Identification of potential biomarkers of head and neck squamous cell carcinoma using iTRAQ based quantitative proteomic approach

Babu, Niraj; Mohan, Sonali V.; Nanjappa, Vishalakshi; Chavan, Sandip; Advani, Jayshree; Khan, Aafaque Ahmad; Renuse, Santosh; Radhakrishnan, Aneesha; Prasad, T. S. Keshava; Kumar, Rekha V.; Ray, Jharna; Biswas, Manjusha; Thiyagarajan, Saravanan; Califano, Joseph A.; Sidransky, David; Gowda, Harsha; Chatterjee, Aditi

doi:10.1016/j.dib.2018.05.100

Cited by 7 publications

(6 citation statements)

References 8 publications

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“…HSPH1 has been reported as one of the many heat shock proteins detected to be abundant in the conditioned media of colon cancer cell lines [52]. A recent study carried out by our own group has reported the overexpression of HSPH1 in HNSCC cell lines CAL 27, FaDu and JHU-O28 in comparison with OKF6/TERT1 [53]. Furthermore, among the differentially secreted proteins we observed lower abundance of MMP9 in OKF6/TERT1-Shisha secretome compared to parental secretome.…”

Section: Discussionsupporting

confidence: 45%

Secretome analysis of oral keratinocytes chronically exposed to shisha

Patil

Babu

Subbannayya

et al. 2019

CBM

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BACKGROUND: Shisha smoking has been associated with multiple diseases including oral cancer. However, a mechanistic study to investigate alteration of secreted proteins in oral cells due to shisha smoking is lacking. OBJECTIVES: Elucidation of differentially secreted proteins by immortalized human normal oral keratinocytes (OKF6/TERT1) upon chronic exposure to shisha. METHODS: OKF6/TERT1 was chronically treated with 0.5% shisha extract for 8 months. Conditioned media from shisha treated (OKF6/TERT1-Shisha) and untreated (OKF6/TERT1-Parental) cells were subjected to TMT-based quantitative proteomic analysis. Bioinformatics analysis of differentially secreted proteins was carried out using SignalP, SecretomeP and TMHMM. Immunoblot validation of selected proteins was carried out to confirm the proteomics results. RESULTS: Proteomic analysis of OKF6/TERT1-Parental and OKF6/TERT1-Shisha secretome resulted in the identification of 1,598 proteins, of which 218 proteins were found to be differentially secreted (≥ 1.5-fold; p-value ≤ 0.05) in shisha treated cells. Bioinformatics analysis using prediction tools showed secretory potential of differentially secreted proteins identified in OKF6/TERT1-Shisha. Western blotting validated the expression of AKR1C2, HSPH1 and MMP9 in OKF6/TERT1-Shisha secretome in agreement with proteomic data. CONCLUSION: This study serves as a useful resource to understand the effect of chronic shisha smoking on the milieu of secreted proteins of oral cells. In vivo studies are warranted to supplement our in vitro data to elucidate the role of these proteins as early diagnostic biomarkers for oral carcinogenesis among shisha smokers.

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Section: Discussionsupporting

confidence: 45%

Secretome analysis of oral keratinocytes chronically exposed to shisha

Patil

Babu

Subbannayya

et al. 2019

CBM

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“…Furthermore, we screened 20 genes as prognostic markers following DEFAMGs analysis. HPSH1 has been reported to be an early detected gene that can be used as a biomarker for HNSCC identification 27 . Similarly, the mRNA expression levels of LDHA isozymes were significantly greater in HNSCC compared to the controls 28 .…”

Section: Discussionmentioning

confidence: 99%

Exploration of a predictive model based on genes associated with fatty acid metabolism and clinical treatment for head and neck squamous cell carcinoma

Yuan

Huang

Teh

et al. 2022

Clinical Laboratory Analysis

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Background Head and neck squamous cell carcinoma (HNSCC) is one of the most prevalent malignant tumors of the head and neck and presents high risks of recurrence and poor prognosis postoperatively. The aim of this study was to establish a predictive model based on fatty acid metabolism (FAM) genes to forecast the prognosis of HNSCC patients and the subsequent treatment strategies. Methods We accessed the TCGA and GEO databases for HNSCC genes and clinical data. The FAM risk score model was created and validated using a combination of univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) regression analysis. Combining risk scores and clinical characteristics, a nomogram was established and assessed. Subsequently, the function, gene mutation, immune difference, and chemotherapeutic drug sensitivity of the groups with high‐ and low‐risk scores were analyzed. Consequently, the mode's validity was evaluated comprehensively by combining single gene analysis. Results The FAM risk score model for predicting HNSCC prognosis had certain validity. Patients in the high‐ and low‐risk groups had genetic mutations, and the prognosis was the poorest for the high‐risk groups with high genetic mutations. The patients with low‐risk scores were suitable for immunotherapy since they had increased infiltration of immune cells. In contrast, the patients in the other groups were more suitable for chemotherapy. Conclusion The results of this study demonstrated that the FAM risk score model may predict the prognosis of HSNCC and has a certain therapeutic guidance value.

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“…Compared with the traditional experimental approaches, advances in high-throughput proteomics analysis can enable researchers to identify the total DEP profiles and abnormal pathological process of SBI after ICH to explore the potentially molecular and pathogenic mechanisms on the macro level. Particularly, further according experiments can be performed to verify the targeted data-derived research hypothesis [ 21 – 24 ]. However, no ICH proteomics studies have been published so far.…”

Section: Discussionmentioning

confidence: 99%

iTRAQ‐Based Quantitative Proteomics Indicated Nrf2/OPTN‐Mediated Mitophagy Inhibits NLRP3 Inflammasome Activation after Intracerebral Hemorrhage

Cheng

Liu

Tang

et al. 2021

Oxidative Medicine and Cellular Longevity

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Intracerebral hemorrhage- (ICH-) induced secondary brain injury (SBI) is a very complex pathophysiological process. However, the molecular mechanisms and drug targets of SBI are highly intricate and still elusive, yet a clear understanding is crucial for the treatment of SBI. In the current study, we aimed to confirm that nuclear factor-E2-related factor 2 (Nrf2)/Optineurin- (OPTN-) mediated mitophagy alleviated SBI by inhibiting nucleotide-binding oligomerization domain-like receptor pyrin domain-containing 3 (NLRP3) inflammasome activation based on the isobaric tag for relative and absolute quantization (iTRAQ) quantification proteomics. Human ICH brain specimens were collected for iTRAQ-based proteomics analysis. Male Nrf2 wild-type (WT) and knockout (KO) mice were employed to establish ICH murine models. The survival rate, hematoma volume, neurofunctional outcomes, blood-brain barrier (BBB) permeability, brain edema, spatial neuronal death, NLRP3 inflammasome, inflammatory response, mitochondrial function, and mitophagy level were evaluated after ICH. The iTRAQ quantification analysis showed that the differentially expressed proteins (DEPs), Nrf2 and NLRP3, were closely associated with the initiation and development of SBI after ICH. The Nrf2 KO mice had a significantly lower survival rate, bigger hematoma volume, worse neurological deficits, and increased BBB disruption, brain edema, and neuronal death when compared with the Nrf2 WT mice after ICH. Furthermore, Nrf2 KO enhanced NLRP3 inflammasome activation and neuroinflammation as evidenced by the NF-κB activation and various proinflammatory cytokine releases following ICH. Moreover, Nrf2 could interact with and modulate the mitophagy receptor OPTN, further mediating mitophagy to remove dysfunctional mitochondria after ICH. Furthermore, OPTN small interfering RNA (siRNA) increased the NLRP3 inflammasome activation by downregulating mitophagy level and enhancing mitochondrial damage in the Nrf2 WT mice after ICH. Together, our data indicated that Nrf2/OPTN inhibited NLRP3 inflammasome activation, possibly via modulating mitophagy, therefore alleviating SBI after ICH.

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Identification of potential biomarkers of head and neck squamous cell carcinoma using iTRAQ based quantitative proteomic approach

Cited by 7 publications

References 8 publications

Secretome analysis of oral keratinocytes chronically exposed to shisha

Secretome analysis of oral keratinocytes chronically exposed to shisha

Exploration of a predictive model based on genes associated with fatty acid metabolism and clinical treatment for head and neck squamous cell carcinoma

iTRAQ‐Based Quantitative Proteomics Indicated Nrf2/OPTN‐Mediated Mitophagy Inhibits NLRP3 Inflammasome Activation after Intracerebral Hemorrhage

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