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Atara Inventory: Contender In Autoimmune Ailments CAR-T Cell Remedy


selvanegra

Thesis overview

Atara Biotherapeutics (NASDAQ:ATRA) is a commercial stage biotech developing allogeneic EBV T cells for oncology and autoimmune indications. Notably, ATRA got a world-first approval of an “off-the-shelf” allogeneic T-cell therapy (tab-cel) by EMA in December 2022 and is nearing FDA approval (following considerable regulatory delays). As explained in my prior coverage, ATRA remains significantly undervalued based on tab-cel alone considering remaining regulatory ($80M) and commercial (up to $520M) milestones as well as significant double-digit royalties of potential peak US sales >$500M.

We know that CAR-T therapies work in both B-cell malignancies and B-cell-dependent autoimmune indications. Therefore we know that ATRA’s CAR-T therapy will most likely work as well. Notably, key features of ATRA’s platform (including EBV-specific T-cell receptor, use of memory phenotype, use of the 1XX costimulatory domain) have already been clinically validated by either academia or the industry. Importantly, ATRA’s platform has been validated by tab-cel approval, the world’s first allogeneic CAR-T approval. Despite fierce competition, ATRA’s CAR-T platform combines all the best attributes of its competition. Therefore, there is promising potential for commercial differentiation in the future. Assuming tab-cel approval in 2024, along with some other reasonable assumptions, ATRA’s cash runway into 2027 should be sufficient to deliver proof-of-concept clinical data for Non-Hodgkin Lymphoma (ph1 data expected Q4 2024) and SLE (ph1 data expected throughout 2025).

Summary of ATRA thesis (Company presentation)

As anticipated, ATRA reported positive clinical data from the ongoing Multicohort Phase 2 EBVision Trial, supporting the label-expansion potential to other EBV-positive immunodeficiency-associated lymphoproliferative diseases. ATRA announced publication of data from the ongoing phase 3 trial in Lancet, highlighting the novelty and importance of the data. Notably, that day ATRA spiked to as high as $37 (split-adjusted price). ATRA announced BLA submission on May 20. The FDA has to decide whether the submission will be accepted within 60 days. Therefore, we should have news in July. ATRA has spent years of regulatory discussion with the FDA, and it has already been more than 2 years since tab-cel approval in Europe. Therefore, I don’t expect any surprises. Considering Breakthrough Therapy Designation, tab-cel should be eligible for a priority review, meaning a PDUFA date within 6 months of submission, i.e. October 2024. EbvalloTM (tab-cel) has been awarded the prestigious 2024 Prix Galien International Award for “Best Product for Orphan/Rare Diseases” further highlighting the scientific achievement by ATRA.

Overview of the partnership with Pierre Fabre (Company presentation)

Overview of tab-cel potential (Company presentation)

ATA3219 (a CD19-targeted allogeneic CAR-T therapy); The asset is currently been evaluated in; An ongoing ph1 study in non-Hodgkin lymphoma (NHL), with initial data expected in Q4 2024. Two planned phase 1 studies in patients with Systemic Lupus Erythematous (SLE). In the first study the treatment will be administered following lymphodepletion and initial data are expected in H1 2025. In the second study the treatment will be administered without lymphodepletion and initial data are expected in H2 2025. ATA3431, a dual CD19/CD20 CAR-T cell therapy being developed for B-cell malignancies and autoimmune indications. The asset is still in the preclinical stage with IND targeted for H2 2025. ATA188, an EBV-targeted CAR-T cell therapy. As explained in prior coverages (1, 2), despite strong scientific rationale, the treatment has failed in EMBOLD ph2 study. Interestingly, the asset is still listed in the pipeline and ATRA is evaluating strategic options. I do not consider ATA188 in my thesis, but it would be a nice surprise if there is any progress in that front, which is a scenario I wouldn’t rule out.

ATRA’s pipeline (Company presentation)

Overview of some good reasons why ATRA is an underestimated CAR-T company (Company presentation)

Overview of ATRA’s CAR-T platform (Company presentation)

EBV specificity reduces Graft vs Host Disease (GvHD) risk due to targeting of viral antigens. This obviates the need for T-cell receptor gene editing, which improves functional persistence. Partial HLA mathing avoids host vs graft rejection and thus enables allogeneic approach. ATRA uses a less differentiated memory phenotype which contributes to potency and durability of responses. 1XX Costimulatory Domain optimizes potency and expansion, mitigates T-cell exhaustion and reduces cytokine release syndrome. All above factors combined seem to obviate the need for lymphodepletion, by allowing ATRA’s EBV CAR-T cells to expand and persist in vivo. Whether this will also work in auto-immune indications, as has clearly worked for tab-cel, remains to be seen (lymphodepletion may prove to be necessary to help “reset” the immune system and achieve durable responses in auto-immune indications).

“Off-the-self” available, no need for lymphodepletion and safety are major advantages of ATRA’s platform (Company presentation)

Key features of ATRA’s CAR-T platform and associated advantages (Company presentation)

Advantages over alternative CAR-T platforms (Company presentation)

Advantages of ATRA’s platform over approved autologous CAR-T therapies, bispecifics and some allogeneic CAR-Ts (Company presentation)

ATRA’s edge in autoimmune indications (Company presentation)

High and durable efficacy against post-transplant B-cell malignancy patients has been shown in a study by Memorial-Sloan Kettering with allogeneic EBV CD19 CAR T. High and durable efficacy using Novartis’ YTB323 (a less differentiated memory phenotype anti-CD19 CAR-T) against both in B-cell malignancies and SLE. Efficacy of CD19 auto CAR T with 1XX domain against B cell malignancies proven by Takeda’s TAK-940.

Advantages of key features of ATRA’s platform have been validated in prior studies by the academia or the industry (Company presentation)

Better persistence and superior efficacy of ATA3219 vs benchmark auto CAR-T. Improved antitumor efficacy of CAR-Ts with the 1XX Costimulatory Domain. Improved efficacy in SLE nephritis model of CAR-Ts with the 1XX Costimulatory Domain. Comparable cytolysis but with lower levels of proinflammatory cytokines vs autologous benchmark (suggesting potential reduction of AEs while preserving efficacy).

Superior persistence and anti-tumor efficacy over benchmark autologous CD19 CAR-T (Company presentation)

1XX Costimulatory Domain increases antitumor efficacy and efficacy in lupus nephritis (Company presentation)

Lower level of proinflammatory cytokines vs autologous bench mark (Company presentation)

Comparable cytolysis with less cytokine release (Company presentation)

Complete B-cell depletion with reduced cytokine release (Company presentation)

Company Asset name Target Donor Lymphodepletion Stage of clinical development

Notes

Cabaletta bio (CABA)

CABA-201 CD19 Autologous Yes. Being tried in pemphigus without lymphodepletion ph1/2 4-1BB costimulatory domain to reduce CRS/ ICANS

Kyverna Therapeutics (KYTX)

KYV-101

CD19

Autologous

Standard lymphodepletion regimen in all registered studies

LN ph1/2

SC ph1/2

MS ph2

MG ph2

KYV-201 preclinical (“multiple indications”)

It was recently announced that 1 SLE patient relapsed within 5 months of KYV-101 treatment despite initial response.

Kyverna Therapeutics (KYTX) KYV-201 CD19 Allogeneic No info (preclinical). Preclinical TCR KO + HLA-A KO + pan HLA Class II

Cartesian Therapeutics (RNAC)

Descartes-08 BCMA Autologous No

MG ph2 completed

SLE/other ph1/2

mRNA CAR-T cell therapy (see text for more details). Current dosing protocol requires 6 weekly infusions. Cartesian Therapeutics (RNAC) Descartes-15 BCMA Autologous No ph1 ready More potent than Descartes-15

Autolus Therapeutics (AUTL)

Obe-cel CD19 Autologous Yes refractory SLE ph1 Obe-cel uses a CD19 binder with fast-off rate which reduces toxicities and improves engraftment and persistence Autolus Therapeutics (AUTL) AUTO8 BCMA/CD19 Autologous Likely yes Preclinical No studies for autoimmune indications yet

BMS (BMY)

BMS-986353/CC-97540 CD19 Autologous Yes Ph1 4-1BB co-stimulatory domain and an epidermal growth factor receptor safety switch

Mustang Bio (MBIO)

MB-106 CD20 Autologous Unclear (preclinical) preclinical Allogene Therapeutics (ALLO) ALLO-329 CD19/CD70 Allogeneic No/ reduced SLE ph1 to start early 2025 uses ALLO’s “Dagger” technology to selectively eliminate alloreactive T cells thus improving persistence of alloCAR-T cells

Fate Therapeutics (FATE)

FT819 CD19 Allogeneic No SLE ph1

1XX costimulatory domain similar to ATRA.

TCR KO.

CRISPR Therapeutics (CRSP)

CTX112 CD19 Allogeneic Preclinical SLE preclinical

incorporates novel edits designed to enhance CAR T potency and reduce CAR T exhaustion.

TCR KO.

Sana Biotechnology (SANA)

SC291 CD19 Allogeneic

Yes

LN/ extrarenal SLE/ AAV ph1

different approach to avoid immune rejection of allogeneic cells which requires gene editing (HLA Ι/ΙΙ knock-out + CD47 overexpression)

TG Therapeutics (TGTX)

Azer-cel CD19 Allogeneic Preclinical Preclinical

Recently acquired from Precision Biosciences for autoimmune indications.

TCR KO

Impact Bio IMPT-514 CD19/CD20 Autologous Yes

SLE ph1/2

SLE/AAV/IIM ph1

JW Therapeutics JWCAR029 (relma-cel) CD19 Autologous Yes

moderate/severe SLE ph1

SS ph1

iCell Gene Therapeutics BCMA-CD19 cCAR T cells BCMA/CD19 Autologous Yes

r/r SLE ph1

MS preclinical

AstraZeneca (AZN) AZD-0120/GC012F BCMA/CD19 Autologous Yes

MG ph1

SLE ph1,

FasTCAR technology which drastically shortens cell production from weeks to overnight AbelZeta Inc C-CAR168 BCMA/CD20 Autologous No lymphodepletion reported in ph1 protocol SLE/MS/NMO/IMNM ph1 Essen Biotech BH002 BCMA/CD19 Autologous Yes refractory SLE ph1 Novartis AG (NVS) YTB323 CD19 Autologous Yes refractory SLE 2-day manufacturing process that preserves T-cell stemness Guangdong Ruishun Biotech Co., Ltd RJMty19 CD19 Allogeneic Yes

refractory SLE ph1

SLE/IIM/SS/AAV ph1

double-negative T cells a subtype of mature T cells that express CD3 and either αβ+ or γδ+ T cell receptor (TCR), but not CD4, CD8 or CD56. The platform has several advantages (including high proportion of stem cell-like memory T cells not causing graft-versus-host disease (GvHD), resistance to host-versus-graft (HvG) rejection, scalability, and storability) but limited clinical evidence so far. Luminary Therapeutics LMY-922 BAFF/BCMA/TACI Allogeneic Preclinical Preclinical “Immune Cloaking” technology that does not require nuclease editing Click to enlarge

Allogeneic platform allowing off-the-shelf availability. Allogeneic competition is relatively limited; KYTX (preclinical), ALLO (ph1 to start early 2025), FATE (ph1), CRISP (preclinical), TGTX. In other words, ATRA is not far behind allogeneic competition and is the only one with already one allogeneic product approved. Notably, all competition requires gene editing (mainly TCR KO) to allow allogeneic CAR-T cell therapy (see point below). On the contrary, most competition insists on the traditional autologous therapies (which requires an apheresis step to isolate T-cells from the patients) and generally takes longer (although newer technologies have drastically reduced the time necessary for manufacturing autologous CAR-T cell therapies to as low as overnight or 2 days). Does not require TCR gene editing or any gene editing at all to avoid GvHD and to avoid immune rejection. This improves the functionality of T-cells, simplifies the manufacturing procedure and reduces the risks associated with extra gene-editing steps.An important obstacle for allogeneic T-cell therapy is GvHD and immune rejection. Most allogeneic competition, including KYTX, FATE, CRISP, TGTX, use T-cell receptor gene editing to avoid these problems. Exceptions are Guangdong Ruishun Biotech Co., Ltd (which uses double-negative T cells, described above), SANA ( HLA Ι/ΙΙ knock-out + CD47 overexpression) and ALLO (CD70 targeting eliminates alloreactive T cells). Does not require lymphodepletion.As of now, only a few companies seem to be attempting a lymphodepletion-free CAR-T cell treatment, including CABA, RNAC, ALLO and FATE. It is safe, although this doesn’t seem to be much of an advantage over competition. In contrast to oncology, in autoimmune indications CRL/ICANS do not seem to be as much of a problem. On the other hand, lymphodepletion is associated with significant adverse events. Therefore, a CAR-T cell therapy that can obviate the need for lymphodepletion (if possible) would be a major commercial advantage, as already discussed. It achieves in vivo expansion, persistence and durable responses. Whether persistence will prove to be beneficial in autoimmune indications remains to be seen. Importantly, ATRA remains the only company with an approved allogeneic CAR T cell therapy.

B-cell expression of various markers, including CD19, CD20 and BMCA at different stages of maturation (KYTX company presentation)

Phase 1 study in NHL (Company presentation)

Phase 1 study in lupus nephritis using a standard lymphodepletion regimen (Company presentation)

Planned cohort using a lymphodepletion-free regimen (Company presentation)

Overview of ATA3431 (Company presentation)

Preclinical data suggest superior anti-tumor efficacy over autologous CD19/CD20 CAR-T benchmark (Company presentation)

anticipated regulatory milestone payments; $20 million upon acceptance of BLA submission (expected by 20 July 2024) and $60 million upon approval (expected October 2024). “anticipated purchases of tab-cel inventory through the manufacturing transfer date by Pierre Fabre”. Total inventories as of March 2024 were $16M. “anticipated reimbursement for tab-cel global development costs through the BLA transfer by Pierre Fabre”. Tab-cel R&D expenses were $22M in 2023 and $6.5M in Q1 2024. “operating efficiencies resulting from completed workforce reductions”; ATRA has guided a 35% reduction in operating expenses in 2024. Based on 2023 total operating expenses of $284.5M, this means that operating expenses for 2024 are expected to be about $185M, with “the large majority of the year-over-year operating expense reduction expected to begin in Q2 2024”. Considering Q1 operating expenses of $58.6M (R&D $45.5M, G&A $11.1M), operating expenses for the rest of 2024 (Q2-Q4) are expected to be about $123M. “the planned transition of substantially all activities relating to tab-cel at the time of the BLA transfer to Pierre Fabre potentially as early as Q1 2025, which will further reduce quarterly operating expenses”; Following this transition Pierre Fabre will be responsible for all tab-cel related expenses (including the ongoing clinical trial, regulatory procedures, manufacturing and commercialization). Notably, costs “relating to performing the services within the Additional Territory Obligation and Process Sciences Obligation” were approximately $12.3M in Q1 2024. anticipated royalties from sales of tab-cel in the U.S.; It is unclear how much royalty revenue ATRA assumes for this guidance. Assuming tab-cel achieves US peak sales >$500M as estimated by ATRA (a reasonable estimation as explained in my last coverage) and considering “significant” double-digit royalties ATRA may in few years have a yearly royalty revenue >$75M (assuming 15% royalties). Interestingly, above assumptions do not seem to include potential commercial milestone payments which can be up to $520M (details of the deal are not yet public), suggesting a conservative estimation of sales growth by ATRA.

There is risk of regulatory delays and/or suboptimal tab-cel sales in US. This will negatively affect ATRA’s cash runway, which is dependent on the pending $80M regulatory milestone payments. ATRA will eventually need to raise considerably more funds to move the CAR-T pipeline to the next stages. Although according to ATRA longer persistence is an advantage of its platform, I have some doubts whether this is an advantage in autoimmune indications. The rationale for CAR-T cell therapy in autoimmune indication is to cause a transient deep depletion of B cells, resulting in resetting of the immune system. This transient depletion is followed by reconstitution of B cells no longer reactive to self-antigens. A longer than necessary B cell depletion may be problematic, unnecessarily prolonging the duration of immunosuppression associated with B-cell depletion. On the other hand, this persistence of CAR-T cells may be important to allow deep B-cell depletion without any lymphodepletion. I was wrong about ATRA before. Despite strong scientific rationale, ATRA failed in multiple sclerosis. Therefore, there is the risk that I am wrong about the rest of ATRA’s CAR-T pipeline as well. There is a theoretical possibility that ATRA may choose to monetize US tab-cel royalties (as it did with EU royalties) to focus on its CAR-T pipeline. This will considerably increase the investment risk. I doubt ATRA would chose to take such an action unless ph1 results in NHL/SEL are very promising.



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