Improving the Management and Survival of Patients with Aggressive, Treatment-Resistant Cancers

NTU research has shaped the design of immunotherapy clinical trials for the treatment, and benefit, of adult patients with aggressive AML. Primary refractory AML, a subtype of the disease, is extremely challenging to treat; the current median survival rate is just four months. To date, no specific treatments have been identified for this patient subset and there is a clear, unmet medical need. Working with MacroGenics, a Nasdaq-listed biopharmaceutical company with annual revenues averaging around $100 million, NTU has carried out an international, multi-centre phase I/II clinical trial to determine the maximum tolerated dose level of an immunotherapy drug flotetuzumab in patients with AML, whose disease is not expected to benefit from cytotoxic chemotherapy. The trial has also studied how the drug acts in the body and evaluated its potential anti-tumour activity.

NTU-led research identified immune signposts or “biomarkers” that predict patients with the chemotherapy-refractory form of acute myeloid leukaemia (AML) who might respond to MacroGenics’ immunotherapy drug flotetuzumab. NTU’s research also informed the development of a paediatric arm of the flotetuzumab clinical trial. NTU’s work, hence promoted the positive perception of the drug by investors and biotech equity analysts, and motivated MacroGenics’ $19.5M investment in developing the drug. NTU’s ‘precision medicine’ approach, advice and testing of molecular profiling techniques enabled successful spatially resolved analyses of bone marrow biopsies at unprecedented depth using NanoString’s GeoMx DSP platform. This development, demonstration and showcasing of the product’s capabilities for research in haematological malignancies has been a key factor in NanoString’s market capitalization growth from $242 million to $1.14 billion in 5 years.

This novel methodological approach extends beyond AML and is informing the development of immunotherapy clinical trials for patients with advanced (metastatic) gastric cancer.

Leading an international team and leveraging financial support from research charities and commercial entities, Professor Sergio Rutella, Director of the John van Geest Cancer Research Centre (JvGCRC), set out to characterise the ‘immune ecosystem’ of AML and to identify immune gene signatures that are reflective of general immune status and predictive of anti-leukaemia immune potential. The research used 3D biology technologies, including targeted immune transcriptomic profiling and spatially resolved digital immunohistochemistry, to characterise the immune ecosystem of the bone marrow tumour microenvironment (TME) in 42 children and 28 adults with AML. This identified heterogeneous immune profiles and concluded that ‘immune enriched’ AMLs might be amenable to immunotherapy approaches tailored to the bone marrow TME.

AML is characterized by clonal expansion of poorly differentiated myeloid precursors, resulting in impaired haematopoiesis and often bone marrow failure. According to Cancer Research UK, an average of 3,200 new cases of AML are diagnosed in the UK annually and 2,600 patients die from AML each year. In the United States, the American Cancer Society estimated that 19,940 people were diagnosed with AML in 2020 and 11,180 people died from the disease. The general therapeutic strategy has not changed substantially in more than 30 years, with chemotherapy remaining the standard of care for most patients with AML despite recent drug approvals by the U.S. Food and Drug Administration. AML is cured in only 35 to 40 per cent of patients below 60 years of age and in 5 to 15 per cent of patients above 60 years of age. While chemotherapy resistance is common, relapse is the most common cause of treatment failure, with only 10% of patients surviving 5 years or longer after disease recurrence.

In the first study of its kind into the genetic make-up of bone marrow cells in leukaemia, the research team used machine learning to identify a gene signature that predicts outcomes for patients with AML. Using an artificial neural network-based machine learning approach to analyse a publicly available dataset for 593 adults with AML, they found that a patient may have a better chance of survival, and may not require intensive treatment, if genes coding for CALCRL, CD109 and LSP1 are switched off. These findings led to the establishment of new sub-categories of risk for which different treatment options should be offered to maximise patient benefit while keeping unwanted toxicity to a minimum, and the early-stage development of a companion diagnostic device to support treatment decision making.

Using innovative RNA/protein expression and digital spatial profiling approaches, researchers led by Professor Rutella carried out high-dimensional analysis of the immunological structure of 442 primary bone marrow samples from patients with AML, unravelling critical differences in immune gene expression across age groups and disease stages. The study also identified those patients that are more likely to fail standard chemotherapy. Crucially, the study found that patients with an interferon dominant TME (the ‘hot’ or ‘inflamed’ AML immune subtype) are more likely to respond to immunotherapy with flotetuzumab (FLZ), a novel CD123×CD3 dual affinity re-targeting molecule currently in a phase I clinical trial sponsored by MacroGenics. This study led to MacroGenics filing three patents, with Professor Rutella and NTU named as a co-inventor, relating to bispecific CD123×CD3 diabodies for the treatment of hematologic malignancies.

The AML research programme as a whole has involved the molecular profiling of an unrivalled cohort of AML samples provided by clinical collaborators (>600 specimens). Professor Rutella used this to generate a compendium of AML gene and protein profiles that provide novel insights into the immunobiology of the disease. These are being made available in the Gene Expression Omnibus, an open-access repository of high throughput transcriptomic data.

Collaboration with MacroGenetics, Nasdaq-listed biopharmaceutical company

Working with MacroGenics, a company with annual revenues averaging around $100 million, NTU has carried out an international, multi-centre phase I/II clinical trial (NCT02152956) to determine the maximum tolerated dose level of an immunotherapy drug flotetuzumab in patients with AML, whose disease is not expected to benefit from cytotoxic chemotherapy. The trial has also studied how the drug acts in the body and evaluated its potential anti-tumour activity.

Reporting its 2018 end-of-year results to investors, MacroGenics highlighted the presentation of clinical trial data and Professor Rutella’s gene signature data at the 2018 American Society of Hematology (ASH) Annual Meeting. Its news release in February 2019 said: “In the study, flotetuzumab demonstrated anti-leukaemic activity and acceptable tolerability in patients with relapsed/refractory AML, with a higher response rate observed in primary refractory patients, an extremely challenging population to treat.”

Historically, patients who do not respond to chemotherapy have remission rates to subsequent interventions in the range of only 5-12%, with a median overall survival of 3.5 months. As shown by the updated clinical data presented at the 2020 ASH Annual Meeting, “a remission rate of 32% with good duration and a manageable safety profile observed in the ongoing registrational study of flotetuzumab is very encouraging”. MacroGenics plans to define a potential registration path for flotetuzumab in patients with primary induction failure and early relapsed AML. In August 2019 MacroGenics submitted a briefing document to the US FDA to seek approval for flotetuzumab under the Biologics Licensure Pathway and to seek guidance on other registrational components.

Professor Rutella’s group has also shown that flotetuzumab modulates the immune TME of individuals who are sensitive to its therapeutic effects by inducing the upregulation of PD-L1, a negative immune checkpoint. This observation has impacted on the development of the next generation of combination immunotherapy clinical trials sponsored by MacroGenics by providing a sound rationale for the administration of flotetuzumab in combination with PD-1-blocking antibodies.

NTU research has informed the correlative biology studies for the first in-child trial of flotetuzumab in patients with relapsed/refractory AML

The first-in-child phase 1 trial studying flotetuzumab in paediatric patients with relapsed/refractory AML opened in January 2020. This is sponsored by the US Children's Oncology Group under the auspices of the US Paediatric Early Phase-Clinical Trial Network. According to the clinical trial description, “Giving flotetuzumab may stop the leukaemia from growing or shrink for a period of time, as well as possibly lessening symptoms, such as pain, that are caused by the leukaemia”.

NTU’s protocols have delivered commercial benefits to NanoString Technologies through the expansion of their product portfolio for molecular profiling of haematological tumours

• Rutella S, Vadakekolathu J, Patel T, Reeder S, Schmitz M, Schaarschmidt H, Warren SE, Liang Y, Hood T, Danaher P, Cesano A, Beechem JM, Pockley AG, Tasian SK, Bornhäuser M. Capturing the complexity of the immune microenvironment of acute myeloid leukemia with 3D biology technology. Journal of Clinical Oncology 2018; 36 (Suppl. 5S; A#50). http://doi.org/10.1200/JCO.2018.36.5_suppl.50.
• Wagner S, Vadakekolathu J, Tasian SK, Altmann H, Bornhäuser M, Pockley AG, Ball GR, Rutella S. A parsimonious 3-gene signature predicts clinical outcomes in an acute myeloid leukemia multicohort study. Blood Advances 2019; 3: 1330-46. https://doi.org/10.1182/bloodadvances.2018030726. PMID: 31015209.
• Vadakekolathu J, Minden MD, Hood T, Church SE, Reeder S, Altmann H, Sullivan AH, Viboch EJ, Patel T, Ibrahimova N, Warren SE, Arruda A, Liang Y, Smith TH, Foulds GA, Bailey MD, Gowen-MacDonald J, Muth J, Schmitz M, Cesano A, Pockley AG, Valk PJM, Löwenberg B, Bornhäuser M, Tasian SK, Rettig MP, Davidson-Moncada JK, DiPersio JF, Rutella S. Immune landscapes predict chemotherapy resistance and immunotherapy response in acute myeloid leukemia. Science Translational Medicine 2020; 12(546): eaaz0463. DOI: https://doi.org/10.1126/scitranslmed.aaz0463. PMID: 32493790.
• Uy GL, Aldoss I, Foster MC, Sayre PH, Wieduwilt MJ, Advani AS, Godwin JE, Arellano ML, Sweet K, Emadi A, Ravandi F, Erba HP, Byrne M, Michaelis LC, Topp MS, Vey N, Ciceri F, Carrabba MG, Paolini S, Huls G, Jongen-Lavrencic M, Wermke M, Chevallier P, Gyan E, Recher C, Stiff P, Pettit K, Löwenberg B, Church S, Anderson EK, Vadakekolathu J, Santaguida MT, Rettig MP, Muth J, Curtis T, Fehr E, Guo K, Zhao J, Bakkacha O, Jacobs K, Tran K, Kaminker P, Kostova M, Bonvini E, Walter RB, Davidson-Moncada JK, Rutella S, DiPersio JF. Flotetuzumab as salvage immunotherapy for refractory acute myeloid leukemia. Blood 2020 Sep 14: blood.2020007732. DOI: 10.1182/blood.2020007732. PMID: 32929488.
• USA Patents Pharmaceutical Formulations of Bispecific CD123 × CD3 Diabodies for the Treatment of Hematologic Malignancies (Attorney Docket No. 1301.0161P; filed on 30 October 2018 and assigned Serial No. 62/752,659); Bispecific CD123 × CD3 Diabodies for the Treatment of Hematologic Malignancies (Attorney Docket No. 1301.0161P2; filed on 19 November 2018 and assigned Serial No. 62/769,078); and Use of Bispecific CD123 × CD3 Diabodies for the Treatment of Hematologic Malignancies (United States Patent Application Serial No. 63/041,051; filed on 20 June 2020).
• Rutella S, Church SE, Vadakekolathu J, Reeder S, Sullivan A, Warren S, Baughman J, Muth J, Park H, Uronis H, Kang YK, Ng M, Enzinger P, Lee KW, Huber K, Wynter-Horton A, Li D, Bang YJ, Davidson-Moncada J, Catenacci D. Evaluation of tumour microenvironment identifies immune correlates of response to combination immunotherapy with margetuximab and pembrolizumab in HER2+ gastroesophageal adenocarcinoma. Annals of Oncology 2019; 30 (Suppl. 5; 123A). DOI: https://doi.org/10.1093/annonc/mdz239.034.