Kodai Kume
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Previous Organizations / Institutes
The organizations / institutes from the scholar's other articles in the past ten years
Kodai Kume has a total of 220 co-authors. Here are the top co-authors by number of shared publications:
- Hideshi Kawakami
Department of Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
17 shared publications Masaki Kamada
Kagawa University Faculty of Medicine
12 shared publicationsKazuyo Ikeda
Department of Neurology, Kagawa University Hospital, Japan
10 shared publicationsTsutomu Masaki
Department of Gastroenterology, Kagawa University Faculty of Medicine, 1750-1 Ikenobe, Miki, Kita, Kagawa, 761-0793, Japan
10 shared publicationsTadayuki Takata
Department of Supportive and Promotive Medicine of the Municipal Hospital, Faculty of Medicine, Kagawa University, Miki, Japan
9 shared publications- Takashi Kurashige
Department of Molecular Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University , Hiroshima, 734-8553
9 shared publications
Latest Publications
- Open Access
- 25 May 2026
- Published by Journal of Neurosurgery Publishing Group (JNSPG) in Journal of Neurosurgery: Case Lessons
- Vol. 11 (21)
Aplastic or twig-like middle cerebral artery with the RNF213 variant: illustrative cases
BACKGROUND: Aplastic or twig-like middle cerebral artery (Ap/T-MCA) is a rare cerebrovascular anomaly characterized by unilateral stenosis of the proximal middle cerebral artery (MCA) with a plexiform arterial network along the horizontal (M1) segment, requiring distinction from moyamoya disease. Genetically confirmed cases remain rare. OBSERVATIONS: We report the cases of 3 patients with Ap/T-MCA carrying the RNF213 (ring finger protein 213) variant. The first patient, a man in his 60s, presented with subarachnoid hemorrhage. The second patient, a woman in her 20s, developed involuntary movement of the left upper limb. The third patient, the older sister of the second patient, experienced transient left hemiparesis in her 40s. In all patients, MR angiography demonstrated unilateral MCA abnormalities, and digital subtraction angiography revealed M1 stenosis with a plexiform arterial network in the subarachnoid space. All patients were managed conservatively, and targeted sequencing confirmed the RNF213 p.R4810K variant in each case. Only 2 Ap/T-MCA patients with this variant have been previously reported. LESSONS: The presence of the RNF213 p.R4810K variant in all 3 patients supports a relationship between twig-like MCA and the RNF213 variant. These findings suggest that Ap/T-MCA may represent the RNF213 -related vasculopathy spectrum, and the occurrence in two sisters indicates a hereditary predisposition. https://thejns.org/doi/10.3171/CASE26186
- 25 May 2026
- Published by Journal of Neurosurgery Publishing Group (JNSPG) in Journal of Neurosurgery: Case Lessons
- Vol. 11 (21)
Open AccessAplastic or twig-like middle cerebral artery with the RNF213 variant: illustrative cases
BACKGROUND: Aplastic or twig-like middle cerebral artery (Ap/T-MCA) is a rare cerebrovascular anomaly characterized by unilateral stenosis of the proximal middle cerebral artery (MCA) with a plexiform arterial network along the horizontal (M1) segment, requiring distinction from moyamoya disease. Genetically confirmed cases remain rare. OBSERVATIONS: We report the cases of 3 patients with Ap/T-MCA carrying the RNF213 (ring finger protein 213) variant. The first patient, a man in his 60s, presented with subarachnoid hemorrhage. The second patient, a woman in her 20s, developed involuntary movement of the left upper limb. The third patient, the older sister of the second patient, experienced transient left hemiparesis in her 40s. In all patients, MR angiography demonstrated unilateral MCA abnormalities, and digital subtraction angiography revealed M1 stenosis with a plexiform arterial network in the subarachnoid space. All patients were managed conservatively, and targeted sequencing confirmed the RNF213 p.R4810K variant in each case. Only 2 Ap/T-MCA patients with this variant have been previously reported. LESSONS: The presence of the RNF213 p.R4810K variant in all 3 patients supports a relationship between twig-like MCA and the RNF213 variant. These findings suggest that Ap/T-MCA may represent the RNF213 -related vasculopathy spectrum, and the occurrence in two sisters indicates a hereditary predisposition. https://thejns.org/doi/10.3171/CASE26186
- Open Access
- 12 September 2025
- Published by Springer Nature in Journal of Human Genetics
- Vol. 71 (1) , 35-39
Whole exome sequencing in Japanese spinocerebellar ataxia identifies novel variants
Spinocerebellar degeneration (SCD) is a clinically and genetically diverse group, and the dominant form of SCD (AD-SCD) is generally referred to as spinocerebellar ataxia (SCA) that primarily affects the cerebellum. Some patients do not have a definitive genetic diagnosis but may carry unknown variants of known causative genes. Here, we screened for known SCA-associated genes in patients with suspected SCA. We examined 174 patients with SCA lacking abnormal repeat expansion of known causative genes. Whole-exome sequencing (WES) was performed to screen for variants in SCA-associated genes. The identified variants were confirmed by Sanger sequencing, and their pathogenicity was determined using five web-based algorithms. WES revealed novel single-nucleotide variants (SNVs) in three genes, ELOVL4 , ELOVL5 , and GRM1 . Patients presented with symptoms other than cerebellar symptoms. One patient with an ELOVL4 variant exhibited skin changes, a typical symptom of ELOVL4 SCA, whereas the other ELOVL4 SCA patient had no skin changes and exhibited mild parkinsonism and calcification in the globus pallidus and dentate nucleus. The patient with an ELOVL5 variant exhibited bladder and rectal disturbances. Finally, patients with GRM1 variants showed few common features beyond the cerebellar symptoms. One patient showed white matter lesions, cognitive decline, and no-no head tremors, whereas the other showed spasticity. The identification of novel SNVs in these known SCA-associated genes will expand our understanding of the genetic landscape of SCA and facilitate the diagnosis of previously undiagnosed patients.
- 12 September 2025
- Published by Springer Nature in Journal of Human Genetics
- Vol. 71 (1) , 35-39
Open AccessWhole exome sequencing in Japanese spinocerebellar ataxia identifies novel variants
Spinocerebellar degeneration (SCD) is a clinically and genetically diverse group, and the dominant form of SCD (AD-SCD) is generally referred to as spinocerebellar ataxia (SCA) that primarily affects the cerebellum. Some patients do not have a definitive genetic diagnosis but may carry unknown variants of known causative genes. Here, we screened for known SCA-associated genes in patients with suspected SCA. We examined 174 patients with SCA lacking abnormal repeat expansion of known causative genes. Whole-exome sequencing (WES) was performed to screen for variants in SCA-associated genes. The identified variants were confirmed by Sanger sequencing, and their pathogenicity was determined using five web-based algorithms. WES revealed novel single-nucleotide variants (SNVs) in three genes, ELOVL4 , ELOVL5 , and GRM1 . Patients presented with symptoms other than cerebellar symptoms. One patient with an ELOVL4 variant exhibited skin changes, a typical symptom of ELOVL4 SCA, whereas the other ELOVL4 SCA patient had no skin changes and exhibited mild parkinsonism and calcification in the globus pallidus and dentate nucleus. The patient with an ELOVL5 variant exhibited bladder and rectal disturbances. Finally, patients with GRM1 variants showed few common features beyond the cerebellar symptoms. One patient showed white matter lesions, cognitive decline, and no-no head tremors, whereas the other showed spasticity. The identification of novel SNVs in these known SCA-associated genes will expand our understanding of the genetic landscape of SCA and facilitate the diagnosis of previously undiagnosed patients.
- Open Access
AGG Repeat Expansion and Aggregation of BIN1 in Multiple System Atrophy
Multiple system atrophy (MSA) is a fatal, sporadic α-synucleinopathy characterized by glial cytoplasmic inclusions (GCIs) in oligodendrocytes. No causative gene for MSA has been identified to date. Herein, we report an intronic AGG repeat expansion in BIN1 , a major susceptibility gene for Alzheimer’s disease, in a familial MSA case and 13% of autopsy-confirmed sporadic cases. In one case, the expansion was detected only in the cerebellum, implicating somatic mosaicism in disease pathogenesis. The BIN1 protein aggregate localized to GCIs and associated with α-synuclein fibrils. Notably, BIN1 was absent from Lewy bodies, highlighting a potential MSA-specific role. Our findings indicate a novel somatically unstable repeat expansion contributing to MSA and support the notion that BIN1 aggregation plays a central role in disease-specific protein pathology. One-Sentence Summary: Repeat expansion and accumulation of BIN1 play an important role in the pathogenesis of multiple system atrophy.
Open AccessAGG Repeat Expansion and Aggregation of BIN1 in Multiple System Atrophy
Multiple system atrophy (MSA) is a fatal, sporadic α-synucleinopathy characterized by glial cytoplasmic inclusions (GCIs) in oligodendrocytes. No causative gene for MSA has been identified to date. Herein, we report an intronic AGG repeat expansion in BIN1 , a major susceptibility gene for Alzheimer’s disease, in a familial MSA case and 13% of autopsy-confirmed sporadic cases. In one case, the expansion was detected only in the cerebellum, implicating somatic mosaicism in disease pathogenesis. The BIN1 protein aggregate localized to GCIs and associated with α-synuclein fibrils. Notably, BIN1 was absent from Lewy bodies, highlighting a potential MSA-specific role. Our findings indicate a novel somatically unstable repeat expansion contributing to MSA and support the notion that BIN1 aggregation plays a central role in disease-specific protein pathology. One-Sentence Summary: Repeat expansion and accumulation of BIN1 play an important role in the pathogenesis of multiple system atrophy.
- Open Access
An R83W mutation in Rab3A causes autosomal-dominant cerebellar ataxia
Spinocerebellar ataxias (SCAs) are a group of progressive neurodegenerative disorders caused by pathogenic variants in more than 40 genes with diverse cellular functions. In this study, we identified the c.247C>T p.(Arg83Trp) variant in RAB3A , encoding a small GTPase involved in membrane-associated regulated exocytosis, in two families with cerebellar ataxia. Affected individuals presented with adult-onset, gradually progressive cerebellar symptoms, often accompanied by mild gait spasticity and tremors. Variable features of neurodevelopmental disorders were also observed. Brain MRI consistently revealed cerebellar atrophy, often accentuated in the vermis, and neuropathological examinations demonstrated diffuse cerebellar cortical degeneration. Functionally, the R83W mutation lies within the conserved switch II region of Rab3A, a domain critical for effector interaction. Although the mutant Rab3A R83W retained GTP-binding affinity, it failed to bind the key effector proteins RIM1 and Rabphilin-3A, highlighting the functional importance of R83 in effector complex formation, as supported by structural analysis. In PC12 cells, the R83W mutant exhibited diffuse cytoplasmic localization, in contrast to the vesicle- and neurite-tip localization of the wild-type and GTP-bound Rab3A mutant. The concordant localization pattern of R83W and GDP-bound Rab3A mutants suggests that R83W-induced mislocalization results from a failure to engage downstream effector proteins. In frozen sections of the mouse cerebellum, Rab3A was predominantly localized to parallel fiber terminals and was absent from postsynaptic Purkinje cells. These findings suggest that disruption of the interaction between Rab3A and its effector proteins may underlie disease pathogenesis, possibly involving presynaptic dysfunction at parallel fiber–Purkinje cell synapses mediated by the Rab3A–RIM1 complex.
Open AccessAn R83W mutation in Rab3A causes autosomal-dominant cerebellar ataxia
Spinocerebellar ataxias (SCAs) are a group of progressive neurodegenerative disorders caused by pathogenic variants in more than 40 genes with diverse cellular functions. In this study, we identified the c.247C>T p.(Arg83Trp) variant in RAB3A , encoding a small GTPase involved in membrane-associated regulated exocytosis, in two families with cerebellar ataxia. Affected individuals presented with adult-onset, gradually progressive cerebellar symptoms, often accompanied by mild gait spasticity and tremors. Variable features of neurodevelopmental disorders were also observed. Brain MRI consistently revealed cerebellar atrophy, often accentuated in the vermis, and neuropathological examinations demonstrated diffuse cerebellar cortical degeneration. Functionally, the R83W mutation lies within the conserved switch II region of Rab3A, a domain critical for effector interaction. Although the mutant Rab3A R83W retained GTP-binding affinity, it failed to bind the key effector proteins RIM1 and Rabphilin-3A, highlighting the functional importance of R83 in effector complex formation, as supported by structural analysis. In PC12 cells, the R83W mutant exhibited diffuse cytoplasmic localization, in contrast to the vesicle- and neurite-tip localization of the wild-type and GTP-bound Rab3A mutant. The concordant localization pattern of R83W and GDP-bound Rab3A mutants suggests that R83W-induced mislocalization results from a failure to engage downstream effector proteins. In frozen sections of the mouse cerebellum, Rab3A was predominantly localized to parallel fiber terminals and was absent from postsynaptic Purkinje cells. These findings suggest that disruption of the interaction between Rab3A and its effector proteins may underlie disease pathogenesis, possibly involving presynaptic dysfunction at parallel fiber–Purkinje cell synapses mediated by the Rab3A–RIM1 complex.
- Open Access
- 15 July 2025
- Published by Rockefeller University Press in Journal of Experimental Medicine
- Vol. 222 (9)
Monoallelic mutations in MMD2 cause autosomal dominant aggressive periodontitis
Aggressive periodontitis causes rapid destruction of periodontal tissue. It occurs at a young age with familial clustering. We report on the first time on molecular and cellular basis of a Mendelian form of autosomal dominant aggressive periodontitis. Monoallelic mutations in the monocyte to macrophage differentiation-associated 2 (MMD2) gene, encoding MMD2, in two Japanese families with autosomal dominant aggressive periodontitis are identified. Mutations, c.347 C>T (p.A116V) and c.377 G>C (p.R126P) in MMD2, disturbed fMLP-induced activation of Ras/ERK signaling. Additionally, abnormalities in the proteins of Golgi apparatus, a crucial contributor to innate immune signaling pathways, were identified in patients’ neutrophils. The knock-in and knockout mice exhibited alveolar bone loss by ligature-induced periodontitis, along with impaired fMLP-induced chemotaxis, as found in the patients with MMD2 mutation. Our studies revealed that monoallelic mutations in MMD2 underlie the impairment of neutrophil chemotaxis, which leads to the development of autosomal dominant aggressive periodontitis.
- 15 July 2025
- Published by Rockefeller University Press in Journal of Experimental Medicine
- Vol. 222 (9)
Open AccessMonoallelic mutations in MMD2 cause autosomal dominant aggressive periodontitis
Aggressive periodontitis causes rapid destruction of periodontal tissue. It occurs at a young age with familial clustering. We report on the first time on molecular and cellular basis of a Mendelian form of autosomal dominant aggressive periodontitis. Monoallelic mutations in the monocyte to macrophage differentiation-associated 2 (MMD2) gene, encoding MMD2, in two Japanese families with autosomal dominant aggressive periodontitis are identified. Mutations, c.347 C>T (p.A116V) and c.377 G>C (p.R126P) in MMD2, disturbed fMLP-induced activation of Ras/ERK signaling. Additionally, abnormalities in the proteins of Golgi apparatus, a crucial contributor to innate immune signaling pathways, were identified in patients’ neutrophils. The knock-in and knockout mice exhibited alveolar bone loss by ligature-induced periodontitis, along with impaired fMLP-induced chemotaxis, as found in the patients with MMD2 mutation. Our studies revealed that monoallelic mutations in MMD2 underlie the impairment of neutrophil chemotaxis, which leads to the development of autosomal dominant aggressive periodontitis.
- Open Access
- 22 March 2025
- Published by Elsevier in Neuroscience Research
- Vol. 216, 104893
Optineurin knock-out forms TDP-43 aggregates to regulate TDP-43 protein levels despite autophagic up-regulation and aberrant TDP-43 expression
- 22 March 2025
- Published by Elsevier in Neuroscience Research
- Vol. 216, 104893
Open AccessOptineurin knock-out forms TDP-43 aggregates to regulate TDP-43 protein levels despite autophagic up-regulation and aberrant TDP-43 expression
- Open Access
- 3 February 2025
- Published by Life Science Alliance, LLC in Life Science Alliance
- Vol. 8 (4) , e202403063
Cholesterol ensures ciliary polycystin-2 localization to prevent polycystic kidney disease
The plasma membrane covering the primary cilium has a diverse accumulation of receptors and channels. To ensure the sensor function of the cilia, the ciliary membrane has higher cholesterol content than other cell membrane regions. A peroxisomal biogenesis disorder, Zellweger syndrome, characterized by polycystic kidney, is associated with a reduced level of ciliary cholesterol in cells. However, the etiological mechanism by which ciliary cholesterol lowering causes polycystic kidney disease remains unclear. Here, we demonstrated that lowering ciliary cholesterol by either pharmacological treatment or genetic depletion of peroxisomes impairs the localization of a ciliary ion channel polycystin-2. We also generated cultured renal medullary cells and mice carrying a missense variant in the cholesterol-binding site of polycystin-2 detected in the patient database of autosomal dominant polycystic kidney disease. This missense protein showed normal channel activity but decreased localization to the ciliary membrane. The homozygous mice exhibited embryonic lethality and the ciliopathy spectrum conditions of situs inversus and polycystic kidney. Our results suggest that cholesterol controls the ciliary localization of polycystin-2 to prevent polycystic kidney disease.
- 3 February 2025
- Published by Life Science Alliance, LLC in Life Science Alliance
- Vol. 8 (4) , e202403063
Open AccessCholesterol ensures ciliary polycystin-2 localization to prevent polycystic kidney disease
The plasma membrane covering the primary cilium has a diverse accumulation of receptors and channels. To ensure the sensor function of the cilia, the ciliary membrane has higher cholesterol content than other cell membrane regions. A peroxisomal biogenesis disorder, Zellweger syndrome, characterized by polycystic kidney, is associated with a reduced level of ciliary cholesterol in cells. However, the etiological mechanism by which ciliary cholesterol lowering causes polycystic kidney disease remains unclear. Here, we demonstrated that lowering ciliary cholesterol by either pharmacological treatment or genetic depletion of peroxisomes impairs the localization of a ciliary ion channel polycystin-2. We also generated cultured renal medullary cells and mice carrying a missense variant in the cholesterol-binding site of polycystin-2 detected in the patient database of autosomal dominant polycystic kidney disease. This missense protein showed normal channel activity but decreased localization to the ciliary membrane. The homozygous mice exhibited embryonic lethality and the ciliopathy spectrum conditions of situs inversus and polycystic kidney. Our results suggest that cholesterol controls the ciliary localization of polycystin-2 to prevent polycystic kidney disease.
- 1 September 2024
- Published by Elsevier in Journal of the Neurological Sciences
- Vol. 466, 123209
C9orf72 repeat expansions in Wakayama: One potential cause of amyotrophic lateral sclerosis in the Kii Peninsula, Japan
- 1 September 2024
- Published by Elsevier in Journal of the Neurological Sciences
- Vol. 466, 123209
C9orf72 repeat expansions in Wakayama: One potential cause of amyotrophic lateral sclerosis in the Kii Peninsula, Japan
- Open Access
- 7 December 2022
- Published by Springer Nature in Acta Neuropathologica Communications
- Vol. 10 (1) , 1-9
Spinocerebellar ataxia type 17-digenic TBP/STUB1 disease: neuropathologic features of an autopsied patient
Spinocerebellar ataxia (SCA) type 17-digenic TBP/STUB1 disease (SCA17-DI) has been recently segregated from SCA17, caused by digenic inheritance of two gene mutations – intermediate polyglutamine-encoding CAG/CAA repeat expansions (polyQ) in TBP (TBP41 − 49) and STUB1 heterozygosity – the former being associated with SCA17, and the latter with SCA48 and SCAR16 (autosomal recessive). In SCA17, most patients carry intermediate TBP41 − 49 alleles but show incomplete penetrance, and the missing heritability can be explained by a new entity whereby TBP41 − 49 requires the STUB1 variant to be symptomatic. The STUB1 gene encodes the chaperone-associated E3 ubiquitin ligase (CHIP) involved in ubiquitin-mediated proteasomal control of protein homeostasis. However, reports of the neuropathology are limited and role of STUB1 mutations in SCA17-DI remain unknown. Here we report the clinicopathologic features of identical twin siblings, one of whom was autopsied and was found to carry an intermediate allele (41 and 38 CAG/CAA repeats) in TBP and a heterozygous missense mutation in STUB1 (p.P243L). These patients developed autosomal recessive Huntington’s disease-like symptoms. Brain MRI showed diffuse atrophy of the cerebellum and T2WI revealed hyperintense lesions in the basal ganglia and periventricular deep white matter. The brain histopathology of the patient shared features characteristic of SCA17, such as degeneration of the cerebellar cortex and caudate nucleus, and presence of 1C2-positive neurons. Here we show that mutant CHIP fails to generate the polyubiquitin chain due to disrupted folding of the entire U box domain, thereby affecting the E3 activity of CHIP. When encountering patients with cerebellar ataxia, especially those with Huntington’s disease-like symptoms, genetic testing for STUB1 as well as TBP should be conducted for diagnosis of SCA17-DI, even in cases of sporadic or autosomal recessive inheritance.
- 7 December 2022
- Published by Springer Nature in Acta Neuropathologica Communications
- Vol. 10 (1) , 1-9
Open AccessSpinocerebellar ataxia type 17-digenic TBP/STUB1 disease: neuropathologic features of an autopsied patient
Spinocerebellar ataxia (SCA) type 17-digenic TBP/STUB1 disease (SCA17-DI) has been recently segregated from SCA17, caused by digenic inheritance of two gene mutations – intermediate polyglutamine-encoding CAG/CAA repeat expansions (polyQ) in TBP (TBP41 − 49) and STUB1 heterozygosity – the former being associated with SCA17, and the latter with SCA48 and SCAR16 (autosomal recessive). In SCA17, most patients carry intermediate TBP41 − 49 alleles but show incomplete penetrance, and the missing heritability can be explained by a new entity whereby TBP41 − 49 requires the STUB1 variant to be symptomatic. The STUB1 gene encodes the chaperone-associated E3 ubiquitin ligase (CHIP) involved in ubiquitin-mediated proteasomal control of protein homeostasis. However, reports of the neuropathology are limited and role of STUB1 mutations in SCA17-DI remain unknown. Here we report the clinicopathologic features of identical twin siblings, one of whom was autopsied and was found to carry an intermediate allele (41 and 38 CAG/CAA repeats) in TBP and a heterozygous missense mutation in STUB1 (p.P243L). These patients developed autosomal recessive Huntington’s disease-like symptoms. Brain MRI showed diffuse atrophy of the cerebellum and T2WI revealed hyperintense lesions in the basal ganglia and periventricular deep white matter. The brain histopathology of the patient shared features characteristic of SCA17, such as degeneration of the cerebellar cortex and caudate nucleus, and presence of 1C2-positive neurons. Here we show that mutant CHIP fails to generate the polyubiquitin chain due to disrupted folding of the entire U box domain, thereby affecting the E3 activity of CHIP. When encountering patients with cerebellar ataxia, especially those with Huntington’s disease-like symptoms, genetic testing for STUB1 as well as TBP should be conducted for diagnosis of SCA17-DI, even in cases of sporadic or autosomal recessive inheritance.
- Open Access
- 7 July 2022
- Published by Springer Nature in Journal of Human Genetics
- Vol. 67 (10) , 621
Correction: Comparison of two families with and without ataxia harboring novel variants in PRKCG
- 7 July 2022
- Published by Springer Nature in Journal of Human Genetics
- Vol. 67 (10) , 621
Open AccessCorrection: Comparison of two families with and without ataxia harboring novel variants in PRKCG