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Pathophysiology Nodes

5
5 shared nodes are defined in this module.
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Cell Types

5
melanocyte CL:0000148 Cell Ontology (CL) Relation: this mechanism module involves this cell type This mechanism module involves melanocyte (CL:0000148). CL:0000148 is a cell type from the Cell Ontology. keratinocyte CL:0000312 Cell Ontology (CL) Relation: this mechanism module involves this cell type This mechanism module involves keratinocyte (CL:0000312). CL:0000312 is a cell type from the Cell Ontology. platelet CL:0000233 Cell Ontology (CL) Relation: this mechanism module involves this cell type This mechanism module involves platelet (CL:0000233). CL:0000233 is a cell type from the Cell Ontology. cytotoxic T cell CL:0000910 Cell Ontology (CL) Relation: this mechanism module involves this cell type This mechanism module involves cytotoxic T cell (CL:0000910). CL:0000910 is a cell type from the Cell Ontology. natural killer cell CL:0000623 Cell Ontology (CL) Relation: this mechanism module involves this cell type This mechanism module involves natural killer cell (CL:0000623). CL:0000623 is a cell type from the Cell Ontology.
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Biological Processes

7
vesicle-mediated transport GO:0016192 ⚠ ABNORMAL Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves abnormal vesicle-mediated transport (GO:0016192). GO:0016192 is a biological process from the Gene Ontology. lysosome organization GO:0007040 ⚠ ABNORMAL Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves abnormal lysosome organization (GO:0007040). GO:0007040 is a biological process from the Gene Ontology. melanosome organization GO:0032438 ⚠ ABNORMAL Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves abnormal melanosome organization (GO:0032438). GO:0032438 is a biological process from the Gene Ontology. melanosome transport GO:0032402 ↓ DECREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves decreased melanosome transport (GO:0032402). GO:0032402 is a biological process from the Gene Ontology. pigmentation GO:0043473 ↓ DECREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves decreased pigmentation (GO:0043473). GO:0043473 is a biological process from the Gene Ontology. platelet dense granule organization GO:0060155 ⚠ ABNORMAL Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves abnormal platelet dense granule organization (GO:0060155). GO:0060155 is a biological process from the Gene Ontology. regulated exocytosis GO:0045055 ↓ DECREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves decreased regulated exocytosis (GO:0045055). GO:0045055 is a biological process from the Gene Ontology.
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Notes

This is a shared mechanism module, not a disease. Disorder-specific substitutions at the trigger node, grouped by which step of the melanosome life cycle the lost component serves: 1. Cargo delivery during biogenesis - the BLOC-1, BLOC-2 and BLOC-3 complexes and adaptor protein complex AP-3 (Hermansky-Pudlak syndrome, HPS1-HPS11). Melanogenic enzymes and structural cargo are not routed into the maturing melanosome, so the organelle forms but is not properly loaded. 2. Organelle size and fission control - LYST (Chediak-Higashi syndrome). The giant inclusion bodies that are the diagnostic hallmark are LROs that have failed to be resolved into normal-sized organelles, and cargo is mis-sorted into them. 3. Peripheral capture and positioning - the RAB27A-melanophilin-myosin Va tripartite complex (Griscelli syndrome types 2, 3 and 1 respectively). The melanosome is built and pigmented normally but is never tethered at the dendrite tip for transfer. Curate the specific step; do not describe all three as "defective melanosome biogenesis", which is true only of the first. **Critical negative boundary: oculocutaneous albinism does NOT conform.** In OCA the lesion is in melanin *synthesis* (TYR, TYRP1, OCA2, SLC45A2) - the melanosome and its trafficking machinery are intact and the organelle is simply empty. Here the opposite holds: pigment is synthesized and retained, so affected melanocytes are *more* densely pigmented than normal while the skin is less so. That inversion, visible on skin histology as melanin-distended melanocytes beside melanin-free keratinocytes, is the single most useful discriminator and the reason this module and the albinism mechanism must not be merged. A disorder whose hypopigmentation comes from absent melanin synthesis does not conform no matter how similar the clinical picture. Distinct from `lysosomal_substrate_accumulation`. That module models the conventional lysosome failing to degrade what it receives; this one models specialized lysosome-*related* organelles failing to be built, sized, or positioned. A conforming entry here has no storage material and no hydrolase deficiency. Not an Xogenesis module: the terminal output is the failure of a normal delivery process, not the formation of a pathological anatomical entity. The Chediak-Higashi giant granule is the one arguable exception - it is a new, pathological structure - but it is an intermediate in this chain rather than its endpoint, and it is a malformed normal organelle rather than a derived new formation, so no anchor stanza is asserted. Conformance requires evidencing a trafficking or biogenesis lesion in the LRO machinery. Hypopigmentation alone, or expression of an LRO gene in melanocytes, is not sufficient. **Attachment points differ, and the difference is informative.** Only the Griscelli route conforms at the central effector, because only there is the melanosome fully built and pigmented and simply never delivered. In Hermansky-Pudlak syndrome the melanosome *is* transferred - it is merely under-loaded, so melanin production itself is reduced - and the entry therefore conforms at the trigger, the melanosome arm and the other-LRO arm but NOT at the delivery node. Chediak-Higashi sits between the two: its giant melanosomes are abnormally distributed and transfer poorly, and its entry attaches at the melanosome arm. Do not "tidy" these into uniform conformance at the central effector; the disagreement is a real statement about where each disorder's pigmentary failure lies, and flattening it would assert something the evidence does not support.
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Used By Disorder Entries

3
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Pathograph

Use the checkboxes to hide or show graph categories. Hover nodes for evidence-backed metadata.
Pathograph: causal mechanism network for Lysosome-Related Organelle Biogenesis and Transport Module Interactive directed graph showing how this shared module's pathophysiology nodes connect.
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Pathophysiology

5
Interrupted Melanosome Maturation or Peripheral Positioning
amplifier
The melanosome fails at one of three steps. Its melanogenic and structural cargo is not routed in, so the organelle is built but not loaded; or its size and fission are uncontrolled, so it enlarges into a giant granule with mis-sorted contents; or it matures normally but is never captured at the dendrite tip, because the RAB27A-melanophilin-myosin Va complex that tethers it to peripheral actin is broken. The three are not interchangeable, and a conforming entry should name which one it has.
melanocyte CL:0000148 Cell Ontology (CL) Relation: this pathophysiological event involves this cell type This pathophysiological event involves melanocyte (CL:0000148). CL:0000148 is a cell type from the Cell Ontology.
melanosome organization GO:0032438 ⚠ ABNORMAL Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves abnormal melanosome organization (GO:0032438). GO:0032438 is a biological process from the Gene Ontology. melanosome transport GO:0032402 ↓ DECREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves decreased melanosome transport (GO:0032402). GO:0032402 is a biological process from the Gene Ontology.
melanosome GO:0042470 Gene Ontology (GO) Relation: this pathophysiological event involves this cellular component This pathophysiological event involves melanosome (GO:0042470). GO:0042470 is a cellular component from the Gene Ontology.
Show evidence (2 references)
PMID:8896560 SUPPORT Human Clinical
"The CHS hallmark is the occurrence of giant inclusion bodies and organelles in a variety of cell types, and protein sorting defects into these organelles."
Documents the size-and-sorting route: LROs that fail to be resolved into normal-sized organelles, with cargo mis-sorted into them.
PMID:14756517 SUPPORT Other
"Once synthesized in the cell body of the epidermal melanocyte, pigmented melanosomes are translocated down the dendrites and captured at the dendritic tips via various cytoskeletal elements. Molecules recently identified that participate in this process consist of Rab27a, myosin-Va and melanophilin."
Documents the peripheral-capture route and names the tripartite complex whose loss defines the Griscelli entry into this module.
Failed Delivery of Functional Melanosomes to Keratinocytes
central effector
Functional, pigment-bearing melanosomes are not transferred from the melanocyte to surrounding keratinocytes. This is the rate-limiting, disorder-agnostic node of the module: all three upstream routes converge here, and conformance should be declared against it. Because skin and hair are almost entirely keratinocyte, visible pigmentation depends on this transfer and not on melanin synthesis alone - which is why the disorders in this module are hypopigmented despite making normal or excess pigment.
melanocyte CL:0000148 Cell Ontology (CL) Relation: this pathophysiological event involves this cell type This pathophysiological event involves melanocyte (CL:0000148). CL:0000148 is a cell type from the Cell Ontology. keratinocyte CL:0000312 Cell Ontology (CL) Relation: this pathophysiological event involves this cell type This pathophysiological event involves keratinocyte (CL:0000312). CL:0000312 is a cell type from the Cell Ontology.
melanosome transport GO:0032402 ↓ DECREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves decreased melanosome transport (GO:0032402). GO:0032402 is a biological process from the Gene Ontology. pigmentation GO:0043473 ↓ DECREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves decreased pigmentation (GO:0043473). GO:0043473 is a biological process from the Gene Ontology.
Show evidence (2 references)
PMID:24662021 SUPPORT Other
"This latter process is absolutely required for visible pigmentation and effective photo-protection because it serves to disperse the pigment in skin and hair."
Establishes that transfer to keratinocytes, not melanin synthesis, is what makes pigmentation visible - the reason this node is the module's rate-limiting step.
PMID:17483661 SUPPORT Human Clinical
"The melanocytes were large and distended with a large volume of melanin (Figure 2). The adjacent keratinocytes were completely devoid of melanin."
Demonstrates this node in patient skin, and demonstrates the inversion that separates the module from albinism: pigment is made and retained rather than absent.
Hypopigmentation with Syndrome-Specific Extracutaneous Disease
consequence
The organ-level endpoint, and the reason these disorders present as syndromes rather than as isolated pigmentary anomalies: hypopigmentation of skin, hair and eye combined with an extracutaneous complication whose identity depends on which other LROs were lost. The pigmentary sign is the diagnostic clue; the extracutaneous arm carries the morbidity and mortality, so recognizing the hypopigmentation is what triggers the surveillance that matters.
pigmentation GO:0043473 ↓ DECREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves decreased pigmentation (GO:0043473). GO:0043473 is a biological process from the Gene Ontology.
Show evidence (2 references)
PMID:33536261 SUPPORT Human Clinical
"Hermansky-Pudlak syndrome (HPS), a rare autosomal recessive disorder characterised by abnormal biogenesis of lysosome-related organelles, manifests with oculocutaneous albinism and excessive bleeding of variable severity."
Documents the paired pigmentary-plus-extracutaneous endpoint and names the LRO biogenesis defect as its cause.
PMID:8896560 SUPPORT Human Clinical
"Chediak-Higashi syndrome (CHS) is a rare, autosomal recessive disorder characterized by hypopigmentation, severe immunologic deficiency with neutropenia and lack of natural killer (NK) cells, a bleeding tendency and neurologic abnormalities. Most patients die in childhood."
Documents the same paired endpoint through a different component, and establishes that the extracutaneous arm rather than the pigmentary one carries the mortality.