Oncofusion

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Proteinmoderate confidence 3 of 5: One strong study, or several smaller consistent ones.Q-scan-hits

CCND3 (cyclin D3) — the scan's rank-4 hit, and the only one of the four with a drug class already in children

also called cyclin D3 · CCND3 · P30281

Cyclin D3 is a protein that pushes a cell from resting into dividing, working with the enzymes CDK4 and CDK6 that existing breast-cancer drugs already block. A computer scan run by this project found leukemia cells carrying the KMT2A fusion need cyclin D3 more than other leukemia cells do, and unlike the other three genes the scan found, there is real published work behind it.

The same thing, for a scientist

CCND3 encodes cyclin D3 (UniProt P30281, 292 aa), the D-type cyclin partner of CDK4/CDK6. It entered this graph through the coordinator's unbiased DepMap scan, ranking 4 of 4,589 genes by KMT2A-rearranged selectivity (difference -0.623; mean Chronos -1.527 in 11 rearranged lines vs -0.904 in 43 other leukemia lines; pan-essentiality -0.348, so not a common essential). The independent literature is unusually supportive for a scan hit: CCND3 is recurrently and **subtype-specifically** mutated in KMT2A-rearranged AML [E2]; CDK6 — not CDK4 — is a direct transcriptional target of KMT2A fusions in both infant ALL [E3] and MLL-AF9 AML [E4]; and CDK4/6 inhibitors produce G1 arrest in KMT2A-rearranged lines [E2][E3]. Two things cut hard against reading this as a clean KMT2A-specific target: CCND3 is reported essential in B-ALL *regardless of driver mutation*, and its anti-apoptotic function appears **independent of CDK4/6 kinase activity**, so a CDK4/6 inhibitor does not phenocopy CCND3 loss [E5]. A palbociclib trial confined to MLL-rearranged acute leukemias completed in 2019 and has posted no results [E6].

What it looks like
loading AF-P30281-F1…
AlphaFold AF-P30281-F1 ↗
colourshape

This is a prediction, not a measurement. No one has seen this protein in this shape. The colours say how much the software trusts itself, and that is worth reading before anything else — the orange stretches are places the model is effectively saying this part has no fixed shape.

very high (90+)confident (70–90)low (50–70)very low (<50)
I have never read one of these pictures before

A protein is one long chain of amino acids that folds up. The ribbon traces that chain from one end to the other; it is not a wire, it is a simplification of where the backbone runs. Drag to rotate, scroll to zoom.

Domains are the stretches of chain that do a particular job, and they are what the coloured blocks above the picture mark out. Click one and the view flies to it. In this project the important question about any domain is usually whether the fusion still has it — the labels say lost where it does not.

Anything in yellow sticks is a bound small molecule, which is usually the drug.

Go deeper
How this gene got into the graph, and what that does and does not license

CCND3 was not found in the literature. It was found by a scan. The coordinator ranked 4,589 protein-coding genes by the difference in mean DepMap Chronos gene effect between 11 Cellosaurus-annotated KMT2A-rearranged leukemia lines and 43 other leukemia lines, with no candidate list. CCND3 came fourth 1.

That licenses exactly one thing: a reason to go and read the literature. It does not establish that CCND3 is a KMT2A-fusion dependency, for reasons the scan's own author recorded — 11 lines, none infant-derived, 24% of the protein-coding genome, and eight of the scan's top twenty are ribosomal or core-machinery genes that scored only because the rearranged panel is more sensitive overall. CCND3 clears that particular filter (pan-essentiality -0.348, far from the -1.4 to -2.6 of the contaminants) but a crude filter is all it is.

What makes CCND3 different from the scan's other three novel hits is that the literature was already there and the scan did not know it. That is the same shape as the scan's rediscovery of ZFP64, and it is the reason this entry exists while the UROS one does not.

The literature: a subtype-specific mutation, and a fusion-driven kinase1 deeper

Two independent lines converge on the D-cyclin/CDK6 axis in KMT2A-rearranged leukemia.

1. CCND3 is recurrently mutated, and the pattern is subtype-specific. Matsuo et al. sequenced pediatric KMT2A-rearranged AML from the Japanese Pediatric Leukemia/Lymphoma Study Group AML-05 study and found novel CCND3 mutations in 5 of 56 pediatric patients (8.9%) and 2 of 30 adults (3.3%). In 105 pediatric t(8;21) AML samples they instead found recurrent CCND1 (n=3, 2.9%) and CCND2 (n=8, 7.6%) mutations and no CCND3 mutations — so the D-type cyclins carry a subtype-specific mutation pattern in AML, and CCND3 is the one that goes with KMT2A rearrangement 2.

2. CDK6, the kinase cyclin D3 activates, is a direct target of the fusion. In infant ALL, CDK6 mRNA is significantly higher in KMT2A-rearranged than wild-type patients (P<0.001); knocking down KMT2A::AFF1 or KMT2A::MLLT1 fusion transcript lowers CDK6; knocking down CDK6 — but not the close homologue CDK4 — inhibits proliferation of the KMT2A::AFF1 line SEM; and KMT2A-rearranged lines are sensitive in vitro to PD0332991 (palbociclib) with a G1 arrest 3. Independently, MLL-AF9-driven AML cells are 'exceptionally reliant' on CDK6 and not CDK4, CDK6 is transcriptionally activated by the mutant MLL protein, and the effect of lowering CDK6 is closely phenocopied by a small-molecule CDK6 inhibitor 4.

So the mechanism is not a story about cyclin D3 as such. It is a story about a fusion-driven CDK6 dependency for which cyclin D3 is the activating partner — and the mutation data say the partner the fusion uses is CCND3 rather than CCND1 or CCND2.

What the mutations are is not established here

Matsuo et al. describe the CCND3 mutations as novel but the paper's body is not open access through PMC or Europe PMC, and this entry was written from the abstract and key-points section only. Whether they are stabilising gain-of-function mutations in the C-terminal degron region (the pattern known for CCND3 in Burkitt lymphoma and for CCND1 in mantle-cell lymphoma), and whether they were functionally characterised, is not established by anything read here and should not be asserted. Anyone building on this must pull the full text.

One detail from the key points is worth recording because it is narrower than the title suggests: the prognostic finding — coexisting mutations shortening relapse-free and overall survival — is reported for pediatric MLL-MLLT3-rearranged patients specifically, not for KMT2A-rearranged AML as a whole 2.

The counter-case, which is strong

CCND3 dependence may be a B-lineage fact, not a fusion fact. Ketzer et al. report that CCND3 is essential for the proliferation and survival of B-ALL independent of the mutational background, that its mRNA exceeds CCND1 and CCND2 in B-ALL, and that FOXO1 is the transcription factor activating it 5. If CCND3 is required by B-ALL generally, then a difference between 11 KMT2A-rearranged lines and 43 mixed leukemia lines — a comparison in which lineage is not controlled — can be produced by lineage composition alone. This graph has already been burned by exactly that confound: ana-depmap-lineage-conditioned exists because a co-dependency claim did not survive lineage conditioning.

The kinase is not the whole target. The same paper reports that CCND3's anti-apoptotic effect is independent of the kinase activity of the CCND3–CDK4/6 complex, that CCND3 contributes to CDK8 transcription, and that increased CCND3 expression is associated with resistance to palbociclib — concluding that downregulating CCND3 may be superior to inhibiting CDK4/6 kinase activity 5. A CDK4/6 inhibitor therefore does not phenocopy the DepMap CCND3 knockout that generated this hit in the first place, and the DepMap number is not evidence for the drug.

The trial that would have settled it reported nothing. AMLSG 23-14 / Palbo-AL-1 (NCT02310243) was a phase Ib/IIa of single-agent palbociclib restricted to acute leukemia with MLL rearrangement, 50 patients planned across 24 German sites, with CDK6 target inhibition as a secondary endpoint. Its recorded completion date is July 2019; its registry status is 'unknown' and no results are posted 6. A negative or uninformative single-agent result that was never written up is the most likely explanation, and it is the single most important missing fact about this target.

Where the clinical evidence actually stands in children

Palbociclib has been given to children with relapsed/refractory ALL. The Children's Oncology Group AINV18P1 phase 1 trial combined palbociclib with standard four-drug re-induction in 12 heavily pretreated children and young adults with B- and T-lymphoblastic leukemia/lymphoma. One dose-limiting haematologic toxicity occurred at the starting dose; the recommended phase 2 dose was 50 mg/m²/day for 21 days; grade 3/4 non-haematologic toxicity was comparable to the chemotherapy platform alone; and five complete responses were seen (2 of 4 T-ALL, 3 of 7 B-ALL) 7.

That establishes deliverability and tolerability of the class in children, which is not nothing. It does not establish activity in KMT2A-rearranged disease: the trial was not selected for fusion status, n=12, and responses in a re-induction combination cannot be attributed to the added agent. Two further pediatric ALL palbociclib studies are on the registry with small or absent yields — NCT03515200 (St. Jude, terminated, n=12) and NCT04996160 (Stanford, completed, n=2).

What this means for the project's central hypothesis

It does not threaten it, and it may quietly support it. CDK6 is a downstream transcriptional output of the fusion, not a component of the fusion complex — the fusion drives CDK6 expression 34. Hitting an output is the strategy that fails when the output is redundant or when the driver simply re-establishes it, which is why this graph separates mechanism-hoxa9-meis1-output-program from the interface targets.

The honest reading is that CCND3/CDK6 is a combination partner hypothesis rather than a competitor to menin inhibition: a proliferative brake on cells that a menin inhibitor is pushing toward differentiation. Nothing read here tested that combination.

Facts and figures
uniprotP30281
gene symbolCCND3
length AA292
alphafold IDAF-P30281-F1
cytoband6p21.1
accession resolutionResolved by fetching https://rest.uniprot.org/uniprotkb/P30281.json on 2026-09-18 and reading back the primary gene name, which is CCND3 with no synonyms listed; UniProtKB ID CCND3_HUMAN; sequence length 292 aa, matching the value stored here. Not resolved by a gene_exact: search, which matches synonyms.
roleD-type cyclin; activating partner of CDK4 and CDK6 in the G1/S transition. Downstream output of the KMT2A fusion via fusion-driven CDK6 transcription, not a component of the fusion complex.
domains noteNo domain coordinates asserted. Cyclin box boundaries were not resolved from a primary source in this cycle, and the graph's rule is that an unverified boundary is left out rather than guessed.
entered graph viaana-depmap-kmt2a-selective-scan (cycle 25), rank 4 of 4,589; no prior entry in this graph
subnuclear localizationNOT MEASURED. Cyclin D3 has no named subnuclear address in any system - no speckle, no nuclear body, no matrix fraction, no chromatin-versus-soluble partition. The closest thing on record is a colocalisation, not a compartment: cyclin D3 colocalises with the transcription factor ATF5 'in the nuclear region' by confocal microscopy [E_q77_loc2], which names a partner rather than a body. UNPUBLISHED rather than not-applicable, and the reason it would be worth having is specific: the same paper reports that cyclin D3 potentiates ATF5 transcription INDEPENDENTLY OF CDK4, and Ketzer et al. report that CCND3's anti-apoptotic function is independent of CDK4/6 kinase activity [E5]. A kinase-independent, chromatin-proximal pool is exactly the thing a subnuclear measurement could resolve, and it is the pool a CDK4/6 inhibitor would not touch.
shown for fusionNO - nobody has looked in any fusion. There is no imaging, fractionation or subnuclear measurement of cyclin D3 in a KMT2A-rearranged cell, an MLL-AF9 mouse or any other fusion system. This is the bare NO in its strict sense and it is uncomfortable here, because CCND3 is the only one of this project's four novel scan hits with a supporting literature and a drug class already in children.
domains
[]
essentiality
{
  "depmap_common_essential": false,
  "chronos_mean_all_lines": -0.3479,
  "chronos_mean_kmt2a_rearranged": -1.5271,
  "chronos_mean_other_leukemia": -0.9041,
  "kmt2a_selectivity_difference": -0.623,
  "scan_rank": 4,
  "scan_n_genes": 4589,
  "scan_percentile": 0.087,
  "empirical_p_vs_scan": 0.00109,
  "n_kmt2a_rearranged_lines": 11,
  "n_other_leukemia_lines": 43,
  "n_all_lines": 1208
}
mutation in kmt2a r
{
  "pediatric_kmt2a_r_aml_pct": 8.9,
  "pediatric_n": 56,
  "adult_kmt2a_r_aml_pct": 3.3,
  "adult_n": 30,
  "t821_aml_ccnd3_mutations": 0,
  "t821_aml_ccnd1_pct": 2.9,
  "t821_aml_ccnd2_pct": 7.6,
  "source_pmid": "30381403",
  "functional_class_of_mutations": "not established here; the paper body was not readable and no gain-of-function claim should be made"
}
druggable partner
{
  "kinase": "CDK6",
  "clinical_inhibitors": [
    "palbociclib",
    "abemaciclib",
    "ribociclib"
  ],
  "note": "CCND3 itself has no ligandable pocket asserted here. The clinical handle is the CDK4/6 ATP site, and one paper argues the CCND3 dependency is partly kinase-independent, in which case the handle does not reach the dependency."
}
localization
{
  "subcellular": "NUCLEUS AND CYTOPLASM - and BOTH rest on ONE paper that is not a localisation study. UniProt P30281 fetched 2026-09-21 carries exactly two locations, 'Nucleus' and 'Cytoplasm', each at ECO:0000269 and each citing the SAME single reference, PubMed:15358120, which is an ATF5 interaction paper [E_q77_loc1][E_q77_loc2]. There is no note, no isoform-scoped statement and no second source. A cleaner, condition-scoped result exists outside the database: influenza A infection triggers REDISTRIBUTION of cyclin D3 from the nucleus to the cytoplasm followed by proteasomal degradation, and the effect is cell-cycle-independent [E_q77_loc3].",
  "subnuclear": "NOT MEASURED. Cyclin D3 has no named subnuclear address in any system - no speckle, no nuclear body, no matrix fraction, no chromatin-versus-soluble partition. The closest thing on record is a colocalisation, not a compartment: cyclin D3 colocalises with the transcription factor ATF5 'in the nuclear region' by confocal microscopy [E_q77_loc2], which names a partner rather than a body. UNPUBLISHED rather than not-applicable, and the reason it would be worth having is specific: the same paper reports that cyclin D3 potentiates ATF5 transcription INDEPENDENTLY OF CDK4, and Ketzer et al. report that CCND3's anti-apoptotic function is independent of CDK4/6 kinase activity [E5]. A kinase-independent, chromatin-proximal pool is exactly the thing a subnuclear measurement could resolve, and it is the pool a CDK4/6 inhibitor would not touch.",
  "how_shown": "in vivo co-immunoprecipitation, in vitro binding and confocal colocalisation with ATF5 [E_q77_loc2]; yeast two-hybrid, GST pull-down, siRNA knockdown and imaging of nucleus-to-cytoplasm redistribution in influenza-infected cells [E_q77_loc3]",
  "systems": "human cultured cells for the ATF5 work; HEK 293T and influenza-infected epithelial cells for the redistribution work. NO haematopoietic system, no B-ALL line, no primary blast and nothing KMT2A-rearranged - which is striking for a protein this entry ranks 4 of 4,589 on KMT2A selectivity.",
  "shown_for_fusion_localisation": "NO - nobody has looked in any fusion. Cyclin D3 has never been imaged or fractionated in a KMT2A-rearranged cell, despite being this project's own scan's rank-4 selectivity hit and despite the mechanism that makes it interesting (CDK6 as a fusion transcriptional target) being a nuclear one.",
  "node": "localization-chromatin-bound-versus-soluble-fraction-kmt2a",
  "the_partition_is_the_unasked_question": "This entry's central unresolved issue is whether the CCND3 dependency is kinase-dependent. Ketzer et al. argue it is not, and propose that down-regulating CCND3 would be superior to inhibiting CDK4/6 kinase activity [E5]. A kinase-independent function implies a pool of cyclin D3 doing something other than activating CDK4/6 at the G1 restriction point - and the only two published hints at what that pool might be are both spatial: a nuclear colocalisation with a transcription factor, and a regulated nucleus-to-cytoplasm redistribution. Nobody has run a fractionation of cyclin D3 in a B-ALL cell, which is a one-week experiment that would tell a CDK4/6 programme whether it is aiming at the right pool."
}
cell type
{
  "evidence_class_key": "concept-expressed-required-maintains-three-evidence-classes",
  "identifier_note": "CCND3 is P30281, 292 aa, primary gene name CCND3 with NO synonyms listed (UniProt, 2026-09-21), which is unusually clean for this tranche. data/symbol-collisions.json was grepped for CCND3 before the first query and has no row; none is proposed. The real hazard here is not the symbol but the PARALOGUES: CCND1 (295 aa) and CCND2 (289 aa) are within 6 residues of CCND3's 292, so the length check gives NO protection across the D-type cyclins, and the subtype-specific mutation pattern this entry records (CCND3 in KMT2A-rearranged AML, CCND1 and CCND2 in t(8;21)) means a paralogue swap inverts the disease association rather than merely naming the wrong protein. Same shape as brief rule 68's RAS family.",
  "expressed_in": {
    "class": 1,
    "summary": "the dominant D-type cyclin in the B lineage: CCND3 mRNA exceeds CCND1 and CCND2 in B-ALL, and FOXO1 is the transcription factor activating it [E5]. So in the lineage this project cares about, the paralogue redundancy that usually protects D-type cyclins is weakest."
  },
  "required_in": {
    "class": 2,
    "claim": "IN MICE, CYCLIN D3 IS UNIQUELY REQUIRED FOR PRE-B CELL DEVELOPMENT - THE CELL COMPARTMENT THIS PROJECT MODELS AS THE ORIGIN OF INFANT t(4;11) B-ALL. A four-way comparison of Ccnd1-/-, Ccnd2-/-, Ccnd3-/- and Ccnd2-/-Ccnd3-/- animals shows the requirement belongs to cyclin D3 alone; Ccnd3 transcription depends on the common gamma-chain, while pre-B-cell-receptor signalling prevents proteasomal degradation of the protein, so cyclin D3 integrates cytokine and pre-BCR signals to expand the pool of pre-B cells that have successfully rearranged the immunoglobulin heavy chain [E_q77_ct1]. Separately, Ccnd3-/- mice fail to expand IMMATURE T LYMPHOCYTES and show greatly reduced susceptibility to T-cell malignancy, and cyclin D3 knockdown inhibits proliferation of human T-ALL derived from immature T cells [E_q77_ct2].",
    "pmids": [
      "16582912",
      "14706337"
    ],
    "system_named_in_the_claim": "murine germline knockouts of the three D-type cyclins in normal lymphopoiesis, plus knockdown in human T-ALL lines - no fusion in any arm",
    "nodes": [
      "cell-type-pre-b",
      "cell-type-early-t-precursor"
    ],
    "why_this_is_the_strongest_cell_type_result_in_the_tranche": "It is a matched four-genotype comparison, it isolates the paralogue, and the cell type it isolates is PRE-B. Almost everything else in this graph's cell-type layer is murine myeloid - brief rule 73 measures 21% myeloid against 18% B-lineage markers in a B-lineage disease. This is B-lineage, and it is specific to the exact paralogue the KMT2A-rearranged AML mutation data independently singles out."
  },
  "the_lineage_confound_this_sharpens": "This entry already states the counter-case: if CCND3 is required by B-ALL regardless of driver [E5], the scan's 11-versus-43 comparison could be reporting lineage rather than fusion. The murine genetics MAKES THAT CONFOUND WORSE, not better: cyclin D3 is required for normal pre-B development in an animal with no leukaemia at all. The defensible reading is that CCND3 is a B-lineage-progenitor requirement that KMT2A-rearranged B-ALL inherits, and that the fusion's own contribution is the CDK6 arm [E3][E4] rather than the cyclin.",
  "context": "murine normal lymphopoiesis and human T-ALL lines; no fusion in any cited arm"
}
cell state
{
  "evidence_class_key": "concept-expressed-required-maintains-three-evidence-classes",
  "maintains_state": {
    "class": 3,
    "states": [
      "cell-state-cell-cycle-g1-cdk6"
    ],
    "claim": "Cyclin D3 maintains the PROLIFERATIVE G1 state of pre-B cells by integrating two signals at the level of protein stability: common-gamma-chain-dependent cytokine signalling drives Ccnd3 TRANSCRIPTION, and pre-B-cell-receptor signalling PREVENTS PROTEASOMAL DEGRADATION of the protein [E_q77_ct1]. That is a checkpoint state, not a generic cell-cycle statement: the pool of cells allowed to expand is the pool that has successfully rearranged the immunoglobulin heavy chain. A second, independent stability switch exists outside the lineage - influenza infection drives cyclin D3 out of the nucleus and into proteasomal degradation, cell-cycle-independently [E_q77_loc3].",
    "pmids": [
      "16582912",
      "28130444"
    ],
    "system_named_in_the_claim": "murine pre-B cells in normal B lymphopoiesis, and influenza-infected human cells for the second stability result - neither involves a fusion"
  },
  "why_the_stability_switch_matters_here": "Both published routes to lowering cyclin D3 are degradation routes, not kinase routes, and this entry's own counter-case says the dependency may be kinase-independent [E5]. Taken together they say a DEGRADER would test the hypothesis that a CDK4/6 inhibitor cannot: if pre-BCR withdrawal and viral infection both act by destabilising the protein, then the cell already has the machinery a degrader would recruit.",
  "confidence": "strong",
  "caveats": "The pre-B result is murine germline knockout in normal lymphopoiesis - no leukaemia, no fusion, and a developmental requirement is not the same as a maintenance requirement in an established blast. The T-cell arm is a different lineage and its human component is knockdown in T-ALL lines. The influenza result is a non-haematopoietic infection model and is included only for the stability mechanism. Three of the four papers behind the murine genetics share the Sicinski laboratory, so the D-type-cyclin knockout series is one group's programme rather than four independent confirmations.",
  "counter_evidence": [
    {
      "note": "The pre-B requirement cuts against the therapeutic reading of this entry's own rank-4 scan hit. If cyclin D3 is UNIQUELY required for normal pre-B development in a wild-type mouse, then a CCND3 degrader or a CCND3-lowering strategy in infant KMT2A::AFF1 B-ALL would be expected to ablate the normal pre-B compartment alongside the leukaemic one - in an infant, in the lineage that is still being built. That is a specific, predictable on-target toxicity that the DepMap selectivity number cannot see, because DepMap contains no normal pre-B cells. It is also the reason the CDK6 arm of this entry [E3][E4] is the more attractive one: CDK6 is the fusion's transcriptional output, and Ccnd3-null mice are viable while the pre-B block is partial.",
      "citation": {
        "title": "A unique function for cyclin D3 in early B cell development.",
        "authors": "Cooper AB, Sawai CM, Sicinska E, Powers SE, Sicinski P, Clark MR, Aifantis I",
        "year": 2006,
        "venue": "Nat Immunol",
        "pmid": "16582912",
        "doi": "10.1038/ni1324",
        "type": "paper"
      }
    }
  ]
}
How this could bite us back
  • CDK4/6 inhibition hits the cell cycle of every proliferating tissue. In infants the growth plate is the concern this graph has already raised for a different agent (risk-revumenib-growth-plate-closure-juvenile-rat), and a chondrocyte is a CDK4/6-driven proliferating cell. No juvenile-animal or pediatric skeletal data for palbociclib were located in this cycle and none is cited here, so this is an unquantified risk, not a documented one.
  • Neutropenia is the dose-limiting toxicity of this class in adults and the one dose-limiting toxicity in the pediatric COG trial was haematologic [E7]. Adding a myelosuppressive agent to re-induction in a disease whose problem is marrow failure is a real cost.
  • Increased CCND3 expression is itself associated with palbociclib resistance [E5]. The cells that most need CCND3 may be the ones least served by inhibiting the kinase it activates.
  • If CCND3's essential function is kinase-independent [E5], then the DepMap knockout that put CCND3 at rank 4 and the drug that would be given to patients are measuring different things, and the entire chain of reasoning from the scan to the clinic breaks at that link.
  • CDK6 is a fusion output, so it is exposed to the same escape route as every other output: a cell that has stopped depending on the fusion, or a lineage-switched clone, need not keep the dependency.
Still open
  1. What happened to AMLSG 23-14 / Palbo-AL-1 (NCT02310243)? It is the only trial ever run in exactly this population with exactly this drug class, it closed in 2019, and it has posted nothing. One email to the Ulm group is worth more than any further analysis in this entry.
  2. Are the CCND3 mutations found in KMT2A-rearranged AML stabilising gain-of-function changes, as the D-cyclin mutations in lymphoma are, or passengers? The paper body was not readable here and the answer changes whether CCND3 is a driver or a bystander.
  3. Does the CCND3 dependency survive lineage conditioning? Re-running the scan's comparison with B-lineage matched controls would separate 'KMT2A-rearranged cells need CCND3' from 'B-ALL cells need CCND3', and this project already has the machinery in ana-depmap-lineage-conditioned.
  4. Is CCND3's requirement in KMT2A-rearranged cells kinase-dependent? A CDK4/6-binding-deficient CCND3 rescue experiment would say whether a CDK4/6 inhibitor can ever reach this dependency, and would decide whether the drug class is worth pursuing at all.
  5. Does a menin inhibitor plus a CDK4/6 inhibitor combine? The mechanistic case is a differentiation agent paired with a proliferative brake, and nothing read here has tested it in a KMT2A-rearranged model.
Every source behind this entry (12)
  1. E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset

    In the coordinator's unbiased scan of 4,589 protein-coding genes, CCND3 ranks 4 by KMT2A-rearranged selectivity (difference -0.623; mean DepMap Chronos gene effect -1.527 across 11 Cellosaurus-annotated KMT2A-rearranged leukemia lines versus -0.904 across 43 other leukemia lines) with a pan-essentiality of -0.348 across 1,208 lines, which places it well outside the pan-essential contaminants that occupy eight of the scan's top twenty places.

    What this evidence cannot show

    This project's own unreviewed computation, not peer reviewed and not independent of ana-depmap-kmt2a-rearranged-specificity (same statistic, same lines). 11 lines, none infant-derived. 24% of the protein-coding genome. The comparison does not condition on lineage, which matters here more than for most hits because the leading counter-hypothesis is that CCND3 dependence is a B-lineage property. Read as the raw results file, not a publication.

    Evidence that argues against this (1)
    • The same scan ranks HOXA9 961 of 4,589, so it cannot see paralogue-buffered dependencies, and eight of its top twenty are ribosomal or core-machinery genes. A rank is a hypothesis, not a result. analysis run by this project 2026
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Novel CCND3 mutations were identified in 5 of 56 pediatric MLL(KMT2A)-rearranged AML patients (8.9%) and 2 of 30 adults (3.3%), while 105 pediatric t(8;21) AML samples carried recurrent CCND1 (2.9%) and CCND2 (7.6%) mutations and no CCND3 mutations, indicating a subtype-specific D-type cyclin mutation pattern; treatment of MLL-rearranged AML cell lines with the CDK4/6 inhibitors abemaciclib and palbociclib blocked G1-to-S cell-cycle progression and impaired proliferation.

    Recurrent CCND3 mutations in MLL-rearranged acute myeloid leukemia · Matsuo H, Yoshida K, Fukumura K, Nakatani K, Noguchi Y, Takasaki S, et al. (Ogawa S, Adachi S, senior authors) · Blood Advances 2:2879-2889 2018
    What this evidence cannot show

    Read as abstract and key-points section only; the body is not retrievable through PMC or Europe PMC and was not read. The mutation frequency rests on 56 pediatric and 30 adult KMT2A-rearranged cases, so 8.9% is 5 patients. Whether the CCND3 mutations are gain-of-function or stabilising, and whether they were functionally characterised, is NOT established by what was read and must not be asserted. The cell lines used for the CDK4/6 inhibitor experiments are not named in the abstract. The prognostic claim in the key points is specific to pediatric MLL-MLLT3-rearranged patients, not to KMT2A-rearranged AML generally. This is AML; the scan's rearranged panel and this project's main interest are mixed lineage.

    Evidence that argues against this (1)
    • A recurrent mutation in 8.9% of cases is a passenger-versus-driver question, not a dependency claim, and a mutation present in 5 of 56 patients cannot explain a dependency seen across 11 cell lines. CCND3 is separately reported to be essential in B-ALL irrespective of driver mutation, which would predict the same DepMap signal with no KMT2A-specific mechanism at all. Ketzer F et al. 2022
  3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    CDK6 is a direct target of the MLL fusion protein in infant ALL: CDK6 mRNA is significantly higher in MLL-rearranged than MLL wild-type infant ALL (P<0.001), siRNA knockdown of MLL-AF4 or MLL-ENL fusion mRNA downregulates CDK6, knockdown of CDK6 but not of the highly homologous CDK4 inhibits proliferation of the MLL-AF4-positive line SEM, and MLL-rearranged leukemia cell lines are sensitive in vitro to the CDK4/6 inhibitor PD0332991 with a remarkable G1 arrest.

    MLL fusion-driven activation of CDK6 potentiates proliferation in MLL-rearranged infant ALL · van der Linden MH, Willekes M, van Roon E, Seslija L, Schneider P, Pieters R, Stam RW · Cell Cycle 13:834-844 2014
    What this evidence cannot show

    Read as abstract only. This is the closest published work to the infant population this project cares about, and it is from the Erasmus/Interfant group. But it is about CDK6, the kinase, not about CCND3, the cyclin — the link from one to the other is the biochemistry of the D-cyclin/CDK6 complex, not an experiment in this paper. Cell-line work plus patient expression; no in vivo or clinical readout. PD0332991 is palbociclib.

    Evidence that argues against this (1)
    • An expression difference plus a knockdown in one cell line is a weaker claim than 'direct target'. Nothing in the abstract read here shows fusion occupancy at the CDK6 locus. Placke T et al. 2014
  4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    AML cells driven by MLL-AF9 are exceptionally reliant on CDK6 but not on its functional homologue CDK4; the preferential growth inhibition from CDK6 depletion is mediated through enhanced myeloid differentiation; CDK6 essentiality extends to cells harbouring alternative MLL fusions and to a mouse MLL-AF9 model; CDK6 is transcriptionally activated by mutant MLL; and the context-dependent effects of lowering CDK6 are closely phenocopied by a small-molecule CDK6 inhibitor then in clinical development.

    Requirement for CDK6 in MLL-rearranged acute myeloid leukemia · Placke T, Faber K, Nonami A, Putwain SL, Salih HR, Heidel FH, Kramer A, Root DE, Barbie DA, Krivtsov AV, Armstrong SA, Hahn WC, Huntly BJ, Sykes SM, Milsom MD, Scholl C, Frohling S · Blood 124:13-23 2014
    What this evidence cannot show

    Read as abstract only. AML, not ALL, and an MLL-AF9 (KMT2A::MLLT3) model rather than the KMT2A::AFF1 biology that dominates infant disease. The CDK4-versus-CDK6 discrimination is the most useful part and is consistent across this and the infant-ALL paper. Again: about CDK6, not about CCND3.

    Evidence that argues against this (1)
    • The mechanism given is differentiation, which is the same mechanism claimed for menin inhibition, DOT1L inhibition and LSD1 inhibition in this disease. When every agent's mechanism is 'induces differentiation', the mechanism is doing little discriminating work, and a differentiation phenotype in a cell line does not predict a clinical response. University of Ulm; Pfizer; National Center for Tumor Diseases et al. 2015
  5. E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    CCND3 is essential for the proliferation and survival of B-ALL independent of the mutational background, its mRNA exceeds that of CCND1 and CCND2, FOXO1 activates its transcription, its anti-apoptotic effect is independent of the kinase activity of the CCND3-CDK4/6 complex, it contributes to CDK8 transcription, and increased CCND3 expression is associated with development of resistance to palbociclib; the authors conclude that downregulating CCND3 might be superior to inhibiting CDK4/6 kinase activity.

    CCND3 is indispensable for the maintenance of B-cell acute lymphoblastic leukemia · Ketzer F, Abdelrasoul H, Vogel M, Marienfeld R, Muschen M, Jumaa H, Wirth T, Ushmorov A · Oncogenesis 11:1 2022
    What this evidence cannot show

    Read as abstract only. This is simultaneously the best support for CCND3 mattering in B-lineage ALL and the strongest argument that the DepMap signal is not KMT2A-specific: 'independent of the mutational background' is exactly the claim that would make a KMT2A-versus-other comparison uninterpretable without lineage conditioning. The kinase-independence claim, if it holds, breaks the inference from a CCND3 CRISPR knockout to a CDK4/6 inhibitor.

    Evidence that argues against this (1)
    • Against 'lineage, not fusion': the subtype-specific mutation pattern is the hardest thing for a pure-lineage explanation to account for. CCND3 mutations occur in KMT2A-rearranged AML — a myeloid disease — while t(8;21) AML from the same study carries CCND1 and CCND2 mutations and no CCND3 mutations. Lineage alone does not predict that. Matsuo H et al. 2018
  6. E6established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.trial_registry

    A phase Ib/IIa trial of single-agent palbociclib restricted to acute leukemia with MLL rearrangement (AMLSG 23-14 / Palbo-AL-1, NCT02310243) planned 50 adult patients across 24 German sites with CDK6 target inhibition as a secondary endpoint, records a completion date of July 2019, carries registry status 'unknown', and has no results posted.

    Phase Ib/IIa Study of Palbociclib in MLL-rearranged Acute Leukemias AMLSG 23-14/Palbo-AL-1 · University of Ulm; Pfizer; National Center for Tumor Diseases, Heidelberg · ClinicalTrials.gov 2015
    What this evidence cannot show

    Registry record read in full via the ClinicalTrials.gov API on 2026-09-18; has_results is false. Absence of posted results is not a published negative result, and no PubMed search run here found a publication reporting this trial. Adults only (age >= 18), single agent, and enrolment against the Simon two-stage design is not reported, so it is not known whether the trial passed its first stage of 21 patients. Treating this as a negative is an inference, and it should be checked with the Ulm group.

    Evidence that argues against this (1)
    • Unreported trials are common for reasons unrelated to efficacy — funding, slow accrual in a rare subtype, investigator turnover. The registry lists 24 sites for a subtype that is roughly 5-10% of adult acute leukemia, so accrual failure is at least as plausible as a negative signal. Raetz EA et al. 2023
  7. E7strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    In the Children's Oncology Group AINV18P1 phase 1 trial, palbociclib combined with standard four-drug re-induction chemotherapy in 12 heavily pretreated children and young adults with relapsed/refractory B- and T-lymphoblastic leukemia and lymphoma produced one dose-limiting haematologic toxicity at the starting dose, a recommended phase 2 dose of 50 mg/m2/day for 21 days, grade 3/4 non-haematologic toxicity comparable to the chemotherapy platform alone, and five complete responses (2 of 4 T-ALL, 3 of 7 B-ALL).

    Palbociclib in combination with chemotherapy in pediatric and young adult patients with relapsed/refractory acute lymphoblastic leukemia and lymphoma: A Children's Oncology Group study (AINV18P1) · Raetz EA, Teachey DT, Minard C, Liu X, Norris RE, Denic KZ, Reid J, Evensen NA, Gore L, Fox E, Loh ML, Weigel BJ, Carroll WL · Pediatric Blood & Cancer 70:e30609 2023
    What this evidence cannot show

    Read as abstract only. n=12, phase 1, no fusion-status selection reported in the abstract, and responses occurred in a combination with four-drug re-induction chemotherapy, so no response can be attributed to palbociclib. No infants. This establishes tolerability and a pediatric dose, nothing about KMT2A-rearranged efficacy.

    Evidence that argues against this (1)
    • Two further pediatric palbociclib ALL trials on the registry did not deliver: NCT03515200 (St. Jude) was terminated after 12 patients and NCT04996160 (Stanford) completed with 2. A class that three separate pediatric groups could not carry past phase 1 has a feasibility problem in this population independent of its biology. St. Jude Children's Research Hospital 2018
  8. E_q77_loc1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database

    Cyclin D3's entire subcellular record in UniProt P30281 (fetched 2026-09-21) is two locations - 'Nucleus' and 'Cytoplasm' - both at ECO:0000269 and both citing the SAME single reference, PubMed:15358120. There is no note, no isoform-scoped statement and no second experimental source for either compartment.

    What this evidence cannot show

    A measurement of the database, reported as such, read from the comment array with evidence attached on 2026-09-21. The ECO:0000269 code is genuine, so this record would pass any experimental-evidence filter - which is the point: a filter cannot see that both compartments of a 292-residue protein rest on one 2004 short communication about an unrelated interaction.

    Evidence that argues against this (1)
    • An experimentally coded record with a single supporting reference is fragile in a way the code does not express. A better-supported and condition-scoped result exists and is NOT in the record: influenza infection redistributes cyclin D3 from nucleus to cytoplasm and then degrades it, cell-cycle-independently. So the annotated cytoplasmic pool may be a regulated state rather than a constitutive compartment, and the database does not say so. Fan Y et al. 2017
  9. E_q77_loc2moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    The single paper UniProt cites for BOTH of cyclin D3's compartments is an interaction study, not a localisation study: Liu et al. 2004 identify ATF5 as a cyclin-D3-specific partner - cyclin D1 and cyclin D2 do not bind it - confirm the interaction by co-IP and in vitro binding, show by CONFOCAL MICROSCOPY that cyclin D3 colocalises with ATF5 in the nuclear region, and show that cyclin D3 potentiates ATF5 transcriptional activity INDEPENDENTLY OF ITS CDK4 PARTNER.

    Cyclin D3 interacts with human activating transcription factor 5 and potentiates its transcription activity. · Liu W, Sun M, Jiang J, Shen X, Sun Q, Liu W, Shen H, Gu J · Biochem Biophys Res Commun 2004
    What this evidence cannot show

    Rule 91 FIRES. The evidence code is correct and there is a microscopy panel in the paper, but the paper's subject is an ATF5 interaction and the localisation is a supporting colocalisation control; it is not the founding observation for cyclin D3's compartments and it is not a quantitative partition. It is also a four-page short communication in BBRC rather than a dedicated cell-biology study. No haematopoietic cells. The reason it is worth reading rather than dismissing is the CDK4-independence of the ATF5 effect, which is the same direction as the kinase-independent anti-apoptotic function this entry records at E5 from an entirely different group.

    Evidence that argues against this (1)
    • Two independent CDK-independent functions for cyclin D3 - transcriptional potentiation of ATF5 here, and anti-apoptosis in B-ALL in Ketzer et al. - are not the same claim and should not be merged. They come from different systems, different decades and different assays, and neither has been reproduced. What they jointly warrant is scepticism that a CDK4/6 ATP-site inhibitor reaches the CCND3 dependency this entry's scan found; they do not jointly establish a mechanism. Ketzer F et al. 2022
  10. E_q77_loc3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper

    Influenza A infection triggers REDISTRIBUTION of cyclin D3 from the NUCLEUS to the CYTOPLASM followed by its proteasomal degradation, and the effect is CELL-CYCLE-INDEPENDENT: knocking down Ccnd3 raises virus titres, and a combined Ccnd3/Rb1 knockdown that restores S-phase progression fails to normalise virus production.

    Cell Cycle-independent Role of Cyclin D3 in Host Restriction of Influenza Virus Infection. · Fan Y, Mok CK, Chan MC, Zhang Y, Nal B, Kien F, Bruzzone R, Sanyal S · J Biol Chem 2017
    What this evidence cannot show

    A virology paper in non-haematopoietic human cells, cited here for one thing only: that cyclin D3's nuclear-versus-cytoplasmic partition is REGULATED and coupled to degradation, rather than being a fixed dual annotation. Nothing about influenza is relevant to this graph. The Rb1 double-knockdown is the control that makes the cell-cycle-independence claim interpretable and is why this is recorded at moderate rather than weak. This paper is not in UniProt's record for P30281.

    Evidence that argues against this (1)
    • Generalising a redistribution seen under viral infection to the resting state of a leukaemic blast is unwarranted, and this entry does not do it. An infected cell is under an interferon programme, and CCND3 has independently been identified as an interferon-stimulated restriction factor, so the redistribution may be part of that programme rather than a general property. The transferable point is narrow: the compartment is regulated by degradation, which is what makes a degrader strategy mechanistically plausible. Liu W et al. 2004
  11. E_q77_ct1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    In MICE, cyclin D3 is UNIQUELY required for pre-B cell development. A matched analysis of Ccnd1-/-, Ccnd2-/-, Ccnd3-/- and Ccnd2-/-Ccnd3-/- animals isolates the requirement to cyclin D3; Ccnd3 transcription depends on the common gamma-chain, while pre-B-cell-receptor expression and downstream signalling PREVENT proteasome-mediated degradation of cyclin D3; the protein thereby integrates cytokine and pre-BCR signals to expand the pool of pre-B cells that have successfully rearranged the immunoglobulin heavy chain.

    A unique function for cyclin D3 in early B cell development. · Cooper AB, Sawai CM, Sicinska E, Powers SE, Sicinski P, Clark MR, Aifantis I · Nat Immunol 2006
    What this evidence cannot show

    Murine germline knockouts in NORMAL lymphopoiesis - no leukaemia and no fusion anywhere in the study. A developmental requirement is not a maintenance requirement in an established blast, and germline loss allows compensation that acute loss would not. The four-genotype design is the strength and it is still one laboratory's mouse series. Brief rule 73: this is murine normal B lymphopoiesis, not human infant KMT2A::AFF1.

    Evidence that argues against this (1)
    • The human leukaemia result points at a broader requirement, which weakens the fusion-specific reading of this entry's scan hit: CCND3 is reported indispensable for B-ALL INDEPENDENT OF MUTATIONAL BACKGROUND, with CCND3 mRNA exceeding CCND1 and CCND2. If the requirement is a property of B-lineage blasts generally, the scan's 11 KMT2A-rearranged versus 43 mixed leukaemia lines is a lineage comparison wearing a fusion label - the confound this graph already owns an analysis about. Ketzer F et al. 2022
  12. E_q77_ct2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    In MICE, cyclin-D3-deficient animals fail to undergo normal expansion of IMMATURE T LYMPHOCYTES and show greatly reduced susceptibility to T-cell malignancies triggered by specific oncogenic pathways; in HUMAN cells, knockdown of cyclin D3 inhibits proliferation of acute lymphoblastic leukaemias derived from immature T lymphocytes.

    Requirement for cyclin D3 in lymphocyte development and T cell leukemias. · Sicinska E, Aifantis I, Le Cam L, Swat W, Borowski C, Yu Q, Ferrando AA, Levin SD, Geng Y, von Boehmer H, Sicinski P · Cancer Cell 2003
    What this evidence cannot show

    The murine arm is germline knockout; the human arm is knockdown in T-ALL lines with no fusion-status annotation. T-lineage, not the index disease - included because it establishes that the cyclin D3 requirement is LYMPHOID-broad rather than B-specific, which is the relevant boundary for reading this entry's scan hit. Same laboratory as the pre-B study.

    Evidence that argues against this (1)
    • Two lymphoid compartments requiring the same cyclin is an argument AGAINST fusion specificity, not for it. Between the pre-B result, the immature-T result and the driver-independent B-ALL result, the simplest account of this entry's rank-4 DepMap selectivity is that lymphoid blasts need cyclin D3 and the comparator arm of the scan is lineage-mixed. The scan's own author recorded the 11-line, non-infant limitation; the lineage composition of the 43 comparator lines is the specific thing that has not been checked. Ketzer F et al. 2022
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