KMT2A-EN1 declined: one spoke-expanded BioID row from an ectopic neural homeobox construct in a kidney cell, and the only screen that ever looked found EN1 unexpressed in AML lines
also called EN1-KMT2A proximity row · engrailed homeobox 1 and KMT2A · IM-28767 EN1 bait KMT2A prey
EN1 is the gene that patterns the midbrain, and it showed up beside KMT2A in a proximity screen done in kidney cells. We are declining it as a partner, because a published screen that deliberately looked for EN1 in leukaemia cell lines found it switched off.
The same thing, for a scientist
**Declined.** EN1 (HGNC:3342, ENSG00000163064, UniProt **Q05925**, 392 aa, 2q14.2) enters this project on a single row - IntAct **IM-28767**, **MI:1314 BioID**, **MI:1060 spoke**, **EN1 bait / KMT2A prey**, MI-score 0.27, HEK293 Flp-In [E1]. Its pair statistic is respectable by the standards of this tail - EN1 recovered 70 preys of 946, ranking 46th of 102, giving **p = 0.123**, second lowest of the eleven KMT2A-TF pairs [E2] - which is exactly why a decline needs a reason beyond the statistic. **The reason is expression.** Nagel et al. screened the EHG homeobox family - **EN1 at 2q14**, GBX2, EN2, GBX1 and HLXB9 - by RT-PCR for dysregulation across AML cell lines with breakpoints at those loci, and report that **"only one EHG-family gene was expressed, HLXB9"** [E3]. **Somebody set out to find EN1 in myeloid leukaemia and did not.** Against that, EN1's HPA imaging call is **nucleoli rim**, its cell-line RNA is cancer-enhanced only in brain (6.7 nTPM) and breast (6.9) lines with no blood entry, and PubMed returns **zero** for EN1 against both KMT2A and MLL [E4][E5].
No three-dimensional model is available for this protein, so the map above is the whole picture. That is itself informative: AlphaFold does not model chains this long, and the parts that have been crystallised are held under the entries for the individual domains.
What the row is
IMEx IM-28767: MI:1314 proximity-dependent biotin identification, MI:1060 spoke expansion, roles MI:0496 bait (EN1) / MI:0498 prey (KMT2A), host taxid:9606(Homo sapiens HEK293flp-in embryonic kidney cell), MI-score 0.27, the deposition-wide floor 1.
The binary pair was never measured. EN1 is a midbrain-hindbrain patterning homeoprotein and the host is an embryonic kidney line, so the construct is ectopic. Nothing about this row is specific to EN1 or to KMT2A, and this beat's own measurement shows KMT2A's 11-of-102 recovery in that panel is 0.9x what its size and abundance predict - KMT2A is not even an unusually recoverable prey there 2.
Why the decline is evidenced rather than assumed
1. A targeted negative exists. The EHG screen is the strongest form of absence this project accepts: not "nobody looked" but "somebody looked with the right assay in the right cells and found nothing". Nagel et al. used RT-PCR across AML cell lines chosen for chromosomal breakpoints at EN1, GBX2, EN2, GBX1 and HLXB9, and only HLXB9 was expressed; their positive result was a t(6;7)(q23;q36) juxtaposing HLXB9 with MYB in GDM-1 3. EN1 was in the panel and was negative.
2. The literature is empty under both operands. EN1[tiab] AND KMT2A[tiab] -> 0; EN1[tiab] AND MLL[tiab] -> 0, both genuine zeros with non-empty translations and a warninglist of No items found. 5.
3. And EN1 is a treacherous search token, which is worth recording. EN1[tiab] AND (leukemia OR leukaemia)[tiab] returns 6 records and all six were read and none is about EN1 in leukaemia: two natural-product cytotoxicity screens against leukaemia cell lines (PMID 34301301, PMID 24252268), a PRDM12 sensory-neuron study where En1 is a marker (PMID 25891934), a Bax-inhibitor-1 embryonic stem cell differentiation paper where En1 is one of seven neuroectodermal markers (PMID 22906541), the EHG screen itself (PMID 15540222), and an EN1 interference-peptide molecular-dynamics paper about breast cancer (PMID 29854286). EN1[tiab] AND (hematopoietic OR haematopoietic)[tiab] returns 1, a skin wound-healing single-cell study in which EN1 labels a myofibroblast subset (PMID 35664010) 5. A three-character symbol plus a common disease word returns a page of false positives, and a beat that counted the 6 without reading them would have recorded a leukaemia literature that does not exist.
4. Localisation does not help it either. HPA's main call is nucleoli rim with nucleoplasm additional, at the Approved tier; UniProt's nucleus call is uncoded. A nucleolar-rim homeoprotein is not obviously in KMT2A's compartment, and neither call is strong 4.
What would reverse this decline
One measurement. If EN1 is expressed in KMT2A-rearranged blasts - infant B-ALL rather than the AML lines Nagel screened - the decline is wrong and EN1 returns to the queue. The EHG screen is 2005, AML-only, cell-line-only, and RT-PCR-based; none of those bounds covers the index disease.
EN1 is also hypermethylated as a cancer biomarker in other tissues (EN1[tiab] AND methylation[tiab] returns 29 records), so a silenced EN1 in a leukaemia would be consistent with the field's general picture and would still mean the proximity row describes nothing. The discriminating experiment is expression in the index disease, not methylation status.
This entry is filed in the style of the existing interface-kmt2a-*-declined-* family - ABT1, ANOS1, FGFBP1, IRF2, KRR1, OASL, PRKRA, TMCO1 - so that the next gap list, which cannot see an interface-* node under a gene-* lookup, finds the decision when it greps the symbol.
| partner a | gene-kmt2a |
|---|---|
| partner b | EN1 (no entry - declined, this node is the record) |
| verdict | DECLINED |
| verdict basis | a targeted AML cell-line expression screen that included EN1 found it unexpressed (PMID 15540222), plus an unsettled localisation and an empty literature under both KMT2A and MLL operands - NOT the interaction statistic, which ranks second of eleven |
| hgnc ID | HGNC:3342 |
| symbol | EN1 |
| ensembl gene ID | ENSG00000163064 |
| uniprot | Q05925 |
| length AA | 392 |
| chromosomal location | 2q14.2 |
| entrez ID | 2019 |
| identifier provenance | HGNC REST fetch/symbol/EN1 and UniProtKB Q05925 retrieved live 2026-09-23; Ensembl id taken from the HGNC record. HGNC lists no previous symbol and no alias symbol, so the name list is complete at one name. |
| subnuclear location hpa | Nucleoli rim (MAIN) with nucleoplasm additional, reliability Approved |
| cell type of the observation | HEK293 Flp-In embryonic kidney - a midbrain-hindbrain patterning factor in a kidney line |
| expression evidence against | RT-PCR screen of the EHG homeobox family across AML cell lines with breakpoints at those loci: only HLXB9 was expressed; EN1 was in the panel and was negative (PMID 15540222) |
| epigenetic role | None as a writer, eraser or reader. EN1 is a homeodomain transcription factor; the epigenetics adjacent to it is that its own promoter is hypermethylated as a biomarker in several solid tumours (EN1[tiab] AND methylation[tiab] -> 29 records), which was not pursued here. |
| shown for fusion | NO - nobody has looked in any fusion, and the one screen that looked for EN1 in AML found it unexpressed. |
| what would reverse this | a measurement of EN1 expression in KMT2A-rearranged blasts, particularly infant B-ALL - the EHG screen is 2005, AML-only, cell-line-only and RT-PCR-based, and none of those bounds covers the index disease |
| filed this way because | a gap list matching own_entry against gene-* and protein-* ids cannot see an interface-*-declined-* node; this beat measured that failure at 2 of 22 partners in its own class, so the decision is filed where a symbol grep will find it |
prev and alias symbols
[]
domains
[
{
"name": "Homeobox (DNA binding)",
"start": 303,
"end": 362
}
]the row
{
"core_protein": "KMT2A",
"core_uniprot": "Q03164",
"partner_experimental_role": "bait",
"core_experimental_role": "prey",
"method": "MI:1314 proximity-dependent biotin identification",
"expansion": "MI:1060 spoke",
"mi_score": 0.27,
"imex": "IM-28767",
"pmid": "35140242",
"host_cell": "HEK293 Flp-In embryonic kidney",
"n_rows": 1,
"n_publications": 1
}adjudication
{
"p_pair_both_margins_held": 0.123,
"rank_among_the_eleven_kmt2a_tf_baits": 2,
"bait_preys_recovered": 70,
"prey_baits_recovering_it": 11,
"of_panel": 102,
"note": "THE STATISTIC DOES NOT SUPPORT THIS DECLINE and the entry says so. Biology overrides the ranking because the ranking is largely an ordering of bait width.",
"source": "analyses/interactome-tail-size-and-abundance-adjudication/pair_null.json"
}subcellular location uniprot
[ "Nucleus (NO evidence code - uncoded annotation)" ]
bounded absence
{
"queries": [
"EN1[tiab] AND KMT2A[tiab] -> 0",
"EN1[tiab] AND MLL[tiab] -> 0",
"EN1[tiab] AND (leukemia[tiab] OR leukaemia[tiab]) -> 6, ALL SIX READ, ALL SIX OFF-TOPIC",
"EN1[tiab] AND (hematopoietic[tiab] OR haematopoietic[tiab]) -> 1, a skin wound-healing study"
],
"querytranslations": [
"\"EN1\"[Title/Abstract] AND \"KMT2A\"[Title/Abstract]",
"\"EN1\"[Title/Abstract] AND \"MLL\"[Title/Abstract]"
],
"false_positive_pmids_read_and_rejected": [
"34301301",
"24252268",
"25891934",
"22906541",
"29854286",
"35664010"
],
"bound": "titles and abstracts only; supporting figures not searched"
}- EN1 interference peptides already exist and produce apoptosis selectively in EN1-overexpressing basal-like breast tumour cells. A tool compound with a published selectivity story is exactly the situation in which a weak proximity row gets cited as a rationale for a misdirected experiment, and this entry exists to make that hard.
- If a future beat reverses this decline on the basis of the p = 0.123 ranking rather than on new expression data, it will be reversing a biology-based call with a statistic that this beat's own analysis shows is mostly a measure of how much the bait labelled.
- Is EN1 expressed in KMT2A::AFF1 infant B-ALL? This is the one measurement that would reverse the decline, and the negative on record covers AML cell lines in 2005 rather than the index disease.
- Should EN1 have a row in data/symbol-collisions.json? Six of six leukaemia hits for a three-character symbol are false positives, and the registry exists for exactly this. Reported rather than edited, since that file belongs to another beat.
- The EHG screen found HLXB9 activated by juxtaposition with MYB in an AML-M4 line. HLXB9 (MNX1) is itself a recurrent partner in paediatric AML through t(7;12), which this graph does not carry. Is the EHG family worth a systematic look that EN1 does not individually deserve?
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
IntAct serves one curated human EN1-KMT2A row: PSI-MI MI:1314 proximity-dependent biotin identification, MI:1060 spoke expansion, EN1 experimental role MI:0496 bait and KMT2A MI:0498 prey, MI-score 0.27, host taxid:9606 Homo sapiens HEK293flp-in embryonic kidney cell, IMEx IM-28767, publication PMID 35140242; EN1 is one of eleven transcription-factor baits in that deposition whose BioID neighbourhood contained KMT2A.
Human transcription factor protein interaction networks. · Göös H, Kinnunen M, Salokas K, Tan Z, Liu X, Yadav L, Zhang Q, Wei GH, Varjosalo M · Nat Commun 2022What this evidence cannot show
Abstract read; full text and supplementary tables not read. The row-level fields were retrieved live from IntAct PSICQUIC MITAB 2.7 on 2026-09-23 (8,331 rows fetched, endpoint-declared count 8,331). Rule 93: PSICQUIC is a floor relative to IntAct REST and a REST query on Q05925/Q03164 was not run. Spoke expansion means the binary pair was never measured. EN1 is a neural patterning factor and the host is an embryonic kidney line.
Evidence that argues against this (1)
- A single spoke-expanded proximity row from an ectopic construct is the weakest evidence class this graph records, and declining it does not require any of the additional arguments below - they are offered because a decline should be checkable. source 2026
- E2moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
In IM-28767's BioID arm EN1 recovered 70 of 946 human preys, ranking 46th of 102 baits by reach against a panel median of 58.5; under a null holding both margins EN1 recovering KMT2A has p = 0.123, second lowest of the eleven KMT2A-TF pairs, which is NOT RESOLVED under the pre-registered thresholds; separately, KMT2A's 11-of-102 recovery in that panel is 0.9 times what a negative-binomial model of length and abundance predicts (p = 0.42).
What this evidence cannot show
20,000 draws, seed 20260923. Bonferroni over the 62 pairs tested is 0.0008 and nothing survives it. NOTE THAT THE STATISTIC DOES NOT SUPPORT THIS DECLINE - p = 0.123 is the second best of the eleven. The decline rests on expression and localisation, and this entry says so rather than implying the numbers agreed.
Evidence that argues against this (1)
- Declining a pair whose interaction statistic ranks second of eleven is a decision to let biology override the ranking. If the ranking is the better instrument, this decline is wrong - and the beat's own analysis says the ranking is largely an ordering of bait width, which is the argument for overriding it. source 2026
- E3moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
Nagel et al. screened members of the EHG family of homeobox genes - EN1 at 2q14, GBX2 at 2q36, and EN2, GBX1 and HLXB9 at 7q36 - by RT-PCR for dysregulation in acute myeloid leukaemia cell lines indicated by chromosomal breakpoints at these sites, and report that only one EHG-family gene was expressed, HLXB9, in the AML-M4 line GDM-1, where a t(6;7)(q23;q36) juxtaposes HLXB9 with regions upstream of MYB.
Activation of HLXB9 by juxtaposition with MYB via formation of t(6;7)(q23;q36) in an AML-M4 cell line (GDM-1). · Nagel S, Kaufmann M, Scherr M, Drexler HG, MacLeod RAF · Genes Chromosomes Cancer 2005What this evidence cannot show
Abstract read; full text not read. THE BOUNDS MATTER AND ARE NARROW: this is 2005, AML only, cell lines only, RT-PCR only, and the lines were selected for breakpoints at these loci rather than as a representative panel. The abstract does not say how many lines were screened or whether any was KMT2A-rearranged. It does NOT test infant B-ALL, which is this project's index disease.
Evidence that argues against this (1)
- An expression screen in a selected AML cell-line panel twenty years ago cannot exclude EN1 expression in KMT2A::AFF1 infant B-ALL, a different lineage and a different disease. This is the strongest negative available and it is still an indirect one. source 2005
- E4moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
UniProt Q05925 is 392 aa with a homeobox DNA-binding domain at residues 303-362 and assigns subcellular location Nucleus with no evidence code; the Human Protein Atlas assigns EN1 a main subcellular location of nucleoli rim with nucleoplasm additional at the Approved reliability tier, and records its cell-line RNA as cancer enhanced with 6.7 nTPM in brain cancer and 6.9 in breast cancer lines and no blood entry.
What this evidence cannot show
The UniProt nucleus call is UNCODED and is therefore a curator assertion, not a measurement. HPA 'Approved' is the lowest usable reliability tier. The nTPM values are HPA's enriched-line summary field, not a full per-line table - the per-cell-line download no longer exists, which is recorded in this beat's parent analysis.
Evidence that argues against this (1)
- A nucleoli-rim call is unusual and could be antibody behaviour rather than biology, so it should not be used as an argument that EN1 is in the wrong compartment either. What the localisation data genuinely support is that EN1's compartment is unsettled, which is a reason to rest the decline on expression instead. source 2026
- E5established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
PubMed returns zero records for EN1 AND KMT2A in titles and abstracts and zero for EN1 AND MLL; EN1 AND (leukemia OR leukaemia) returns 6 records, all six of which were read and none of which concerns EN1 in leukaemia; EN1 AND (hematopoietic OR haematopoietic) returns 1, a skin wound-healing single-cell study in which EN1 labels a myofibroblast subset.
What this evidence cannot show
Both zeros carry a non-empty querytranslation and a warninglist reading 'No items found.'. HGNC lists no previous symbol and no alias for EN1, so the name list is complete at one name - but EN1 is a THREE-CHARACTER TOKEN and the six leukaemia hits are all false positives (two natural-product cytotoxicity screens against leukaemia lines, a PRDM12 sensory-neuron paper, a Bax-inhibitor-1 stem-cell differentiation paper, the EHG screen, and a breast-cancer interference-peptide simulation). Bounded by titles and abstracts only.
Evidence that argues against this (1)
- Six of six hits being off-topic is a demonstration that a short symbol plus a common disease word produces a literature that is not there. A beat that reported '6 records link EN1 to leukaemia' would have been wrong six times, and this is the same failure this project's symbol-collision registry exists to catch. source 2026
- related to →KMT2A / MLL1 — the gene that breaks
declined: one spoke-expanded BioID row from an ectopic neural homeobox construct in a kidney cell
EN1 is one of the eleven TF baits recovering KMT2A in IM-28767; this node records its adjudication
declined on biology AGAINST its own ranking (p = 0.123, second of eleven) - a case where the pair statistic and the evidence disagree