POLD1

Researchers have identified biological markers in triple negative breast cancer that are associated with resistance to chemotherapy treatment. Researchers at Baylor College of Medicine and the Broad Institute of MIT and Harvard and clinicians at Washington University in St. Louis have identified biological markers in triple negative breast cancer (TNBC) that are associated with resistance to chemotherapy treatment. The study is published in the journal Cancer Discovery and was funded by the National Cancer Institute's Clinical Proteomics Tumor Analysis Consortium (CPTAC). "TNBC is the most difficult to treat form of breast cancer, with standard treatment requiring multiple chemotherapy drugs that unfortunately often fail to cure the patient," said first and co-corresponding author Dr. Meenakshi Anurag, assistant professor of medicine at the Lester and Sue Smith Breast Center at Baylor. "It is imperative that we develop approaches to predict response so that only effective treatments are given. Furthermore, patients who don't respond to standard drugs need entirely new treatment approaches. The discovery of therapeutic alternatives will depend on new insights into how TNBC arises." The research team used an innovative analytic approach called "microscaled proteogenomics" that they previously developed (Satpathy et al, 2020) to analyze tumor biopsies taken from TNBC patients prior to treatment with carboplatin and docetaxel combination chemotherapy. Data from standard DNA and RNA sequencing approaches were integrated with mass spectrometry-based proteomics and phosphoproteomic analyses to derive more complete molecular portraits of treatment-responsive versus treatment-resistant tumors. "The proteomic analysis of pretreatment biopsies uniquely revealed metabolic pathways that were associated with resistance to treatment, including fatty acid metabolism," said Anurag, also a member of Baylor's Dan L Duncan Comprehensive Cancer Center. When the team considered both proteomics and gene expression data together, they observed that sensitivity to chemotherapy was marked by higher DNA repair signatures, interferon gamma signaling and immune checkpoint components. These data suggest a multi-omics predictor for chemotherapy response is within reach. The team then conducted analyses that triangulated treatment response, chromosomal deletion or gain and concordant decreases or increases in mRNA and protein expression. This led the team to determine that a deletion on chromosome 19, located in a region called 19q13.31-33, was associated with resistance to chemotherapy treatment. Of the hundreds of genes deleted in this location, expression of the DNA ligase gene LIG1 was one of the mostly consistently suppressed genes at both the mRNA and protein level. In model systems, and in other TNBC data sets, loss of expression and/or deletion of LIG1 was associated with selective carboplatin resistance and poor clinical outcome. "LIG1 loss was also associated with poor prognosis in other cancer types, showing that this deletion has broader clinical significance," Anurag said. The researchers are currently working on clinical grade assays to confirm that LIG1 loss can be safely used to direct carboplatin chemotherapy in TNBC. Dr. Matthew Ellis, a McNair Scholar at Baylor and director of the Lester and Sue Smith Breast Center at the time of this research, and Dr. Steve Carr, senior director of the Proteomics Platform and an institute scientist at Broad, who together orchestrated the analysis, said, "This groundbreaking study clearly reveals the power of combining microscaled proteogenomic analyses with careful clinical research to produce new insights into the nature of cancer." LIG1 is a critical component of lagging strand DNA synthesis that connects Okazaki fragments (small DNA segments that must be connected to complete the synthesis reaction). Interestingly, the lagging stand DNA polymerase POLD1 is frequently co-deleted with LIG1, suggesting a multigenic mechanism is in play. Lagging-strand synthesis components are generally considered essential to cellular survival but here reductions in the levels of these enzymes are associated with marked chromosomal instability in multiple cancer types and selective carboplatin resistance in TNBC. Mechanistic studies are underway to determine how the genome is destabilized and how tumors with LIG1 deletion can be more effectively treated. "This is an exciting result that is a testament to the remarkably close collaboration between patients, oncology care teams and laboratory scientists. In our view, proteogenomic analyses should be routine in clinical trials to discover clinically useful biomarkers, new biological insight and therapeutic hypotheses," said Dr. Shankha Satpathy, co-corresponding author of the study and senior group leader at in the Proteomics Platform at Broad.

New research shows that pathogenic polymerase epsilon and delta (POLE/POLD1) genetic mutations lead to improved response to immune checkpoint blockade, a powerful class of immunotherapy drugs. The findings contribute to a growing list of discoveries that prove certain classes of drugs are more effective in cases where the genetic makeup of the tumor -- and not the type or origin of the tumor -- should determine the decision-making process for treatment. New research from Cleveland Clinic is demonstrating that pathogenic polymerase epsilon and delta (POLE/POLD1) genetic mutations lead to improved response to immune checkpoint blockade, a powerful class of immunotherapy drugs. The findings, published in Nature Genetics, contribute to a growing list of discoveries that prove certain classes of drugs are more effective in cases where the genetic makeup of the tumor -- and not the type or origin of the tumor -- should determine the decision-making process for treatment. "To date, this is the most comprehensive analysis of the mutations in POLE/POLD1 genes in patients with cancer," said Timothy Chan, M.D., Ph.D., chair of the Center for Immunotherapy and Precision Immuno-Oncology at Cleveland Clinic. "Our research here shows that patients with POLE/POLD1 mutations should get immune checkpoint blockade therapy as a preferred treatment, and that POLE/POLD1 mutations are a potential indication for immunotherapy regardless of the cancer type or where the cancer started in the body." POLE/POLD1 are DNA repair genes that are genetically altered in nearly 4% of tumors across all cancer types. Not all the POLE/POLD1 mutations are pathogenic (predisposed to a certain disease) or functional that could lead to sensitivity to immunotherapy. Tumors containing pathogenic POLE/POLD1 mutations have high levels of immune cell infiltrations, and until this point, it was challenging to distinguish these pathogenic mutations from non-functional ones. It had remained unclear how these mutations would affect patients' response to anti-tumor immunity therapy. In preclinical models, the growth of tumors introduced with well-established POLE/POLD1 pathogenic mutations was dramatically inhibited by immune checkpoint blockade therapies. In contrast, treatment had little effect on growth of the parental POLE/POLD1 non-mutated tumors. To determine whether similar phenomena could be observed in patients, the team generated statistical learning models based on mutational signatures of the POLE/POLD1 mutant tumors. These signatures could identify the telltale DNA fingerprints of functional POLE/POLD1 mutations. Modeling demonstrated high accuracy for distinguishing the tumors with pathogenic POLE/POLD1 mutations from tumors with the functional mutation. The researchers further found that their model outperformed other traditional approaches for identifying the patients with pathogenic POLE/POLD1 mutations that are more likely to benefit from immunotherapy. It was able to identify mutations that sensitize tumors to immunotherapy that would otherwise have been missed. Further analysis indicated that the underlying mechanism is associated with the increased quantity and quality of the immunogenic mutations, as well as the improved immune microenvironment in the tumors harboring pathogenic POLE/POLD1 mutations. "The short-term impact of this study on cancer immunotherapy is that we demonstrated that tumors with functional POLE/POLD1 mutations are sensitive to immunotherapy," said Xiaoxiao Ma, Ph.D., a postdoctoral researcher at Cleveland Clinic and lead author of the study. "The long-term impact is that we demonstrated it's possible to utilize genomic features, such as mutational signatures, to identify a major indication for immune checkpoint therapy." The study was funded in part by the National Cancer Institute (part of the National Institutes of Health) and Brian and Diana Taussig.