Cue Biopharma, Inc. (CUE)·Q1 2025 Earnings Summary

Executive Summary

• Q1 2025 revenue was $0.42M, down sharply year over year due to the Ono collaboration termination in March; EPS was $(0.17). Versus Wall Street, revenue missed consensus $1.27M* and EPS was modestly below $(0.153)* .
• Liquidity actions and partnering improved the balance sheet: $20M gross capital raise (closed April 16) and $12M upfront from Boehringer Ingelheim for CUE-501; cash was $13.1M at quarter-end, then +$18M net proceeds in April and +$12M upfront, materially extending runway .
• Operating expenses fell year over year on lower clinical trial costs and compensation; R&D was $8.5M (vs $10.2M LY) and G&A held flat at $4.2M .
• Strategic narrative pivoted to autoimmune: regained worldwide rights to lead program CUE-401, and BI collaboration validated the CUE-500 platform; management scheduled a May 15 “Novel Biologics Portfolio” event that highlighted CUE-401’s preclinical data .

What Went Well and What Went Wrong

What Went Well

• Validating external partnership: Boehringer Ingelheim collaboration for CUE-501 with $12M upfront and ~$345M in potential milestones supports and accelerates autoimmune strategy .
• Cost discipline: R&D decreased to $8.5M driven by lower clinical trial costs and employee compensation; G&A stable at $4.2M, showing controlled OpEx despite pipeline transition .
• Strengthened liquidity: ~$20M gross follow-on offering and $12M upfront from BI, plus ~$18M net proceeds received in April, bolstering resources for advancing CUE-401 toward the clinic .
• Quote: “We believe the strategic collaboration with Boehringer Ingelheim for CUE-501 combined with our capital raise, places us in a position of strength to advance CUE-401 toward the clinic” – CEO Daniel Passeri .

What Went Wrong

• Material top-line decline: collaboration revenue fell to $0.4M vs $1.7M LY due to termination of Ono agreement in March, creating a significant revenue vacuum .
• Estimate miss: revenue missed consensus materially and EPS modestly missed, highlighting near-term model uncertainty as the company pivots to autoimmune development (consensus: revenue $1.27M*, EPS $(0.153)*) [GetEstimates].
• Continuing losses: net loss was $(12.3)M with loss from operations $(12.3)M; interest income declined vs LY, reflecting lower cash balances prior to April financing .

Financial Results

KPIs and Operating Detail

Versus Estimates (S&P Global consensus)

Values marked with * retrieved from S&P Global.

Context and drivers:

• Revenue decline was attributed to the Ono Pharmaceutical agreement termination in March 2025, which eliminated collaboration revenue streams tied to that agreement .
• R&D decrease reflected lower clinical trial costs and compensation; G&A remained flat year over year .

Guidance Changes

No formal financial guidance was provided (revenue, margins, EPS, OpEx) for upcoming periods. Management emphasized advancing CUE-401 toward IND-enabling studies and leveraging the BI collaboration to accelerate CUE-501 development .

Earnings Call Themes & Trends

Note: The company did not hold a traditional Q1 earnings call; instead, it hosted a May 15 “Novel Biologics Portfolio” event with extensive prepared remarks and Q&A.

Management Commentary

• “We believe the strategic collaboration with Boehringer Ingelheim for CUE-501 combined with our capital raise, places us in a position of strength to advance CUE-401 toward the clinic…” – CEO Daniel Passeri .
• “CUE-401… designed to bind to destructive autoimmune effector cells, transforming them into anti-inflammatory regulatory Tregs… enabling simultaneous signaling of TGF-β and IL-2” – CMO Matteo Levisetti .
• “We believe this data could form the basis of an important strategic oncology partnership” – CEO Daniel Passeri (on CUE-100 series survival data) .
• “Under the terms… Cue will receive an upfront payment of $12 million… eligible to receive up to $345 million in success-based milestone payments…” – CBO Lucinda Warren (BI collaboration details) .

Q&A Highlights

• Indication prioritization for CUE-401: management is assessing dermatologic, GI (IBD), MS, transplantation; final selection will be data- and opportunity-driven .
• CUE-500 scope: beyond B-cell lineage (BI), potential targets include mast cells, eosinophils, fibroblasts (FAP), monocyte subsets, and pathogenic T-cell subsets; oncology applications envisioned .
• Treg durability and safety: consistent activation markers with durable tolerance in GVHD and autoimmune models; well tolerated across dosing regimens in preclinical studies .
• Dosing durability vision: potential for measurable durable effects enabling personalized, intermittent dosing as biology and PK/PD become clearer (expert view) .

Estimates Context

• Q1 2025 revenue of $0.421M missed S&P Global consensus of $1.268M*, driven by the March termination of the Ono collaboration revenue stream .
• Q1 2025 EPS of $(0.17) was slightly below consensus $(0.153)*; continuing operating losses reflect early-stage R&D intensity and reduced interest income from lower pre-offering cash balances .
  Values marked with * retrieved from S&P Global.

Where estimates may need to adjust:

• Sell-side models should reflect the removal of Ono-related revenue and incorporate BI collaboration economics (upfront recognized outside Q1 and future milestones contingent), lowering near-term revenue but enhancing funding of autoimmune programs .

Key Takeaways for Investors

• Near-term top-line remains minimal post-Ono termination; stock narrative is likely driven by pipeline progress (CUE-401), BI collaboration validation, and funding runway rather than quarterly P&L prints .
• The BI deal and April financing constitute meaningful liquidity catalysts; subsequent cash inflows de-risk near-term execution on IND-enabling for CUE-401 and continued CUE-501 advancement .
• Autoimmune thesis strengthening: first-in-class TGF-β/IL-2 bispecific for Treg induction and effector conversion shows durable preclinical effects across models; Pre-IND feedback (June) supports IND filing path .
• Oncology assets (CUE-101/102) exhibit encouraging survival/response metrics; management is exploring strategic alternatives/partnering—potential non-dilutive catalysts .
• Expect estimate recalibration: consensus should reflect lower collaboration revenue in 2025 and potential milestone/non-dilutive inflows from partnerships; monitor milestones and regulatory events as drivers of sentiment .
• Near-term trading implications: news flow sensitivity to regulatory updates (CUE-401 IND-enabling progress, IND timeline) and business development; limited revenue means P&L beats/misses less likely to drive stock than strategic events .
• Medium-term thesis: platform validation plus partnering economics could finance clinical entry of autoimmune programs; clinical data readouts will be key inflection points for valuation re-rating .

Notes:

• No non-GAAP adjustments were disclosed in the Q1 press release; comparisons use GAAP metrics .
• Revenue decline was explicitly tied to the termination of the Ono Pharmaceutical agreement in March 2025 .
• Liquidity subsequent events: ~$18M net proceeds in April offering and $12M upfront from BI improved quarter-end cash position .