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aTYR PHARMA INC (ATYR)·Q3 2025 Earnings Summary

Executive Summary

  • Q3 2025 EPS was ($0.26), missing consensus of ($0.19); revenue was $0.19M, above a $0.00 consensus, driven by license/collaboration revenue . EPS miss likely reflects a step-up in R&D tied to EFZO-FIT and manufacturing for potential BLA/commercial supply .*
  • R&D rose to $22.1M (Q/Q +$6.7M; Y/Y +$7.3M), and G&A was $4.8M (Q/Q -$0.1M; Y/Y +$1.5M) .
  • Cash, cash equivalents, restricted cash and investments were $92.9M at 9/30/25 (vs. $83.2M at 6/30/25, $78.8M at 3/31/25), improving liquidity despite higher spend .
  • Clinical update: EFZO-FIT did not meet the primary endpoint, but showed quality-of-life improvements (KSQ-Lung, FAS, KSQ-General Health) and higher complete steroid withdrawal in the 5.0 mg/kg arm vs placebo; company plans FDA meeting in Q1 2026 to determine path forward in pulmonary sarcoidosis .

What Went Well and What Went Wrong

What Went Well

  • Quality-of-life outcomes: 5.0 mg/kg efzofitimod improved KSQ-Lung at week 48 (p=0.0479), FAS total score (p=0.0226), and KSQ-General Health (p=0.0197) vs placebo . “These consistent clinical benefits reinforce our belief in efzofitimod’s potential to meaningfully improve quality of life and reduce reliance on chronic steroids” — Sanjay S. Shukla, M.D., M.S., CEO .
  • Steroid withdrawal signal: 52.6% complete steroid withdrawal at week 48 in 5.0 mg/kg vs 40.2% placebo (p=0.0919); a higher proportion achieved withdrawal with KSQ-Lung improvement (29.5% vs 14.4%, p=0.0199) .
  • Balance sheet strengthened: Cash/investments rose to $92.9M at quarter end, providing flexibility for regulatory interactions and ongoing trials .

What Went Wrong

  • Primary endpoint miss: EFZO-FIT did not meet change from baseline in mean daily OCS dose at week 48; 5.0 mg/kg reduced to 2.79 mg vs 3.52 mg for placebo (p=0.3313), triggering nominal reporting for secondary endpoints .
  • EPS miss vs consensus: ($0.26) vs ($0.19) consensus as elevated R&D ($22.1M) weighed on results; manufacturing prep for potential BLA/commercial supply also contributed .*
  • Placebo response: Management cited “higher than anticipated placebo response,” complicating demonstration of the steroid reduction endpoint .

Financial Results

Quarterly P&L (Q1–Q3 2025)

Metric (Units)Q1 2025Q2 2025Q3 2025
Total Revenues ($USD Thousands)$0 $0 $190
R&D Expenses ($USD Thousands)$11,814 $15,384 $22,130
G&A Expenses ($USD Thousands)$3,959 $4,929 $4,805
Total Operating Expenses ($USD Thousands)$15,773 $20,313 $26,935
Net Loss Attributable to ATYR ($USD Thousands)$(14,880) $(19,531) $(25,744)
Net Loss per Share ($USD)($0.17) ($0.22) ($0.26)
Shares Used (Basic/Diluted)86,485,126 90,120,235 97,153,541

YoY Comparison (Q3 2025 vs Q3 2024)

Metric (Units)Q3 2024Q3 2025
Total Revenues ($USD Thousands)$0 $190
R&D Expenses ($USD Thousands)$14,807 $22,130
G&A Expenses ($USD Thousands)$3,336 $4,805
Total Operating Expenses ($USD Thousands)$18,143 $26,935
Net Loss Attributable to ATYR ($USD Thousands)$(17,259) $(25,744)
Net Loss per Share ($USD)($0.23) ($0.26)
Shares Used (Basic/Diluted)75,801,666 97,153,541

Liquidity and Cash

Metric (Units)Q1 2025Q2 2025Q3 2025
Cash & Investments ($USD Millions)$78.8 $83.2 $92.9

Estimates vs Actuals

MetricQ1 2025Q2 2025Q3 2025
EPS Consensus Mean ($)($0.19)*($0.18)*($0.19)*
EPS Actual ($)($0.17) ($0.22) ($0.26)
EPS Beat/Miss ($)+$0.02-$0.04-$0.07
Revenue Consensus Mean ($USD Millions)$0.00*$0.00*$0.00*
Revenue Actual ($USD Millions)$0.00 $0.00 $0.19
Revenue Beat/Miss ($USD Millions)$0.00$0.00+$0.19

Values with an asterisk were retrieved from S&P Global.

Clinical KPIs (EFZO-FIT Week 48)

Measure5.0 mg/kg EfzofitimodPlacebop-value
Mean daily OCS dose change (mg)2.79 3.52 0.3313
Complete steroid withdrawal (%)52.6% 40.2% 0.0919
KSQ-Lung score change10.36 6.19 0.0479
KSQ-Lung improvement + complete withdrawal (%)29.5% 14.4% 0.0199
FAS Total Score improvementImproved —0.0226
KSQ-General Health improvementImproved —0.0197
FVC (% predicted change)-1.81 -2.11 0.7875

Guidance Changes

MetricPeriodPrevious GuidanceCurrent GuidanceChange
FDA meeting to determine efzofitimod pathQ1 2026Not specified priorPlan to meet FDA in Q1 2026 Raised (added timeline)
EFZO-CONNECT (SSc-ILD) enrollment completionH1 2026Enrollment ongoing; interim data Q2 2025 Expect completion in H1 2026 Raised (added completion target)
Cash runwayPost EFZO-FIT readoutSufficient for one year post readout No update in Q3 releaseMaintained/Not updated
Manufacturing readiness for BLA/commercial supplyOngoingManufacturing for efzofitimod program Manufacturing costs for potential BLA filing and commercial supply Progressing execution
ATYR0101 (pulmonary fibrosis) INDH2 2026File IND in H2 2026 No update in Q3 releaseMaintained

Earnings Call Themes & Trends

Note: Q3 2025 earnings call transcript not available in the dataset; themes derived from company releases.

TopicPrevious Mentions (Q-2 and Q-1)Current Period (Q3 2025)Trend
Regulatory path (efzofitimod)Topline data expected Q3; major inflection point flagged FDA meeting planned Q1 2026 to determine path forward Greater clarity on timeline
Clinical efficacy signalsTrial design, endpoints; interim SSc-ILD skin biomarkers KSQ-Lung improvement, FAS, KSQ-General Health nominal wins; steroid withdrawal higher in 5.0 mg/kg QoL benefits strengthened despite primary miss
R&D executionEFZO-FIT last patient visit; EFZO-CONNECT interim data Elevated R&D due to clinical activity and manufacturing prep Spend rising with program execution
Funding/liquidityCash $78.8–$83.2M; ATM raise $30.7M gross post-Q2 Cash $92.9M at Q3 end Liquidity improved
Pipeline (ATYR0101)IND targeted H2 2026 No updateStable
Market presenceAdded to Russell 2000/3000 No updateStable

Management Commentary

  • “While we did not meet the primary endpoint, efzofitimod is the first investigational therapy to exhibit improvements in quality of life across multiple disease-related health outcomes while also reducing steroid burden” — Sanjay S. Shukla, M.D., M.S., CEO .
  • “In spite of a higher than anticipated placebo response, we found that treatment with efzofitimod was associated with a greater amount of steroid reduction and an improvement in the KSQ-Lung score” — Sanjay S. Shukla, M.D., M.S. .
  • “Based on the findings… we plan to meet with the U.S. Food and Drug Administration (FDA) in the first quarter of 2026 to review the results and determine the path forward” — Sanjay S. Shukla, M.D., M.S. .
  • “This upcoming readout represents a major inflection point for aTyr… and we look forward to sharing the results” — Sanjay S. Shukla, M.D., M.S. (pre-readout) .

Q&A Highlights

  • Q3 2025 earnings call transcript was not available in the dataset; the company hosted a 9/15/25 webcast for EFZO-FIT topline results, but no transcript was retrievable here . No additional Q&A clarifications could be extracted.

Estimates Context

  • Q3 2025 EPS of ($0.26) missed consensus ($0.19) by $0.07; Q3 2025 revenue of $0.19M beat consensus $0.00 by $0.19M. The miss aligns with elevated R&D and manufacturing costs related to EFZO-FIT and potential BLA/commercial supply .*
  • Prior quarters: Q1 2025 EPS beat by $0.02; Q2 2025 EPS missed by $0.04; revenue aligned with $0.00 for Q1/Q2 .*
  • With the primary endpoint miss and nominal secondary wins, estimate revisions may bias toward wider EPS losses near term unless spend moderates; any FDA feedback in Q1 2026 is likely to drive scenario-dependent valuation adjustments .*

Values with an asterisk were retrieved from S&P Global.

Key Takeaways for Investors

  • EPS miss versus consensus is primarily expense-driven; watch R&D normalization post-EFZO-FIT as a lever for near-term EPS stabilization .*
  • Quality-of-life endpoints (KSQ-Lung, FAS, KSQ-General Health) and steroid withdrawal signals support clinical activity despite the primary endpoint miss; narrative shifts to regulatory dialogue on totality of evidence .
  • Liquidity improved to $92.9M, supporting operations through FDA meeting and EFZO-CONNECT enrollment milestones without immediate financing pressure .
  • Near-term stock catalyst: FDA meeting outcome in Q1 2026; medium-term, EFZO-CONNECT completion and any clarity on efzofitimod’s regulatory path in pulmonary sarcoidosis .
  • Risk factors: placebo response magnitude in EFZO-FIT, nominal nature of secondary endpoints, and continued high R&D outlays until regulatory path is clarified .
  • Pipeline depth (ATYR0101) offers optionality into H2 2026; however, efzofitimod program trajectory will likely dominate the thesis near term .
  • Actionable: Monitor updated guidance post-FDA meeting; track operating expense trends and cash burn; reassess probability-weighted valuation contingent on regulatory feedback and potential pathway leveraging QoL endpoints.

Optional notes

  • Non-GAAP: The company did not provide non-GAAP adjustments or measures in these releases .