Tier 4 — mechanistic

Mechanisms of the antiproliferative effects of SIRT6 inhibition in melanoma: a multi-omics analysis

Karla B. Anaya Aldrete, Durdana Muntaqua, Liz M. Garcia-Peterson, Mary A. Ndiaye, Jeong Ha Nam, Nihal Ahmad
Cancers 2026 Volume 18, issue 4, article 590

Bibliography

PubMed
PMID 41749843
PubMed Central
PMC12938699
DOI
10.3390/cancers18040590
Funding
Department of Veterans Affairs (Merit Review Awards I01CX002210 and I01BX005917 to N.A.; Senior Research Career Scientist Award IK6BX006041 to N.A.); National Institutes of Health R01CA261937 (to N.A.); University of Wisconsin Foundation's Dr. Frederic E. Mohs Skin Cancer Research Chair.
Competing interests
The authors declare no conflicts of interest.

Study snapshot

DesignGenetic SIRT6 knockdown in two human melanoma cell lines followed by proliferation and clonogenic survival assays, RNA sequencing, LC-MS/MS proteomics, and Ingenuity Pathway Analysis (IPA) for upstream regulator prediction.
ModelA375 and G361 human melanoma cell lines with SIRT6 knockdown by CRISPR/Cas9 or lentiviral shRNA. No matched normal melanocyte control in the omics arms.
SampleThree biological replicates per condition for RNA-seq and proteomics; clonogenic assays plated at 250 cells per well; independent CRISPR and shRNA arms as orthogonal validation.
InterventionLoss-of-function SIRT6 perturbation: CRISPR/Cas9 knockout and shRNA-mediated knockdown compared to scrambled or non-targeting controls. No pharmacological intervention.
DurationNot applicable to cell-line multi-omics readouts; clonogenic assays scored after standard 10 to 14 day colony growth.
EndpointsCell proliferation and clonogenic survival; differential gene expression (RNA-seq); differential protein expression (LC-MS/MS); predicted upstream regulators and canonical pathways (IPA); transcription-translation concordance for cell cycle, invasion, migration, apoptosis, and immunomodulation genes including AURKB, ANLN, MYC, FOXM1, RABL6, E2F2, TP53, RBL1, OSM, TNF, IL1B, IL6, IFNG.

What the study showed, in plain terms

Melanoma is the most dangerous form of skin cancer. Even with modern targeted and immune therapies, drug resistance and relapse remain common. SIRT6 is overexpressed in melanoma tumours and had previously been shown by this same laboratory to help melanoma cells grow. This study asked exactly what happens inside melanoma cells when SIRT6 is switched off.

The authors knocked down SIRT6 in two human melanoma cell lines using two independent genetic techniques — CRISPR/Cas9 gene editing and lentiviral shRNA. In both models, losing SIRT6 sharply reduced cell growth and the ability of individual cells to form colonies. They then measured every gene the cells transcribed (RNA sequencing) and every protein the cells produced (mass spectrometry proteomics), and looked for coordinated changes.

The picture that emerged was consistent at both the RNA and protein level. Genes driving cell division, mitosis, and invasion were downregulated. Genes driving apoptosis, necrosis, and cellular senescence were upregulated. Immune signalling molecules such as TNF, IL1B, IL6, and IFNG were induced. Pathway analysis pointed to reduced activity of several master regulators of melanoma proliferation, including MYC, MAP3K20, MKNK, and HMGCR (the cholesterol-synthesis enzyme).

The authors conclude that SIRT6 is pro-tumorigenic in melanoma and that inhibiting SIRT6 — not activating it — is the therapeutic direction for this cancer. This is the opposite of SIRT6's role in most other tissues, where activation is protective.

Key findings

  • SIRT6 knockdown in A375 and G361 human melanoma cell lines caused a significant decrease in cell proliferation and clonogenic survival, reproduced with both CRISPR/Cas9 knockout and lentiviral shRNA.
  • RNA sequencing identified coordinated downregulation of mitotic and cell-cycle regulators including AURKB, ANLN, MYC, FOXM1, RABL6, E2F2, and RBL1, alongside upregulation of TP53 and cell-death pathway genes.
  • Label-free LC-MS/MS proteomics confirmed transcript-level changes at the protein level, with concordant downregulation of proliferation, invasion, and migration factors and upregulation of apoptosis and necrosis effectors.
  • Immunomodulatory cytokines OSM, TNF, IL1B, IL6, and IFNG were upregulated in SIRT6-deficient melanoma cells, indicating a possible pro-inflammatory shift on top of the pro-death programme.
  • Ingenuity Pathway Analysis predicted downregulation of the upstream signalling nodes MAP3K20, MYC, MKNK, and HMGCR in SIRT6-deficient cells.
  • The study confirms and extends the same laboratory's earlier finding that SIRT6 acts as an oncogene in melanoma, in contrast to its tumour-suppressor role in colorectal, pancreatic, and hepatocellular cancers.

What this study can and cannot tell us

All findings are from two human melanoma cell lines cultured in vitro. There are no animal xenograft results in this paper and no patient-derived tissue analysis. The two cell lines both carry BRAF V600E mutations, so the results may not generalise to BRAF wild-type or NRAS-driven melanomas.

The multi-omics work compared SIRT6-knockdown melanoma cells to scrambled-control melanoma cells only. There was no comparison to normal human epidermal melanocytes, so the transcriptomic and proteomic changes reflect what SIRT6 loss does inside a transformed cell rather than what SIRT6 does to a healthy melanocyte.

Ingenuity Pathway Analysis predictions (MAP3K20, MYC, MKNK, HMGCR) are computational inferences from expression signatures. They were not confirmed with rescue experiments, phospho-signalling assays, or genetic epistasis in this paper.

The authors disclose using Microsoft Co-Pilot (GPT-5) during manuscript preparation for literature search and sentence rephrasing. This does not affect the underlying experiments but is worth noting for readers assessing text-level claims.

The oncogenic role of SIRT6 in melanoma reported here contradicts SIRT6's tumour-suppressor role documented in colorectal, pancreatic, hepatocellular, and other cancers. The paper does not resolve this tissue-specific reversal mechanistically. Any therapeutic strategy targeting SIRT6 must be matched to the specific tumour context, and a systemic SIRT6 activator would be contraindicated in patients with melanoma or at elevated melanoma risk.

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