Singapore's Cancer Research Frontier: Decoding BAP1's Role in Aggressive Tumors

In a landmark achievement for Singapore's biomedical research landscape, scientists from the National Cancer Centre Singapore (NCCS) and Duke-NUS Medical School have published groundbreaking findings in Science Translational Medicine. Their study delves into the intricate mechanisms of BRCA1-associated protein 1 (BAP1), a key tumor suppressor frequently inactivated in deadly cancers. This research not only maps BAP1's deubiquitination targets but also identifies promising combination therapies that could transform treatment for patients with BAP1-deficient malignancies.

The work highlights Singapore's rising stature in global oncology research, where higher education institutions like Duke-NUS—a graduate medical school jointly established by the National University of Singapore (NUS) and Duke University—play a pivotal role. By fostering clinician-scientists through its rigorous MD-PhD programs, Duke-NUS bridges basic science and clinical application, producing leaders who drive such innovations.

Understanding BAP1: The Tumor Suppressor's Hidden Functions

BAP1, or BRCA1-associated protein 1, is a deubiquitinating enzyme (DUB) that removes ubiquitin molecules from target proteins, regulating their stability and function. Ubiquitination is a post-translational modification akin to tagging proteins for degradation by the proteasome, a cellular recycling system. When BAP1 is mutated or lost, this quality control falters, leading to genomic instability and unchecked cell proliferation.

Inactivating BAP1 mutations occur in 10-20% of certain aggressive cancers worldwide, including mesothelioma (pleura/peritoneum lining), uveal melanoma (eye), cholangiocarcinoma (bile duct), and clear cell renal cell carcinoma (ccRCC, kidney). In Singapore, where cancer incidence rises—averaging 50 new cases daily per recent national registry data—these BAP1-driven tumors pose significant challenges due to poor prognosis and limited therapies.

The NCCS-Duke-NUS team employed ubiquitin remnant motif pulldown coupled with mass spectrometry to comprehensively profile BAP1's substrates. This revealed BAP1's critical involvement in global genome nucleotide excision repair (GG-NER), a DNA repair pathway that excises bulky lesions like UV-induced thymine dimers or chemotherapy adducts.

Mapping BAP1's Deubiquitination Network: Key Insights from Advanced Proteomics

The study's proteomics approach identified damage-specific DNA binding protein 1 (DDB1), UV excision repair protein RAD23 homolog B (RAD23B), and COP9 signalosome complex subunit 7B (COPS7B) as direct BAP1 targets. BAP1 deubiquitinates these GG-NER components, preventing their proteasomal degradation and ensuring efficient DNA damage recognition and repair.

Step-by-step, GG-NER initiates with DDB1-CUL4-RBX1 (DCR1) complex binding UV lesions, recruiting XPC for verification. RAD23B shuttles XPC to the site, while COPS7B aids complex assembly. Without BAP1, ubiquitinated forms accumulate, impairing repair and allowing mutations to persist—a hallmark of cancer progression.

Integrative multi-omics—ChIP-seq, ATAC-seq, and transcriptomics—confirmed BAP1, along with lysine-specific demethylase 1 (LSD1) and poly(ADP-ribose) polymerase 1 (PARP1), colocalize at chromatin. LSD1 demethylates histones for chromatin relaxation, enabling transcription-coupled NER (TC-NER) overlap, while PARP1 PARylates proteins for lesion flagging.

Synthetic Lethality: LSD1 and PARP1 as Achilles' Heels in BAP1-Loss Tumors

High-throughput screening of 422 anti-cancer agents pinpointed LSD1 inhibitors (e.g., SP2509, SP2577) and PARP inhibitors (PARPi, e.g., olaparib) as selectively toxic to BAP1-deficient cells. Synthetic lethality occurs when two non-lethal defects combine fatally: BAP1 loss cripples GG-NER baseline, LSD1 inhibition blocks chromatin access, and PARPi traps PARP at lesions, overwhelming repair capacity.

In vitro, combination treatment induced DNA damage accumulation, apoptosis via caspase activation, and halted proliferation in BAP1-mutant lines from mesothelioma, uveal melanoma, cholangiocarcinoma, and ccRCC. Patient-derived organoids mirrored this sensitivity, underscoring translational relevance.

Photo by TSquared Lab on Unsplash

Preclinical Validation: From Cells to Xenografts

Mouse xenograft models engrafted with BAP1-deficient human tumors demonstrated profound synergy. Oral SP2509/SP2577 plus olaparib reduced tumor volumes by over 80% versus monotherapy, extending median survival from 25 to 55 days in mesothelioma models. No overt toxicity occurred, with normal cells spared due to intact BAP1-mediated repair.

These results, detailed in the full study (Science Translational Medicine), position BAP1 status as a biomarker for stratifying patients likely to benefit from this regimen.

Singapore's Ecosystem: NCCS and Duke-NUS Driving Translational Excellence

NCCS, Singapore's premier cancer center under SingHealth Duke-NUS Academic Medical Centre, integrates clinical care with research. Prof. Teh Bin Tean, NCCS Deputy CEO (Venture & Enterprise) and Duke-NUS researcher, co-led this effort, leveraging NCCS's biobanks and clinical cohorts.

Duke-NUS's Cancer & Stem Cell Biology Programme trains next-gen researchers via PhD/MD-PhD tracks, emphasizing precision oncology. First author Dr. Hong Jing Han exemplifies this, funded by NMRC awards. Such collaborations exemplify Singapore's biomedical hub status, with over SGD 25B invested in RIE2025.

Higher education plays central: NUS/NTU provide foundational biosciences, feeding into Duke-NUS graduate programs.

Addressing Singapore's Cancer Burden: Relevance of BAP1 Research

Singapore faces rising cancer rates; kidney cancer (ccRCC subset) ranks among top 10, cholangiocarcinoma links to chronic liver disease prevalent in Asia. Mesothelioma, though rarer (asbestos legacy), and uveal melanoma demand specialized care NCCS provides.

This study offers hope amid 1 in 2 lifetime risk, per National Registry. By targeting unmet needs, it aligns with Healthier SG initiatives for personalized medicine. NCCS news release (here) quotes Prof. Teh: "...encouraging... shift to mechanism-based combination strategies."

Path to Clinic: Trials, Challenges, and Opportunities

LSD1i and PARPi are clinically advanced; olaparib FDA-approved for BRCA cancers. Ongoing trials explore expansions; Singapore's Phase I/II units at NCCS/Nuh ideal for testing. Challenges: biomarker validation, resistance mechanisms, Asia-specific genetics.

Future: multi-omics for BAP1 subtypes, AI integration (e.g., CAN-Scan from recent GIS study). Singapore's Clinical Research Institute supports rapid translation.

Photo by Albert Vincent Wu on Unsplash

Careers in Singapore's Cancer Research: Thriving Academic Landscape

This breakthrough underscores vibrant opportunities. Duke-NUS offers postdoc fellowships; NCCS clinician-scientist tracks blend patient care/research. PhD programs at NUS/NTU in oncology booming, with grants like NMRC STS.

Stakeholders: A*STAR, SingMass for proteomics. Regional context: Asia's cancer surge demands local talent; SG's ecosystem attracts global experts.

• Postdoctoral positions in epigenetics/DNA repair
• Research assistant roles in organoid modeling
• MD-PhD pathways for clinician-researchers

Global Impact and Future Outlook

Beyond Singapore, findings apply pancancer; BAP1 mutations ~1-5% solid tumors. Collaboration potential with global hubs. Prof. Teh notes: "new opportunities to test drug combinations... biomarkers to personalize treatment."

Singapore positions as Asia's oncology leader, via higher ed investments yielding high-impact papers (e.g., recent engineered bacteria in Sci Transl Med). Actionable: monitor BAP1 in biopsies, advocate combo trials.