What changed in this filing

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Item 2. Management’s Discussion and Analysis

2025-11-13 compared with 2025-08-12 · 175 added, 123 removed, 184 unchanged (62% of the section changed)

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Factors that could cause or contribute to these differences include those discussed below and elsewhere in this Quarterly Report, particularly in "Special Note Regarding Forward-Looking Statements" and "Risk Factors." The forward-looking statements included in this Quarterly Report are made only as of the date hereof.

We are a dedicated discovery and clinical-stage biopharmaceutical company advancing the next generation of gene and cell therapies with the overall goal of improving outcomes for patients with significant unmet medical needs.

We are a biopharmaceutical company specializing in the advancement of innovative precision medicines to address difficult-to-treat diseases with high unmet patient need.

Precigen is dedicated to advancing scientific breakthroughs from proof-of-concept through commercialization.

We are leveraging our proprietary technology platforms to develop product candidates designed to target urgent and intractable diseases in our core therapeutic areas of immuno-oncology, autoimmune disorders, and infectious diseases.

We have developed an extensive pipeline of therapies across multiple indications.

We believe that our array of technology platforms uniquely positions us among other biotechnology companies to advance precision medicine.

Precision medicine is the practice of therapeutic product development that takes into account specific genetic variations within populations impacted by a disease to design targeted therapies to improve outcomes for a disease or patient population.

Our proprietary and complementary technology platforms provide a strong foundation to realize the core promise of precision medicine by supporting our efforts to construct powerful gene programs to drive efficacy, deliver these programs through viral, non-viral, and microbe-based approaches to drive lower costs, and control gene expression to drive safety.

Our therapeutic platforms, including UltraCAR-T, AdenoVerse immunotherapy, and ActoBiotics, are designed to allow us to precisely control the level and physiological location of gene expression and modify biological molecules to control the function and output of living cells to treat underlying disease conditions.

Our therapeutic platforms, including AdenoVerse immunotherapy, UltraCAR-T, and ActoBiotics, are designed to allow us to precisely control the level and physiological location of gene expression and modify biological molecules to control the function and output of living cells to treat underlying disease conditions.

We have developed a proprietary electroporation device, UltraPorator, designed to further streamline and ensure the rapid and cost-effective manufacturing of UltraCAR-T therapies.

UltraPorator has received Food and Drug Administration ("FDA") clearance for manufacturing UltraCAR-T cells in clinical trials, and we have dosed patients with UltraCAR-T cells manufactured with UltraPorator in our clinical trials.

Our clinical pipeline includes PRGN-2012 and PRGN-2009, which are based on our AdenoVerse immunotherapy platform;

Our commercial product, Papzimeos™ (zopapogene imadenovec-drba, PRGN-2012), is the first and only US Food and Drug Administration (“FDA”) approved therapy for the treatment of adults with recurrent respiratory papillomatosis (“RRP”).

Papzimeos is a non-replicating adenoviral vector-based immunotherapy designed to express a fusion antigen comprising selected regions of human papillomavirus (HPV) types 6 and 11 proteins.

Papzimeos is designed to generate an immune response directed against HPV 6 and HPV 11 proteins in patients with recurrent respiratory papillomatosis ("RRP").

Discovered and designed in Precigen's labs using Precigen's proprietary AdenoVerse therapeutic platform, Papzimeos represents a new therapeutic paradigm for RRP.

Our clinical pipeline includes PRGN-2009, which are based on our AdenoVerse immunotherapy platform;

and PRGN-3005, PRGN-3006 and PRGN-3007, which are built on our UltraCAR-T platform.

We have completed enrollment in the Phase 1b clinical trial of PRGN-3006.

As part of the strategic prioritization of our pipeline, we have paused enrollment in the PRGN-3005 and PRGN-3007 clinical trials.

In August 2024, we announced the strategic prioritization of our pipeline to focus on development of our lead program, PRGN-2012.

We have minimized UltraCAR-T spending and plan to focus on strategic partnerships to further advance UltraCAR-T programs.

As part of this restructuring, we paused enrollment in PRGN-3005 and PRGN-3007 UltraCAR-T clinical trials.

In addition, we plan to continue PRGN-2009 Phase 2 clinical trials under a cooperative research and development agreement ("CRADA") with the National Cancer Institute ("NCI") in recurrent/metastatic cervical cancer and in newly diagnosed HPV-associated oropharyngeal cancer.

As part of the strategic prioritization of our pipeline announced in August 2024, we paused enrollment in the PRGN-3005 and PRGN-3007 clinical trials, minimized UltraCAR-T spending and plan to focus on strategic partnerships to further advance UltraCAR-T programs.

In addition, we previously announced plans to continue PRGN-2009 Phase 2 clinical trials under a cooperative research and development agreement ("CRADA") with the National Cancer Institute ("NCI") in recurrent/metastatic cervical cancer and in newly diagnosed HPV-associated oropharyngeal cancer.

We have reduced our focus on preclinical programs, while continuing select projects that we believe could provide further near-term validation of our technology platforms.

These strategic changes were designed to enable us to focus on the pre-commercialization efforts for PRGN-2012, including supporting regulatory approval, conducting the confirmatory clinical trial, and manufacturing of commercial product.

Additionally, we have continued commercial readiness efforts for a potential launch.

We have completed submission of a Biologics License Application ("BLA") for PRGN-2012 for the treatment of adults with Recurrent Respiratory Papillomatosis ("RRP") and the FDA has granted priority review with a Prescription Drug User Fee Act ("PDUFA") target action date set for August 27, 2025.

We are developing therapies built on our "off-the-shelf" AdenoVerse immunotherapy platform and our UltraCAR-T therapeutics platform.

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We believe that our proprietary gorilla adenovectors, part of the AdenoVerse technology, have superior performance characteristics as compared to current competition, including standard human adenovirus serotype 5, rare human adenovirus types and other non-human primate adenovirus types.

PRGN-2012 is an investigational AdenoVerse immunotherapy with optimized antigen design that uses our gorilla adenovector technology, part of our proprietary AdenoVerse platform, to elicit immune responses directed against cells infected with HPV6 and HPV11.

We have completed the Phase 1/2 pivotal clinical trial of PRGN-2012 in adults with RRP.

The Phase 1/2 pivotal study met the primary safety and efficacy endpoints.

The confirmatory clinical trial of PRGN-2012 is enrolling patients.

PRGN-2012 has been granted Breakthrough Therapy Designation and Orphan Drug designation for the treatment of RRP by the FDA.

PRGN-2012 has received Orphan Drug Designation for the Treatment of RRP from the European Commission as well.

We have completed the submission of, and received priority review for Precigen's BLA for PRGN-2012, which is intended for treating adults with RRP.

The PDUFA target action date is set for August 27, 2025.

PRGN-2009 is an investigational AdenoVerse immuno-therapy designed to activate the immune system to recognize and target human papillomavirus-positive, or HPV+, solid tumors.

In August 2025, the FDA granted full approval of Papzimeos for the treatment of adults with RRP.

RRP is a rare, debilitating,

and potentially life-threatening disease caused by chronic HPV 6 or HPV 11 infection, which results in recurrent benign tumors in the respiratory tract.

RRP can lead to severe voice disturbance, a compromised airway, and recurrent post-obstructive pneumonias.

Management of RRP has primarily consisted of repeated surgeries, which do not address the root cause of the disease and can be associated with significant morbidity as well as significant patient and health system burden.

The approval of Papzimeos marks a historic milestone for the RRP patient community as the first and only FDA-approved therapy for the treatment of adults with RRP.

As a result of Papzimeos receiving full FDA approval, a confirmatory clinical trial is no longer required.

Papzimeos is a non-replicating adenoviral vector-based immunotherapy designed to express a fusion antigen comprising selected regions of HPV types 6 and 11 proteins—the root cause of RRP.

Papzimeos is delivered via four subcutaneous injections over a 12-week interval.

Papzimeos approval is supported by safety and efficacy data from the pivotal Phase 1/2 clinical trial published in the Lancet Respiratory Medicine.

The pivotal study successfully met its primary safety and pre-specified primary efficacy endpoints.

Papzimeos was well-tolerated with no dose-limiting toxicities and no treatment-related adverse events greater than Grade 2.

51% (18 out of 35) of study patients achieved Complete Response, requiring no surgeries in the 12 months after treatment with Papzimeos.

These Complete Responses remained durable for over 12 months.

Complete responses have been durable after Papzimeos treatment with median follow-up of 36 months as of a September 19, 2025 data cutoff.

PRGN-2012 had been granted Breakthrough Therapy Designation and Orphan Drug designation for the treatment of RRP by the FDA.

In addition, PRGN-2012 has received Orphan Drug Designation for the Treatment of RRP from the European Commission as well.

PRGN-2009 is an investigational AdenoVerse immunotherapy designed to activate the immune system to recognize and target human papillomavirus-positive, or HPV+, solid tumors.

PRGN-2009 leverages our UltraVector and AdenoVerse platforms to optimize HPV type 16 ("HPV 16") and HPV type 18 ("HPV 18"), antigen designed for delivery via a proprietary gorilla adenovector with a large genetic payload capacity and the ability for repeat administrations.

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In addition, a Phase 2 randomized-controlled clinical trial of PRGN-2009 in combination with pembrolizumab to treat patients with recurrent or metastatic cervical cancer is ongoing pursuant to a CRADA.

As part of the strategic prioritization of our pipeline announced in August 2024, we plan to enroll patients in the PRGN-2009 clinical trials only at NCI under a CRADA.

In August 2024, as part of the strategic prioritization of our pipeline, we announced plan to enroll patients in the PRGN-2009 clinical trials only at NCI under a CRADA.

Through our UltraCAR-T therapeutics platform, we are able to precision-engineer UltraCAR-T cells to produce a homogeneous cell product that simultaneously expresses antigen-specific chimeric antigen receptor, or CAR, kill switch, and our proprietary membrane-bound interleukin-15, or mbIL15, genes in any genetically modified UltraCAR-T cell.

Our decentralized and rapid proprietary manufacturing process allows us to manufacture UltraCAR-T cells overnight at a medical center's current good manufacturing practices facility, or cGMP, and reinfuse the patient the following day after gene transfer.

Our decentralized and rapid proprietary manufacturing process allows us to manufacture UltraCAR-T cells overnight at a medical center's current good manufacturing practices facility ("cGMP") and reinfuse the patient the following day after gene transfer.

This process improves upon current approaches to CAR-T manufacturing, which require extensive ex vivo expansion following viral vector transduction to achieve clinically relevant cell numbers that we believe can result in the exhaustion of CAR-T cells prior to their administration, limiting their potential for persistence in patients.

We have developed a proprietary electroporation device, UltraPorator, designed to further streamline and ensure the rapid and cost-effective manufacturing of UltraCAR-T therapies.

The UltraPorator system includes proprietary hardware and software solutions and potentially represents a major advancement s over current electroporation devices by significantly reducing the processing time and contamination risk.

The UltraPorator system includes proprietary hardware and software solutions and potentially represents a major advancement over current electroporation devices by significantly reducing the processing time and contamination risk.

UltraPorator is intended to be a viable scale-up and commercialization solution for decentralized UltraCAR-T manufacturing.

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We have completed the Phase 1 dose escalation portion of the PRGN-3005 Phase 1/1b study.

As part of the strategic

prioritization of our pipeline announced in August 2024, we have paused enrollment in the Phase 1b clinical trial of PRGN-3005.

As part of the strategic prioritization of our pipeline announced in August 2024, we have paused enrollment in the Phase 1b clinical trial of PRGN-3005.

PRGN-3007 is an investigational autologous CAR-T therapy that utilizes the next generation UltraCAR-T platform to express a CAR which targets ROR1, mbIL15, a kill switch, and a novel mechanism for the intrinsic blockade of the programmed death 1, or PD-1, gene expression.

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The target patient population for Arm 2 includes locally advanced unresectable or metastatic histologically confirmed TNBC.

The trial is designed to enroll in two parts:

an initial 3+3 dose escalation in each arm followed by a dose expansion at the maximum tolerated dose.

As part of the strategic prioritization of our pipeline announced in August 2024, we have paused enrollment in the Phase 1 clinical trial of PRGN-3007.

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We have incurred significant losses since our inception.

We anticipate that we may continue to incur significant losses in the foreseeable future, and we may never achieve or maintain profitability.

We may continue to incur significant losses in the foreseeable future, and we may never achieve or maintain profitability.

Our historical collaboration and licensing revenues were generated under a business model from which we have gradually transitioned, and we do not expect to expend significant resources servicing our historical collaborations in the future.

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We continue to generate product and service revenues through our Exemplar subsidiary.

Papzimeos was approved by the FDA in August 2024, and we expect to begin recognizing revenue on that product in future periods.

Products currently in our clinical pipeline will require regulatory approval and/or commercial scale-up before they may commence significant product sales and operating profits.

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These efforts could result in us identifying impairment indicators or recording impairment charges in future periods.

In addition, market changes and changes in judgements, assumptions, and estimates that we have made in assessing the fair value of goodwill could cause us to consider some portion or all of certain assets to become impaired.

See further discussion regarding our ability to continue as a going concern below under the Liquidity and capital resources section of Item 2.

In addition, market changes and changes in judgments, assumptions, and estimates that we have made in assessing the fair value of goodwill could cause us to consider some portion or all of certain assets to become impaired.

Sources of revenue

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We recognize revenue when control of the promised product or service is transferred to the customer.

In future periods, our revenues will primarily depend on our ability to advance and create our own programs and the extent to which we bring products enabled by our technologies to market.

Other than for collaboration revenues recognized upon cancellation or modification of an existing collaboration or for revenues generated pursuant to future strategic transactions for any of our existing platforms or programs, we expect our collaboration revenues will continue to be minimal or zero in the near term, although if any new collaboration agreements or strategic transactions are entered into, revenue could be positively impacted.

Our revenues will also depend upon our ability to maintain or improve the volume and pricing of Exemplar's current product and service offerings.

We anticipate that our expenses will increase substantially if, and as, we continue to advance the preclinical and clinical development of our existing product candidates and our research programs.

We expect some period of time, and in most cases a significant period of time, could pass before commercialization of our various product candidates or before the achievement of contractual milestones and the realization of royalties on product candidates commercialized under our collaborations.

In future periods, our revenue profile is expected to evolve significantly with the commercialization of Papzimeos, our newly approved gene therapy for recurrent respiratory papillomatosis.

As we transition to a commercial-stage company, our revenues will increasingly depend on our ability to successfully launch Papzimeos, advance our proprietary programs, and bring additional products enabled by our technology platforms to market.

We currently have not generated any revenue from commercial product sales of Papzimeos.

We anticipate that collaboration revenue will remain minimal in the near term, except in cases where revenue is recognized upon cancellation or modification of existing agreements, or through future strategic transactions involving our platforms or programs.

Should new collaboration agreements or strategic transactions be executed, revenue could be positively impacted.

Accordingly, there can be no assurance as to the timing, magnitude, and predictability of revenues, if any, to which we might be entitled.

Cost of products and services

Cost of products and services, all which are related to our Exemplar reporting segment, includes primarily labor and related costs, drugs and supplies, feed used in production, and facility charges, including rent and depreciation.

Currently, cost of products and services, all which are currently related to our Exemplar business, includes primarily labor and related costs, drugs and supplies, feed used in production, and facility charges, including rent and depreciation.

Fluctuations in the price of livestock and feed have not had a significant impact on our operating margins and no derivative financial instruments are used to mitigate the price risk.

In future periods, we expect our costs of products to be driven by the commercialization of Papzimeos.

These costs will include manufacturing (including labor and other direct costs), packaging, quality assurance, and other production-related expenses, including labor and facility charges, such as rent and depreciation.

As Papzimeos becomes our primary revenue-generating product, its associated cost structure will represent a significant portion of our overall cost of goods sold.

Research and development expenses

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Prior to August 2024, the Company was progressing preclinical and clinical programs that targeted urgent and intractable diseases in our core therapeutic areas of immuno-oncology, autoimmune disorders, and infectious diseases, including PRGN-3005, PRGN-3006, PRGN-3007, PRGN-2009, PRGN-2012 and AG019.

As discussed above in the Overview, in August 2024, we announced a strategic prioritization of our clinical portfolio and streamlining of resources, to focus on potential commercialization of the PRGN-2012

AdenoVerse ® gene therapy for the treatment of RRP.

The Company's research and development activities also include the development of new and improved pig research models.

In addition to the strategic prioritization, the amount of research and development expenses may be impacted by, among other things, the number and nature of our own proprietary programs, the number and size of programs we may support on behalf of collaboration agreements, and the potential approval of the PRGN-2012 BLA by the FDA, as certain manufacturing costs will be recorded into inventory post approval.

Selling, general and administrative expenses

Selling, general and administrative, or SG&A, expenses consist primarily of salaries and related costs, including stock-based compensation expense and severance benefits, for employees in executive, operational (including commercialization), finance, information technology, legal, and corporate communications functions.

Other significant SG&A expenses include rent and utilities, insurance, accounting, external commercialization costs, and legal services (including the cost of settling any claims and lawsuits), and expenses associated with obtaining and maintaining our intellectual property.

SG&A expenses may fluctuate in the future depending on the scaling of our corporate functions required to support our corporate initiatives, the strategic prioritization, the build-up of our commercialization efforts and the outcomes of legal claims and assessments against us.

Following the FDA approval of Papzimeos in August 2025, we no longer expect to record research and development expenses related to PRGN-2012 for adults.

Future costs associated with this product for adults are expected to be classified as costs of products or capitalized as inventory.

In addition to the strategic prioritization announced in August 2024, the amount of research and development expenses may be impacted by, among other things, the number and nature of our own proprietary programs.

Selling, general and administrative expenses (SG&A)

Selling, general and administrative expenses consist of salaries and related costs, including stock-based compensation expense and severance benefits, for employees in executive, commercial (including sales), operational, finance, information technology,

legal, and corporate communications functions.

Other significant SG&A expenses include rent and utilities, insurance, marketing and promotion activities, sales operations, accounting, and legal services (including the cost of settling any claims and lawsuits), and expenses associated with obtaining and maintaining our intellectual property.

SG&A expenses may fluctuate in the future depending on the scaling of our corporate functions required to support our corporate initiatives, the strategic prioritization of assets, the build-up of our commercialization efforts and the outcomes of legal claims and assessments against us.

Other income (expense), net

Other income and expense net, consists of changes in the fair value of warrant liabilities and interest earned on our cash and cash equivalents and short-term and long-term investments, which may fluctuate based on amounts invested and current interest rates.

Other income and expense, net consists primarily of changes in the fair value of warrant liabilities, interest expense related to the term loans entered into in 2025 that mature in 2030, and interest earned on our cash and cash equivalents and short-term and long-term investments, which may fluctuate based on amounts invested and current interest rates.

Results of operations

Comparison of the three months ended June 30, 2025 and the three months ended June 30, 2024

The following table summarizes our results of operations for the three months ended June 30, 2025 and 2024 (dollars in thousands):

Comparison of the three months ended September 30, 2025 and the three months ended September 30, 2024

The following table summarizes our results of operations for the three months ended September 30, 2025 and 2024 (dollars in thousands):

Three Months Ended

June 30, Dollar

September 30, Dollar

Change Percent

Collaboration and licensing revenues $ 1,818 $ — $ 1,818 N/A

Product revenues 162 66 96 145.5 %

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Selling, general and administrative 23,991 9,836 14,155 143.9 %

Impairment of goodwill 3,907 1,630 2,277 139.7 %

Impairment of other noncurrent assets — 32,915 (32,915) (100.0) %

Total operating expenses 37,403 22,215 15,188 68.4 %

Operating loss (34,481) (21,262) (13,219) 62.2 %

Total other income (expense), net

Total other expense, net

(111,863) (2,704) (109,159) >200%

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(146,344) (23,966) (122,378) >200%

Income tax (expense) benefit

Income tax expense

— (12) 12 (100.0) %

Net loss $ (26,642) $ (58,792) $ 32,150 (54.7) %

Product, service and other revenues

Product, service and other revenues increased $0.1 million, or 19%, compared to the three months ended June 30, 2024.

This increase was primarily related to increased volume of products sold and services rendered at Exemplar.

$ (146,344) $ (23,978) $ (122,366) <200%

Deemed dividend on preferred stock

$ (179,000) $ — $ (179,000) — %

Net loss attributable to common shareholders

$ (325,344) $ (23,978) $ (301,366) <200%

Net loss per share attributable to common shareholders, basic and diluted

$ (1.06) $ (0.09) $ (0.97) <200%

Total revenues

Total revenues increased by $2.0 million, or >200% primarily driven by the increase in collaboration and licensing revenues.

In September 2025, the Company and PTC Therapeutics mutually agreed to terminate their existing exclusive channel collaboration ("ECC") agreement.

As a result, the Company recognized the remaining deferred revenue associated with the agreement, totaling $1.8 million.

There was no comparable revenue recognized in the prior year period.

Cost of product and services

Cost of product and services slightly increased, primarily as a result of higher revenues at Exemplar.

Cost of product and services slightly increased, primarily as a result of higher product and service revenues at our Exemplar subsidiary.

Research and development expenses

Research and development expenses decreased by $4.2 million, or 27%, compared to the three months ended June 30, 2024.

The decrease was primarily due to a $3.8 million decrease in costs associated with ActoBio, including depreciation, amortization, personnel and other research and development costs after the Company closed ActoBio operations in late 2024.

Additionally, there was a decrease of $0.5 million incurred at contract research organizations as a result of the Company's asset prioritization announced in the third quarter of 2024.

Research and development expenses increased by $1.0 million, or 9%, compared to the three months ended September 30, 2024.

The increase was primarily driven by increased manufacturing expenses and lab supplies related to commercial manufacturing costs of Papzimeos prior to its FDA approval, professional fees incurred in connection with regulatory filing procedures as well as increased employee-related expenses pertaining to the vesting of performance-based stock unit ("PSU") awards upon the FDA's approval of Papzimeos in the third quarter of 2025.

These increases were offset by the capitalization of inventory related costs subsequent to the FDA's approval of Papzimeos.

Selling, general and administrative expenses

SG&A expenses increased by $5.8 million, or 57%, compared to the three months ended June 30, 2024.

This increase was primarily associated with PRGN-2012 commercial readiness.

This increase was partially offset by a reduction in costs associated with ActoBio, legal fees, insurance rates and license and patent fees compared to the prior year period.

Impairment of Goodwill and other noncurrent assets

In the second quarter of 2025, we recorded $3.9 million in impairment related to our Exemplar reporting unit.

Additionally, in conjunction with the suspension of ActoBio’s operations, we recorded $34.5 million of impairment charges related to goodwill and long-lived assets in the second quarter of 2024.

SG&A expenses increased by $14.2 million, or 144%, compared to the three months ended September 30, 2024.

This increase was primarily due to $9.0 million increase in costs incurred related to Papzimeos commercial readiness, including sales and marketing efforts as well as professional and consulting fees to support our business growth and commercial leadership.

In addition, other employee-related costs increased approximately $4.0 million, which includes increased costs associated with the vesting of certain PSU awards which was tied to the FDA's approval of Papzimeos, and professional and legal fees increased $1.0 million primarily due to costs incurred related to general corporate matters.

Total other income (expense), net

Total other income (expense) increased $4.8 million, compared to the three months ended June 30, 2024.

This change was primarily driven by $4.5 million decrease in the fair value of warrant liabilities, which was influenced by a decrease in the stock price of Precigen common stock compared to the first quarter of 2025 and to a lesser extent, a decrease in the liability to account for the additional warrants that will be issued as part of the paid-in-kind dividends related to the Company's Series A Preferred Stock,which was also influenced by a decrease in the stock price of Precigen common stock compared to the first quarter of 2025.

Additionally, interest income rose by $0.4 million resulting from increased investment balances.

Comparison of the six months ended June 30, 2025 and the six months ended June 30, 2024

The following table summarizes our results of operations for the six months ended June 30, 2025 and 2024 (dollars in thousands):

Six months ended

June 30, Dollar

Total other (expense), net increased by $109.2 million compared to the three months ended September 30, 2024.

This change was primarily due to a $111.5 million increase in the fair value of warrant liabilities prior to their reclassification into permanent equity in the third quarter of 2025.

Substantially all of the increase in the fair value of warrant liabilities was as a result of an increase in the Company's common stock price at the valuation date compared to June 30, 2025.

This increase was partially offset by a decrease of $3.0 million third quarter 2024 charge related to the reclassification of cumulative translation losses resulting from the final closing of the ActoBio facilities in the third quarter of 2024.

Deemed dividend on preferred stock

On September 15, 2025, all Series A Preferred Stockholders converted 79,000 shares (stated value of $79.0 million) into 54,937,411 shares of common stock at the then-current conversion rate of 695.4103 shares per $1,000.

Because the conversion feature resulted in a variable number of common shares to be issued, the conversion was accounted for as a redemption under Accounting Standards Codification ("ASC") 260, resulting in the recording of a $179.0 million non-cash deemed dividend as a reduction to additional paid-in capital (and an increase in net loss attributable to common shareholders when computing net loss per share).

Net loss per share attributable to common shareholders

Net loss per share attributable to common shareholders (basic and diluted) increased to $1.06 for the three months ended September 30, 2025, compared to $0.09 for the three months ended September 30, 2024.

The increase was primarily driven by the changes noted above (including the $111.5 million change in fair value of warrant liabilities, representing $0.36 per basic and diluted share) plus the deemed dividend, as discussed above (representing $0.58 per basic and diluted share), partially offset by a higher weighted-average number of shares outstanding, primarily due to the conversion of preferred shares into common shares during the third quarter of 2025.

Comparison of the nine months ended September 30, 2025 and the nine months ended September 30, 2024

The following table summarizes our results of operations for the nine months ended September 30, 2025 and 2024 (dollars in thousands):

Nine months ended

September 30, Dollar

Change Percent

Collaboration and licensing revenues $ 1,818 $ — $ 1,818 N/A

Product revenues 406 235 $ 171 72.8 %

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Operating loss (88,841) (106,513) 17,672 (16.6) %

Total other income (expense), net

Total other expense, net

(138,295) (1,701) (136,594) >200%

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$ (227,139) $ (106,508) $ (120,631) 113.3 %

Product and service revenues

Product and service revenues increased by $0.4 million, or 22%, compared to the six months ended June 30, 2024.

This increase was primarily related to increased volume of products sold and services rendered at Exemplar.

Deemed dividend on preferred stock

$ (179,000) $ — $ (179,000) — %

Net loss attributable to common shareholders

$ (406,139) $ (106,508) $ (299,631) >200%

Net loss per share attributable to common shareholders, basic and diluted

$ (1.36) $ (0.41) $ (0.95) <200%

Total revenues

Total revenues increased by $2.4 million, or 87% primarily driven by the increase in collaboration and licensing revenues.

In September 2025, the Company and PTC Therapeutics mutually agreed to terminate their existing ECC agreement.

As a result, the Company recognized the remaining deferred revenue associated with the agreement, totaling $1.8 million.

There was no comparable revenue recognized in the prior year period.

In addition, Product and Service revenues increased by $0.5 million, or 20%, compared to the nine months ended September 30, 2024.

This increase was primarily related to increased volume of products sold and services rendered at our subsidiary, Exemplar.

Cost of product and services

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Research and development expenses

Research and development expenses decreased by $8.0 million, or (27)%, compared to the six months ended June 30, 2024.

The decrease was primarily due to a $5.6 million decrease in costs associated with ActoBio, including depreciation, amortization, personnel and other research and development costs after the Company closed ActoBio operations in late 2024.

Additionally, there was a decrease of $1.5 million at contract research organizations and a $1 million reduction in personnel expenses due to the Company's asset prioritization announced in the third quarter of 2024.

Research and development expenses decreased by $7.0 million, or 17%, compared to the nine months ended September 30, 2024.

The decrease was primarily driven by a $5.4 million decrease in costs associated with ActoBio, including depreciation, amortization, personnel and other research and development costs after the Company closed its operations in late 2024.

Additionally, external services declined by $3.5 million, primarily due to reduced activity for contract research organizations as a result of the strategic prioritization of our pipeline announced in the third quarter of 2024.

These decreases were partially offset by increased manufacturing costs related to Papzimeos prior to its FDA approval and higher professional fees incurred in connection with regulatory filing procedures.

Selling, general and administrative expenses

SG&A expenses increased by $8.0 million, or 39%, compared to the six months ended June 30, 2024.

This increase was primarily associated with PRGN-2012 commercial readiness.

This increase was partially offset by a reduction in costs associated with ActoBio, legal fees, insurance rates and license and patent fees compared to the prior year period.

SG&A expenses increased by $22.2 million, or 73%, compared to the nine months ended September 30, 2024.

This increase was primarily due to an $18.0 million increase in costs incurred related to Papzimeos commercial readiness, including sales and marketing efforts as well as professional and consulting fees to support our business growth and commercial leadership.

In addition, other employee-related costs increased by approximately $4.7 million, which includes increased costs associated with the vesting of certain PSU awards which was tied to the FDA's approval of Papzimeos.

Impairment of goodwill and other noncurrent assets

In the second quarter of 2025, we recorded $3.9 million in impairment related to our Exemplar reporting unit.

In conjunction with the suspension of ActoBio’s operations, we recorded $34.5 million of impairment charges related to goodwill and long-lived assets in the second quarter of 2024.

Impairment of goodwill and other noncurrent assets decreased by $30.6 million, or 89%, from the nine months ended September 30, 2024.

In the second quarter of 2025, we recorded an impairment charge of $3.9 million related to our Exemplar reporting unit.

In the second quarter of 2024, in conjunction with the suspension of ActoBio’s operations, we recognized $34.5 million of goodwill and other noncurrent asset impairment charges.

Total other income (expense), net

Total other income (expense), net changed from income of $1.0 million in the six months ended June 30, 2024 to expense of $26.4 million in the six months ended June 30, 2025.

This change was primarily driven by the recording of a $28.0 million increase in the fair value of warrant liabilities, which was influenced by an increase in the stock price of Precigen common stock compared to the end of 2024 and, to a lesser extent, an increase in the liability to account for the additional warrants that will be issued as part of the paid-in-kind dividends related to the Company's Series A Preferred Stock, which was also influenced by an increase in the stock price of Precigen common stock since December 31, 2024.

Total other (expense), net increased by $136.6 million compared to the nine months ended September 30, 2024, primarily driven by a $139.5 million increase in the fair value of warrant liabilities prior to their reclassification into permanent equity in the third quarter of 2025.

Substantially all of the increase in the fair value of warrant liabilities was as a result of an increase in our common stock price at the valuation date compared to December 31, 2024.

This increase was partially offset by a $3.0 million 2024 charge related to the reclassification of cumulative translation losses resulting from the final closing of the ActoBio facilities in the third quarter of 2024.

Deemed dividend on preferred stock

Because the conversion feature resulted in a variable number of common shares to be issued, the conversion was accounted for as a redemption under ASC 260, resulting in the recording of a $179.0 million non-cash deemed dividend as a reduction to additional paid-in capital (and an increase in net loss attributable to common shareholders when computing net loss per share).

Net loss per share attributable to common shareholders

Net loss per share attributable to common shareholders increased to $1.36, compared to $0.41 for the nine months ended September 30, 2024.

The increase was primarily driven by the changes noted above (including the $139.5 million change in fair value of warrant liabilities, representing $0.47 per basic and diluted share) plus the deemed dividend, as discussed above (representing $0.60 per basic and diluted share), partially offset by a higher weighted-average number of shares outstanding, primarily due to the conversion of preferred shares to common shares during the third quarter of 2025.

Liquidity and capital resources

Sources of liquidity

We have incurred losses from continuing operations since our inception, and as of June 30, 2025, we had an accumulated deficit of $2.2 billion.

From our inception through June 30, 2025, we have funded our operations principally with proceeds received from private and public equity and debt offerings, cash received from our collaborators, and through product and service sales made directly to customers.

As of June 30, 2025, we had cash and cash equivalents of $13.8 million and investments of $46.0 million.

We have incurred losses from continuing operations since our inception, and as of September 30, 2025, we had an accumulated deficit of $2.3 billion.

From our inception through September 30, 2025, we have funded our operations principally with proceeds received from private and public equity and debt offerings, cash received from our collaborators, cash received through sales of businesses, and through product and service sales made directly to customers.

As of September 30, 2025, we had cash and cash equivalents of $14.3 million and investments of $109.3 million.

Cash in excess of immediate requirements is typically invested primarily in money market funds, certificate of deposits and U.S.

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In August 2024, we closed a public offering of 39,878,939 shares of our common stock, resulting in net proceeds to us of $30.9 million, after deducting underwriting discounts, fees, and an estimate of other offering expenses.

In December 2024, we issued 79,000 shares of 8.00% Series A Convertible Perpetual Preferred Stock with an initial liquidation preference and stated value of $1,000 per share, together with warrants to purchase 52,666,669 shares of common stock for net proceeds of approximately $78,463, after deducting offering expenses.

In September 2025, all of the holders of the Series A Convertible Perpetual Preferred Stock converted their 79,000 shares into 54,937,411 shares of our common stock.

In September 2025, the Company entered into a Loan Agreement with investment entities managed by Pharmakon Advisors,

The Company received net proceeds of $92,818 after deducting underwriting discounts and offering expenses of $7,182.

The following table sets forth the significant sources and uses of cash for the periods set forth below:

Six Months Ended

Nine Months Ended

September 30,

(In thousands)

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Cash flows from operating activities:

During the six months ended June 30, 2025, our net loss was $80.8 million, which includes the following significant noncash expenses and benefits totaling $36.8 million:

(i) $28.0 million of unrealized appreciation in the fair value of warrant liabilities, (ii) $3.9 million impairment of goodwill, (iii) $4.3 million of stock-based compensation expense, (iv) $1.3 million of depreciation and amortization expense, and (v) $0.5 million of shares issued as payment for services, partially offset by non-cash benefits of $1.2 million due to amortization of discounts on investments.

During the nine months ended September 30, 2025, our net loss was $227.1 million, which includes the following significant noncash expenses and benefits totaling $153.3 million:

(i) $139.5 million of appreciation in the fair value of warrant liabilities prior to their reclassification to permanent equity in the third quarter of 2025, (ii) $3.9 million impairment of goodwill, (iii) $8.7 million of stock-based compensation expense, (iv) $2.1 million of depreciation and amortization expense, (v) $0.5 million for shares issued as payment for services, and (vi) $0.1 million related to accretion of debt discount and amortization of financing cost, partially offset by non-cash benefits of $1.5 million due to amortization of discounts on investments.

In addition, changes in operating assets and liabilities provided $9.5 million of cash for operating activities.

During the six months ended June 30, 2024, our net loss was $82.5 million, which includes the following significant noncash expenses and benefits totaling $40.4 million:

(i) $34.5 million of impairment losses, (ii) $4.5 million of stock-based compensation expense, (iii) $3.2 million of depreciation and amortization expense, and (iv) $0.5 million of shares issued as payment for services, offset by non-cash benefits of $1.7 million due to deferred income taxes and $0.6 million due to amortization of discounts on investments.

During the nine months ended September 30, 2024, our net loss was $106.5 million, which includes the following significant noncash expenses and benefits totaling $46.1 million:

(i) $34.5 million of impairment losses, (ii) $6.6 million of stock-based compensation expense, (iii) $3.9 million of depreciation and amortization expense, (iv) $2.9 million due to reclassification of cumulative translation losses, and (v) $0.6 million of shares issued as payment for services, offset by non-cash benefits of $1.7 million due to deferred income taxes and $0.7 million due to amortization of discounts on investments.

In addition, changes in operating assets and liabilities provided $0.5 million of cash for operating activities.

Cash flows from investing activities:

During the six months ended June 30, 2025, we received $23.6 million of investments, from sales and maturities, net of purchases, and purchased $1.6 million of property, plant and equipment, primarily related to the build-out of our manufacturing facility.

During the six months ended June 30, 2024, we received $45.7 million of investments, from sales and maturities, net of purchases, and purchased $6.7 million of property, plant and equipment, primarily related to the build-out of our manufacturing facility.

During the nine months ended September 30, 2025, we purchased $39.4 million of investments, net of sales and maturities, and purchased $2.0 million of property, plant and equipment, primarily related to the build-out of our manufacturing facility.

During the nine months ended September 30, 2024, we received $52.1 million from sales and maturities of investment, net of purchases, and purchased $7.6 million of property, plant and equipment, primarily related to the build-out of our manufacturing facility.

Cash flows from financing activities:

During the six months ended June 30, 2025, we paid $0.4 million in issuance costs related to a prior year equity issuance, $0.5 million related to the prior year preferred stock issuance costs, and $1.8 million to taxing authorities related to vesting of equity awards, and received $0.2 million from the exercise of stock options.

During the six months ended June 30, 2024, we received $0.1 million of proceeds from stock option exercises.

During the nine months ended September 30, 2025, we received $93.5 million under the Loan Agreement with entities managed by Pharmakon Advisors LP (see "Notes to the Condensed Consolidated Financial Statements (Unaudited) - Note 9" appearing elsewhere in this Quarterly Report) and $1.1 million from the exercise of stock options, and made the following financing activity payments:

$0.4 million for costs related to a prior year equity issuance, $0.5 million for costs related to the prior year preferred stock issuance, $1.8 million to taxing authorities related to vesting of equity awards, and $1.3 million for performance share units settled in cash.

During the nine months ended September 30, 2024, we received $31.8 million of proceeds, net of certain issuance costs, from the sale of our common stock in an underwritten public offering and $0.3 million of proceeds from stock option exercises.

Future capital requirements

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• progress in our research and development programs, as well as the magnitude and speed of development of these programs;

• capital expenditures to building out our manufacturing capabilities, including the potential manufacturing of other product candidates;

• capital expenditures to expanding our manufacturing capabilities, including the potential manufacturing of other product candidates;

• the speed and scale of building our commercial operations as we prepare for commercial readiness;

• the timing of regulatory approval of our product candidates and those of our collaborations;

• the sales price and availability of adequate third-party coverage and reimbursement for Papzimeos;

• selling and marketing activities undertaken in connection with the commercialization of Papzimeos, potential

commercialization of any future product candidates, if approved, and costs involved in the creation of an effective

sales and marketing organization;

• the timing of regulatory approval of our product candidates;

• the timing, receipt, and amount of any payments received in connection with strategic transactions;

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• the timing and capital requirements to scale up our various product candidates and service offerings and customer acceptance thereof;

• the timing of and amount of payments under our indemnification accruals;

• our ability to maintain and establish new collaborative arrangements and/or new strategic initiatives;

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To the extent that we raise additional capital through the sale of equity or convertible debt securities, the ownership interests of our common shareholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of our common shareholders.

Our current stock price may make it more

difficult to pursue equity financings and lead to substantial dilution if the price of our common stock does not increase.

Our current stock price may make it more difficult to pursue equity financings and lead to substantial dilution if the price of our common stock does not increase.

Debt financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures, or declaring dividends.

If we raise additional funds through strategic transactions, collaborations, or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs, or product candidates, or to grant licenses on terms that may not be favorable to us.

We are subject to a number of risks similar to those of other companies conducting high-risk, early-stage research and development of product candidates.

We are subject to a number of risks similar to those of other companies conducting high-risk, early-stage research and development of product candidates, as well as launching a first commercial product.

Principal among these risks are dependence on key individuals and intellectual property, competition from other products and companies, and the technical risks associated with the successful research, development, and clinical manufacturing of its product candidates.

Our success is dependent upon our ability to continue to raise additional capital in order to fund ongoing research and development, obtain regulatory approval of our products, successfully commercialize our products, generate revenue, meet our obligations, and, ultimately, attain profitable operations.

Our consolidated financial statements as of June 30, 2025 have been prepared on the basis that we will continue as a going concern, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business.

Based on current projections, management believes that its existing cash, cash equivalents and short-term investments, combined with anticipated potential revenue from the commercialization of PRGN-2012, which is outside of our direct control, will enable us to continue our operations for at least one year from the date of this filing.

These assumptions include the receipt of future payments that are dependent upon the successful FDA approval of the PRGN-2012 BLA, and therefore revenue from this product is uncertain at this time.

Based on this factor, we do not know when, or if, we will generate sufficient revenue from commercialization to offset our operating expenses.

We are subject to all of the risks inherent in the development of new products, and we may encounter unforeseen expenses, difficulties, complications, delays and other unknown factors that may adversely affect our business.

In addition, because our forecasted potential revenues are currently outside of our direct control, they have not been included in our going concern analysis.

These conditions raise substantial doubt about our ability to continue as a going concern for at least 12 months after the issuance of the accompanying condensed consolidated financial statements appearing elsewhere in this Quarterly Report.

Our financial statements do not include any adjustments that might result from the outcome of this uncertainty.

Our ability to continue as a going concern is dependent upon the successful execution of management’s plans, which include the successful commercialization of PRGN-2012.

Our consolidated financial statements as of September 30, 2025 have been prepared on the basis that we will continue as a going concern, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business.

Based on current projections, management believes that its existing cash, cash equivalents and short and long-term investments, combined with anticipated potential revenue from the commercialization of Papzimeos, will enable us to continue our operations for at least one year from the date of this filing.

We are subject to all of the risks inherent in the development of new products (including commercialization of Papzimeos), and we may encounter unforeseen expenses, difficulties, complications, delays and other unknown factors that may adversely affect our business.

Our ability to continue as a going concern is dependent upon the successful execution of management’s plans, which include the successful commercialization of Papzimeos.

In addition, we may decide, or be required to raise additional capital.

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There can be no assurance that new financings or other transactions will be available to us on commercially acceptable terms, or at all, and such financings may adversely affect the holdings or rights of our stockholders and may cause significant dilution to existing stockholders.

The condensed consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty, which could have a material adverse effect on our financial condition.

See the section entitled "Risk Factors" in our 2024 Annual Report for additional risks associated with our substantial capital requirements.

Contractual obligations and commitments

The following table summarizes our significant contractual obligations and commitments from continuing operations as of June 30, 2025 and the effects such obligations are expected to have on our liquidity and cash flows in future periods:

The following table summarizes our significant contractual obligations and commitments from continuing operations as of September 30, 2025 and the effects such obligations are expected to have on our liquidity and cash flows in future periods:

Total Less Than 1 Year 1 - 3 Years 3 - 5 Years More Than 5 Years

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Operating leases $ 6,805 $ 1,689 $ 2,953 $ 2,163 $ —

Purchase commitments 278 115 163 — —

Cash interest payable on long-term debt (*)

43,666 10,582 21,253 11,831 —

Long-term debt

100,000 — — 100,000 —

Total $ 150,749 $ 12,386 $ 24,369 $ 113,994 $ —

In addition to the obligations in the table above, as of June 30, 2025, we are party to license agreements with various third parties that contain future milestones and royalty payment obligations related to development milestones and/or commercial sales of products that incorporate or use their technologies.

(*) Interest is calculated using static annual rate of 10.67%, although our long-term debt carries a variable interest rate (see "Notes to the Condensed Consolidated Financial Statements (Unaudited) - Note 9" appearing elsewhere in this Quarterly Report).

In addition to the obligations in the table above, as of September 30, 2025, we are party to license agreements with various third parties that contain future milestones and royalty payment obligations related to development milestones and/or commercial sales of products that incorporate or use their technologies.

Because these agreements are generally subject to termination by us or are dependent on certain condition precedents within our control, no amounts are included in the tables above.

As of June 30, 2025, we also had research and development commitments with third parties totaling $4.6 million that had not yet been incurred.

As of September 30, 2025, we also had research and development commitments with third parties totaling $6.4 million that had not yet been incurred.

Off-balance sheet arrangements

We did not have during the periods presented, and we do not currently have, any off-balance sheet arrangements as defined under SEC rules.

We did not have during the periods presented, and we do not currently have, any off-balance sheet arrangements as defined under Security and Exchange Commission rules.

Critical accounting policies and estimates

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Our actual results may differ from these estimates under different assumptions or conditions.

There have been no material changes to our critical accounting policies from those described in "Management's Discussion and Analysis of Financial Condition and Results of Operations" included in our Annual Report.

Beginning with the FDA's approval of Papzimeos in the third quarter of 2025, we began to capitalize inventory at Precigen related to Papzimeos.

Inventory is stated at the lower of cost or net realizable value, and is determined using the first-in, first-out method.

The Company evaluates inventory recoverability at each reporting period and adjusts net realizable value for excess, slow-moving, or obsolete inventory.

If the net realizable value is lower than cost, the inventory is written down accordingly, and the resulting impairment charge is recognized as a component of cost of goods sold.

Inventory used for clinical development purposes is expensed to research and development expense when consumed.

Shipping and handling costs for product shipments to customers are recorded as incurred in cost of products sold.

Recent accounting pronouncements

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Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 2. Management’s Discussion and Analysis