Research Directions
EXPLORATORY22 research directions spanning spatial multi-omics, regenerative biology, and computational approaches to SMA. Each direction connects to specific molecular targets, key concepts, and therapeutic modalities.
6
Harvard Cutting Edge
4
Querdenker (Gemini)
6
Unconventional
1
Circuit Biology
1
Drug Repurposing
4
Querdenker Sprint
Harvard Cutting Edge
Spatial Multi-Omics
Slide-seqV2 and MERFISH mapping drug penetration zones and resistant niches in SMA spinal cord tissue.
SMN2SMN_PROTEIN
Concepts: spatial transcriptomics, slide-seq, MERFISH, niche, drug penetration
Harvard Cutting Edge
NMJ-on-a-Chip
Wyss Institute microphysiological systems modeling neuromuscular junction, EV drug delivery, and retrograde muscle→nerve signaling.
NMJ_MATURATIONPLS3
Concepts: organ-on-chip, neuromuscular junction, extracellular vesicle, retrograde signal, microphysiological
Harvard Cutting Edge
Bioelectric Reprogramming
Michael Levin's Vmem manipulation and electroceuticals for activating endogenous regeneration in motor neurons.
ANK3NCALD
Concepts: bioelectric, Vmem, ion channel, electroceutical, satellite cell, Michael Levin
Querdenker (Gemini)
Epigenetic Dimming
dCas9/CRISPRi silencing disease-causing genes without DNA cuts, modeled on FSHD/DUX4 approach for SMN2 upregulation.
DNMT3BSMN2
Concepts: CRISPRi, dCas9, epigenetic, DUX4, chromatin remodeling, methylation
Querdenker (Gemini)
Bear Hibernation / Muscle Preservation
Hibernating bears preserve muscle mass through SUMOylation and protein homeostasis — mechanisms potentially applicable to SMA.
UBA1SPATA18CAST
Concepts: hibernation, torpor, muscle preservation, SUMOylation, protein homeostasis
Harvard Cutting Edge
NDRG1 / Atrofish / Dormancy
Cell dormancy and quiescence as neuroprotection strategy, inspired by zebrafish survivorship and NDRG1 stress response.
LDHASPATA18NCALD
Concepts: NDRG1, dormancy, quiescence, zebrafish, survivorship, stress response
Harvard Cutting Edge
SMA as Multisystem Disease
Lee Rubin (Harvard) — liver/metabolic involvement in SMA suggests combination therapy targeting both neuronal and systemic pathways.
MTOR_PATHWAYLDHASMN_PROTEIN
Concepts: multisystem, liver, metabolic, energy metabolism, fatty acid, systemic
Querdenker (Gemini)
ECM Engineering / Fibrosis Reversal
Targeting extracellular matrix remodeling and fibrosis in SMA muscle, including SULF1/CD44 pathway connections.
SULF1CD44CTNNA1GALNT6
Concepts: extracellular matrix, fibrosis, decellularized, MMP, SULF1, CD44
Querdenker (Gemini)
Cross-Species Regeneration
Axolotl and zebrafish splicing programs for regeneration — identifying silenced regeneration genes in human SMA motor neurons.
PLS3SMN2
Concepts: axolotl, regeneration, splicing program, newt, salamander, zebrafish motor neuron
Harvard Cutting Edge
Dual-Target Molecules
Designing compounds that modify SMN2 splicing AND influence ion channels or anti-fibrotic pathways simultaneously.
SMN2ANK3
Concepts: dual target, bifunctional, multitarget, polypharmacology, SMN2 splicing modifier
Unconventional
RNA Decoy / Sponge Strategy
Sequestering hnRNP A1 via RNA decoys to prevent SMN2 exon 7 skipping — inspired by splicing factor competition models.
SMN2
Concepts: RNA decoy, sponge, hnRNP, splicing factor, decoy oligonucleotide
Unconventional
Mitochondrial Overdrive / PGC-1alpha
Bioenergetic rescue via PGC-1alpha activation and NAD+ supplementation to compensate for SMN-dependent metabolic deficits.
MTOR_PATHWAYLDHA
Concepts: PGC-1alpha, mitochondrial, NAD+, bioenergetic, AMPK, energy metabolism
Unconventional
DUBTACs — Protein Stabilization
Reverse PROTACs: targeted deubiquitination to stabilize SMN protein and prevent degradation.
UBA1SMN_PROTEIN
Concepts: DUBTAC, deubiquitin, PROTAC, ubiquitin, protein stabilization, degradation
Unconventional
Mechanotransduction / Vibration Therapy
Mechanical stimulation activating HSP chaperones for neuroprotection — whole body vibration as adjunct SMA therapy.
PLS3NMJ_MATURATION
Concepts: mechanotransduction, vibration, HSP, chaperone, mechanical stimulation
Unconventional
Engineered Probiotics / Microbiome
Gut-brain axis modulation via engineered probiotics producing butyrate/HDAC inhibitors for systemic SMN upregulation.
SMN2MTOR_PATHWAY
Concepts: probiotic, microbiome, gut-brain, butyrate, HDAC, living therapeutic
Unconventional
Spinal Cord Stimulation in SMA
Epidural spinal cord stimulation targeting proprioceptive circuits to reactivate dormant motor neurons — Capogrosso (Pittsburgh) / Simon (Leipzig) / ESPACE Europe. Sub-motor threshold stimulation activates Ia afferents, re-establishing proprioceptive-motor circuit. Pilot results show 'spectacular' motor improvement after 1 month of 2h/day stimulation.
NMJ_MATURATIONANK3STMN2
Concepts: epidural stimulation, spinal cord stimulation, proprioception, Capogrosso, Ia afferent, H-reflex, motor neuron reactivation, ESPACE consortium, neuromodulation
Circuit Biology
Proprioceptive Circuit Dysfunction
SMA is increasingly recognized as a circuit disease, not just motor neuron death. Mentis lab (Columbia) showed Ia afferent synapse loss on motor neurons precedes motor neuron degeneration. DRG neuron dysfunction, disrupted sensory-motor connectivity, and proprioceptive innervation specificity loss contribute to motor circuit failure. Motor neuron counting varies 0-80% across labs — methodology problems confound disease understanding. Therapeutic window may be larger than thought if circuit rescue happens before cell death.
SMN1SMN2STMN2NMJ_MATURATIONBDNF
Concepts: proprioception, Ia afferent, DRG neuron, sensory-motor circuit, Mentis lab, non-cell-autonomous, circuit disease, motor neuron counting, NMJ vulnerability, glial contribution
Drug Repurposing
Actin-ROCK-Cofilin Pathway / Fasudil
SMN directly interacts with Profilin 1 (PFN1) in motor neurons (PMID 26401655). Pathway: SMN→PFN1→RhoA→ROCK→LIMK→CFL2→actin-cofilin rods→TDP-43 aggregation. ROCK1/2 elevated in SMNΔ7 mice, phospho-cofilin elevated in SMA models + patient fibroblasts. Fasudil (ROCK inhibitor, approved in Japan/China for stroke) crosses BBB, Phase 2 in ALS (NCT03792490). Nobody has tested ROCK inhibitors in SMA — first-in-field opportunity. MDI-117740 (LIMK inhibitor, published 2025) is more specific alternative.
PFN1CFL2ROCK2CORO1CPLS3TARDBP
Concepts: Fasudil, ROCK inhibitor, cofilin phosphorylation, actin-cofilin rods, TDP-43, LIMK, MDI-117740, profilin, SMA-ALS convergence, drug repurposing, BBB penetration
Querdenker Sprint
Accelerated Aging & Senescence in SMA
Do SMA patients on therapy face accelerated cellular aging? Chronic SMN deficiency may activate senescence pathways (p16/p21), SASP, and mitochondrial dysfunction — all hallmarks of aging. Senolytics (dasatinib + quercetin) could reduce senescent cell burden. The mTOR pathway is dysregulated in SMA and is a central aging regulator. As more SMA patients survive into adulthood, understanding long-term cellular effects becomes critical.
MTOR_PATHWAYTP53BCL2CASP3
Concepts: cellular senescence, SASP, senolytics, telomere, mTOR, aging hallmarks, dasatinib, quercetin, mitochondrial dysfunction, proteostasis
Querdenker Sprint
Epigenetic Editing of SMN2
Beyond HDAC inhibitors: permanently alter SMN2 expression via targeted epigenetic editing. dCas9-p300 could activate the SMN2 promoter without DNA cuts. DNA methylation at the SMN2 locus may suppress expression — DNMT inhibitors could reverse this. EZH2 (H3K27me3) and DOT1L (H3K79me2) may regulate SMN2 chromatin state. Non-coding RNAs (lncRNAs, circRNAs) provide additional regulatory layers.
SMN2HDAC_PATHWAYDNMT3B
Concepts: epigenetic editing, dCas9-p300, DNA methylation, DNMT inhibitor, EZH2, H3K27me3, lncRNA, circRNA, chromatin remodeling, 5-azacytidine, permanent SMN2 activation
Querdenker Sprint
Gut-Brain Axis & Microbiome in SMA
The gut microbiome influences neuroinflammation and neurotrophic factor production. SMA is increasingly recognized as a multisystem disease affecting GI tract. Butyrate (microbial metabolite) is a natural HDAC inhibitor that could increase SMN levels. Engineered probiotics could deliver SMN-enhancing compounds locally. SMA mouse models show GI dysfunction — is the microbiome altered?
HDAC_PATHWAYSMN2BDNFIGF1
Concepts: gut-brain axis, microbiome, butyrate, HDAC inhibitor, engineered probiotics, GI dysfunction, neuroinflammation, fecal transplant, short-chain fatty acids
Querdenker Sprint
Necroptosis & Axon Degeneration in SMA
Necroptosis (RIPK1/RIPK3/MLKL pathway) is activated in SMA motor neurons, Schwann cells, and skeletal muscle. Martinez-Espana (SMA Europe 2026) showed 4-AP prevents motoneuron deafferentation via necroptotic mechanisms. SARM1 (axon degeneration master regulator) may cooperate with necroptosis. Necrostatin-1 shows mixed results in SMA mice. RIPK1 inhibitors in Phase 2 for Alzheimer's. SARM1 inhibitors in trials for neuropathy. Combination of necroptosis inhibitor + SMN therapy could address downstream damage.
RIPK1SARM1CASP3TP53BCL2
Concepts: necroptosis, RIPK1, RIPK3, MLKL, SARM1, necrostatin-1, axon degeneration, NAD+ depletion, 4-aminopyridine, deafferentation, combination therapy