Up to 80% of breast cancer deaths occur in patients with tumors that express estrogen receptor-alpha. Although these estrogen receptor-positive (ER+) breast cancers often initially respond to standard treatment combining endocrine therapies with CDK4/6 inhibitors, drug resistance frequently develops, leading to lethal metastatic disease that spreads from the breast and does not respond to available treatments.
Researchers at Baylor College of Medicine and collaborating institutions have focused on identifying new vulnerabilities in this type of cancer that could lead to improved therapies. Specifically, they studied proteins produced by ER+ breast cancers resistant to combination therapy, searching for enzymes called kinases whose expression is typically altered in cancer. Their promising results are now published in Molecular Cancer Therapeutics, a journal of the American Association for Cancer Research.
“Kinases have proven to be effective therapeutic targets for cancer and there are many inhibitors of these enzymes that are already approved by the Food and Drug Administration for human use that could be tested for their potential therapeutic value in breast cancers,” said corresponding author Dr. Charles Foulds, assistant professor in the Lester and Sue Smith Breast Center and member of the Dan L Duncan Comprehensive Cancer Center at Baylor. “The challenge was to identify the kinase among hundreds of kinases in these treatment-resistant tumors that would help us turn the tide in the fight against this cancer.”
The researchers had previously developed a laboratory method called kinase inhibitor pull-down assay (KIPA) that significantly sped up the process of kinase identification among hundreds of potential candidates.
Working with 22 patient-derived xenografts (PDXs), human breast cancer tumors grown in immune-compromised mouse models, the team used KIPA to identify and then compare the kinases produced by tumors whose growth depended on the hormone estradiol with those produced by tumors whose growth was independent of estrogen.
“The goal was to identify the difference between the estrogen-dependent group, which clinically represents cancers that respond to endocrine therapy (this therapy makes the estrogen the tumor needs to grow unavailable, therefore reducing cancer growth), versus tumors whose growth is independent of estrogen, which clinically typically correlates with the group that does not respond to endocrine therapy,” said first author Dr. Anran Chen, a graduate student in Dr. Matthew Ellis's former lab and later a post-doctoral associate in Foulds's lab during this project. Chen is currently a senior scientist at Repare Therapeutics. “Our comprehensive analyses showed that the protein kinase membrane-associated tyrosine/threonine one or PKMYT1 was our best candidate.”
Furthermore, patient clinical samples and breast cancer cell lines with high PKMYT1 mRNA levels—an indicator of PKMYT1 gene expression—were associated with resistance to both endocrine therapy and CDK4/6 inhibition. “These findings suggested that a high PKMYT1 level could be an indicator for treatment response in ER+ breast cancer tumors,” Chen said. “Because this kinase is involved in regulating cell division, we decided to investigate what effect a PKMYT1 inhibitor in clinical development would have on cancer growth.”
Working with PDXs, organoids (mini-tumors grown in the lab), cell lines, and clinical samples, researchers discovered that combining PKMYT1 inhibitor lunresertib (also called RP-6306) with chemotherapy drug gemcitabine selectively and synergistically reduced viability of ER+ breast cancer cells resistant to endocrine therapy and CDK4/6 inhibitor palbociclib while also lacking functional tumor suppressor protein p53. The absence of functional p53 disturbs cell cycle regulation in response to DNA damage leading to poor clinical outcomes.
“We were excited to find that combining a PKMYT1 inhibitor with gemcitabine led to DNA damage and cell death in p53 dysfunctional cancer cells grown in lab conditions," Foulds said. "It markedly reduced size of PDX organoids grown in labs as well as tumors grown within immune-compromised mice compared against treatment using either drug alone."
“Our study shows PKMYT1 is not only a potential marker for these tumors’ response but also has clinical potential as therapeutic target treating drug-resistant mutant p53 ER+ breast cancers,” Chen concluded. “Our pre-clinical findings support further investigations determining value novel potential therapy treating one most challenging human cancers.”
Additional co-authors include Beom-Jun Kim; Aparna Mitra; Craig T. Vollert; Jonathan T. Lei; Diana Fandino; Meenakshi Anurag; Matthew V Holt; Xuxu Gou; Jacob B Pilcher; Matthew P Goetz; Donald W Northfelt; Susan G Hilsenbeck; C Gary Marshall; Marc L Hyer; Robert Papp; Shou-Yun Yin; Carmine De Angelis; Rachel Schiff Suzanne A.W Fuqua Cynthia X Ma Matthew J Ellis.
Authors affiliated institutions: Baylor College Medicine Repare Therapeutics Adrienne Helis Malvin Medical Research Foundation Mayo Clinic University Naples Federico II Washington University School Medicine St Louis
This work supported grants Susan G Komen Foundation SAC190059 PG12220321 SAC130059 BCTR0707808 National Cancer Institute P50CA186784 U54CA233223 U01CA214125 Susan G Komen Foundation Scholarship McNair Scholarship supported McNair Medical Institute Robert Janice McNair Foundation CPRIT Established Investigator Award RR140033 SPORE Developmental Research Project grant P50CA186784 SRA Repare Therapeutics charitable gift Golfers Against Cancer P50CA186784 NIH grant R01CA072038 Breast Cancer Research Foundation grant BCRF 22-055 This work partly supported Breast Cancer Research Foundation grants BCRF 20-145 21-145 22-145 Cancer Prevention & Research Institute Texas CPRIT grant RP140102 CPRIT training grant RP210027 NIH training grant T32CA203690 grants U54CA224076 U54CA224083 Further support provided CPRIT Core Facility Support Grant P30 Cancer Center Support Grant P30CA125123 Researchers gratefully acknowledge Pfizer funding NeoPalAna clinical trial
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