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Discovering and Targeting Neo-epitopes in Cancer

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Antibody Engineering & Therapeutics, held in December 2021, offered many opportunities to hear exciting and informative presentations by experts in the field. We are pleased to present here a summary of a plenary lecture by Prof. James Wells (USCF), kindly written by Dr. Czeslaw Radziejewski.

 


Discovering and Targeting Neo-epitopes in Cancer.
James Wells, Professor and Chair, Department of Pharmaceutical Chemistry, UCSF

Professor Wells presented the plenary lecture on the identification of cancer-associated proteolytic neo-epitopes in cell membrane proteins and the identification of novel cancer-specific MHC-1 peptide complexes. Cell surface proteins are the targets of most biologic and small molecule drugs. Professor Wells and colleagues use cell surface proteomics to examine changes in the cell surface proteins upon transformation with oncogenes such as KRAS, HER2, EGFR, BRAF, MEK, and Myc. Ecto-domains of identified proteins, which generally belong to the single pass trans-membrane class, are expressed as Fc fusion proteins and antibodies are generated against these proteins via screening phage libraries. Specificities of the antibodies are verified by testing against full-length trans-membrane proteins expressed by cells transfected with appropriate vectors.

Proteolysis is a primary post-translational modification of cell surface proteins. There are approximately 500 human proteases, and proteolysis plays an important role in disease progression, such as angiogenesis, invasion and metastasis, inflammation, and immune evasion. Well’s lab is exploring methods to identify proteolytic cleavage sites on the surfaceome of cancer cells.[1] To accomplish this, they devised a technology called N-terminomics, which uses the peptide ligase called subtiligase. Subtiligase ligates peptide esters to the N-terminus of a protein or a peptide. This enzyme can be used for other purposes, such as peptide cyclization and protein bioconjugation. The lab used peptides tagged with biotin or fluorescently labelled in conjunction with mass spectrometry to identify sites of proteolytic cleavage.[2,3] Prof. Wells showed an example of this strategy used to identify sites of cleavage by caspase in the proteome of a human cell line in which apoptosis was induced. This approach, however, identified only a limited number of cleaved proteins. In the next implementation of the strategy, cells were directly transfected with subtiligase. This strategy allowed the identification of hundreds of extracellular proteins that were proteolytically modified.

The newest strategy invented in Prof. Wells’ lab (unpublished) involves tethering subtiligase to glycans of cell surface proteins instead of transacting cells. Using this latest strategy in Kras-transformed cells, 611 cell surface cleavage events were observed. In HER2-transfected cells, 267 cleavage events were observed and the majority of events were not related to cleavage of signal peptide from extracellular proteins. Interestingly, the extent of proteolytic modification of some proteins in oncogene-transformed cells can either increase or decrease. Similarly, expression levels of the same proteins also change in both directions. N-terminomics of Kras- and HER2-transformed cells was thus different.

This study also identified an interesting protein called CDCP1, which has cleavage and expression that is upregulated in pancreatic cancer. The cleavage is indeed specific to cancer cells. Three closely nested cleavage sites were found in CDCP1. Antibodies (CL03.2) were developed in the lab against the cleaved form  of CDCP1. Cells containing the cleaved form were efficiently killed by the anti-CDCP1 antibody formatted as an antibody-drug conjugate (ADC). In Jurkat cells, an anti-CD3/anti-CDCP1 bispecific single-chain variable fragment showed killing activity. For in vivo studies, mouse-specific antibodies toward the truncated form of CDCP1 were generated and used to produce an auristatin (MMAF)-based ADC. An ADC against the truncated form of CDCp1 was well tolerated in non-tumor-bearing mouse, but the animals lost weight when treated with an ADC targeting the full-length protein. In a study of mice bearing xenograph tumors, the animals were administered antibody against the truncated form that was radiolabeled with isotope Lu 177 and a dramatic decrease of tumor growth was observed.

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FDA approves Vabysmo™ (faricimab-svoa) for ophthalmic disorders

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On January 28, 2022, Genentech announced that the U.S. Food and Drug Administration has approved Vabysmo ™ (faricimab-svoa) for the treatment of wet, or neovascular, age-related macular degeneration (AMD) and diabetic macular edema (DME). Faricimab (RO6867461, RG7716) is an anti-vascular endothelial growth factor-A (VEGF-A) and anti-angiopoietin-2 (Ang-2) bispecific antibody derived from Roche’s CrossMab technology.

The approval was based in part on results from four Phase 3 studies in wet AMD and DME. The randomized, double-masked, and active comparator-controlled TENAYA (NCT03823287) and LUCERNE (NCT03823300) studies evaluated the effects of faricimab (6.0 mg administered at fixed intervals of every two, three, or four months) and aflibercept (Eylea®) (2.0 mg administered at fixed two-month intervals) in wet AMD patients. The primary endpoint of the studies, average change in best-corrected visual acuity (BCVA) from baseline through week 48, was met in both studies. The average vision gains from baseline in the faricimab arms were +5.8 and +6.6 letters, compared to +5.1 and +6.6 letters in the aflibercept arms, in the TENAYA and LUCERNE studies, respectively, demonstrating the non-inferiority of faricimab compared to aflibercept. The study also showed that faricimab’s treatment interval could be longer than that of aflibercept – nearly 80% of patients treated with faricimab were able to go three months or longer between treatments during the first year.

The 3-arm, randomized, double-masked, active comparator-controlled YOSEMITE (NCT03622580) and RHINE studies (NCT03622593) compared the effects of faricimab (6.0 mg administered at personalized treatment intervals (PTI) of up to four months or 6.0 mg administered at fixed two-month intervals) to those of aflibercept (2.0 mg administered at fixed two-month intervals) in DME patients. The primary endpoint, average change in BCVA score from baseline at one year, was met, with faricimab again showing non-inferiority in visual acuity gains compared to aflibercept. In the YOSEMITE study, the average vision gains from baseline were +11.6, +10.7, and +10.9 letters eye chart letters in the faricimab PTI, faricimab two-month, and aflibercept arms, respectively. The average vision gains from baseline were +10.8, +11.8, and +10.3 letters in the faricimab PTI, faricimab two-month, and aflibercept arms, respectively, in the RHINE study.

Further details for the TENAYA and LUCERNE and YOSEMITE and RHINE studies were published in The Lancet.

The European Medicines Agency has accepted the submission of a Marketing Authorisation Application for faricimab.

Vabysmo ™ is the 2nd antibody-based therapeutic granted a first approval for marketing in the EU or US in 2022. Explore our searchable table of antibody therapeutics approved in the EU or US for details.

Bispecific antibodies come to the fore

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Bispecific antibodies are a versatile class of targeted therapeutics designed to bind two different sites, which can be located on a single antigen or on two antigens. Although bispecific antibodies were conceptualized ~60 years ago, various challenges associated with protein engineering, stability and manufacturing delayed their wide-spread development. However, as of 2020, numerous validated platforms, i.e., those that have produced bispecific clinical candidates, are readily available (1). Using these platforms, the commercial clinical pipeline has grown to over 100 bispecific antibodies, ranging from tandem single-chain variable fragments (scFv) to full-length immunoglobulins with dual variable domains. Substantial growth in the pipeline has occurred only relatively recently, though. During the early 2010s, bispecific antibodies comprised less than 10% of the total number of antibody therapeutics entering clinical study per year, but this number rose to 25% by 2018. Reflecting the general success of antibody therapeutics, the entry of all types of new, innovative antibody candidates into clinical study also grew substantially during this period, from 63 on average during the early 2010s to over 140 in 2018.

As is the case for the overall pipeline of antibody therapeutics, the majority of bispecific antibodies that have entered clinical study recently are being evaluated as treatments for cancer. Among these, the most common approach involves guiding T cells to cancer cells via a bispecific antibody, which binds to a tumor-associated antigen on a cancer cell and CD3 on T cells. Bispecifics that use this mechanism of action comprise ~45% of the pipeline. Of the T-cell engaging bispecifics now in the clinic, B-cell maturation antigen is the tumor-associated antigen most frequently targeted, followed by CD20, CD33, CD123 and prostate-specific membrane antigen. Of the bispecific antibodies in the clinical pipeline that do not re-direct T cells, the most frequent targets are programmed cell death 1 (PD1) and its ligand (PD-L1), human epidermal growth factor 2 (HER2) and vascular endothelial growth factor (VEGF). The most frequently paired targets are HER2/HER2 (different epitopes), PD1/CTLA4, PD-L1/4-1BB, VEGF/Ang-2 and VEGF/Delta-like ligand 4. Immune checkpoint proteins are frequent targets, including PD1 paired with LAG3, ICOS and TIM3, as well as PD-L1 paired with LAG3 and CTLA4.

The increased number of antibody therapeutics in the commercial clinical pipeline is due, at least in part, to the relatively high approval success rate of these molecules. Since 2014, at least 6 antibody therapeutics have been approved in either the US or European Union each year, and the number of approvals in 2020 is expected to exceed that of the all-time high of 13 approvals set in 2018 (2). Overall, antibody therapeutics have a 22% approval success rate, defined as the percentage of molecules that successfully transitioned from Phase 1 to approval of all that entered Phase 1 (3). For each clinical phase transition, the lowest rates are for the transition from Phase 1 to 2 (69%) and from Phase 2 to 3 (45%). So far, bispecific antibodies are very similar to the broader category of antibody therapeutics in their Phase 1 to 2 (71%) and Phase 2 to 3 (46%) transition rates. Since so few bispecific antibodies have reached Phase 3 or been approved, there is insufficient data for the calculation of meaningful transition rates for Phase 3 to regulatory review and regulatory review to approval. Despite this, the favorable early phase transition rates are good news for bispecific antibody developers.

In addition to success rates, the length of time required for clinical development and regulatory review is a key drug development metric. Typically for antibody therapeutics, 4-6 years is considered a relatively short period, ~ 8 years is about average, and a period of 10-12 years is considered lengthy. As with success rates, a meaningful average development period for bispecific antibodies is not available because only 3 have been approved (emicizumab, catumaxomab, blinatumomab), and 2 of these are likely not representative of bispecifics currently in clinical development. Of the 3 approved products, emicizumab, a humanized IgG4 targeting Factor IXa and Factor X approved for hemophilia, proceeded through clinical development to approval the fastest (~5.25 years), and it is most similar in structure to a canonical IgG antibody. In contrast, blinatumomab took the longest (~13 years), and it is the most dissimilar to a canonical IgG, which is typically includes human or humanized protein sequence. Blinatumomab is a tandem scFv composed of murine protein sequence with such a short half-life (2.1 hours) that continuous intravenous dosing is required for efficacy.

Because most bispecific antibodies in the commercial pipeline entered clinical studies in just the past few years, marketing approvals, if granted, may not occur for at least 4-5 years. However, two bispecific antibodies, tebentafusp and faricimab, qualify as ‘Antibodies to Watch’ (2) with late-stage clinical study primary completion dates in 2020. Tebentafusp, which is composed of a soluble T cell receptor fused to an anti-CD3 scFv (4), is being evaluated in a pivotal Phase 2 study with a primary completion date in July 2020. Faricimab is a bispecific CrossMAb (5) targeting VEGF-A and Ang-2 undergoing evaluation in several Phase 3 studies with primary completion dates in September 2020. Tebentafusp and faricimab are being studied as treatments for uveal melanoma and diabetic macular edema, respectively. Results from the clinical studies, which will help determine whether the molecules advance to regulatory review, may be available in the second half of 2020.

In summary, bispecific antibodies are entering clinical studies in record numbers, with most developed for cancer. Data available to date indicates that these molecules have similar early clinical phase transition rates, and the potential for similar development periods, compared with canonical IgG antibodies. Data discussed here will be updated and presented at PEGS Boston in the “Clinical Validation of Platforms” session of the “Engineering Bispecific Antibodies” track on Friday May 8, 2020.

1.      Labrijn AF, Janmaat ML, Reichert JM, Parren PWHI. Bispecific antibodies: a mechanistic review of the pipeline. Nat Rev Drug Discov. 2019;18(8):585–608. doi:10.1038/s41573-019-0028-1

2.      Kaplon H, Muralidharan M, Schneider Z, Reichert JM. Antibodies to watch in 2020. MAbs. 2020;12(1):1703531. doi:10.1080/19420862.2019.1703531

3.      Kaplon H, Reichert JM. Antibodies to watch in 2019. MAbs. 2019;11(2):219–238. doi:10.1080/19420862.2018.1556465

4.      Damato BE, Dukes J, Goodall H, Carvajal RD. Tebentafusp: T cell redirection for the treatment of metastatic uveal melanoma. Cancers (Basel). 2019;11(7):971. Published 2019 Jul 11. doi:10.3390/cancers11070971.

5.      Klein C, Schaefer W, Regula JT. The use of CrossMAb technology for the generation of bi- and multispecific antibodies [published correction appears in MAbs. 2018 Nov 13;11(1):217]. MAbs. 2016;8(6):1010–1020. doi:10.1080/19420862.2016.1197457

Most read from mAbs, Nov/Dec 2019

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The Antibody Society is pleased to be affiliated with mAbs, a multi-disciplinary journal dedicated to advancing the art and science of antibody research and development. We hope you enjoy these summaries based on the abstracts of the most read papers published in a recent issue.

All the articles are open access; PDFs can be freely downloaded by following the links below.

Issue 11.8 (Nov/Dec 2019)

Insights into the IgG heavy chain engineering patent landscape as applied to IgG4 antibody development

In this new Perspective, Dumet et al., present the results from their study of the patent landscape of IgG4 Fc engineering, i.e., patents claiming modifications in the heavy chain. Thirty-seven relevant patent families were identified, comprising hundreds of IgG4 Fc variants focusing on removal of residual effector functions (since IgG4s bind to FcγRI and weakly to other FcγRs), half-life enhancement and IgG4 stability. Given the number of expired or soon to expire major patents in those 3 areas, companies developing blocking antibodies now have, or will in the near future, access to free tools to design silenced, half-life extended and stable IgG4 antibodies.

Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells

Parola et al. describe an antibody engineering and screening approach where complete variable light (VL) and heavy (VH) chain cassette libraries are stably integrated into the genome of hybridoma cells by enhanced Cas9-driven homology-directed repair (HDR), resulting in their surface display and secretion. By developing an improved HDR donor format that utilizes in situ linearization, they were able to achieve >15-fold improvement of genomic integration, resulting in a screening workflow that only requires a simple plasmid electroporation. This proved suitable for different applications in antibody discovery and engineering. By integrating and screening an immune library obtained from the variable gene repertoire of an immunized mouse, they isolated a diverse panel of >40 unique antigen-binding variants. They also successfully performed affinity maturation by directed evolution screening of an antibody library based on random mutagenesis, leading to the isolation of several clones with affinities in the picomolar range.

DuoMab: a novel CrossMab-based IgG-derived antibody format for enhanced antibody-dependent cell-mediated cytotoxicity

In this new Report,  Sustmann et al. present a generic approach to generate two novel IgG-derived antibody formats that are based on a modification of the CrossMab technology. MoAbs harbor two heavy chains (HCs) resulting in one binding entity and one Fc, whereas DuoMabs are composed of four HCs harboring two binding entities and two Fc regions linked at a disulfide-bridged hinge. The latter bivalent format is characterized by avidity-enhanced target cell binding while simultaneously increasing the ‘Fc-load’ on the surface. DuoMabs were shown to be producible in high yield and purity and bind to surface cells with affinities comparable to IgGs. The increased Fc load directed at the surface of target cells by DuoMabs modulates their ADCC competency toward target cells, making them attractive for applications that require or are modulated by FcR interactions.

Single-step Protein A and Protein G avidity purification methods to support bispecific antibody discovery and development

Heavy chain (Hc) heterodimers represent a majority of bispecific antibodies (bsAbs) under clinical development. Although recent technologies achieve high levels of Hc heterodimerization (HD), traces of homodimer contaminants are often present, and as a consequence robust purification techniques for generating highly pure heterodimers in a single step are needed. Ollier et al. describe two different purification methods that exploit differences in Protein A (PA) or Protein G (PG) avidity between homo- and heterodimers. Differential elution between species was enabled by removing PA or PG binding in one of the Hcs of the bsAb. The PA method allowed the avidity purification of heterodimers based on the VH3 subclass, which naturally binds PA and interferes with separation, by using a combination of IgG3 Fc and a single amino acid change in VH3, N82aS. The PG method relied on a combination of three mutations that completely disrupts PG binding, M428G/N434A in IgG1 Fc and K213V in IgG1 CH1. Both methods achieved a high level of heterodimer purity as single-step techniques without Hc HD (93–98%). Since PA and PG have overlapping binding sites with the neonatal Fc receptor (FcRn), they investigated the effects of the engineering both in vitro and in vivo. Mild to moderate differences in FcRn binding and Fc thermal stability were observed, but these did not significantly change the serum half-lives of engineered control antibodies and heterodimers. The methods are conceptually compatible with various Hc HD platforms such as BEAT® (Bispecific Engagement by Antibodies based on the T cell receptor), in which the PA method has already been successfully implemented.

Most read from mAbs, October 2019

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The Antibody Society is pleased to be affiliated with mAbs, a multi-disciplinary journal dedicated to advancing the art and science of antibody research and development. We hope you enjoy these summaries based on the abstracts of the most read papers published in a recent issue.

All the articles are open access; PDFs can be freely downloaded by following the links below.

 

 

Issue 11.7 (Oct 2019)

Glycoform-resolved FcɣRIIIa affinity chromatography–mass spectrometry

Lippold et al. describe a method to determination the impact of individual antibody glycoforms on FcɣRIIIa affinity, and consequently antibody-dependent cell-mediated cytotoxicity (ADCC) without performing high purity glycoengineering. They hyphenated FcɣRIIIa affinity chromatography to mass spectrometry, which allowed direct affinity comparison of glycoforms of intact monoclonal antibodies. The approach enabled reproduction and refinement of known glycosylation effects, and insights on afucosylation pairing as well as on low-abundant, unstudied glycoforms. Their method greatly improves the understanding of individual glycoform structure–function relationships, and it is highly relevant for assessing Fc-glycosylation critical quality attributes related to ADCC.

Looking for therapeutic antibodies in next-generation sequencing repositories

It is now possible to query the great diversity of natural antibody repertoires using next-generation sequencing (NGS) using methods capable of producing millions of sequences in a single experiment. In this new article, Krawczyk et al. compare clinical-stage therapeutic antibodies to the ~1b sequences from 60 independent sequencing studies in the Observed Antibody Space database, which includes antibody sequences from NGS analysis of immunoglobulin gene repertoires. Of 242 post-Phase 1 antibodies, they found 16 with sequence identity matches of 95% or better for both heavy and light chains. There were also 54 perfect matches to therapeutic CDR-H3 regions in the NGS outputs, suggesting a nontrivial amount of convergence between naturally observed sequences and those developed artificially. The authors discuss the potential implications for both the legal protection of commercial antibodies and the discovery of antibody therapeutics.

Elucidating heavy/light chain pairing preferences to facilitate the assembly of bispecific IgG in single cells

Joshi et al. report that a high yield (>65%) of bispecific IgG1 (BsIgG1) without Fab engineering can be a surprisingly common occurrence, i.e., observed for 33 of the 99 different antibody pairs evaluated. Installing charge mutations at both CH1/CL interfaces was sufficient for near quantitative yield (>90%) of BsIgG1 for most (9 of 11) antibody pairs tested with this inherent cognate chain pairing preference. Mechanistically, they demonstrate that a strong cognate pairing preference in one Fab arm can be sufficient for high BsIgG1 yield. These observed chain pairing preferences are apparently driven by variable domain sequences and can result from a few specific residues in the complementarity-determining region (CDR) L3 and H3. Transfer of these CDR residues into other antibodies increased BsIgG1 yield in most cases. Mutational analysis revealed that the disulfide bond between heavy and light chains did not affect the yield of BsIgG1. This study provides some mechanistic understanding of factors contributing to antibody heavy/light chain pairing preference and subsequently contributes to the efficient production of BsIgG in single host cells.

Antibody Fc engineering for enhanced neonatal Fc receptor binding and prolonged circulation half-life

The neonatal Fc receptor (FcRn) promotes antibody recycling through rescue from normal lysosomal degradation. The binding interaction is pH-dependent with high affinity at low pH, but not under physiological pH conditions. In this new article, Mackness et al. describe how they combined rational design and saturation mutagenesis to generate novel antibody variants with prolonged half-life and acceptable development profiles. First, a panel of saturation point mutations was created at 11 key FcRn-interacting sites on the Fc region of an antibody. Multiple variants with slower FcRn dissociation kinetics than the wildtype (WT) antibody at pH 6.0 were successfully identified. The mutations were further combined and characterized for pH-dependent FcRn binding properties, thermal stability and the FcγRIIIa and rheumatoid factor binding. The most promising variants, YD (M252Y/T256D), DQ (T256D/T307Q) and DW (T256D/T307W), exhibited significantly improved binding to FcRn at pH 6.0 and retained similar binding properties as WT at pH 7.4. The pharmacokinetics in human FcRn transgenic mice and cynomolgus monkeys demonstrated that these properties translated to significantly prolonged plasma elimination half-life compared to the WT control. The novel variants exhibited thermal stability and binding to FcγRIIIa in the range comparable to clinically validated YTE and LS variants, and showed no enhanced binding to rheumatoid factor compared to the WT control. These engineered Fc mutants are promising new variants that are widely applicable to therapeutic antibodies, to extend their circulation half-life with obvious benefits of increased efficacy, and reduced dose and administration frequency.

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