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Vallés-Martí A, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Verheij J, Dijk F, Halfwerk H, Giovannetti E, Jiménez CR, Bijlsma MF. Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues. Mol Oncol 2024. [PMID: 38650175 DOI: 10.1002/1878-0261.13625] [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: 07/19/2023] [Revised: 12/12/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited number of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a direct read-out of aberrant signaling and the resultant clinically relevant phenotype. Mass spectrometry (MS)-based proteomics and phosphoproteomics were applied to 42 PDAC tumors. Data encompassed over 19 936 phosphoserine or phosphothreonine (pS/T; in 5412 phosphoproteins) and 1208 phosphotyrosine (pY; in 501 phosphoproteins) sites and a total of 3756 proteins. Proteome data identified three distinct subtypes with tumor intrinsic and stromal features. Subsequently, three phospho-subtypes were apparent: two tumor intrinsic (Phos1/2) and one stromal (Phos3), resembling known PDAC molecular subtypes. Kinase activity was analyzed by the Integrative iNferred Kinase Activity (INKA) scoring. Phospho-subtypes displayed differential phosphorylation signals and kinase activity, such as FGR and GSK3 activation in Phos1, SRC kinase family and EPHA2 in Phos2, and EGFR, INSR, MET, ABL1, HIPK1, JAK, and PRKCD in Phos3. Kinase activity analysis of an external PDAC cohort supported our findings and underscored the importance of PI3K/AKT and ERK pathways, among others. Interestingly, unfavorable patient prognosis correlated with higher RTK, PAK2, STK10, and CDK7 activity and high proliferation, whereas long survival was associated with MYLK and PTK6 activity, which was previously unknown. Subtype-associated activity profiles can guide therapeutic combination approaches in tumor and stroma-enriched tissues, and emphasize the critical role of parallel signaling pathways. In addition, kinase activity profiling identifies potential disease markers with prognostic significance.
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Affiliation(s)
- Andrea Vallés-Martí
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Richard R de Goeij-de Haas
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Alex A Henneman
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Frederike Dijk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Hans Halfwerk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Italy
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Maarten F Bijlsma
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, University of Amsterdam, The Netherlands
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Reyaz I, Khan B, James N, Azhar H, Rehman A, Younas MW, Rashid H, Al-Shaikhly FF, Almomani MM, I Kh Almadhoun MK, Abdullah Yahya N, Bokhari SFH, Shehzad A. Emerging Horizons in the Diagnosis of Pancreatic Cancer: The Role of Circulating microRNAs as Early Detection Biomarkers for Pancreatic Ductal Adenocarcinoma. Cureus 2024; 16:e53023. [PMID: 38410292 PMCID: PMC10895207 DOI: 10.7759/cureus.53023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with a poor prognosis, primarily due to a late diagnosis. Recent studies have focused on identifying non-invasive biomarkers for early detection, with microRNAs (miRNAs) emerging as promising candidates. This systematic review aims to evaluate the potential of circulating miRNAs as biomarkers for the early detection of PDAC, analyzing their diagnostic accuracy, specificity, and sensitivity. Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a comprehensive search across PubMed, Embase, and the Cochrane Library was conducted. Studies published from January 2013 to October 2023 focusing on miRNA biomarkers for early PDAC detection were included. Data synthesis was performed through a narrative approach due to the heterogeneity of the studies. Nine studies met the inclusion criteria. Key findings include the elevated levels of specific miRNAs, such as miR-18a, miR-106a, and miR-25, in early-stage PDAC patients compared to controls. The integration of miRNA profiles with traditional biomarkers like CA19-9 showed improved diagnostic performance. However, challenges in the standardization of miRNA evaluation methodologies were noted. Circulating miRNAs demonstrate significant potential as non-invasive biomarkers for early PDAC detection. Despite promising results, further research and standardization are necessary for clinical application.
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Affiliation(s)
- Ibrahim Reyaz
- Internal Medicine, Christian Medical College and Hospital Ludhiana, Ludhiana, IND
| | - Bilal Khan
- Internal Medicine, Jinnah Postgraduate Medical Centre, Karachi, PAK
| | - Neha James
- General Medicine, Rehman Medical Institute, Peshawar, PAK
| | - Hammad Azhar
- Accident and Emergency, Sahiwal Teaching Hospital, Sahiwal, PAK
- General Medicine, King Edward Medical University, Lahore, PAK
| | | | - Muhammad Waqas Younas
- Accident and Emergency, Sahiwal Teaching Hospital, Sahiwal, PAK
- General Medicine, Faisalabad Medical University, Faisalabad, PAK
| | - Hamza Rashid
- Medicine, Pak Medical Centre & Hospital, Peshawar, PAK
| | | | | | | | | | | | - Ahsan Shehzad
- Surgery, King Edward Medical University, Lahore, PAK
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3
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Temaj G, Chichiarelli S, Saha S, Telkoparan-Akillilar P, Nuhii N, Hadziselimovic R, Saso L. An intricate rewiring of cancer metabolism via alternative splicing. Biochem Pharmacol 2023; 217:115848. [PMID: 37813165 DOI: 10.1016/j.bcp.2023.115848] [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] [Received: 08/24/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
All human genes undergo alternative splicing leading to the diversity of the proteins. However, in some cases, abnormal regulation of alternative splicing can result in diseases that trigger defects in metabolism, reduced apoptosis, increased proliferation, and progression in almost all tumor types. Metabolic dysregulations and immune dysfunctions are crucial factors in cancer. In this respect, alternative splicing in tumors could be a potential target for therapeutic cancer strategies. Dysregulation of alternative splicing during mRNA maturation promotes carcinogenesis and drug resistance in many cancer types. Alternative splicing (changing the target mRNA 3'UTR binding site) can result in a protein with altered drug affinity, ultimately leading to drug resistance.. Here, we will highlight the function of various alternative splicing factors, how it regulates the reprogramming of cancer cell metabolism, and their contribution to tumor initiation and proliferation. Also, we will discuss emerging therapeutics for treating tumors via abnormal alternative splicing. Finally, we will discuss the challenges associated with these therapeutic strategies for clinical applications.
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Affiliation(s)
- Gazmend Temaj
- Faculty of Pharmacy, College UBT, 10000 Prishtina, Kosovo
| | - Silvia Chichiarelli
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, 00185 Rome, Italy.
| | - Sarmistha Saha
- Department of Biotechnology, GLA University, Mathura 00185, Uttar Pradesh, India
| | | | - Nexhibe Nuhii
- Department of Pharmacy, Faculty of Medical Sciences, State University of Tetovo, 1200 Tetovo, Macedonia
| | - Rifat Hadziselimovic
- Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University, 00185 Rome, Italy.
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4
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Vahabi M, Dehni B, Antomás I, Giovannetti E, Peters GJ. Targeting miRNA and using miRNA as potential therapeutic options to bypass resistance in pancreatic ductal adenocarcinoma. Cancer Metastasis Rev 2023; 42:725-740. [PMID: 37490255 PMCID: PMC10584721 DOI: 10.1007/s10555-023-10127-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with poor prognosis due to early metastasis, low diagnostic rates at early stages, and resistance to current therapeutic regimens. Despite numerous studies and clinical trials, the mortality rate for PDAC has shown limited improvement. Therefore, there is a pressing need to attain. a more comprehensive molecular characterization to identify biomarkers enabling early detection and evaluation of treatment response. MicroRNA (miRNAs) are critical regulators of gene expression on the post-transcriptional level, and seem particularly interesting as biomarkers due to their relative stability, and the ability to detect them in fixed tissue specimens and biofluids. Deregulation of miRNAs is common and affects several hallmarks of cancer and contribute to the oncogenesis and metastasis of PDAC. Unique combinations of upregulated oncogenic miRNAs (oncomiRs) and downregulated tumor suppressor miRNAs (TsmiRs), promote metastasis, characterize the tumor and interfere with chemosensitivity of PDAC cells. Here, we review several oncomiRs and TsmiRs involved in chemoresistance to gemcitabine and FOLFIRINOX in PDAC and highlighted successful/effective miRNA-based therapy approaches in vivo. Integrating miRNAs in PDAC treatment represents a promising therapeutic avenue that can be used as guidance for personalized medicine for PDAC patients.
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Affiliation(s)
- Mahrou Vahabi
- Department of Medical Oncology, Amsterdam UMC, location VUMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Bilal Dehni
- Department of Medical Oncology, Amsterdam UMC, location VUMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Inés Antomás
- Department of Medical Oncology, Amsterdam UMC, location VUMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam UMC, location VUMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
- Cancer Pharmacology Lab, Fondazione Pisana per La Scienza, Pisa, Italy
| | - Godefridus J Peters
- Department of Medical Oncology, Amsterdam UMC, location VUMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands.
- Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland.
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Marima R, Francies FZ, Hull R, Molefi T, Oyomno M, Khanyile R, Mbatha S, Mabongo M, Owen Bates D, Dlamini Z. MicroRNA and Alternative mRNA Splicing Events in Cancer Drug Response/Resistance: Potent Therapeutic Targets. Biomedicines 2021; 9:1818. [PMID: 34944633 PMCID: PMC8698559 DOI: 10.3390/biomedicines9121818] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer is a multifaceted disease that involves several molecular mechanisms including changes in gene expression. Two important processes altered in cancer that lead to changes in gene expression include altered microRNA (miRNA) expression and aberrant splicing events. MiRNAs are short non-coding RNAs that play a central role in regulating RNA silencing and gene expression. Alternative splicing increases the diversity of the proteome by producing several different spliced mRNAs from a single gene for translation. MiRNA expression and alternative splicing events are rigorously regulated processes. Dysregulation of miRNA and splicing events promote carcinogenesis and drug resistance in cancers including breast, cervical, prostate, colorectal, ovarian and leukemia. Alternative splicing may change the target mRNA 3'UTR binding site. This alteration can affect the produced protein and may ultimately affect the drug affinity of target proteins, eventually leading to drug resistance. Drug resistance can be caused by intrinsic and extrinsic factors. The interplay between miRNA and alternative splicing is largely due to splicing resulting in altered 3'UTR targeted binding of miRNAs. This can result in the altered targeting of these isoforms and altered drug targets and drug resistance. Furthermore, the increasing prevalence of cancer drug resistance poses a substantial challenge in the management of the disease. Henceforth, molecular alterations have become highly attractive drug targets to reverse the aberrant effects of miRNAs and splicing events that promote malignancy and drug resistance. While the miRNA-mRNA splicing interplay in cancer drug resistance remains largely to be elucidated, this review focuses on miRNA and alternative mRNA splicing (AS) events in breast, cervical, prostate, colorectal and ovarian cancer, as well as leukemia, and the role these events play in drug resistance. MiRNA induced cancer drug resistance; alternative mRNA splicing (AS) in cancer drug resistance; the interplay between AS and miRNA in chemoresistance will be discussed. Despite this great potential, the interplay between aberrant splicing events and miRNA is understudied but holds great potential in deciphering miRNA-mediated drug resistance.
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Affiliation(s)
- Rahaba Marima
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
| | - Flavia Zita Francies
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
| | - Rodney Hull
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
| | - Thulo Molefi
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
- Department of Medical Oncology, Steve Biko Academic Hospital, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Meryl Oyomno
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Richard Khanyile
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
- Department of Medical Oncology, Steve Biko Academic Hospital, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Sikhumbuzo Mbatha
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Mzubanzi Mabongo
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
- Department of Maxillofacial and Oral Surgery, School of Dentistry, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - David Owen Bates
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
- Centre for Cancer Sciences, Division of Cancer and Stem Cells, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfiel, Pretoria 0028, South Africa; (R.M.); (F.Z.F.); (R.H.); (T.M.); (M.O.); (R.K.); (S.M.); (M.M.); (D.O.B.)
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