The paralogue that covers for LEDGF: HRP-2 carries the only other IBD in the human proteome, substitutes for LEDGF in HIV integration, and the double knockout is embryonic lethal
also called HRP-2 · HDGFL2 · HDGFRP2 · LEDGF paralogue buffering
There is a second human protein with the same grip module as LEDGF. In viral infection it can take over when LEDGF is gone, and mice missing both die before birth while mice missing either one alone survive. A drug against LEDGF alone may simply be covered for.
The same thing, for a scientist
HRP-2 (HDGFL2/HDGFRP2) is the **only cellular protein besides LEDGF/p75 that contains an integrase-binding domain**, and the two are the closest members of the HRP family. Three published results define the buffering problem. In virology, a human somatic cell line with the LEDGF IBD exons deleted still supported residual HIV-1 replication, and that replication ran through **HRP-2's IBD**. In development, Hdgfrp2 knockout mice are normal and fertile and Psip1 knockout mice are perinatally lethal, but **Psip1/Hdgfrp2 double-deficient embryos die at about E13.5 with a ventricular septal defect** - the classic signature of a redundant pair. In leukaemia, HRP-2 interacts with MLL through a conserved interface that is **less menin-dependent** than the MLL-LEDGF interaction; HRP-2 knockout primary cells are still efficiently transformed by MLL-ENL, so HRP-2 is dispensable for transformation, yet HRP-2 depletion reduces colony formation in leukaemic lines **independently of MLL rearrangement**. The net for this beat: the paralogue does not rescue transformation, but it does carry an MLL contact, it does substitute for the IBD in at least one system, and the only existing LEDGF chemistry binds it too.
Three experiments, three different answers
| System | Manipulation | Result | What it says about buffering |
|---|---|---|---|
| HIV replication, human somatic cells 1 | LEDGF IBD exons 11-14 deleted | residual replication, mediated by HRP-2's IBD; LEDGINs still active | HRP-2 substitutes for the LEDGF IBD |
| Mouse development 2 | Hdgfrp2 KO; Psip1 KO; double KO | single Hdgfrp2 KO normal and fertile; double KO lethal at E13.5 with VSD | redundant pair in development |
| MLL-ENL transformation 3 | HRP-2 KO primary murine cells | transformed efficiently | HRP-2 does not substitute for LEDGF in transformation |
| Leukaemic line survival 3 | HRP-2 miRNA knockdown | reduced colony formation, independent of MLL rearrangement | HRP-2 has its own requirement, and it is not KMT2A-selective |
The third and fourth rows are the ones that matter for a drug. HRP-2 will not rescue a LEDGF-directed agent's effect on transformation - but nobody has asked whether it rescues the effect on maintenance, which is the setting the whole beat turns on, and which is the setting where the two proteins' shared MLL interface could matter.
The interface difference, and why it is a design opportunity
The MLL-HRP-2 interface is conserved but 'less dependent on menin than the MLL-LEDGF/p75 interaction' 3. That is a genuine structural distinction and it cuts in a useful direction: menin inhibition should therefore disturb the MLL-HRP-2 contact less than it disturbs the MLL-LEDGF contact. If LEDGF occupancy falls under revumenib, HRP-2 occupancy might not, and HRP-2 would be the residual IBD-mediated tether in a menin-inhibitor-treated cell. Nobody has profiled HRP-2 occupancy under a menin inhibitor, and it is one more antibody in the CUT&RUN panel already proposed in exp-ledgf-occupancy-menin-inhibitor-monotherapy-panel.
What this does to the drug case
- For an IBD ligand: selectivity is the question. The IBD fold is shared, so an IBD ligand is a candidate dual agent by default, and counter-screening against HRP-2's IBD must be part of any programme from the first hit.
- For a PWWP ligand: dual engagement is already a fact, not a risk. The published LEDGF PWWP fragment series binds HRP-2 PWWP as well, because the screen was run on HRP-2 crystals.
- For the safety case: the double knockout is embryonic lethal, so a dual agent's on-target liability is larger than either single-gene phenotype suggests, and both proteins contribute to homologous recombination.
| paralogue | HDGFL2 / HRP-2 / HDGFRP2 |
|---|---|
| unique fact | the only other human protein carrying an IBD |
| single ko hdgfrp2 | normal and fertile |
| single ko psip1 | perinatal lethality |
| double ko | embryonic lethal ~E13.5, ventricular septal defect |
shared domains
[ "PWWP", "IBD" ]
substitutes for ledgf in
[ "HIV-1 integration (residual replication)" ]
does not substitute in
[ "MLL-ENL transformation" ]
untested
[ "maintenance of established KMT2A-rearranged leukaemia", "HRP-2 occupancy under a menin inhibitor" ]
- An LEDGF-selective agent may be buffered by a paralogue that carries the same two domains and the same MLL contact.
- A dual LEDGF/HRP-2 agent removes a pair whose combined loss is embryonic lethal in mice, and both members contribute to homologous recombination.
- HRP-2 depletion impairs leukaemic colony formation regardless of MLL rearrangement, so dual engagement converts a KMT2A-selective hypothesis into a general leukaemia cytotoxic.
- Does HRP-2 buffer LEDGF loss in MAINTENANCE of established KMT2A-rearranged leukaemia? The transformation answer is no; the maintenance answer is unknown and is the one that matters for a drug.
- Does HRP-2 occupancy at fusion target genes survive menin inhibition? Its MLL interface is less menin-dependent, so it may be the residual IBD tether in a treated cell - one extra antibody in an already-proposed CUT&RUN panel.
- Is a LEDGF-IBD-selective ligand achievable against the HRP-2 IBD, or is dual engagement structurally forced? No IBD ligand exists for either protein, so nobody knows.
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
In a human somatic cell line in which the exons encoding the LEDGF/p75 IBD were knocked out, residual HIV-1 replication was predominantly mediated by HRP-2, the only cellular protein besides LEDGF/p75 that contains an IBD, and LEDGINs remained active by blocking the interaction with HRP-2's IBD.
LEDGF/p75-independent HIV-1 replication demonstrates a role for HRP-2 and remains sensitive to inhibition by LEDGINs. · Schrijvers R, De Rijck J, et al. · PLoS Pathog 2012What this evidence cannot show
A virology system. A PubMed correction notice exists for this paper (PMID 32870932) which was not retrieved; the primary record was used and the correction's content is unknown here.
Evidence that argues against this (1)
- Substitution in HIV integration does not imply substitution at the KMT2A IBM, because the two ligands bind the same IBD surface with very different affinities and the KMT2A contact is cooperatively enhanced by menin while the integrase contact is not. Murai MJ et al. 2014
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
Hdgfrp2 knockout mice develop normally and are fertile, Psip1 knockout causes perinatal lethality, and Psip1/Hdgfrp2 double-deficient mice die at approximately embryonic day 13.5 with a ventricular septal defect; among known LEDGF/p75 binding factors only Nova1 was significantly deregulated, and TGF-beta signalling was the only pathway significantly deregulated by the double knockout.
Embryonic Lethality Due to Arrested Cardiac Development in Psip1/Hdgfrp2 Double-Deficient Mice. · Wang H, Shun MC, et al. · PLoS One 2015What this evidence cannot show
Developmental phenotype in mice; the mechanistic attribution to TGF-beta signalling is the authors' speculation from RNA-seq. Open access (PMC4569352). The Psip1 allele removes both p75 and p52.
Evidence that argues against this (1)
- Embryonic redundancy in cardiac morphogenesis says nothing about whether the paralogues are redundant in an adult haematopoietic or leukaemic cell, where their expression ratio and partner availability differ. Van Belle S et al. 2021
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
MLL and HRP-2 interact through a conserved interface that is less menin-dependent than the MLL-LEDGF/p75 interaction; HRP-2 knockout primary murine cells were efficiently transformed by MLL-ENL, so HRP-2 is dispensable for MLL-ENL leukaemogenesis; but HRP-2 depletion in leukaemic cell lines and transformed primary murine cells reduced colony formation independently of MLL rearrangement, and systemic HRP-2 knockout mice showed only an increase in peripheral blood neutrophils.
Unlike Its Paralog LEDGF/p75, HRP-2 Is Dispensable for MLL-R Leukemogenesis but Important for Leukemic Cell Survival. · Van Belle S, El Ashkar S, et al. · Cells 2021What this evidence cannot show
Murine transformation and human cell-line knockdown; the interaction work is co-immunoprecipitation plus NMR with recombinant proteins. Open access (PMC7835958).
Evidence that argues against this (1)
- That HRP-2 depletion impairs colony formation regardless of MLL rearrangement means HRP-2 is not a KMT2A-selective target, so co-engagement by a LEDGF agent imports a non-selective liability rather than a second selective effect. Van Belle S et al. 2021
- E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
HRP-2/HDGFL2 promotes DNA repair by homologous recombination, so the two paralogues overlap in genome-maintenance function as well as in domain architecture.
Hepatoma-derived growth factor-related protein 2 promotes DNA repair by homologous recombination. · Baude A, Aaes TL, et al. · Nucleic Acids Res 2016What this evidence cannot show
Cited for the HRP-2 repair function; the overlap inference is this entry's.
Evidence that argues against this (1)
- Overlapping function does not mean interchangeable function, and the single knockouts' very different phenotypes argue that the two proteins are not simply substitutable in vivo. Wang H et al. 2015
- E5strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
The only published small-molecule chemistry against the LEDGF PWWP domain was developed on HRP-2 PWWP crystals and binds both LEDGF and HRP-2 PWWP domains.
Rational fragment-based design of compounds targeting the PWWP domain of the HRP family. · Vantieghem T, Aslam NA, et al. · Eur J Med Chem 2024What this evidence cannot show
Abstract only; Europe PMC returns no PMCID for this record.
Evidence that argues against this (1)
- Dual engagement could be desirable if HRP-2 buffering is real in the leukaemic setting, so this is only a liability under the assumption that HRP-2 inhibition contributes nothing therapeutically - an assumption the colony-formation data partly contradict. Van Belle S et al. 2021
the paralogue that shares both of this protein's domains
the existing PWWP chemistry binds both paralogues
the knockout experiment that proves both points at once
adds an HRP-2 arm to the proposed panel