeks, with reinvigoration in the blood observed as early as 1 week. Transcriptional analysis demonstrated a pretreatment immune signature (neoadjuvant response signature) that was associated with clinical benefit. In contrast, patients with disease recurrence displayed mechanisms of resistance including immune suppression, mutational escape, and/or tumor evolution. Neoadjuvant anti-PD-1 treatment is effective in high-risk resectable stage III/IV melanoma. Pathological response and immunological analyses after a single neoadjuvant dose can be used to predict clinical outcome and to dissect underlying mechanisms in checkpoint blockade. Neoadjuvant PD-1 blockade in patients with resectable melanoma followed by adjuvant maintenance results in early immunological effects driving clinical benefit and reveals transcriptional and genomic mechanisms of response.
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- 2019
33. Abstract 3579: T cell intrinsic DNA damage and repair response as a novel marker associated with clinical response to PD-1 blockade
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Yuki Muroyama, Sasikanth Manne, Derek A. Oldridge, Nils Wellhausen, Allison R. Greenplate, Lakshmi Chilukuri, Divij Mathew, Caiyue Xu, Ramin S. Herati, Alexander C. Huang, Dmitriy Zamarin, Claire F. Friedman, and E. John Wherry
- Subjects
Cancer Research ,Oncology - Abstract
Despite the high tumor mutational burden (TMB), immune check point blockade (ICB) still fails in about half of microsatellite instability-high (MSI-H) cancer patients, suggesting underlying immune dysregulation. Immune profiling of peripheral blood from chemotherapy-resistant MSI-H uterine cancer patients treated with nivolumab identified a rapid proliferative CD8 T cell response 2-4 weeks post PD-1 blockade (N = 32). This immunological response, however, did not correlate with clinical response, suggesting additional parameters may be relevant. We focused on DNA damage and repair (DDR) in T cells as potential novel parameters. DDR has been extensively studied in the context of inducing cell death in highly-proliferating tumor cells. However, despite induction of rapid proliferation of T cells upon ICB, whether T cell-intrinsic DDR impacts T cell function, and how the coordination of DDR affects immunological and clinical response to ICBs have been largely unexplored. We hypothesized that the T celI-intrinsic DDR responses to proliferative and genotoxic stress might contribute to the disparity between immunological and clinical response. To test the hypothesis, we developed a novel high-dimensional cytometry platform. This DDR-Immune platform enables simultaneous analysis of T cell differentiation state with changes in major DDR pathways at single-cell resolution. The DDR-Immune platform revealed consistent T cell subset specific patterns of DDR, as well as specific DDR pathways induced by different types of DNA damage, such as γ-irradiation (IR), UV irradiation (UV) or proliferative stress (i.e. anti-CD3/CD28 stimulation). For example, terminally differentiated effector T cells accumulated higher DNA damage and cell death. In contrast, stem cell memory (TSCM) and regulatory T cells (Treg) displayed high DDR with less cell death, suggesting that effective cell-intrinsic DDR against genotoxic stress in T cells confers a survival advantage. We applied the platform to MSI-H uterine cancer cohort to test if T cell-intrinsic DDR distinguish the clinical response. Indeed, we found that in clinical responders but not clinical non-responders, Ki67+ CD8 T cells responding to PD-1 blockade exhibited rapid induction of DDR represented as a spike increase of phosphorylated-ATM (pATM). This likely indicates the T cell ‘fitness’ response to proliferative stress induced by PD-1 blockade. Furthermore, patients with higher induction of pATM in responding CD8 T cells at the peak of the immunological response to PD-1 blockade had longer progression-free survival (PFS). Collectively, the new platform reveals previously unrecognized roles for T cell-intrinsic DDR as a novel determinant of immune responsiveness and clinical outcome to ICB and has potential application to other cancer therapies including chemotherapy and radiotherapy. Citation Format: Yuki Muroyama, Sasikanth Manne, Derek A. Oldridge, Nils Wellhausen, Allison R. Greenplate, Lakshmi Chilukuri, Divij Mathew, Caiyue Xu, Ramin S. Herati, Alexander C. Huang, Dmitriy Zamarin, Claire F. Friedman, E. John Wherry. T cell intrinsic DNA damage and repair response as a novel marker associated with clinical response to PD-1 blockade [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 3579.
- Published
- 2022
34. PD-1 restricts the development and effector function of tissue regulatory T cells in experimental autoimmune encephalomyelitis
- Author
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Dan Liang, Jennifer Judge, Samuel Markson, Samantha Guinn, Jenna Lynn Collier, Osmaan Shahid, Sasikanth Manne, Juhi Kuchroo, Megan Fung, Kristen E Pauken, Dario AA Vignali, John E Wherry, and Arlene H Sharpe
- Subjects
Immunology ,Immunology and Allergy - Abstract
PD-1 restricts T cell effector functions, regulates T cell tolerance, and maintains immune homeostasis, thereby playing pivotal roles in cancer, autoimmune and infectious diseases. Our studies and others show that PD-1 can restrain Treg suppressive function in autoimmunity and cancer. Here, we investigate the role of Treg intrinsic PD-1 in regulating pathogenic and protective CD4+ T cell responses in experimental autoimmune encephalomyelitis (EAE) by inducing PD-1 deletion on FoxP3+ cells prior to disease development. This deletion of PD-1 only in Treg protects mice from severe disease, and both flow cytometry and transcriptional analysis of central nervous system (CNS) CD4+ T cells show enrichment of tissue effector Treg (eTreg) subsets at peak of disease. We find that PD-1 restrains the generation and suppressive function of these effector Treg. This tissue eTreg signature is also observed in human and mouse Treg subsets from the tumor microenvironment, and are potent suppressor populations. Further studies are underway to determine how PD-1 impacts TCR signaling and FoxP3 transcriptional co-activators in Treg cells. Our study provides deeper insights into how PD-1 regulates T cell tolerance, underscoring the important role of PD-1 in regulating Treg differentiation and suppressive function during autoimmune diseases, and provide mechanistic insights for PD-1 modulation in cancer and autoimmunity. Supported by NIH P01AI108545
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- 2022
35. Inhibitory signaling sustains a distinct early memory CD8 + T cell precursor that is resistant to DNA damage
- Author
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Kristen E. Pauken, Zhangying Cai, Bertram Bengsch, Jonathan B. Johnnidis, Shin Foong Ngiow, Dario A. A. Vignali, Michael A. Paley, Yuki Muroyama, Sasikanth Manne, Arlene H. Sharpe, Shufei Song, Christelle Harly, Jason M. Schenkel, John Attanasio, Jesse M. Platt, Zeyu Chen, Allison R. Greenplate, Avinash Bhandoola, Steven L. Reiner, F. Bradley Johnson, Mohamed S. Abdel-Hakeem, Kito Nzingha, Jean Christophe Beltra, Makoto Kurachi, Mohammed Alkhatim A. Ali, Josephine R. Giles, Vesselin T. Tomov, E. John Wherry, University of Pennsylvania [Philadelphia], Washington University in Saint Louis (WUSTL), Massachusetts General Hospital [Boston], Brigham & Women’s Hospital [Boston] (BWH), Harvard Medical School [Boston] (HMS), Massachusetts Institute of Technology (MIT), Immunobiology of Human αβ and γδ T Cells and Immunotherapeutic Applications (CRCINA-ÉQUIPE 1), Centre de Recherche en Cancérologie et Immunologie Nantes-Angers (CRCINA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH), LabEX IGO Immunothérapie Grand Ouest, Freiburg University Medical Center, Centre for Biological Signaling Studies [Freiburg] (BIOSS), University of Freiburg [Freiburg], Kanazawa University (KU), University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE), UPMC Hillman Cancer Center [Pittsburgh, PA, États-Unis], Columbia University [New York], University of Pennsylvania, Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université d'Angers (UA)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre hospitalier universitaire de Nantes (CHU Nantes), Nantes Université (Nantes Univ), Universitäts Klinikum Freiburg = University Medical Center Freiburg (Uniklinik), and Bernardo, Elizabeth
- Subjects
0301 basic medicine ,Effector ,DNA damage ,Chemistry ,T cell ,Lymphocyte ,Immunology ,Eomesodermin ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,General Medicine ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,[SDV.CAN] Life Sciences [q-bio]/Cancer ,medicine ,Cytotoxic T cell ,CD5 ,CD8 ,030215 immunology - Abstract
International audience; The developmental origins of memory T cells remain incompletely understood. During the expansion phase of acute viral infection, we identified a distinct subset of virus-specific CD8 + T cells that possessed distinct characteristics including expression of CD62L, T cell factor 1 (TCF-1), and Eomesodermin; relative quiescence; expression of activation markers; and features of limited effector differentiation. These cells were a quantitatively minor subpopulation of the TCF-1 + pool and exhibited self-renewal, heightened DNA damage surveillance activity, and preferential long-term recall capacity. Despite features of memory and somewhat restrained proliferation during the expansion phase, this subset displayed evidence of stronger TCR signaling than other responding CD8 + T cells, coupled with elevated expression of multiple inhibitory receptors including programmed cell death 1 (PD-1), lymphocyte activating gene 3 (LAG-3), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), CD5, and CD160. Genetic ablation of PD-1 and LAG-3 compromised the formation of this CD62L hi TCF-1 + subset and subsequent CD8 + T cell memory. Although central memory phenotype CD8 + T cells were formed in the absence of these cells, subsequent memory CD8 + T cell recall responses were compromised. Together, these results identify an impor tant link between genome integrity maintenance and CD8 + T cell memory. Moreover, the data indicate a role for inhibitory receptors in preserving key memory CD8 + T cell precursors during initial activation and differentiation. Identification of this rare subpopulation within the memory CD8 + T cell precursor pool may help reconcile models of the developmental origin of long-term CD8 + T cell memory.
- Published
- 2021
36. The identity of human tissue-emigrant CD8(+) T cells
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Sian Llewellyn-Lacey, Son Nguyen, Ali Naji, Takuya Sekine, Maxim Itkin, Ernesto Sparrelid, Michael R. Betts, Alberto Sada Japp, Irene Bukh Brody, Johan K. Sandberg, E. John Wherry, Samuel Darko, Sasikanth Manne, Jack P. Antel, Golnaz Vahedi, Ian Frank, Andrew D. Wells, Niklas K. Björkström, Jean Baptiste Gorin, Martin A. Ivarsson, Marcus Buggert, Colby R. Maldini, Louis J. Picker, Emma Gostick, André Perez-Potti, Leticia Kuri-Cervantes, Afam A. Okoye, David Price, Vincent H. Wu, Matthew E. Johnson, Terri M. Laufer, Daniel C. Douek, Amy Ransier, Yoav Dori, Amit Bar-Or, David H. Canaday, Laura A. Vella, Zeyu Chen, Olga Rivera-Ballesteros, and Laura Hertwig
- Subjects
Cytotoxicity, Immunologic ,Transcription, Genetic ,T cell ,Lymphocyte ,Biology ,CD8-Positive T-Lymphocytes ,General Biochemistry, Genetics and Molecular Biology ,Article ,Epigenesis, Genetic ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,T-Lymphocyte Subsets ,Gene expression ,medicine ,Cytotoxic T cell ,Animals ,Humans ,Epigenetics ,030304 developmental biology ,0303 health sciences ,Cell Differentiation ,Macaca mulatta ,Cell biology ,Clone Cells ,medicine.anatomical_structure ,Lymphatic system ,Lymph Nodes ,Transcriptome ,Immunologic Memory ,030217 neurology & neurosurgery ,CD8 - Abstract
Lymphocyte migration is essential for adaptive immune surveillance. However, our current understanding of this process is rudimentary, because most human studies have been restricted to immunological analyses of blood and various tissues. To address this, we used an integrated approach to characterize tissue-emigrant immune cells in thoracic duct lymph (TDL). The most prevalent immune cells in human and non-human primate efferent lymph were T cells. Cytolytic CD8(+) T cell subsets with effector-like epigenetic and transcriptional signatures were clonotypically skewed and selectively confined to the intravascular circulation, whereas non-cytolytic CD8(+) T cell subsets with stem-like epigenetic and transcriptional signatures predominated in tissues and TDL. Moreover, these anatomically distinct gene expression profiles were recapitulated within individual antigen-specific clonotypes, suggesting parallel differentiation programs independent of the expressed antigen receptor. Our collective dataset provides a framework of the migratory immune system and defines the nature of tissue-emigrant CD8(+) T cells that recirculate via TDL.
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- 2020
37. 186 Distinct immune signatures predicting clinical response to PD-1 blockade therapy in gynecological cancers revealed by high-dimensional immune profiling
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Yuki Muroyama, Sasikanth Manne, Alexandar Huang, Divij Mathew, Lakshmi Chilukuri, Allison Greenplate, Takuya Ohtani, Dmitriy Zamarin, Claire Friedman, and John Wherry
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business.industry ,medicine.medical_treatment ,T cell ,Immunotherapy ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,lcsh:RC254-282 ,Immune checkpoint ,medicine.anatomical_structure ,Immune system ,Uterine cancer ,medicine ,Cancer research ,Nivolumab ,business ,Lung cancer ,Ovarian cancer - Abstract
Background Although immune checkpoint blockade revolutionized cancer therapy, response rates have been mixed in gynecological malignancies. While uterine endometrial cancer with high microsatellite instability (MSIHI) and high tumor mutational burden (TMB) respond robustly to checkpoint blockade, high-grade serous ovarian cancer (HGSOC) with low TMB respond modestly. Currently, there has been no known immune signature or T cell phenotype that predicts clinical response in gynecological tumors. Methods To dissect the immune landscape and T cell phenotypes in gynecological cancer patients receiving PD-1 blockade, we used high-dimensional cytometry (flow cytometry and mass cytometry (CyTOF)). We performed longitudinal deep immune profiling of PBMC from patients with recurrent uterine endometrial cancer receiving single-arm nivolumab, and HSGOC patients receiving neoadjuvant nivolumab plus platinum-based chemotherapy prior to debulking surgery. Results Chemotherapy-resistant MSI-H uterine cancer patients treated with nivolumab had a proliferative T cell response 2–4 weeks post PD-1 blockade, consistent with responses seen in high TMB melanoma and lung cancer. The responding Ki67+ CD8 T cell population was largely CD45RAloCD27hi or CD45RAloCD27lo and highly expressed PD1, CTLA-4, and CD39, consistent with the phenotype of exhausted T cells (TEX). These exhausted-like cells are enriched in responders, whereas early expansion Tregs are enriched in non-responders. Unlike patients with uterine endometrial cancer, patients with TMBlo ovarian cancer did not have a clear proliferative CD8 T cell response after neoadjuvant nivolumab plus chemotherapy treatment, suggesting systemic immune suppression. At baseline, ovarian cancer without recurrence have more terminally differentiated effector-like CD8 T cells, and patients with recurrence have more naive-like cells. Thus, both high and low TMB gynecological tumors have distinct immune landscapes associated with clinical response. Additionally, in MSI-H uterine endometrial cancer patients, the length of time between the prior chemotherapy and the initiation of immunotherapy was negatively correlated with T cell reinvigoration post immunotherapy and clinical response. This suggests the importance of optimize therapeutic timing to maximize the therapeutic efficacy when combining immunotherapy and chemotherapy. Conclusions Collectively, our immune profiling revealed the distinct immune signatures associated with clinical response to PD-1 blockade in gynecological cancers. Our results also suggest that TMBhi inflamed versus TMBlo cold tumor microenvironment, and timing of chemo/immunotherapy could impact differentiation and functions of T cells. Ethics Approval The study was approved by MSKCC Ethics Board, approval number 17–180 and 17–182.
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- 2020
38. Inhibitory signaling sustains a distinct early memory CD8
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Jonathan B, Johnnidis, Yuki, Muroyama, Shin Foong, Ngiow, Zeyu, Chen, Sasikanth, Manne, Zhangying, Cai, Shufei, Song, Jesse M, Platt, Jason M, Schenkel, Mohamed, Abdel-Hakeem, Jean-Christophe, Beltra, Allison R, Greenplate, Mohammed-Alkhatim A, Ali, Kito, Nzingha, Josephine R, Giles, Christelle, Harly, John, Attanasio, Kristen E, Pauken, Bertram, Bengsch, Michael A, Paley, Vesselin T, Tomov, Makoto, Kurachi, Dario A A, Vignali, Arlene H, Sharpe, Steven L, Reiner, Avinash, Bhandoola, F Bradley, Johnson, and E John, Wherry
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Male ,Mice, Knockout ,Precursor Cells, T-Lymphoid ,Programmed Cell Death 1 Receptor ,Cell Differentiation ,CD8-Positive T-Lymphocytes ,Lymphocytic Choriomeningitis ,Lymphocyte Activation ,Listeria monocytogenes ,Lymphocyte Activation Gene 3 Protein ,Article ,Disease Models, Animal ,Memory T Cells ,Mice ,Antigens, CD ,Animals ,Humans ,Lymphocytic choriomeningitis virus ,Female ,Listeriosis ,Hepatocyte Nuclear Factor 1-alpha ,Immunologic Memory ,DNA Damage - Abstract
The developmental origins of memory T cells remain incompletely understood. During the expansion phase of acute viral infection, we identified a distinct subset of virus-specific CD8(+) T cells that possessed distinct characteristics including expression of CD62L, TCF-1 and Eomes; relative quiescence; expression of activation markers; and features of limited effector differentiation. These cells were a quantitatively minor subpopulation of the TCF-1(+) pool and exhibited self-renewal, heightened DNA damage surveillance activity, and preferential long-term recall capacity. Despite features of memory and somewhat restrained proliferation during the expansion phase, this subset displayed evidence of stronger TCR signaling than other responding CD8(+) T cells, coupled with elevated expression of multiple inhibitory receptors including PD-1, LAG-3, CTLA-4, CD5, and CD160. Indeed, genetic ablation of PD-1 and LAG-3 compromised the formation of this CD62L(hi) TCF-1(+) subset and subsequent CD8(+) T cell memory. Although central memory phenotype CD8(+) T cells (T(CM)) were formed in the absence of these cells, subsequent memory CD8(+) T cell recall responses were compromised. Together, these results identify an important link between genome integrity maintenance and CD8(+) T cell memory. Moreover, the data indicate a role for inhibitory receptors in preserving key memory CD8(+) T cell precursors during initial activation and differentiation. Identification of this rare subpopulation within the memory CD8(+) T cell precursor pool may help reconcile models of the developmental origin of long-term CD8(+) T cell memory.
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- 2020
39. Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications
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Ariel R. Weisman, Ajinkya Pattekar, Fang Chen, Caroline A. G. Ittner, Cécile Alanio, Sasikanth Manne, Zeyu Chen, E. John Wherry, Holly Ramage, M. Betina Pampena, Scott E. Hensley, Kito Nzingha, Justin Kim, Amy E. Baxter, Jeanette Dougherty, Divij Mathew, Michael R. Betts, Allison R. Greenplate, Claudia P. Arevalo, Yinghui Jane Huang, Leticia Kuri-Cervantes, Josephine R. Giles, Derek A. Oldridge, Nuala J. Meyer, Jennifer E. Wu, Marcus J. Bolton, Laura A. Vella, John P. Reilly, Alexander C. Huang, Elizabeth M. Anderson, Eileen C. Goodwin, Madison E. Weirick, Simon F. Lacey, Sokratis A. Apostolidis, Sara Cherry, Kurt D'Andrea, Nicholas Han, Sigrid Gouma, and Oliva Kuthuru
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Multidisciplinary ,biology ,business.industry ,R-Articles ,T cell ,Immunology ,Acquired immune system ,Virus ,medicine.anatomical_structure ,Immune system ,biology.protein ,Medicine ,Antibody ,business ,Cytometry ,Research Articles ,B-Lymphocyte Subsets ,B cell ,Research Article - Abstract
Immune profiling of COVID-19 patients Coronavirus disease 2019 (COVID-19) has affected millions of people globally, yet how the human immune system responds to and influences COVID-19 severity remains unclear. Mathew et al. present a comprehensive atlas of immune modulation associated with COVID-19. They performed high-dimensional flow cytometry of hospitalized COVID-19 patients and found three prominent and distinct immunotypes that are related to disease severity and clinical parameters. Arunachalam et al. report a systems biology approach to assess the immune system of COVID-19 patients with mild-to-severe disease. These studies provide a compendium of immune cell information and roadmaps for potential therapeutic interventions. Science , this issue p. eabc8511 , p. 1210
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- 2020
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40. In vivo CRISPR screening identifies Fli1 as a transcriptional safeguard that restrains effector CD8 T cell differentiation during infection and cancer
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E. John Wherry, Kito Nzingha, Viktoriya Ekshyyan, Zhangying Cai, Josephine R. Giles, Allison R. Greenplate, Sasikanth Manne, Omar Khan, Zhendong Cao, Mohammed Alkhatim A. Ali, Zhuoyu Wen, Junwei Shi, Shelley L. Berger, Zhen Zhang, Nancy A. Speck, Hua Huang, Alexis Battle, Shin Foong Ngiow, Makoto Kurachi, Elizabeth Freilich, Yuan He, Jennifer E. Wu, Eri Arai, Amy E. Baxter, and Zeyu Chen
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Effector ,Cellular differentiation ,T cell ,medicine.medical_treatment ,fungi ,Biology ,Chromatin ,Cell biology ,medicine.anatomical_structure ,Cancer immunotherapy ,parasitic diseases ,medicine ,Cytotoxic T cell ,CRISPR ,Transcription factor - Abstract
SummaryImproving effector activity of antigen specific T cells is a major goal in cancer immunotherapy. Despite the identification of several effector T cell (TEFF)-driving transcription factors (TF), the transcriptional coordination of TEFF biology remains poorly understood. We developed an in vivo T cell CRISPR screening platform and identified a novel mechanism restraining TEFF biology through the ETS family TF, Fli1. Genetic deletion of Fli1 enhanced TEFF responses without compromising memory or exhaustion precursors. Fli1 restrained TEFF lineage differentiation by binding to cis-regulatory elements of effector-associated genes. Loss of Fli1 increased chromatin accessibility at ETS:RUNX motifs allowing more efficient Runx3-driven TEFF biology. CD8 T cells lacking Fli1 provided substantially better protection against multiple infections and tumors. These data indicate that Fli1 safeguards the developing CD8 T cell transcriptional landscape from excessive ETS:RUNX-driven TEFF cell differentiation. Moreover, genetic deletion of Fli1 improves TEFF differentiation and protective immunity in infections and cancer.
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- 2020
41. In vivo CD8
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Divij Mathew, Yuan He, Viktoriya Ekshyyan, E. John Wherry, Junwei Shi, Josephine R. Giles, Hua Huang, Omar Khan, Sasikanth Manne, Alexis Battle, Zhuoyu Wen, Eri Arai, Nancy A. Speck, Allison R. Greenplate, Makoto Kurachi, Shin Foong Ngiow, Zeyu Chen, Qingzhou Chen, Kito Nzingha, Elizabeth Freilich, Amy E. Baxter, Mohammed Alkhatim A. Ali, Zhen Zhang, Jennifer E. Wu, Mohamed A. Hakeem, Zhangying Cai, Zhendong Cao, and Shelley L. Berger
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medicine.medical_treatment ,Cellular differentiation ,Biology ,CD8-Positive T-Lymphocytes ,Infections ,General Biochemistry, Genetics and Molecular Biology ,Article ,Epigenesis, Genetic ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Cancer immunotherapy ,Neoplasms ,parasitic diseases ,medicine ,Cytotoxic T cell ,CRISPR ,Animals ,Gene Regulatory Networks ,Transcription factor ,030304 developmental biology ,0303 health sciences ,Effector ,Proto-Oncogene Protein c-fli-1 ,fungi ,Cell Differentiation ,Chromatin ,Cell biology ,Core Binding Factor Alpha 3 Subunit ,FLI1 ,Chronic Disease ,CRISPR-Cas Systems ,030217 neurology & neurosurgery - Abstract
Improving effector activity of antigen specific T cells is a major goal in cancer immunotherapy. Despite the identification of several effector T cell (T(EFF))-driving transcription factors (TF), the transcriptional coordination of T(EFF) biology remains poorly understood. We developed an in vivo T cell CRISPR screening platform and identified a key mechanism restraining T(EFF) biology through the ETS family TF, Fli1. Genetic deletion of Fli1 enhanced T(EFF) responses without compromising memory or exhaustion precursors. Fli1 restrained T(EFF) lineage differentiation by binding to cis-regulatory elements of effector-associated genes. Loss of Fli1 increased chromatin accessibility at ETS:RUNX motifs allowing more efficient Runx3-driven T(EFF) biology. CD8(+) T cells lacking Fli1 provided substantially better protection against multiple infections and tumors. These data indicate that Fli1 safeguards the developing CD8(+) T cell transcriptional landscape from excessive ETS:RUNX-driven T(EFF) cell differentiation. Moreover, genetic deletion of Fli1 improves T(EFF) differentiation and protective immunity in infections and cancer.
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- 2020
42. Exploration of T-Cell Diversity Using Mass Cytometry
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Kaitlin C, O'Boyle, Takuya, Ohtani, Sasikanth, Manne, Bertram, Bengsch, Sarah E, Henrickson, E John, Wherry, and Cecile, Alanio
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Cohort Studies ,Staining and Labeling ,T-Lymphocyte Subsets ,Metals, Heavy ,Systems Biology ,Humans ,Single-Cell Analysis ,Flow Cytometry ,Lymphocyte Activation ,Antibodies ,High-Throughput Screening Assays ,Immunophenotyping ,Workflow - Abstract
T-cell diversity is multifactorial and includes variability in antigen specificity, differentiation, function, and cell-trafficking potential. Spectral overlap limits the ability of traditional flow cytometry to fully capture the diversity of T-cell subsets and function. The development of mass cytometry permits deep immunoprofiling of T-cell subsets, activation state, and function simultaneously from even small volumes of blood. This chapter describes our methods for mass cytometry and high-throughput data analysis of T cells in patient cohorts. We provide a pipeline that includes practical considerations when customizing a panel for mass cytometry. We also provide protocols for the conjugation and titration of metal-labeled antibodies (including two T-cell panels) and a staining procedure. Finally, with the aim to support translational science, we provide R scripts that contain a detailed workflow for initial evaluation of high-dimensional data generated from cohorts of patients.
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- 2020
43. Exploration of T-Cell Diversity Using Mass Cytometry
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E. John Wherry, Takuya Ohtani, Bertram Bengsch, Sarah E. Henrickson, Cécile Alanio, Kaitlin C. O'Boyle, and Sasikanth Manne
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0301 basic medicine ,medicine.diagnostic_test ,Computer science ,Systems biology ,T cell ,Antigen specificity ,Computational biology ,Flow cytometry ,High throughput analysis ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,medicine ,In patient ,Mass cytometry ,030217 neurology & neurosurgery - Abstract
T-cell diversity is multifactorial and includes variability in antigen specificity, differentiation, function, and cell-trafficking potential. Spectral overlap limits the ability of traditional flow cytometry to fully capture the diversity of T-cell subsets and function. The development of mass cytometry permits deep immunoprofiling of T-cell subsets, activation state, and function simultaneously from even small volumes of blood. This chapter describes our methods for mass cytometry and high-throughput data analysis of T cells in patient cohorts. We provide a pipeline that includes practical considerations when customizing a panel for mass cytometry. We also provide protocols for the conjugation and titration of metal-labeled antibodies (including two T-cell panels) and a staining procedure. Finally, with the aim to support translational science, we provide R scripts that contain a detailed workflow for initial evaluation of high-dimensional data generated from cohorts of patients.
- Published
- 2020
44. In vivo CRISPR Screening Identifies Fli1 as a Transcriptional Safeguard that Restrains Effector CD8 T Cell Differentiation During Infection and Cancer
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Sasikanth Manne, Zeyu Chen, Makoto Kurachi, Jennifer E. Wu, Junwei Shi, Hua Huang, Amy E. Baxter, Omar Khan, Shin Foong Ngiow, Allison R. Greenplate, Zhen Zhang, Eri Arai, Zhuoyu Wen, Viktoriya Ekshyyan, Nancy A. Speck, Josephine R. Giles, Kito Nzingha, E. John Wherry, Elizabeth Freilich, Alexis Battle, Zhendong Cao, Yuan He, Shelley L. Berger, Zhangying Cai, and Mohammed Alkhatim A. Ali
- Subjects
Effector ,T cell ,medicine.medical_treatment ,fungi ,Cell ,Biology ,Cell biology ,Chromatin ,medicine.anatomical_structure ,Cancer immunotherapy ,medicine ,CRISPR ,Cytotoxic T cell ,Transcription factor - Abstract
Improving effector activity of antigen specific T cells is a major goal in cancer immunotherapy. Despite the identification of several effector T cell (TEFF)-driving transcription factors (TF), the transcriptional coordination of TEFF biology remains poorly understood. We developed an in vivo T cell CRISPR screening platform and identified a novel mechanism restraining TEFF biology through the ETS family TF, Fli1. Genetic deletion of Fli1 enhanced TEFF responses without compromising memory or exhaustion precursors. Fli1 restrained TEFF lineage differentiation by binding to cis-regulatory elements of effector-associated genes. Loss of Fli1 increased chromatin accessibility at ETS:RUNX motifs allowing more efficient Runx3-driven TEFF biology. CD8 T cells lacking Fli1 provided substantially better protection against multiple infections and tumors. These data indicate that Fli1 safeguards the developing CD8 T cell transcriptional landscape from excessive ETS:RUNX-driven TEFF cell differentiation. Moreover, genetic deletion of Fli1 improves TEFF differentiation and protective immunity in infections and cancer.
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- 2020
45. Chronic viral infection promotes early germinal center exit of B cells and impaired antibody development
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Ramin S. Herati, Amy E. Baxter, Laura A. Vella, Omar Khan, E. John Wherry, Josephine R. Giles, Jennifer E. Wu, Eline T. Luning Prak, Sasikanth Manne, Wenzhao Meng, and Ryan P. Staupe
- Subjects
Affinity maturation ,Chronic infection ,medicine.anatomical_structure ,Humoral immunity ,Immunology ,medicine ,biology.protein ,Germinal center ,Biology ,Antibody ,Plasma cell ,Memory B cell ,B cell - Abstract
SUMMARYChronic viral infections disrupt B cell responses leading to impaired affinity maturation and delayed control of viremia. Previous studies have identified early pre-germinal center (GC) B cell attrition but the impact of chronic infections on B cell fate decisions in the GC remains poorly understood. To address this question, we used single-cell transcriptional profiling of virus-specific GC B cells to test the hypothesis that chronic viral infection disrupted GC B cell fate decisions leading to suboptimal humoral immunity. These studies revealed a critical GC differentiation checkpoint that is disrupted by chronic infection, specifically at the point of dark zone re-entry. During chronic viral infection, virus-specific GC B cells were shunted towards terminal plasma cell (PC) or memory B cell (MBC) fates at the expense of continued participation in the GC. Early GC exit was associated with decreased B cell mutational burden and antibody quality. Persisting antigen and inflammation independently drove facets of dysregulation, with a key role for inflammation in directing premature terminal GC B cell differentiation and GC exit. Thus, these studies define GC defects during chronic viral infection and identify a critical GC checkpoint that is short-circuited, preventing optimal maturation of humoral immunity.
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- 2019
- Full Text
- View/download PDF
46. TCF-1-centered transcriptional network drives an effector versus exhausted CD8 T cell fate decision
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Zeyu Chen, Jean Christophe Beltra, Sasikanth Manne, Golnaz Vahedi, Caiyue Xu, Amy E. Baxter, Sixiang Yu, Chi Wai Lau, Josephine R. Giles, Erietta Stelekati, John L. Johnson, Zhicheng Ji, Omar Khan, Bertram Bengsch, Jennifer E. Wu, Alexander C. Huang, Laura A. Vella, Hongkai Ji, Ramin S. Herati, Shin Foong Ngiow, E. John Wherry, Ryan P. Staupe, Laura M. McLane, Shelley L. Berger, Xiaolu Yang, Makoto Kurachi, and Zhangying Cai
- Subjects
0301 basic medicine ,animal structures ,Transcription, Genetic ,Immunology ,Population ,Programmed Cell Death 1 Receptor ,Biology ,CD8-Positive T-Lymphocytes ,Article ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Transcription (biology) ,Precursor cell ,T Cell Transcription Factor 1 ,Immunology and Allergy ,Cytotoxic T cell ,Animals ,Gene Regulatory Networks ,education ,Transcription factor ,Progenitor ,education.field_of_study ,Effector ,Gene Expression Profiling ,Cell Differentiation ,Cell biology ,Gene expression profiling ,030104 developmental biology ,Infectious Diseases ,Virus Diseases ,030220 oncology & carcinogenesis ,Chronic Disease ,Host-Pathogen Interactions ,embryonic structures - Abstract
TCF-1 is a key transcription factor in progenitor exhausted CD8 T cells (Tex). Moreover, this Tex cell subset mediates responses to PD-1 checkpoint pathway blockade. However, the role of the transcription factor TCF-1 in early fate decisions and initial generation of Tex cells is unclear. Single cell RNA-sequencing (scRNA-seq) and lineage tracing identified a TCF-1(+)Ly108(+)PD-1(+) CD8 T cell population early during chronic infection that seeds development of mature Tex cells. TCF-1 mediated the bifurcation between divergent fates, repressing development of terminal KLRG1(Hi) effectors while fostering KLRG1(Lo) Tex precursor cells, and PD-1 stabilized this TCF-1(+) Tex precursor cell pool. TCF-1 mediated a T-bet to Eomes transcription factor transition in Tex precursors by promoting Eomes expression and drove c-Myb expression that controlled Bcl-2 and survival. These data define a role for TCF-1 in early fate bifurcation driving Tex precursor cells, and also identify PD-1 as a protector of this early TCF-1 subset.
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- 2019
47. Therapeutic Targeting of Vasculature in the Premetastatic and Metastatic Niches Reduces Lung Metastasis
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Jalpa Patel, Surya Kumari Vadrevu, Sanjay K. Srivastava, Sasikanth Manne, Shanawaz M. Ghouse, Magdalena Karbowniczek, Niraj Lodhi, Ashok Silwal, Yvonne Paterson, Maciej M. Markiewski, Bhaumik Patel, and Britney Reese
- Subjects
Lung Neoplasms ,Angiogenesis ,medicine.medical_treatment ,Immunology ,Angiogenesis Inhibitors ,Complement C5a ,Cancer Vaccines ,C5a receptor ,Article ,Metastasis ,Neovascularization ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Antineoplastic Agents, Immunological ,Downregulation and upregulation ,Cell Line, Tumor ,medicine ,Tumor Microenvironment ,Immunology and Allergy ,Animals ,Humans ,Neoplasm Metastasis ,Lung ,Receptor, Anaphylatoxin C5a ,Mice, Knockout ,Tumor microenvironment ,Neovascularization, Pathologic ,business.industry ,Myeloid-Derived Suppressor Cells ,Mammary Neoplasms, Experimental ,Immunotherapy ,medicine.disease ,Combined Modality Therapy ,Listeria monocytogenes ,Matrix Metalloproteinase 9 ,Myeloid-derived Suppressor Cell ,Cancer research ,Female ,medicine.symptom ,business ,030215 immunology - Abstract
In the metastasis-targeted organs, angiogenesis is essential for the progression of dormant micrometastases to rapidly growing and clinically overt lesions. However, we observed changes suggesting angiogenic switching in the mouse lungs prior to arrival of tumor cells (i.e., in the premetastatic niche) in the models of breast carcinoma. This angiogenic switching appears to be caused by myeloid-derived suppressor cells recruited to the premetastatic lungs through complement C5a receptor 1 signaling. These myeloid cells are known to secrete several proangiogenic factors in tumors, including IL-1β and matrix metalloproteinase-9, and we found upregulation of these genes in the premetastatic lungs. Blockade of C5a receptor 1 synergized with antiangiogenic Listeria monocytogenes–based vaccines to decrease the lung metastatic burden by reducing vascular density and improving antitumor immunity in the lungs. This was mediated even when growth of primary breast tumors was not affected by these treatments. This work provides initial evidence that angiogenesis contributes to the premetastatic niche in rapidly progressing cancers and that inhibiting this process through immunotherapy is beneficial for reducing or even preventing metastasis.
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- 2019
48. Long-Term Persistence of Exhausted CD8 T Cells in Chronic Infection Is Regulated by MicroRNA-155
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Zeyu Chen, Keith Lewy, Kito Nzingha, Peter D. Katsikis, Makoto Kurachi, Sasikanth Manne, Jennifer L. Hope, Erietta Stelekati, Laura M. McLane, E. John Wherry, Adam J. Fike, Zhangying Cai, Mohammed-Alkhatim Ali, and Immunology
- Subjects
0301 basic medicine ,Cell signaling ,Time Factors ,Transcription, Genetic ,T cell ,Cell ,Fos-Related Antigen-2 ,CD8-Positive T-Lymphocytes ,Biology ,Lymphocytic choriomeningitis ,Communicable Diseases ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,microRNA ,medicine ,Animals ,Cytotoxic T cell ,Transcription factor ,Cell Proliferation ,Cell Differentiation ,medicine.disease ,Lymphocyte Subsets ,Cell biology ,Mice, Inbred C57BL ,Transcription Factor AP-1 ,MicroRNAs ,Chronic infection ,Phenotype ,030104 developmental biology ,medicine.anatomical_structure ,Gene Expression Regulation ,Chronic Disease ,030215 immunology - Abstract
Persistent viral infections and tumors drive development of exhausted T (TEX) cells. In these settings, TEX cells establish an important host-pathogen or host-tumor stalemate. However, TEX cells erode over time, leading to loss of pathogen or cancer containment. We identified microRNA (miR)-155 as a key regulator of sustained TEX cell responses during chronic lymphocytic choriomeningitis virus (LCMV) infection. Genetic deficiency of miR-155 ablated CD8 T cell responses during chronic infection. Conversely, enhanced miR-155 expression promoted expansion and long-term persistence of TEX cells. However, rather than strictly antagonizing exhaustion, miR-155 promoted a terminal TEX cell subset. Transcriptional profiling identified coordinated control of cell signaling and transcription factor pathways, including the key AP-1 family member Fosl2. Overexpression of Fosl2 reversed the miR-155 effects, identifying a link between miR-155 and the AP-1 transcriptional program in regulating TEX cells. Thus, we identify a mechanism of miR-155 regulation of TEX cells and a key role for Fosl2 in T cell exhaustion. During persistent viral infections, exhausted T cells (TEX) erode quantitatively and qualitatively and therefore fail to provide protection. Stelekati et al. identified microRNA (miR)-155 as a key molecule that can enhance and sustain TEX responses long-term during chronic viral infection.
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- 2018
49. 310 T cell intrinsic DNA damage and repair response as a novel marker associated with clinical response to PD-1 blockade
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Ramin S. Herati, Claire F. Friedman, Divij Mathew, Yuki Muroyama, Caiyue Xu, Alexander C. Huang, Allison R. Greenplate, E. John Wherry, D. Zamarin, Lakshmi Chilukuri, Derek A. Oldridge, and Sasikanth Manne
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Pharmacology ,Cancer Research ,Chemistry ,DNA damage ,T cell ,Immunology ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,body regions ,medicine.anatomical_structure ,Oncology ,Cancer research ,medicine ,Molecular Medicine ,Immunology and Allergy ,Pd 1 blockade ,RC254-282 - Abstract
BackgroundDespite the success of immune checkpoint blockade (ICB), many patients still fail to achieve durable clinical benefit. Previous studies have shown that CD8 T cells are reinvigorated by ICB. However, not all patients with this immunological response experience an effective clinical response, suggesting additional parameters may be relevant.DNA damage and repair (DDR) has been extensively studied in the context of inducing cell death of highly-proliferating tumor cells. However, whether T cell-intrinsic DDR impacts T cell differentiation and function, and how the coordination of DDR affects immunological and clinical response to proliferation-inducing ICBs have been largely unexplored. We hypothesized that the T celI-intrinsic DDR responses to proliferative and genotoxic stress might contribute to the disparity between immunological and clinical response.MethodsTo understand the impact of cell-intrinsic DDR on T cell differentiation and responses to cancer therapies, we developed a novel high-dimensional cytometry platform. This DDR-Immune platform enables simultaneous analysis of T cell differentiation state and multiple DDR pathways at single cell resolution. We then investigated immune reinvigoration and its association with DDR, in a cohort of chemotherapy-resistant hypermutated or microsatellite instability-high (MSI-H) uterine cancer patients treated with nivolumab. Peripheral blood samples were examined every 2–4 weeks after initiating anti-PD-1 treatment (N = 21).ResultsThe DDR-Immune platform revealed consistent T cell subset specific patterns of DDR, as well as specific DDR pathways induced by different types of DNA damage, such as γ-irradiation (IR), UV irradiation (UV) or proliferative stress (i.e. anti-CD3/CD28 stimulation). For example, terminally differentiated effector cells had higher DNA damage accumulation and cell death. In contrast, stem cell memory (TSCM) and regulatory T cells (Treg) displayed high DDR with less cell death, suggesting better cell-intrinsic DDR against genotoxic stress for survival advantage. In hypermutated MSI-H uterine cancer patients, CD8 T cells underwent rapid pharmacodynamic proliferation 2–4 weeks after starting PD-1 blockade, which did not correlate with clinical response. Application of the DDR-Immune platform to this cohort revealed, however, that in clinical responders but not clinical non-responders, Ki67+ CD8 T cells responding to PD-1 blockade had rapid induction of DDR represented as a spike increase of phosphorylated-ATM, presumably adapting T cell ‘fitness’ in response to proliferative stress induced by PD-1 blockade.ConclusionsCollectively, the new platform reveals previously unrecognized roles for T cell-intrinsic DDR as a novel determinant of immune responsiveness and clinical outcome to ICB and have potential application to other cancer therapies including chemotherapy and radiotherapy.Ethics ApprovalThe study was approved by MSKCC Ethics Board, approval number 17–180 (NCT03241745).
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- 2021
50. Author Correction: Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation
- Author
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Sasikanth Manne, Golnaz Vahedi, Allison R. Greenplate, Erietta Stelekati, Josephine R. Giles, Zeyu Chen, E. John Wherry, Divij Mathew, Mohamed S. Abdel-Hakeem, Mohammed-Alkhatim Ali, Kito Nzingha, Jean-Christophe Beltra, and John L. Johnson
- Subjects
Antigenic stimulation ,Text mining ,business.industry ,Immunology ,Immunology and Allergy ,Medicine ,Epigenetics ,Bioinformatics ,business - Published
- 2021
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