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    Drug repositioning in non-small cell lung cancer (NSCLC) using gene co-expression and drug-gene interaction networks analysis
    (Nature, 2022) MotieGhader, Habib; Tabrizi-Nezhadi, Parinaz; Abad Paskeh, Mahshid Deldar; Baradaran, Behzad; Mokhtarzadeh, Ahad; Hashemi, Mehrdad; Lanjanian, Hossein; Jazayeri, Seyed Mehdi; Maleki, Masoud; Khodadadi, Ehsan; Nematzadeh, Sajjad; Maghsoudloo, Mazaher; Masoudi-Nejad, Ali; Kiani, Farzad
    Lung cancer is the most common cancer in men and women. This cancer is divided into two main types, namely non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). Around 85 to 90 percent of lung cancers are NSCLC. Repositioning potent candidate drugs in NSCLC treatment is one of the important topics in cancer studies. Drug repositioning (DR) or drug repurposing is a method for identifying new therapeutic uses of existing drugs. The current study applies a computational drug repositioning method to identify candidate drugs to treat NSCLC patients. To this end, at frst, the transcriptomics profle of NSCLC and healthy (control) samples was obtained from the GEO database with the accession number GSE21933. Then, the gene co-expression network was reconstructed for NSCLC samples using the WGCNA, and two signifcant purple and magenta gene modules were extracted. Next, a list of transcription factor genes that regulate purple and magenta modules’ genes was extracted from the TRRUST V2.0 online database, and the TF–TG (transcription factors–target genes) network was drawn. Afterward, a list of drugs targeting TF–TG genes was obtained from the DGIdb V4.0 database, and two drug–gene interaction networks, including drug-TG and drug-TF, were drawn. After analyzing gene co-expression TF–TG, and drug–gene interaction networks, 16 drugs were selected as potent candidates for NSCLC treatment. Out of 16 selected drugs, nine drugs, namely Methotrexate, Olanzapine, Haloperidol, Fluorouracil, Nifedipine, Paclitaxel, Verapamil, Dexamethasone, and Docetaxel, were chosen from the drug-TG sub-network. In addition, nine drugs, including Cisplatin, Daunorubicin, Dexamethasone, Methotrexate, Hydrocortisone, Doxorubicin, Azacitidine, Vorinostat, and Doxorubicin Hydrochloride, were selected from the drug-TF sub-network. Methotrexate and Dexamethasone are common in drug-TG and drug-TF sub-networks. In conclusion, this study proposed 16 drugs as potent candidates for NSCLC treatment through analyzing gene co-expression, TF–TG, and drug–gene interaction networks.
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    Molecular landscape of LncRNAs in prostate cancer: A focus on pathways and therapeutic targets for intervention
    (PMC, 2022) Mirzaei, Sepideh; Abad Paskeh, Mahshid Deldar; Okina, Elena; Gholami, Mohammad Hossein; Hushmandi, Kiavash; Hashemi, Mehrdad; Kalu , Azuma; Zarrabi, Ali; Nabav, Noushin; Rabiee, Navid; Sharifi, Esmaeel; Karimi-Maleh, Hassan; Ashrafizadeh, Milad; Kumar, Alan Prem; Wang, Yuzhuo
    Background: One of the most malignant tumors in men is prostate cancer that is still incurable due to its heterog? enous and progressive natures. Genetic and epigenetic changes play signifcant roles in its development. The RNA molecules with more than 200 nucleotides in length are known as lncRNAs and these epigenetic factors do not encode protein. They regulate gene expression at transcriptional, post-transcriptional and epigenetic levels. LncRNAs play vital biological functions in cells and in pathological events, hence their expression undergoes dysregulation. Aim of review: The role of epigenetic alterations in prostate cancer development are emphasized here. Therefore, lncRNAs were chosen for this purpose and their expression level and interaction with other signaling networks in prostate cancer progression were examined. Key scientifc concepts of review: The aberrant expression of lncRNAs in prostate cancer has been well-docu? mented and progression rate of tumor cells are regulated via afecting STAT3, NF-?B, Wnt, PI3K/Akt and PTEN, among other molecular pathways. Furthermore, lncRNAs regulate radio-resistance and chemo-resistance features of prostate tumor cells. Overexpression of tumor-promoting lncRNAs such as HOXD-AS1 and CCAT1 can result in drug resistance. Besides, lncRNAs can induce immune evasion of prostate cancer via upregulating PD-1. Pharmacological compounds such as quercetin and curcumin have been applied for targeting lncRNAs. Furthermore, siRNA tool can reduce expression of lncRNAs thereby suppressing prostate cancer progression. Prognosis and diagnosis of prostate tumor at clinical course can be evaluated by lncRNAs. The expression level of exosomal lncRNAs such as lncRNA-p21 can be investigated in serum of prostate cancer patients as a reliable biomarker