Long non-coding RNA implicated in triple negative breast cancer

A slice of RNA that doesn’t code for a protein manages to stifle tumor-suppressing genes and wreck the cellular mechanism that flags cancer cells for destruction by the immune system.

Writing this month in Nature Immunology, a team led by scientists at MD Anderson shows that the long, non-coding RNA (lncRNA) called LINK-A is a potential therapeutic target for triple negative breast cancer.

Working in a uniquely developed mouse model of the disease, the team showed that inhibiting LINK-A restored immune function and thwarted tumor growth. Its presence in a tumor also could serve as a biomarker for treatment with immune checkpoint blockade.

“We believe that these research findings successfully demonstrate the integral role of specific lncRNAs as oncogenes in the development and progression of breast cancer and highlight the potential for lncRNAs to serve as promising therapeutic targets in future clinical avenues,” says co-senior author Liuqing Yang, Ph.D., assistant professor of Molecular and Cellular Biology.

While scientists have long worked with shorter portions of non-coding RNA, longer RNA is subject to recent research and is defined as having a length of more than 200 nucleotides.

The team had previously shown that LINK-A is abundantly expressed in triple negative breast cancer and its presence is associated with poor outcomes.

About half of triple-negative tumors respond to chemotherapy. The cancer lacks expression of the therapeutic target HER2 and both targets for hormonal therapy -- estrogen and progesterone receptors.  Only 10-18% of patients respond to immune checkpoint inhibitors that block the connection between PD-L1 and the PD-1 brake on immune T cells.

When LINK-A is up, immune cell penetration is down

The researchers examined data from The Cancer Genome Atlas, finding LINK-A is heavily expressed not only in breast cancer but also kidney, ovarian, uterine, head and neck, and squamous cell lung cancer.

Among breast cancer patients, they found an inverse correlation between levels of LINK-A and penetration of tumors by immune cells – both antigen-presenting cells and T cells.  High LINK-A tumors had low immune cell penetration.

An analysis of triple negative breast cancer patients who had been treated with the PD-1 immune checkpoint inhibitor pembrolizumab showed that non-responders had high levels of LINK-A and notably lower expression of proteins involved in presenting antigens on the cell surface for immune targeting.

Those same crucial proteins in the antigen-presenting machinery were marked for destruction by the cell’s proteasome – further evidence that LINK-A helps tumors evade immune system detection.

Uncovering the cancer-promoting pathway

The team developed a mouse model of triple negative breast cancer that induced expression of LINK-A in mammary tissues, ultimately developing breast cancer. “This provided us with a powerful tool for assessing these associations,” says co-first author Qingsong Hu, Ph.D., research scientist in Molecular and Cellular Oncology.

Subsequent experiments established that LINK-A activates G-coupled protein receptor pathways (GPCR), which in turn downregulates cyclic AMP (cAMP) and inactivates protein kinase A (PKA).  PKA depletion was previously associated with cancer formation, but the mechanism for this effect was unknown.

The team showed PKA inactivation by LINK-A leads to tumor-suppressing proteins p53 and Rb being tagged with ubiquitins, marking them for destruction by the proteasome.  Rb and p53 are both notably suppressed in breast cancer compared to nearby normal tissue.

They also found that non-responders to pembrolizumab had lower levels of PKA and its crucial target, TRIM71, that protects Rb and p53, and higher levels of LINK-A.

Additionally, they found that the LINK-A-to-TRIM71 connection degrades all six components of the antigen peptide-loading complex that finds potential immune system target peptides inside the cell, packages them and transports them through the MHC 1 complex to the cell surface, where they can trigger an immune response by T cells.

LINK-A downregulates this immune system mechanism during tumor initiation in their mouse model.

Potential breast cancer treatment

Treating mice with GPCR-antagonist Rauwolscine or locked nucleic acids that target LINK-A reduced tumor development and increased penetration of T cells into tumors.  Both drugs also stabilized the antigen-presenting machinery. The team is working to advance either approach to clinical trial.

Their findings point to developing LINK-A expression as a biomarker for treating patients with immunotherapy and as a drug target to sensitize breast tumors to immune checkpoint blockade.

“Given the scarcity of viable drug targets, lack of targeted therapies, and relatively poor prognoses of patients with TNBC, an improved understanding of the immunogenicity of triple negative breast cancer, as reported in our study, helps define the role of immune checkpoint blockade in treatment and provides a targeted lncRNA-based immunotherapeutic combinational treatment for this breast cancer,” says Chunru Lin, Ph.D., co-senior author and assistant professor of Molecular and Cellular Oncology.

Co-senior author Leng Han, Ph.D., assistant professor of Biochemistry and Molecular Biology, and co-first author Youqiong Ye, Ph.D., a post-doctoral fellow in Han’s lab, led the University of Texas Health Science Center at Houston McGovern Medical School team involved in this research.

Co-first author Li-Chuan Chan is a graduate student in the MD Anderson/UTHealth Graduate School of Biomedical Sciences.