Exhibit 99.1
® THERAPEUTICS Pioneering mRNA Cell Therapy for Autoimmunity January 2024 C
A R T ES I AN T H E R APEUT I CS
Forward-Looking Statements Disclosures For the purposes of this notice, the
“presentation” that follows shall mean and include the slides that follow, the oral presentation of the slides by members of management of Cartesian Therapeutics, Inc. (the “Company”) or any person on their behalf, any question-and-answer
session that follows such oral presentation, hard copies of this document and any materials distributed at, or in connection with, such oral presentation. Forward-looking Statements Any statements in this presentation about the future
expectations, plans and prospects of the Company, including without limitation, statements regarding the Company’s expected cash resources and cash runway, the Company’s estimated cash on hand, the expected receipt of proceeds from the
Company’s November 2023 private placement, conversion of the Company’s Series A Non-Voting Convertible Preferred Stock, the potential of RNA Armory® to enable precision control and optimization of engineered cells for diverse cell therapies
leveraging multiple modalities, the potential of Descartes-08, Descartes-15, Descartes-33 and the Company’s other product candidates to treat myasthenia gravis, systemic lupus erythematosus, or any other disease, the anticipated timing or the
outcome of ongoing and planned clinical trials, studies and data readouts, the anticipated timing or the outcome of the FDA’s review of the Company’s regulatory filings, the Company’s ability to conduct its clinical trials and preclinical
studies, the timing or making of any regulatory filings, the anticipated timing or outcome of selection of developmental product candidates, the ability of the Company to consummate any expected agreements and licenses and to realize the
anticipated benefits thereof, the novelty of treatment paradigms that the Company is able to develop, the potential of any therapies developed by the Company to fulfill unmet medical needs, the Company’s ability to enter into and maintain its
strategic partnerships, and enrollment in the Company’s clinical trials and other statements containing the words “anticipate,” “believe,” “continue,” “could,” “estimate,” “expect,” “hypothesize,” “intend,” “may,” “plan,” “potential,”
“predict,” “project,” “should,” “target,” “would,” and similar expressions, constitute forward-looking statements within the meaning of The Private Securities Litigation Reform Act of 1995. Actual results may differ materially from those
indicated by such forward-looking statements as a result of various important factors, including, but not limited to, the following: the uncertainties inherent in the initiation, completion and cost of clinical trials including proof of
concept trials, including uncertain outcomes, the availability and timing of data from ongoing and future clinical trials and the results of such trials, whether preliminary results from a particular clinical trial will be predictive of the
final results of that trial and whether results of early clinical trials will be indicative of the results of later clinical trials, the ability to predict results of studies performed on human beings based on results of studies performed on
non-human subjects, the unproven approach of the Company’s RNA Armory® technology, potential delays in enrollment of patients, undesirable side effects of the Company’s product candidates, its reliance on third parties to conduct its clinical
trials, the Company’s inability to maintain its existing or future collaborations, licenses or contractual relationships, its inability to protect its proprietary technology and intellectual property, potential delays in regulatory approvals,
the availability of funding sufficient for its foreseeable and unforeseeable operating expenses and capital expenditure requirements, the Company’s recurring losses from operations and negative cash flows, substantial fluctuation in the price
of the Company’s common stock, risks related to geopolitical conflicts and pandemics and other important factors discussed in the “Risk Factors” section of the Company’s most recent Annual Report on Form 10-K and Quarterly Reports on Form
10-Q, and in other filings that the Company makes with the Securities and Exchange Commission. In addition, any forward-looking statements included in this presentation represent the Company’s views only as of the date of its publication and
should not be relied upon as representing its views as of any subsequent date. The Company specifically disclaims any intention to update any forward-looking statements included in this presentation, except as required by law. 2
3 Clinical-stage company pioneering mRNA cell therapies designed to expand
the reach of cell therapy to autoimmunity Pipeline of mRNA cell therapies designed to be dosed more reliably and safely in an outpatient setting without lymphodepletion Descartes-08: Potential first-in-class mRNA CAR T-cell (CAR-T)
demonstrated deep and durable clinical responses in Phase 2a study in patients with myasthenia gravis (MG) Wholly-owned GMP manufacturing designed to enable rapid optimization of processes in iterative manner MULTIPLE ANTICPATED NEAR-TERM
CATALYSTS $118M as of end of 2023; expected to fund currently planned operations into 2H26 Expected to provide for continued clinical development of Descartes-08 in MG through Phase 3 and multiple additional clinical programs PRO FORMA
CASH RESOURCES* DESCARTES-08 Phase 2b topline data in MG expected mid-2024 Initiation of Phase 2 study in SLE expected in 1H 2024 Initiation of studies in additional autoimmune indications expected in 2H
2024 DESCARTES-15 Next-generation mRNA CAR-T candidate IND cleared, with first-in-human Phase 1 planning activities underway *Reflects the anticipated receipt of $40M through two delayed settlement payments previously announced as part of
the November 2023 financing, which are expected in January 2024 and February 2024 CAR, Chimeric antigen receptor SLE, Systemic Lupus Erythematosus
Experienced management team to lead the mRNA cell therapy company of the
future Matthew Bartholomae General Counsel Metin Kurtoglu, MD, PhD COO Milos Miljkovic, MD CMO Blaine Davis CFO Chris Jewell, PhD Chief Scientific Officer Carsten Brunn, PhD President and CEO MANAGEMENT Emily English, PhD VP,
Quality 4 Murat Kalayoglu, MD, PhD Director | Cartesian Co- Founder & pre-merger CEO Timothy Springer, PhD Director Carrie S. Cox Chairman BOARD MEMBERS Michael Singer, MD, PhD Director | Cartesian Co- Founder & pre-merger
Chief Strategy Officer Timothy Barabe Director Nishan De Silva, MD Director Aymeric Sallin, MS Director Patrick Zenner Director
DNA CAR-T cell therapy creates increased patient burden Patients receiving DNA
CAR-T require inpatient administration and pre-treatment chemotherapy (lymphodepletion) Indirect costs high due to monitoring/treatment of toxicities DNA transduced CAR-T associated with: Cytokine release syndrome (CRS) Neurotoxicity and
parkinsonism Cytopenia (from pre-treatment chemo) Infections Secondary malignancies Death 5 Conventional engineered cell therapy uses DNA, which can lead to toxicity and increased patient burden Effector function of cell therapy
engineered with DNA amplifies exponentially with cell replication and frequently leads to uncontrollable PK/PD Cells administered at subtherapeutic levels quickly proliferate beyond therapeutic window
6 Time Therapeutic window Subtherapeutic Toxicity CAR+ Cells 6
Doses Expectation for cells to be administered at the therapeutic but sub-toxic doses Descartes-08 has been administered to 66 patients with autoimmune diseases and cancer1 with no CRS, neurotoxicity, or infections observed Ability to
treat in outpatient setting offers potential to be administered in community clinics Potential for safe re-dosing mRNA CAR-Ts have potential to overcome challenges of DNA CAR-Ts No expected need for hospitalization, lymphodepletion,
toxicity management, and monitoring Produces multiple cycles from one apheresis Lower manufacturing costs 1All open-label patients treated with Descartes-08 as of Oct 30, 2023 Cartesian’s mRNA approach is designed to expand the reach of
potent cell therapy products to address potential autoimmune indications mRNA does not replicate predictable half-life with more controllable PK/PD defined by the dose No requirement for cell proliferation no expected need for
pre-treatment chemotherapy no Grade 3-4 cytopenias
Wholly-owned pipeline targets autoimmune disease AAAD, autoantibody-associated
autoimmune diseases SLE, Systemic Lupus Erythematosus mRNA MSC, Mesenchymal Stem Cells transfected with mRNA LN, Lymph node BCMA, B-cell maturation antigen Asset Indications Discovery/Preclinical Phase 1 Phase 2 Pivotal Descartes-08
Autologous mRNA CAR-T Myasthenia Gravis SLE, other AAAD Descartes-15 Autologous mRNA CAR-T AAAD Descartes-33 Allogeneic mRNA MSC AAAD In situ LN transfection Undisclosed 7 Data from Phase 2b study expected in mid-2024 Expect to
initiate Phase 2 studies in SLE and additional autoimmune indications in 2024 Next-gen anti-BCMA mRNA CAR-T with >10x preclinical potency
® THERAPEUTICS 8 Descartes-08 is believed to be the first mRNA CAR-T in
clinical development for autoimmune disease Engineered by transfection of autologous CD8+ T cells with mRNA encoding anti-BCMA CAR Typical lot processed for infusion within ~3 weeks Positive Phase 2a data in myasthenia gravis underscores
potential for deep and durable responses Granted U.S. FDA orphan designation for generalized myasthenia gravis
® THERAPEUTICS Initial indication for Descartes-08: Myasthenia
gravis Affects over 120,000 patients in US and EU Characterized by debilitating weakness: limbs, respiratory, ocular, facial muscles Standard of care includes chronic use of immunosuppressants, which are often toxic: Progressive disease
that is fatal in 1/3 of patients without immunosuppressants Newer agents include complement inhibitors and anti-FcRn mAbs, which must be administered chronically to maintain responses Pathogenesis is similar across many autoimmune
diseases; involves attack on self by both T cells and B/plasma cells 9
Phase 2 study of Descartes-08 in MG (NCT04146051) All doses observed to be safe
and well-tolerated 10 Patient eligibility MG-ADL > 6 MGFA Class II-IV Stable medication dosing > 8 wks prior to infusion 4-week washout for biologics IVIg and plasma exchange not allowed after starting Descartes-08 Patients on
immunosuppression or complement inhibitors expected to be able to continue their treatment while receiving Descartes-08 Cell manufacturing platform tolerates most standard immunosuppressive therapies Part 1 Identify safe dose (n =
3) Complete Part 2 Determine optimal dosing schedule (n = 11) Complete1 Part 3 Phase 2b comparing Descartes-08 to placebo (n = 30) Enrolling 1 Continues to enroll patients with MuSK MG and subjects who are otherwise not eligible for
Part 3 MG-ADL, Myasthenia Gravis Activities of Daily Living scale MGFA, Myasthenia Gravis Foundation of America Six weekly infusions led to observed deep, durable responses Placebo-controlled trial for engineered adoptive cell therapy
® THERAPEUTICS Phase 1/2a study population comprises patients with
significant disease Baseline MG-ADL mean score of 10 79% were MGFA Class III-IV at screening All patients presented with disease that was not controlled with standard of care therapies Volume 22, Issue 7, July 2023, Pages
578-590 11 Mean age, years (SD) 52 (18) Female 10 (71%) Male 4 (29%) Mean weight, kg (SD) 84 (21) Mean BMI, kg/m2 (SD) 31.6 (8.1) Race and ethnicity White, non-Hispanic 11 (79%) White, Hispanic 1 (7%) Asian 2 (14%) MGFA
class at screening II 3 (21%) III 10 (71%) IV 1 (7%) Median age of disease onset, years (range) 40 (14-79) Median duration of disease, years (range) 14 (3-27) Myasthenia gravis antibody status Anti-AChR antibody 11
(79%) Anti-MuSK antibody 2 (14%) Seronegative (for AChR, MuSK, and LRP4 antibodies) 1 (7%) Mean baseline scores (SD) QMG 15.3 (4.1) MG-ADL 10.0 (3.2) MGC 21.9 (5.7) MG-QoL-15r 19.9 (5.8) Previous myasthenia gravis therapies
(standard of care) Pyridostigmine 14 (100%) Prednisone 14 (100%) Other immunosuppressants 14 (100%) Eculizumab 2 (14%) Rituximab 2 (14%) Previous intravenous immunoglobin 12 (86%) Previous plasma exchange 8 (57%) Diagnosis of
thymoma 0 Previous thymectomy 6 (43%) Previous myasthenia gravis crisis requiring intubation 4 (29%) Myasthenia gravis ongoing therapy Pyridostigmine 11 (79%) Prednisone 10 (71%) Azathioprine 1 (7%) Mycophenolate mofetil 1 (7%)
® THERAPEUTICS Descartes-08 was observed to be safe and well-tolerated in
MG KEY OBSERVATIONS: No dose-limiting toxicities No cytokine release syndrome No neurotoxicity No pre-treatment chemotherapy and related cytopenias Outpatient treatment Volume 22, Issue 7, July 2023, Pages 578-590 12 Grade* Part 1
(n=3) Part 2: all groups (n=11) Part 2: group 1 (n=3) Part 2: group 2 (n=7) Part 2: group 3 (n=1) Hand numbness 2 1 (33%) 0 0 0 0 Headache 1 1 (33%) 5 (45%) 1 (33%) 3 (43%) 1 (100%) Muscle soreness 1 1 (33%) 1
(9%) 0 1 (14%) 0 Nausea 1 1 (33%) 4 (36%) 2 (67%) 2 (29%) 0 Rash 3 0 1 (9%) 1 (33%) 0 0 Itchy throat 1 0 2 (18%) 0 1 (14%) 1 (100%) Vomiting 1 0 3 (27%) 2 (67%) 1 (14%) 0 Weakness 1 0 2 (18%) 2
(67%) 0 0 Line infiltration 1 0 1 (9%) 1 (33%) 0 0 Fever 1 0 4 (36%) 1 (33%) 3 (43%) 0 Shortness of breath1 1 0 2 (18%) 1 (33%) 1 (14%) 0 Chills 1 0 2 (18%) 1 (33%) 1 (14%) 0 Diarrhoea 1 0 1 (9%) 1 (33%) 1
(14%) 0 Gum inflammation 1 0 1 (9%) 0 1 (14%) 0 Teeth sensitivity 1 0 1 (9%) 0 1 (14%) 0 Night sweats 1 0 1 (9%) 0 1 (14%) 0 Restless leg 1 0 1 (9%) 0 1 (14%) 0 Light-headedness 1 0 1 (9%) 0 1
(14%) 0 *There were no adverse events of grade 3 or higher reported in part 1, and no grade 2 or grade 4 events reported in part 2, where grade 1 is mild, grade 2 is moderate, grade 3 is severe, and grade 4 is life- threatening. 1Not
associated with hypoxia
® THERAPEUTICS Descartes-08 observed to induce deep and durable
clinical improvement in MG Notable magnitude and duration of response across all 4 standard MG severity scales Responses appear to deepen after completing treatment at Week 6 Positive twelve-month follow-up data from Phase 2a study
reinforce prior findings published in Lancet Neurology 13 Manuscript submitted for peer review; pre-print available at medRxiv.org Efficacy dataset includes all MG patients completing the 6-dose once-weekly regimen (n=7). Data are mean
score improvement (point) and standard error (light blue shading). Note that QOL scale does not have an agreed-upon threshold for clinically meaningful disease improvement; MG-ADL, MGC and QMG scales are validated, quantitated, standardized
instruments of disease severity and have been acceptable endpoints for registration studies.
Retreated patient experienced rapid improvement in clinical scores which was
ongoing at Month 6 of retreatment follow-up with minimal symptom expression 14 Descartes-08 demonstrated durable depletion of autoantibodies and retreatment potential in MG Lasting reductions in autoantibody titers are consistent with the
observed clinical responses and mechanism of action
Informed Consent/Screening (Days -61 to -12) Screening (Days -60 to
-11) Leukapheresis & Cell Processing (Days -59 to -10) Descartes-08 (Day 1, 8, 15, 22, 29, 36) Placebo (Day 1, 8, 15, 22, 29, 36) Follow up visits Day 57 (± 7 days) Day 85* (± 7 days) Day 113 (± 7 days) Month 6 (± 2 weeks) Month
9 (± 2 weeks) Month 12 (± 2 weeks) Descartes-08 (Crossover Day 1, 8, 15, 22, 29, 36) Follow up visits Crossover Day 57 (± 7 days) Crossover Day 85* (± 7 days) Crossover Day 113 (± 7 days) Crossover Month 6 (± 2 weeks) Crossover Month 9
(± 2 weeks) Crossover Month 12 (± 2 weeks) Phase 2b randomized, placebo-controlled, double-masked study of Descartes-08 in MG Enrollment underway, with top-line results expected in mid-2024 Plan to treat ~30 patients PRIMARY
ENDPOINT Proportion of MG Composite responders (≥5-point reduction) at Day 85 SECONDARY OBJECTIVES Safety and tolerability Quantify clinical effect of Descartes-08 over 1 year QMG, MG QoL 15R, MG ADL, and MG PIS (change from baseline to
Day 85) Compare effect of Descartes-08 versus placebo on MG scales (change from baseline to Day 85) in patients who cross over from placebo to Descartes-08 15 Randomization MG QMG, Quantitative MG Scores MG QOL15R, MG Quality of Life
15-revised MG ADL, MG Activities of Daily Living MG PIS, MG Post-intervention Status
Exploring potential of Descartes-08 in Systemic Lupus Erythematosus
(SLE) 16 IND CLEARED PHASE 2 STUDY ON TRACK FOR 1H 2024 Open-label study in up to 30 adults with moderate to severe multi-refractory SLE and no CNS involvement Designed to assess safety, tolerability, and manufacturing feasibility of
Descartes-08 in patients with SLE Secondary objectives include standard measures of clinical activity in SLE: Systemic Lupus Erythematosus Disease Activity Index 2000 (SLEDAI-2K) Physician Global Assessment (PGA) Systemic Lupus
Erythematosus Responder Index (SRI) British Isles Lupus Assessment Group (BILAG)–based Composite Lupus Assessment (BICLA) Screening (Days -60 to -15) Leukapheresis & Cell Processing (Days -59 to -14) 2 - 3 Weeks Descartes-08 (Day 1,
8, 15, 22, 29, 36) Safety/Response Assessment (Day 50) Follow up visits (Months 3, 6, 9, 12)
Exploring additional applications for Descartes-08 in autoantibody- associated
autoimmune diseases (AAAD) 17 Potential significant Descartes-08-associated improvement observed in a patient with autoimmune retinitis (AIR) 61-year-old man with DPPX antibody-positive AIR, colitis, encephalitis refractory to prednisone,
rituximab, bortezomib, IVIg; positive for 5/5 disease-associated autoantibodies pre-treatment Post-treatment: experienced a clinically-significant, 2-line improvement in visual acuity; 3 of 5 autoantibodies became
undetectable Test Pre-treatment Month 2 Month 4 Month 6 Visual acuity 20/60 20/40 20/40 20/40 Carbonic anhydrase II Ab + - - NP* Tubulin Ab + - - NP* PKM2 Ab + - - NP* Aldolase Ab + + + NP* Enolase
Ab + + + NP* *NP – not performed Clinical data suggest that Descartes-08 could lead to clinical benefit along with disappearance of disease-associated autoantibodies, suggesting potential in additional autoimmune indications DPPX, ,
Dipeptidyl-peptidase–like protein 6 IVIg, Intravenous immunoglobulin
RNA Armory® example: Descartes-15, a next generation anti-BCMA mRNA CAR-T with
>10x potency observed in preclinical studies Potent killing (single target exposure) Persistent killing (multiple exposures) (1:2) (1:8) (1:32) 0 50 100 % Specific Killing DC-15 DC-08 Vehicle EP Descartes-15 Descartes-08
Control (1:2) (1:8) (1:32) 0 100 50 % Specific Killing DC-15 DC-08 Vehicle EP Descartes-15 Descartes-08 Control Descartes-15 is an anti-BCMA mRNA CAR-T with potential disruptive features: Engineered for maximum potency and CAR
stability, even in the presence of target-driven suppression of CAR Clinical strategy expected to leverage safety and clinical activity data from Descartes-08 0 Day 0 Day 1 Day 2 Day 5 Day 7 Day 9 1000 2000 MFI DC-15 DC-08 Vehicle
EP Control Superior CAR expression 3000 Descartes-15 Descartes-08 Control Descartes-15 0 2×108 4×108 6×108 8×108 Day 21 Total Flux (p/s) Control Descartes-15 Control Descartes-15 0 1×107 2×107 3×107 Day 11 Total Flux
(p/s) Day 21 Day 11 Efficient killing of BCMA+ target cells1 Day 11 1 MM1-S disseminated myeloma model in NSG mice infused with either control T-cells or Descartes-15 18
® THERAPEUTICS 19 In-house manufacturing enhances control of product
quality, production schedules and costs cGMP Cell Manufacturing ISO14644 certified aseptic facility with dedicated QMS cGMP mRNA Synthesis Clinical grade mRNA production Quality Control Internal assay validation and lot release MSC
Cell Banking Part 1271, FDA- reviewed huMSC collection & banking Process Development Processes optimized through >200 cGMP runs
Platform offers potential development opportunities via three modalities:
autologous, allogeneic and in situ 20 Autologous mRNA CAR-T Descartes-08 Descartes-15: next generation anti- BCMA mRNA CAR-T with >10x potency observed in clinical studies Allogeneic mRNA MSC Descartes-33 rLN: In situ lymph node
transfection Undisclosed program
Maturing pipeline offers potential for multiple catalysts 21 Descartes- 08 in
MG Descartes- 08 in SLE Descartes- 08 Additional Indications Descartes- 15 Expect to report Phase 2b data mid-2024 Plan to initiate Phase 2 in 1H 2024 Plan to initiate basket studies in additional autoimmune indications in 2H
2024 IND cleared, with first-in-human Phase 1 planning activities underway Mid 2024 1H 2024 2H 2024 2024 Funding expected to support development of Descartes-08 through Phase 3 and advance additional programs
® THERAPEUTICS Strong Financial Position Expected to
Support Pipeline Through Key Milestones <50 employees Based in Gaithersburg, MD Anticipated cash runway into 2H 2026 162M common 696M basic** Shares outstanding as of 12/31/23 ~$118M Pro forma cash as of 12/31/23* *Reflects the
anticipated receipt of $40M through two delayed settlement payments previously announced as part of the November 2023 financing, which are expected in January 2024 and February 2024 **Reflects 534,261 shares of Series A Non-Voting
Convertible Preferred stock outstanding, which are convertible into approximately 534.3 million shares of common stock.
® THERAPEUTICS P I O NE E RI NG m RNA CE L L T HE RA P I E S Pipeline
designed to expand the reach of cell therapy to autoimmunity M AT U RI N G PI PEL I NE W I T H EX PE C T E D N EAR - T E R M CAT AL YS T S Validated lead program, Descartes-08, with Phase 2b data expected mid-year CA S H RE S O UR C E S E
X P E C T E D T O F U ND O P E R A T I O NS I NT O 2 H 2 0 2 6 Expected to support Descartes-08 through Phase 3 and advance additional programs ® THERAPEUTICS EX PE R I E N C E D L EAD ER S H I P T EAM Focused on disciplined investment
and creating value for stockholders and patients
