Raw file for, "Differential role of SALL Transcription Factors in Breast Cancer: Potential biomarkers"

Differential role of SALL Transcription Factors in Breast Cancer: Potential biomarkers Sandeep Sisodiyaa,b, Payal Singha,c, Tannu joshia,d, Asiya Khane, Neetu Mishrab*, Sandeep Kumara, Pranay Tanwarf, Usha Agrawalg, Showket Hussaina* aCellular and Molecular Diagnostics (Molecular Biology Group), ICMR-National Institute of Cancer Prevention and Research, Noida, India. bSymbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University) (SIU), Pune, India cDepartment of Biosciences, Jamia Millia Islamia, New Delhi, India. dAcademy of Scientific and Innovative Research (AcSIR), Ghaziabad, India eThe All India Institute of Ayurveda (AIIA), New Delhi, India. fLab Oncology Unit, Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India. gFormer director, ICMR National Institute of Pathology, New Delhi, India. Background Aberrant alterations in transcription factors frequently disrupt key signaling pathways and contribute to oncogenesis, including breast cancer. The Spalt-like (SALL) family of transcription factors encodes highly conserved zinc finger proteins with context-dependent roles in tumorigenesis. Despite emerging evidence implicating SALL family members in cancer progression, their comprehensive molecular and clinical relevance in breast cancer remains insufficiently explored. Methods This dataset comprises integrated in-silico, in-vitro, and clinical validation data generated to investigate the expression, regulation, and prognostic significance of SALL transcription factors in breast cancer. Bioinformatics analyses were performed using publicly available omics platforms, including cBioPortal, UALCAN, GeneMania, Human Protein Atlas (HPA), Kaplan–Meier Plotter, STRING, TIMER 3.0, and miRNA.ca, to assess mRNA expression, protein expression, DNA methylation, survival associations, immune correlations, and regulatory networks. Experimental validation was conducted using breast cancer cell lines and clinical tissue samples to evaluate mRNA expression (RT-qPCR), protein expression and localization (immunohistochemistry and immunoblotting), with appropriate biological and technical replicates. Statistical analyses were performed using GraphPad Prism. Results The dataset reveals distinct molecular and clinical patterns of SALL family members in breast cancer. Differential mRNA expression, protein abundance, DNA methylation profiles, and survival associations were observed across breast cancer subtypes. SALL1 and SALL2 exhibited significantly reduced expression in aggressive subtypes, particularly triple-negative breast cancer (TNBC), whereas SALL3 showed elevated expression predominantly in luminal breast cancer. In contrast, SALL4 demonstrated higher expression across luminal, HER2-positive, and TNBC subtypes compared with adjacent normal tissues, suggesting a dual functional role of SALL transcription factors in breast cancer biology. Survival analyses further demonstrated significant associations between SALL gene expression and patient outcomes, highlighting their potential prognostic relevance. Conclusion This dataset provides a comprehensive molecular and clinical resource characterizing the role of SALL transcription factors in breast cancer. The findings support the potential utility of SALL family members as biomarkers and therapeutic targets and offer a valuable reference for future transcription-based and precision oncology studies. Keywords Breast cancer; SALL transcription factors; gene expression; DNA methylation; survival analysis; biomarkers