Cancer evolution converging on common resistance mechanisms to PARP inhibition: A Molecular Tumor Board discussion.

Jan 7, 2025 | Blog Post

Precision oncology is revolutionizing the way we treat cancer by tailoring therapies to the genetic makeup of individual tumors. As our understanding of cancer’s molecular biology continues to expand, therapies are becoming more targeted, effective, and individualized. This shift toward personalized medicine is gradually becoming the standard of care, offering hope for better outcomes in patients with advanced cancers.

Molecular Tumor Boards (MTBs), are multidisciplinary teams of experts that play a pivotal role in the application of precision oncology and the translation of research findings into clinical practice. The Molecular Tumor Board routinely reviews cases of individuals with advanced cancer and interprets the genomic data obtained through next-generation sequencing (NGS) to ultimately explore molecularly-informed treatment recommendations. These MTBs however, are most commonly available in tertiary cancer centers, making access to them still limited. That is why our team at the Johns Hopkins Molecular Tumor Board (JH MTB) recently published a case report (DOI) in The Journal of Clinical Oncology (JCO), to open up an educational discussion on the genomically informed treatment paradigm. This case report leverages a discussion held at our Molecular Tumor Board that highlights the important role of the MTB in the management of metastatic breast cancer, and it details the journey of a patient whose tumor developed resistance to targeted therapy, identified using NGS, and interpreted by the JH MTB.

We discussed the case of a young woman diagnosed with early stage hormone receptor–positive, HER2-negative breast cancer, who as per standard of care, received neoadjuvant chemotherapy followed by bilateral mastectomy. Germline testing identified a heterozygous pathogenic loss-of-function PALB2 frameshift mutation which is known to be associated with an increased lifetime risk of breast, pancreatic, and ovarian cancer. The patient’s cancer recurred four years after the initial diagnosis and as biopsy of a metastatic site showed hormone receptor–positive breast cancer, she received letrozole monotherapy. Following further disease progression 15 months later she received the PARP inhibitor olaparib as part of a clinical trial given the presence of the PALB2 germline mutation.

PALB2 is one of the genes involved in DNA repair, specifically in homologous recombination (HR). Loss of function of PALB2 leads to the inability to properly repair DNA, specifically double-strand breaks, which can result in genetic instability and contribute to cancer progression. This is referred to as homologous recombination deficiency (HRD), and, as in this case, it can be driven by loss-of-function mutations in one of the genes of the HR pathway. Cancers with DNA repair deficiency rely on alternate DNA repair mechanisms and this creates an opportunity for therapies that block these alternate DNA repair pathways such as PARP inhibitors (PARPi) to block DNA repair in cancer cells ultimately leading to tumor cell death.

However, some tumors can develop resistance to PARPi through acquired mutations that restore homologous recombination, like in this case. At the time of disease progression on olaparib, a liquid biopsy detected the germline PALB2 mutation, together with a plethora of new PALB2 mutations that all restored the PALB2 reading frame, practically negating the effect of the germline loss-of-function mutation. The JH MTB reasoned that these reversion mutations all restored homologous recombination that allowed the metastatic clones to escape synthetic lethality through PARPi therapy. A large number of different PALB2 reversion mutations were detected in the bloodstream, which represents the reservoir where circulating DNA from any metastatic site is shed. As such, the JH MTB team hypothesized that different PALB2 reversion mutations were acquired and selected for in various metastatic sites and potentially at different timepoints during PARPi therapy. This essentially means that these reversion mutations, although all driven by a shared selective pressure of PARPi therapy, emerged separately at different metastatic sites and at different times during tumor evolution.

The emergence of polyclonal reversion mutations in PALB2, following PARP inhibition, suggest convergence evolution in this tumor, through independent genomic events, in response to the shared selective pressure of target therapy, ultimately restoring homologous recombination and DNA repair, and leading to a clinically refractory phenotype. Such reversion mutations have been observed in ovarian, breast, pancreatic, and prostate cancer with a prevalence of approximately 26% and the cancer clones harbouring these reversion mutations gain a fitness advantage, followed by positive selection that clinically manifests as therapy resistance. As seen in this case, different subclones can develop genomically distinct but phenotypically similar resistance when subjected to a shared selective pressure.

This case highlights the importance of elucidating the underlying mechanism of resistance and uncovering the molecular biology driving the refractory phenotype. By leveraging advanced genomic techniques like next-generation sequencing and the multi-disciplinary expertise of Molecular Tumor Boards, we can uncover the intricate mechanisms behind treatment resistance, such as the polyclonal reversion mutations observed in this patient. Our findings also illustrate the importance of real-time monitoring to adapt treatment approaches. As personalized therapies continue to evolve, the integration of genomic profiling into clinical decision-making remains essential for identifying the most effective treatment options and overcoming resistance. This case additionally highlights the advantage of liquid biopsy to both allow for minimally invasive real-time serial monitoring for arising resistance variants and to enable comprehensive assessment of the genomic landscape across metastatic sites in heterogeneous tumors. The collaborative, multidisciplinary MTB review process exemplified by this case is a powerful model for translating molecular insights into actionable treatment strategies, ultimately improving outcomes for patients with advanced cancer. Lastly, we emphasise the need for broadening access to MTBs, ensuring that genomically informed care is available to a wider range of patients.

Bridging liquid biopsy discoveries with clinical cancer: Harnessing ctDNA Molecular Response to Predict Clinical Outcomes and Guide Therapeutic Decision Making for Individuals with Lung Cancer.

Nov 20, 2024 | Blog Post

Posing hypothesis-driven and clinically relevant questions represents one of the pillars of scientific discovery that can be translated in interventions that may improve patient outcomes. And that’s exactly what our research team was able to do with BR.36; a multi-center, randomized, ctDNA-directed, phase 2 trial of molecular response-adaptive immuno-chemotherapy for individuals with lung cancer. Recently published in Nature Medicine (DOI), and building on years of work on minimally invasive liquid biopsies in capturing therapy response to immunotherapy, our group formed, asked, and investigated the clinical value of using a molecular readout of therapy response during immunotherapy.

Evaluation of therapy response on immunotherapy represents a challenge.  Imaging that is predominantly used to evaluate cancer’s response to treatment, often falls short in rapidly and accurately capturing the therapeutic effect. The limitations of imaging are intensified in patients with radiographic stable disease or mixed responses, both representing heterogenous and hard to assess patient groups. In addition, already existing snapshot tumor-based biomarkers such as PD-L1 expression and tumor mutation burden (TMB), that can help guide therapy selection, are imperfect and inconsistently predict clinical outcomes with immunotherapy.

That’s where liquid biopsies and analyses of cell-free circulating tumor DNA (ctDNA) have gained momentum and can be particularly informative. As cells in our body die, they shed fragments of their DNA in the bloodstream. Cancer cells do so as well and these cell-free circulating tumor DNA remnants can be picked up by liquid biopsies (LB). From a LB assay standpoint, cell-free DNA is isolated from blood, followed by ultra-sensitive techniques that allow us to focus on specific regions of DNA and look for changes in the genetic code, known as mutations. These minimally invasive, innovative approaches allow for real-time tracking of circulating tumor burden, thereby molecularly assessing cancer’s response to treatment.

After identifying mutations in ctDNA, we are faced with the challenge of deciphering which of the mutations detected by the LB are truly tumor-derived. Here comes another challenge, that of identifying which mutations are coming from cancer cells and which ones come from other tissues and as such represent “biological noise”. These confounding mutations can be germline, meaning mutations passed down from previous generations, or can be originating from blood cells, which is termed “clonal hematopoiesis” (CH). To solely focus on tumor-derived mutations in our study, we used matched normal DNA genomic data, obtained through next generation sequencing of white blood cells (WBCs), which in turn allowed for filtering out CH-derived and germline mutations.

With that background in mind, let us dive deeper into the fundamental questions posed. Starting with the definition: What is ctDNA response? How soon after immunotherapy initiation should we look for it? How concordant is ctDNA molecular response with imaging response? And how does it relate to survival and clinical outcomes? Are there specific patients that would benefit most from a molecular assessment of their cancer’s response?

Let us rewind and unfold these one by one. Fifty patients with metastatic non-small cell lung cancer (NSCLC) were enrolled in the first observational phase of our trial and received immunotherapy as standard of care. LBs were performed with each of the first three  cycles of immunotherapy and ctDNA load was estimated. Molecular response (mR) was defined as clearance of ctDNA mutation levels, whereas persistence or rise of ctDNA levels was classified as molecular disease progression (mPD). Our findings reveal that the median time necessary for achievement of mR was 2.1 months, or in other words, after 2 cycles of immunotherapy. We found that most patients with radiographic complete (CR) or partial (PR) response prior to cycle 3 of immunotherapy had mR on their liquid biopsy testing. We additionally and importantly found a strong correlation between molecular response and improved clinical outcomes, as patients in the mR group attained longer overall survival (OS) and progression-free survival (PFS) than patients showing mPD.

These findings suggest a unique actionable opportunity to use molecular response assessment to more optimally decipher the true therapy response including the heterogeneous group of patients with radiographically stable disease. Molecular responses were largely concordant with radiographic responses, however the former were more informative and effective in predicting clinical outcomes and survival.

Upon investigating these questions, what is next? Clinical translation. Eager to implement the aforementioned findings in clinical practice, we designed the second phase of BR.36; a ctDNA molecular response-driven interventional randomized stage of the trial that will assess the value of ctDNA molecular response in guiding therapeutic decision making (NCT04093167) and inform which patients should receive immunotherapy monotherapy vs. a combination of immunotherapy with chemotherapy. Looking at the expanding landscape of immunotherapy treatments for individuals with metastatic lung cancer, our vision is that ctDNA molecular response can rapidly and accurately predict therapy response and allow us to navigate treatments, tailoring therapies to the right patient populations at the right time.

Interested in more reading? Here’s a list of liquid biopsy studies from our group:

Neoadjuvant nivolumab or nivolumab plus LAG-3 inhibitor relatlimab in resectable esophageal/gastroesophageal junction cancer: a phase Ib trial and ctDNA analyses. (DOI)

Liquid biopsy approaches to capture tumor evolution and clinical outcomes during cancer immunotherapy. (DOI)

Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer. (DOI)