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Chen Y, Lee K, Woo J, Kim DW, Keum C, Babbi G, Casadio R, Martelli PL, Savojardo C, Manfredi M, Shen Y, Sun Y, Katsonis P, Lichtarge O, Pejaver V, Seward DJ, Kamandula A, Bakolitsa C, Brenner SE, Radivojac P, O’Donnell-Luria A, Mooney SD, Jain S. Evaluating predictors of kinase activity of STK11 variants identified in primary human non-small cell lung cancers. RESEARCH SQUARE 2024:rs.3.rs-4587317. [PMID: 39011112 PMCID: PMC11247923 DOI: 10.21203/rs.3.rs-4587317/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Critical evaluation of computational tools for predicting variant effects is important considering their increased use in disease diagnosis and driving molecular discoveries. In the sixth edition of the Critical Assessment of Genome Interpretation (CAGI) challenge, a dataset of 28 STK11 rare variants (27 missense, 1 single amino acid deletion), identified in primary non-small cell lung cancer biopsies, was experimentally assayed to characterize computational methods from four participating teams and five publicly available tools. Predictors demonstrated a high level of performance on key evaluation metrics, measuring correlation with the assay outputs and separating loss-of-function (LoF) variants from wildtype-like (WT-like) variants. The best participant model, 3Cnet, performed competitively with well-known tools. Unique to this challenge was that the functional data was generated with both biological and technical replicates, thus allowing the assessors to realistically establish maximum predictive performance based on experimental variability. Three out of the five publicly available tools and 3Cnet approached the performance of the assay replicates in separating LoF variants from WT-like variants. Surprisingly, REVEL, an often-used model, achieved a comparable correlation with the real-valued assay output as that seen for the experimental replicates. Performing variant interpretation by combining the new functional evidence with computational and population data evidence led to 16 new variants receiving a clinically actionable classification of likely pathogenic (LP) or likely benign (LB). Overall, the STK11 challenge highlights the utility of variant effect predictors in biomedical sciences and provides encouraging results for driving research in the field of computational genome interpretation.
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Affiliation(s)
- Yile Chen
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, 98105, WA, USA
| | - Kyoungyeul Lee
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Junwoo Woo
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Dong-wook Kim
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Changwon Keum
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Matteo Manfredi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, TX, USA
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, TX, USA
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - David J. Seward
- Department of Pathology, University of Vermont, Burlington, 5445, VT, USA
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
| | | | | | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
| | - Anne O’Donnell-Luria
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, 02115, MA, USA
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Sean D. Mooney
- Center for Information Technology, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Shantanu Jain
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
- The Institute for Experiential AI, Northeastern University, Boston, 02115, MA, USA
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Yoshida H, Hiranuma K, Nakahara M, Kobayashi-Kato M, Tanase Y, Uno M, Shiraishi K, Ishikawa M, Kato T. Ovarian Mucinous Tumor Presenting Atypical Lobular Endocervical Glandular Hyperplasia-Like Appearance in a Patient With Germline STK11 p.F354L Variant: A Case Report. Int J Surg Pathol 2024; 32:394-400. [PMID: 37226494 DOI: 10.1177/10668969231177256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Peutz-Jeghers syndrome (PJS) is associated with female genital lesions, such as cervical gastric-type adenocarcinoma and lobular endocervical glandular hyperplasia (LEGH). However, ovarian mucinous borderline tumors (OMBT) with atypical LEGH-like histology have not been described. The patient was a 60-year-old female with PJS clinically diagnosed at 23 years old with gastrointestinal polyposis. Abdominal distension was noted, and computed tomography scan revealed bilateral breast masses, multiple lung nodules, and a multicystic ovarian tumor. A needle biopsy revealed invasive ductal carcinoma of the breast. For the ovarian tumor, simple hysterectomy and bilateral salpingo-oophorectomy were performed. The left ovarian tumor was 25 × 20 × 12 cm in size and a multicystic tumor containing yellowish mucus without a solid part. Histologically, the cyst wall was covered with mucus cells with focal mild-to-moderate cellular atypia, forming LEGH-like architectures. The glandular cells were immunohistochemically positive for MUC5AC, MUC6 (focal), HIK1083 (focal), and HNF4α. Stromal invasion was not observed. Cervical lesions were not observed. The final pathological diagnosis was OMBT showing atypical LEGH morphology. Targeted sequencing of nontumor tissues revealed the germline STK11 p.F354L variant. Six months later, peritoneal dissemination of adenocarcinoma showing features similar to those of the ovarian tumor was observed, and the patient died of the disease. In summary, we report a case of OMBT with an atypical LEGH-like appearance in a patient with germline STK11 p.F354L variant. This case provides us with unresolved questions regarding the pathogenicity of this STK11 variant and the malignant potential of OMBT with this unusual morphology.
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Affiliation(s)
- Hiroshi Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Kengo Hiranuma
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Mariko Nakahara
- Department of Gynecology, National Cancer Center Hospital, Tokyo, Japan
| | | | - Yasuhito Tanase
- Department of Gynecology, National Cancer Center Hospital, Tokyo, Japan
| | - Masaya Uno
- Department of Gynecology, National Cancer Center Hospital, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Mitsuya Ishikawa
- Department of Gynecology, National Cancer Center Hospital, Tokyo, Japan
| | - Tomoyasu Kato
- Department of Gynecology, National Cancer Center Hospital, Tokyo, Japan
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Lenahan SM, Sarausky HM, Deming P, Seward DJ. STK11 loss leads to YAP1-mediated transcriptional activation in human KRAS-driven lung adenocarcinoma cell lines. Cancer Gene Ther 2024; 31:1-8. [PMID: 37968341 PMCID: PMC10794139 DOI: 10.1038/s41417-023-00687-y] [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: 06/30/2023] [Revised: 10/16/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023]
Abstract
Serine Threonine Kinase 11 (STK11) loss of function (LoF) correlates with anti-PD-1 therapy resistance in patients with KRAS-driven lung adenocarcinoma (LUAD). The molecular mechanisms governing this observation remain unclear and represent a critical outstanding question in the field of lung oncology. As an initial approach to understand this phenomenon, we knocked-out (KO) STK11 in multiple KRAS-driven, STK11-competent human LUAD cell lines and performed whole transcriptome analyses to identify STK11-loss-dependent differential gene expression. Subsequent pathway enrichment studies highlighted activation of the HIPPO/YAP1 signaling axis, along with the induction of numerous tumor-intrinsic cytokines. To validate that YAP1-mediated transcriptional activation occurs in response to STK11 loss, we pursued YAP1 perturbation as a strategy to restore an STK11-competent gene expression profile in STK11-KO LUAD cell lines. Together, our data link STK11 loss with YAP1-mediated transcriptional activation, including the upregulation of immune-evasion promoting cytokines IL-6, CXCL8 and CXCL2. Further, our results raise the intriguing possibility that YAP1 antagonism may represent a therapeutic approach to counter anti-PD-1 therapy resistance in STK11-null, KRAS-driven LUADs by modulating tumor-intrinsic gene expression to promote a "hot" tumor immune microenvironment.
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Affiliation(s)
- Sean M Lenahan
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA
| | - Hailey M Sarausky
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA
| | - Paula Deming
- Department of Biomedical and Health Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, VT, USA
- University of Vermont Cancer Center, Burlington, VT, USA
| | - David J Seward
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA.
- University of Vermont Cancer Center, Burlington, VT, USA.
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Mohan D, Sherman HL, Mitra A, Lawlor R, Shanthalingam S, Ullom J, Pobezinskaya EL, Zhang G, Osborne BA, Pobezinsky LA, Tew GN, Minter LM. LKB1 isoform expression modulates T cell plasticity downstream of PKCθ and IL-6. Mol Immunol 2023; 157:129-141. [PMID: 37018939 DOI: 10.1016/j.molimm.2023.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 03/12/2023] [Accepted: 03/26/2023] [Indexed: 04/05/2023]
Abstract
Following activation, CD4 T cells undergo metabolic and transcriptional changes as they respond to external cues and differentiate into T helper (Th) cells. T cells exhibit plasticity between Th phenotypes in highly inflammatory environments, such as colitis, in which high levels of IL-6 promote plasticity between regulatory T (Treg) cells and Th17 cells. Protein Kinase C theta (PKCθ) is a T cell-specific serine/threonine kinase that promotes Th17 differentiation while negatively regulating Treg differentiation. Liver kinase B1 (LKB1), also a serine/threonine kinase and encoded by Stk11, is necessary for Treg survival and function. Stk11 can be alternatively spliced to produce a short variant (Stk11S) by transcribing a cryptic exon. However, the contribution of Stk11 splice variants to Th cell differentiation has not been previously explored. Here we show that in Th17 cells, the heterogeneous ribonucleoprotein, hnRNPLL, mediates Stk11 splicing into its short splice variant, and that Stk11S expression is diminished when Hnrnpll is depleted using siRNA knock-down approaches. We further show that PKCθ regulates hnRNPLL and, thus, Stk11S expression in Th17 cells. We provide additional evidence that exposing induced (i)Tregs to IL-6 culminates in Stk11 splicing downstream of PKCθAltogether our data reveal a yet undescribed outside-in signaling pathway initiated by IL-6, that acts through PKCθ and hnRNPLL to regulate Stk11 splice variants and facilitate Th17 cell differentiation. Furthermore, we show for the first time, that this pathway can also be initiated in developing iTregs exposed to IL-6, providing mechanistic insight into iTreg phenotypic stability and iTreg to Th17 cell plasticity.
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Zhou W, Yan LD, Yu ZQ, Li N, Yang YH, Wang M, Chen YY, Mao MX, Peng XC, Cai J. Role of STK11 in ALK‑positive non‑small cell lung cancer (Review). Oncol Lett 2022; 23:181. [PMID: 35527776 PMCID: PMC9073580 DOI: 10.3892/ol.2022.13301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/01/2022] [Indexed: 11/10/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) inhibitors have been shown to be effective in treating patients with ALK-positive non-small cell lung cancer (NSCLC), and crizotinib, ceritinib and alectinib have been approved as clinical first-line therapeutic agents. The availability of these inhibitors has also largely changed the treatment strategy for advanced ALK-positive NSCLC. However, patients still inevitably develop resistance to ALK inhibitors, leading to tumor recurrence or metastasis. The most critical issues that need to be addressed in the current treatment of ALK-positive NSCLC include the high cost of targeted inhibitors and the potential for increased toxicity and resistance to combination therapy. Recently, it has been suggested that the serine/threonine kinase 11 (STK11) mutation may serve as one of the biomarkers for immunotherapy in NSCLC. Therefore, the main purpose of this review was to summarize the role of STK11 in ALK-positive NSCLC. The present review also summarizes the treatment and drug resistance studies in ALK-positive NSCLC and the current status of STK11 research in NSCLC.
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Affiliation(s)
- Wen Zhou
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Lu-Da Yan
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Zhi-Qiong Yu
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Na Li
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Yong-Hua Yang
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Meng Wang
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Yuan-Yuan Chen
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Meng-Xia Mao
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Xiao-Chun Peng
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Jun Cai
- Department of Oncology, First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434023, P.R. China
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