RNA sequencing (RNA-seq) has transformed cancer research by providing a detailed analysis of gene expression in cancerous and healthy cells. This technology enables the identification of differentially expressed genes, novel transcripts, and molecular pathways associated with tumor progression. (Siavoshi et al., 2022a, Siavoshi et al., 2022b) A study by Abbas et al. (2023) highlights the significance of RNA-seq in cancer research by comparing gene expression in two-dimensional (2D) and three-dimensional (3D) colorectal cancer (CRC) models. Their findings demonstrated that 3D cultures more closely resemble patient-derived tumors, emphasizing the role of the tumor microenvironment in gene expression. This research underscores the importance of RNA-seq in developing accurate cancer models for preclinical studies.(Abbas et al., 2023; Maynard et al., 2020)Additionally, RNA-seq plays a crucial role in identifying fusion genes—hybrid genes formed due to chromosomal rearrangements—which are common in many cancers and serve as potential diagnostic markers or therapeutic targets. (Guo et al., 2019)This technology also helps in discovering novel biomarkers by analyzing gene expression at different disease stages. RNA-seq enables differential expression analysis to investigate altered biological functions using gene ontology (GO) and pathway enrichment through the Kyoto Encyclopedia of Genes and Genomes (KEGG).(Ogata et al., 1998) (Chen et al., 2017; Young et al., 2010)These analytical approaches contribute to cancer drug development, aiding research across multiple cancers, including ovarian, lung, colorectal, and gastric cancers.(Yasui et al., 2004)(Wang et al., 2018).

Ovarian cancer is the leading cause of death among gynecological cancers due to late detection and recurrence. According to WHO GLOBOCAN 2022, it had an incidence of over 324,000 cases and nearly 207,000 deaths. Asia reported the highest incidence (54.9 %) and mortality (52.9 %). The five-year survival rate is only 21–29 % since 60 % of cases are diagnosed at advanced stages, whereas early detection increases survival to 87–93 %. (Barani et al., 2021; Miller et al., 2021) Current treatments—surgery, radiotherapy, and chemotherapy—face challenges due to chemotherapy resistance, emphasizing the need for improved therapies targeting cancer cells more effectively to enhance treatment outcomes and reduce recurrence.

Cadmium sulfide nanoparticles have been recognized as a promising candidate for cancer cell treatments due to favorable physicochemical characteristics, low cytotoxicity, and biocompatibility.(Shivaji et al., 2019) The utilization of plant extracts as stabilizing agents in the synthesis of CdSNPs is a promising approach for the control of quantum dot size while ensuring low toxicity and cost-effectiveness. It is suitable for in vitro studies, as it has been shown not to cause significant cellular damage.(Borovaya et al., 2014)(Chen et al., 2012) Recent research has shown tremendous potential for usage in in vivo bioimaging and cancer therapeutics using Camellia sinensis extract as a stabilizing agent for CdS quantum dots.(Shivaji et al., 2018).

In this study, Berberis aristata (Daruharidra) extract was used as the particle stabilizing agent to manufacture CdS nanoparticles. The ayurvedic plant Berberis aristata is used to cure various ailments, including hepatitis, malaria, jaundice, fever, bleeding, and diarrhea.(Jahan et al., 2022) It is a hardy, yellow, and spiny erect shrub commonly found in the sub-Himalayan regions.(Malhotra et al., 2021) Daruharidra is composed of various significant phytochemicals, including alkaloids of the proto-berberine and isoquinoline type, as well as bis benzyl-isoquinoline and flavonoids and phenolic acids, which play an important role in Cadmium sulfide quantum dots synthesis.(Potdar et al., 2012).

This study is an extended research of our previous published study, which presented a potential treatment option for ovarian cancer.(Bhatnagar and Mishra, 2023) To brief, our previous study was in the context of the treatment of ovarian cancer (PA1 cell line) with the green synthesized (Daruharidra (Berberis aristata) mediated) CdSNPs (Cadmium sulfide Nanoparticles). The treatment with the CdSNPs projected an IC50 value of 95.74 μg/ml. and an apoptotic-mediated cell arrest at the G2/M stage. The results of our previous work showed CdSNPs as a potential agent for the treatment of the PA1 ovarian cancer cell line.(Bhatnagar and Mishra, 2023) Further, to investigate the molecular alterations, i.e., to explore the differentially expressed genes and their proposed role in apoptosis or cancer growth was carried out.

Therefore, we present a novel application of RNA-sequencing and transcriptomic analysis to identify gene targets and insight into molecular alterations in the PA1 ovarian cancer cell line upon treatment with Cadmium sulfide nanoparticles derived from Berberis aristata extract.