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Di Modugno F, Di Carlo A, Spada S, Palermo B, D'Ambrosio L, D'Andrea D, Morello G, Belmonte B, Sperduti I, Balzano V, Gallo E, Melchionna R, Panetta M, Campo G, De Nicola F, Goeman F, Antoniani B, Carpano S, Frigè G, Warren S, Gallina F, Lambrechts D, Xiong J, Vincent BG, Wheeler N, Bortone DS, Cappuzzo F, Facciolo F, Tripodo C, Visca P, Nisticò P. Tumoral and stromal hMENA isoforms impact tertiary lymphoid structure localization in lung cancer and predict immune checkpoint blockade response in patients with cancer. EBioMedicine 2024; 101:105003. [PMID: 38340557 PMCID: PMC10869748 DOI: 10.1016/j.ebiom.2024.105003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Tertiary Lymphoid Structures (TLS) correlate with positive outcomes in patients with NSCLC and the efficacy of immune checkpoint blockade (ICB) in cancer. The actin regulatory protein hMENA undergoes tissue-specific splicing, producing the epithelial hMENA11a linked to favorable prognosis in early NSCLC, and the mesenchymal hMENAΔv6 found in invasive cancer cells and pro-tumoral cancer-associated fibroblasts (CAFs). This study investigates how hMENA isoforms in tumor cells and CAFs relate to TLS presence, localization and impact on patient outcomes and ICB response. METHODS Methods involved RNA-SEQ on NSCLC cells with depleted hMENA isoforms. A retrospective observational study assessed tissues from surgically treated N0 patients with NSCLC, using immunohistochemistry for tumoral and stromal hMENA isoforms, fibronectin, and TLS presence. ICB-treated patient tumors were analyzed using Nanostring nCounter and GeoMx spatial transcriptomics. Multiparametric flow cytometry characterized B cells and tissue-resident memory T cells (TRM). Survival and ICB response were estimated in the cohort and validated using bioinformatics pipelines in different datasets. FINDINGS Findings indicate that hMENA11a in NSCLC cells upregulates the TLS regulator LTβR, decreases fibronectin, and favors CXCL13 production by TRM. Conversely, hMENAΔv6 in CAFs inhibits LTβR-related NF-kB pathway, reduces CXCL13 secretion, and promotes fibronectin production. These patterns are validated in N0 NSCLC tumors, where hMENA11ahigh expression, CAF hMENAΔv6low, and stromal fibronectinlow are associated with intratumoral TLS, linked to memory B cells and predictive of longer survival. The hMENA isoform pattern, fibronectin, and LTβR expression broadly predict ICB response in tumors where TLS indicates an anti-tumor immune response. INTERPRETATION This study uncovers hMENA alternative splicing as an unexplored contributor to TLS-related Tumor Immune Microenvironment (TIME) and a promising biomarker for clinical outcomes and likely ICB responsiveness in N0 patients with NSCLC. FUNDING This work is supported by AIRC (IG 19822), ACC (RCR-2019-23669120), CAL.HUB.RIA Ministero Salute PNRR-POS T4, "Ricerca Corrente" granted by the Italian Ministry of Health.
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Affiliation(s)
- Francesca Di Modugno
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy.
| | - Anna Di Carlo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Sheila Spada
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Belinda Palermo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Lorenzo D'Ambrosio
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Daniel D'Andrea
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, New Hall Block - Room 171, Clifton Campus - NG11 8NS, Nottingham, United Kingdom
| | - Gaia Morello
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Corso Tukory 211, 90134, Palermo, Italy
| | - Beatrice Belmonte
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Corso Tukory 211, 90134, Palermo, Italy
| | - Isabella Sperduti
- Biostatistics and Scientific Direction, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Vittoria Balzano
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Enzo Gallo
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Roberta Melchionna
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Mariangela Panetta
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Giulia Campo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Francesca De Nicola
- SAFU Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Frauke Goeman
- SAFU Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Barbara Antoniani
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Silvia Carpano
- Second Division of Medical Oncology, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Gianmaria Frigè
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, Milan, Italy
| | - Sarah Warren
- NanoString Technologies Inc., 530 Fairview Ave N, Seattle, WA, 98109, USA
| | - Filippo Gallina
- Thoracic-Surgery Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Diether Lambrechts
- Center for Cancer Biology, Herestraat 49 box 912, VIB, 3000, Leuven, Belgium
| | - Jieyi Xiong
- Center for Cancer Biology, Herestraat 49 box 912, VIB, 3000, Leuven, Belgium
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 5206 Marsico Hall, Chapel Hill, NC, 27599, USA
| | - Nathan Wheeler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 5206 Marsico Hall, Chapel Hill, NC, 27599, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 5206 Marsico Hall, Chapel Hill, NC, 27599, USA
| | - Federico Cappuzzo
- Second Division of Medical Oncology, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Francesco Facciolo
- Thoracic-Surgery Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144 Rome, Italy
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Corso Tukory 211, 90134, Palermo, Italy
| | - Paolo Visca
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Paola Nisticò
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy.
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Lindenboim L, Zohar H, Gundersen GG, Worman HJ, Stein R. LINC complex protein nesprin-2 has pro-apoptotic activity via Bcl-2 family proteins. Cell Death Discov 2024; 10:29. [PMID: 38225256 PMCID: PMC10789774 DOI: 10.1038/s41420-023-01763-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/13/2023] [Accepted: 12/06/2023] [Indexed: 01/17/2024] Open
Abstract
The apoptotic intrinsic pathway is initiated by perforation of the mitochondrial outer membrane by the effector pro-apoptotic proteins of the Bcl-2 family, Bax and Bak. Bax and Bak need to be activated, a process facilitated by the action of BH3-only pro-apoptotic members of the Bcl-2 family. The latter either directly activates the effector proteins or antagonizes the action of pro-survival Bcl-2 family members such as Bcl-xL. The nuclear envelope is a known target of the apoptotic machinery; however, it may also act as mediator of apoptosis. We showed previously that the nuclear envelope protein nesprin-2, a component of the linker of nucleoskeleton and cytoskeleton (LINC) complex, can bind to Bax in close proximity to the mitochondria and that the binding increases in apoptotic cells. We now show that depleting nesprin-2 inhibits the apoptotic mitochondrial pathway as measured by Bax and Bak activation and cytochrome c release. This survival effect was Bcl-xL-dependent. Nesprin-2 depletion also inhibited spontaneous exposure of the N-terminus of Bak in cells lacking Bcl-xL and increased the presence of Bcl-xL and Bax in the mitochondria. These results indicate that nesprin-2 promotes Bak activation and regulates mitochondrial translocation/retrotranslocation of Bcl-2 family proteins. Our findings demonstrate a new apoptotic pathway whereby the nuclear envelope, via nesprin-2, regulates apoptosis.
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Affiliation(s)
- Liora Lindenboim
- Department of Neurobiology, School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Hila Zohar
- Department of Neurobiology, School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Gregg G Gundersen
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Howard J Worman
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Reuven Stein
- Department of Neurobiology, School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.
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Melchionna R, Trono P, Di Carlo A, Di Modugno F, Nisticò P. Transcription factors in fibroblast plasticity and CAF heterogeneity. J Exp Clin Cancer Res 2023; 42:347. [PMID: 38124183 PMCID: PMC10731891 DOI: 10.1186/s13046-023-02934-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
In recent years, research focused on the multifaceted landscape and functions of cancer-associated fibroblasts (CAFs) aimed to reveal their heterogeneity and identify commonalities across diverse tumors for more effective therapeutic targeting of pro-tumoral stromal microenvironment. However, a unified functional categorization of CAF subsets remains elusive, posing challenges for the development of targeted CAF therapies in clinical settings.The CAF phenotype arises from a complex interplay of signals within the tumor microenvironment, where transcription factors serve as central mediators of various cellular pathways. Recent advances in single-cell RNA sequencing technology have emphasized the role of transcription factors in the conversion of normal fibroblasts to distinct CAF subtypes across various cancer types.This review provides a comprehensive overview of the specific roles of transcription factor networks in shaping CAF heterogeneity, plasticity, and functionality. Beginning with their influence on fibroblast homeostasis and reprogramming during wound healing and fibrosis, it delves into the emerging insights into transcription factor regulatory networks. Understanding these mechanisms not only enables a more precise characterization of CAF subsets but also sheds light on the early regulatory processes governing CAF heterogeneity and functionality. Ultimately, this knowledge may unveil novel therapeutic targets for cancer treatment, addressing the existing challenges of stromal-targeted therapies.
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Affiliation(s)
- Roberta Melchionna
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy.
| | - Paola Trono
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Rome, Italy
| | - Anna Di Carlo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Francesca Di Modugno
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Paola Nisticò
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
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Trono P, Tocci A, Palermo B, Di Carlo A, D'Ambrosio L, D'Andrea D, Di Modugno F, De Nicola F, Goeman F, Corleone G, Warren S, Paolini F, Panetta M, Sperduti I, Baldari S, Visca P, Carpano S, Cappuzzo F, Russo V, Tripodo C, Zucali P, Gregorc V, Marchesi F, Nistico P. hMENA isoforms regulate cancer intrinsic type I IFN signaling and extrinsic mechanisms of resistance to immune checkpoint blockade in NSCLC. J Immunother Cancer 2023; 11:e006913. [PMID: 37612043 PMCID: PMC10450042 DOI: 10.1136/jitc-2023-006913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Understanding how cancer signaling pathways promote an immunosuppressive program which sustains acquired or primary resistance to immune checkpoint blockade (ICB) is a crucial step in improving immunotherapy efficacy. Among the pathways that can affect ICB response is the interferon (IFN) pathway that may be both detrimental and beneficial. The immune sensor retinoic acid-inducible gene I (RIG-I) induces IFN activation and secretion and is activated by actin cytoskeleton disturbance. The actin cytoskeleton regulatory protein hMENA, along with its isoforms, is a key signaling hub in different solid tumors, and recently its role as a regulator of transcription of genes encoding immunomodulatory secretory proteins has been proposed. When hMENA is expressed in tumor cells with low levels of the epithelial specific hMENA11a isoform, identifies non-small cell lung cancer (NSCLC) patients with poor prognosis. Aim was to identify cancer intrinsic and extrinsic pathways regulated by hMENA11a downregulation as determinants of ICB response in NSCLC. Here, we present a potential novel mechanism of ICB resistance driven by hMENA11a downregulation. METHODS Effects of hMENA11a downregulation were tested by RNA-Seq, ATAC-Seq, flow cytometry and biochemical assays. ICB-treated patient tumor tissues were profiled by Nanostring IO 360 Panel enriched with hMENA custom probes. OAK and POPLAR datasets were used to validate our discovery cohort. RESULTS Transcriptomic and biochemical analyses demonstrated that the depletion of hMENA11a induces IFN pathway activation, the production of different inflammatory mediators including IFNβ via RIG-I, sustains the increase of tumor PD-L1 levels and activates a paracrine loop between tumor cells and a unique macrophage subset favoring an epithelial-mesenchymal transition (EMT). Notably, when we translated our results in a clinical setting of NSCLC ICB-treated patients, transcriptomic analysis revealed that low expression of hMENA11a, high expression of IFN target genes and high macrophage score identify patients resistant to ICB therapy. CONCLUSIONS Collectively, these data establish a new function for the actin cytoskeleton regulator hMENA11a in modulating cancer cell intrinsic type I IFN signaling and extrinsic mechanisms that promote protumoral macrophages and favor EMT. These data highlight the role of actin cytoskeleton disturbance in activating immune suppressive pathways that may be involved in resistance to ICB in NSCLC.
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Affiliation(s)
- Paola Trono
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
- Institute of Biochemistry and Cell Biology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Annalisa Tocci
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Belinda Palermo
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Anna Di Carlo
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Lorenzo D'Ambrosio
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Daniel D'Andrea
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Francesca Di Modugno
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Frauke Goeman
- SAFU Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giacomo Corleone
- SAFU Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Sarah Warren
- NanoString Technologies Inc, Seattle, Washington, USA
| | - Francesca Paolini
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Mariangela Panetta
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Isabella Sperduti
- Biostatistics Unit, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Silvia Baldari
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Paolo Visca
- Pathology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Silvia Carpano
- Second Division of Medical Oncology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Federico Cappuzzo
- Second Division of Medical Oncology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Vincenzo Russo
- Department of Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Claudio Tripodo
- Department of Health Sciences, Human Pathology Section, Tumor Immunology Unit, University of Palermo, Palermo, Italy
| | - Paolo Zucali
- Department of Oncology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Vanesa Gregorc
- Department of Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Federica Marchesi
- Department of Immunology and Inflammation, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Paola Nistico
- Tumor of Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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