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Article ; Online: Challenges and opportunities for discovering the biology of rare genetic diseases of the brain.

Raghu, Padinjat / Sharma, Yojet / Suseela Devi, Aswathy Bhuvanendran Nair / Krishnan, Harini

2024 Volume 49

Abstract: Diseases of the human nervous system are an important cause of morbidity and mortality worldwide. These disorders arise out of multiple aetiologies of which rare genetic mutations in genes vital to nervous system development and function are an important ...

Abstract	Diseases of the human nervous system are an important cause of morbidity and mortality worldwide. These disorders arise out of multiple aetiologies of which rare genetic mutations in genes vital to nervous system development and function are an important cause. The diagnosis of such rare disorders is challenging due to the close overlap of clinical presentations with other diseases that are not of genetic origin. Further, understanding the mechanisms by which mutations lead to altered brain structure and function is also challenging, given that the brain is not readily accessible for tissue biopsy. However, recent developments in modern technologies have opened up new opportunities for the analysis of rare genetic disorders of the brain. In this review, we discuss these developments and strategies by which they can be applied effectively for better understanding of rare diseases of the brain. This will lead to the development of new clinical strategies to manage brain disorders.
MeSH term(s)	Humans ; Rare Diseases/diagnosis ; Rare Diseases/genetics ; Brain ; Mutation ; Biology
Language	English
Publishing date	2024-02-21
Publishing country	India
Document type	Review ; Journal Article
ZDB-ID	756157-x
ISSN	0973-7138 ; 0250-5991
ISSN (online)	0973-7138
ISSN	0250-5991
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Article ; Online: IMPA1 dependent regulation of phosphatidylinositol 4,5-bisphosphate and calcium signalling by lithium.

Saha, Sankhanil / Krishnan, Harini / Raghu, Padinjat

Life science alliance

2023 Volume 7, Issue 2

Abstract: Lithium (Li) is widely used as a mood stabilizer to treat bipolar affective disorder. However, the molecular targets of Li that underpin its therapeutic effect remain unresolved. Inositol monophosphatase (IMPA1) is an enzyme involved in ... ...

Abstract	Lithium (Li) is widely used as a mood stabilizer to treat bipolar affective disorder. However, the molecular targets of Li that underpin its therapeutic effect remain unresolved. Inositol monophosphatase (IMPA1) is an enzyme involved in phosphatidylinositol 4,5-bisphosphate (PIP
MeSH term(s)	Humans ; Lithium/pharmacology ; Phosphatidylinositols ; Calcium ; Calcium Signaling
Chemical Substances	Lithium (9FN79X2M3F) ; Phosphatidylinositols ; myo-inositol-1 (or 4)-monophosphatase (EC 3.1.3.25) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2023-12-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202302425
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Article ; Online: Biochemical characterization of the Drosophila insulin receptor kinase and longevity-associated mutants.

Krishnan, Harini / Ahmed, Sultan / Hubbard, Stevan R / Miller, W Todd

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

2023 Volume 38, Issue 1, Page(s) e23355

Abstract: Drosophila melanogaster (fruit fly) insulin receptor (D-IR) is highly homologous to the human counterpart. Like the human pathway, D-IR responds to numerous insulin-like peptides to activate cellular signals that regulate growth, development, and lipid ... ...

Abstract	Drosophila melanogaster (fruit fly) insulin receptor (D-IR) is highly homologous to the human counterpart. Like the human pathway, D-IR responds to numerous insulin-like peptides to activate cellular signals that regulate growth, development, and lipid metabolism in fruit flies. Allelic mutations in the D-IR kinase domain elevate life expectancy in fruit flies. We developed a robust heterologous expression system to express and purify wild-type and longevity-associated mutant D-IR kinase domains to investigate enzyme kinetics and substrate specificities. D-IR exhibits remarkable similarities to the human insulin receptor kinase domain but diverges in substrate preferences. We show that longevity-associated mutations reduce D-IR catalytic activity. Deletion of the unique kinase insert domain portion or mutations proximal to activating tyrosines do not influence kinase activity, suggesting their potential role in substrate recruitment and downstream signaling. Through biochemical investigations, this study enhances our comprehension of D-IR's role in Drosophila physiology, complementing genetic studies and expanding our knowledge on the catalytic functions of this conserved signaling pathway.
MeSH term(s)	Humans ; Animals ; Drosophila/metabolism ; Receptor, Insulin/genetics ; Receptor, Insulin/metabolism ; Drosophila melanogaster/metabolism ; Longevity/genetics ; Signal Transduction/physiology ; Insulin/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism
Chemical Substances	Receptor, Insulin (EC 2.7.10.1) ; Insulin ; Drosophila Proteins
Language	English
Publishing date	2023-12-09
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	639186-2
ISSN	1530-6860 ; 0892-6638
ISSN (online)	1530-6860
ISSN	0892-6638
DOI	10.1096/fj.202301948R
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Article: Emerging perspectives on multidomain phosphatidylinositol transfer proteins

Raghu, Padinjat / Basak, Bishal / Krishnan, Harini

Biochimica et biophysica acta. 2021 Sept., v. 1866, no. 9

2021

Abstract: The phosphatidylinositol transfer protein domain (PITPd) is an evolutionarily conserved protein that is able to transfer phosphatidylinositol between membranes in vitro and in vivo. However some animal genomes also include genes that encode proteins ... ...

Abstract	The phosphatidylinositol transfer protein domain (PITPd) is an evolutionarily conserved protein that is able to transfer phosphatidylinositol between membranes in vitro and in vivo. However some animal genomes also include genes that encode proteins where the PITPd is found in cis with a number of additional domains and recent large scale genome sequencing efforts indicate that this type of multidomain architecture is widespread in the animal kingdom. In Drosophila photoreceptors, the multidomain phosphatidylinositol transfer protein RDGB is required to regulate phosphoinositide turnover during G-protein activated phospholipase C signalling. Recent studies in flies and mammalian cell culture models have begun to elucidate functions for the non-PITPd of RDGB and its vertebrate orthologs. We review emerging evidence on the genomics, functional and cell biological perspectives of these multi-domain PITPd containing proteins.
Keywords	Drosophila ; G-proteins ; cell culture ; genomics ; mammals ; phospholipase C ; protein domains
Language	English
Dates of publication	2021-09
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1388-1981
DOI	10.1016/j.bbalip.2021.158984
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Article ; Online: Interdomain interactions regulate the localization of a lipid transfer protein at ER-PM contact sites.

Basak, Bishal / Krishnan, Harini / Raghu, Padinjat

Biology open

2021 Volume 10, Issue 3

Abstract: During phospholipase C-β (PLC-β) signalling ... ...

Abstract	During phospholipase C-β (PLC-β) signalling in
MeSH term(s)	Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Carrier Proteins/chemistry ; Carrier Proteins/metabolism ; Cell Membrane/metabolism ; Drosophila ; Endoplasmic Reticulum/metabolism ; Models, Biological ; Photoreceptor Cells/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Transport ; Signal Transduction
Chemical Substances	Carrier Proteins ; lipid transfer protein
Language	English
Publishing date	2021-03-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2632264-X
ISSN	2046-6390 ; 2046-6390
ISSN (online)	2046-6390
ISSN	2046-6390
DOI	10.1242/bio.057422
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Article ; Online: Emerging perspectives on multidomain phosphatidylinositol transfer proteins.

Raghu, Padinjat / Basak, Bishal / Krishnan, Harini

Biochimica et biophysica acta. Molecular and cell biology of lipids

2021 Volume 1866, Issue 9, Page(s) 158984

Abstract: The phosphatidylinositol transfer protein domain ( ... ...

Abstract	The phosphatidylinositol transfer protein domain (PITP
MeSH term(s)	Animals ; Humans ; Phospholipid Transfer Proteins/chemistry ; Phospholipid Transfer Proteins/metabolism ; Protein Domains
Chemical Substances	Phospholipid Transfer Proteins
Language	English
Publishing date	2021-06-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2618 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2618 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbalip.2021.158984
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Article ; Online: Structural organization of RDGB (retinal degeneration B), a multi-domain lipid transfer protein: a molecular modelling and simulation based approach.

Krishnan, Harini / Basak, Bishal / Nath, Vaisaly R / Mishra, Shirish / Raghu, Padinjat

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 22, Page(s) 13368–13382

Abstract: Lipid transfer proteins (LTPs) that shuttle lipids at membrane contact sites (MCS) play an important role in maintaining cellular homeostasis. One such important LTP is the Retinal Degeneration B (RDGB) protein. RDGB is localized at the MCS formed ... ...

Abstract	Lipid transfer proteins (LTPs) that shuttle lipids at membrane contact sites (MCS) play an important role in maintaining cellular homeostasis. One such important LTP is the Retinal Degeneration B (RDGB) protein. RDGB is localized at the MCS formed between the endoplasmic reticulum (ER) and the apical plasma membrane (PM) in
MeSH term(s)	Animals ; Membrane Proteins/metabolism ; Retinal Degeneration/metabolism ; Molecular Docking Simulation ; Drosophila Proteins ; Eye Proteins/metabolism ; Drosophila/metabolism ; Phosphatidylinositols/metabolism ; Endoplasmic Reticulum ; Cell Membrane/metabolism
Chemical Substances	lipid transfer protein ; Membrane Proteins ; Drosophila Proteins ; Eye Proteins ; Phosphatidylinositols
Language	English
Publishing date	2023-02-20
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2179545
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Article ; Online: Heterocellular N-cadherin junctions enable nontransformed cells to inhibit the growth of adjacent transformed cells.

Sheehan, Stephanie A / Retzbach, Edward P / Shen, Yongquan / Krishnan, Harini / Goldberg, Gary S

Cell communication and signaling : CCS

2022 Volume 20, Issue 1, Page(s) 19

Abstract: Background: The Src tyrosine kinase phosphorylates effector proteins to induce expression of the podoplanin (PDPN) receptor in order to promote tumor progression. However, nontransformed cells can normalize the growth and morphology of neighboring ... ...

Abstract	Background: The Src tyrosine kinase phosphorylates effector proteins to induce expression of the podoplanin (PDPN) receptor in order to promote tumor progression. However, nontransformed cells can normalize the growth and morphology of neighboring transformed cells. Transformed cells must escape this process, called "contact normalization", to become invasive and malignant. Contact normalization requires junctional communication between transformed and nontransformed cells. However, specific junctions that mediate this process have not been defined. This study aimed to identify junctional proteins required for contact normalization. Methods: Src transformed cells and oral squamous cell carcinoma cells were cultured with nontransformed cells. Formation of heterocellular adherens junctions between transformed and nontransformed cells was visualized by fluorescent microscopy. CRISPR technology was used to produce cadherin deficient and cadherin competent nontransformed cells to determine the requirement for adherens junctions during contact normalization. Contact normalization of transformed cells cultured with cadherin deficient or cadherin competent nontransformed cells was analyzed by growth assays, immunofluorescence, western blotting, and RNA-seq. In addition, Src transformed cells expressing PDPN under a constitutively active exogenous promoter were used to examine the ability of PDPN to override contact normalization. Results: We found that N-cadherin (N-Cdh) appeared to mediate contact normalization. Cadherin competent cells that expressed N-Cdh inhibited the growth of neighboring transformed cells in culture, while cadherin deficient cells failed to inhibit the growth of these cells. Results from RNA-seq analysis indicate that about 10% of the transcripts affected by contact normalization relied on cadherin mediated communication, and this set of genes includes PDPN. In contrast, cadherin deficient cells failed to inhibit PDPN expression or normalize the growth of adjacent transformed cells. These data indicate that nontransformed cells formed heterocellular cadherin junctions to inhibit PDPN expression in adjacent transformed cells. Moreover, we found that PDPN enabled transformed cells to override the effects of contact normalization in the face of continued N-Cdh expression. Cadherin competent cells failed to normalize the growth of transformed cells expressing PDPN under a constitutively active exogenous promoter. Conclusions: Nontransformed cells form cadherin junctions with adjacent transformed cells to decrease PDPN expression in order to inhibit tumor cell proliferation. Cancer begins when a single cell acquires changes that enables them to form tumors. During these beginning stages of cancer development, normal cells surround and directly contact the cancer cell to prevent tumor formation and inhibit cancer progression. This process is called contact normalization. Cancer cells must break free from contact normalization to progress into a malignant cancer. Contact normalization is a widespread and powerful process; however, not much is known about the mechanisms involved in this process. This work identifies proteins required to form contacts between normal cells and cancer cells, and explores pathways by which cancer cells override contact normalization to progress into malignant cancers. Video Abstract.
MeSH term(s)	Adherens Junctions/metabolism ; Antigens, CD/metabolism ; Cadherins/metabolism ; Cell Transformation, Neoplastic ; Humans ; Mouth Neoplasms/metabolism ; Mouth Neoplasms/pathology ; Squamous Cell Carcinoma of Head and Neck/metabolism ; Squamous Cell Carcinoma of Head and Neck/pathology
Chemical Substances	Antigens, CD ; CDH2 protein, human ; Cadherins
Language	English
Publishing date	2022-02-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2126315-2
ISSN	1478-811X ; 1478-811X
ISSN (online)	1478-811X
ISSN	1478-811X
DOI	10.1186/s12964-021-00817-9
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Article ; Online: Independent effects of Src kinase and podoplanin on anchorage independent cell growth and migration.

Retzbach, Edward P / Sheehan, Stephanie A / Krishnan, Harini / Zheng, Haiyan / Zhao, Caifeng / Goldberg, Gary S

Molecular carcinogenesis

2022 Volume 61, Issue 7, Page(s) 677–689

Abstract: The Src tyrosine kinase is a strong tumor promotor. Over a century of research has elucidated fundamental mechanisms that drive its oncogenic potential. Src phosphorylates effector proteins to promote hallmarks of tumor progression. For example, Src ... ...

Abstract	The Src tyrosine kinase is a strong tumor promotor. Over a century of research has elucidated fundamental mechanisms that drive its oncogenic potential. Src phosphorylates effector proteins to promote hallmarks of tumor progression. For example, Src associates with the Cas focal adhesion adaptor protein to promote anchorage independent cell growth. In addition, Src phosphorylates Cas to induce Pdpn expression to promote cell migration. Pdpn is a transmembrane receptor that can independently increase cell migration in the absence of oncogenic Src kinase activity. However, to our knowledge, effects of Src kinase activity on anchorage independent cell growth and migration have not been examined in the absence of Pdpn expression. Here, we analyzed the effects of an inducible Src kinase construct in knockout cells with and without exogenous Pdpn expression on cell morphology migration and anchorage independent growth. We report that Src promoted anchorage independent cell growth in the absence of Pdpn expression. In contrast, Src was not able to promote cell migration in the absence of Pdpn expression. In addition, continued Src kinase activity was required for cells to assume a transformed morphology since cells reverted to a nontransformed morphology upon cessation of Src kinase activity. We also used phosphoproteomic analysis to identify 28 proteins that are phosphorylated in Src transformed cells in a Pdpn dependent manner. Taken together, these data indicate that Src utilizes Pdpn to promote transformed cell growth and motility in complementary, but parallel, as opposed to serial, pathways.
MeSH term(s)	Cell Adhesion ; Cell Movement ; Humans ; Neoplasms ; Phosphorylation ; src-Family Kinases/genetics ; src-Family Kinases/metabolism
Chemical Substances	src-Family Kinases (EC 2.7.10.2)
Language	English
Publishing date	2022-04-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1004029-8
ISSN	1098-2744 ; 0899-1987
ISSN (online)	1098-2744
ISSN	0899-1987
DOI	10.1002/mc.23410
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Zs.A 2664: Show issues

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Article ; Online: PI3P-dependent regulation of cell size and autophagy by phosphatidylinositol 5-phosphate 4-kinase.

Ghosh, Avishek / Venugopal, Aishwarya / Shinde, Dhananjay / Sharma, Sanjeev / Krishnan, Meera / Mathre, Swarna / Krishnan, Harini / Saha, Sankhanil / Raghu, Padinjat

Life science alliance

2023 Volume 6, Issue 9

Abstract: Phosphatidylinositol 3-phosphate (PI3P) and phosphatidylinositol 5-phosphate (PI5P) are low-abundance phosphoinositides crucial for key cellular events such as endosomal trafficking and autophagy. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K) is an ... ...

Abstract	Phosphatidylinositol 3-phosphate (PI3P) and phosphatidylinositol 5-phosphate (PI5P) are low-abundance phosphoinositides crucial for key cellular events such as endosomal trafficking and autophagy. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K) is an enzyme that regulates PI5P in vivo but can act on both PI5P and PI3P in vitro. In this study, we report a role for PIP4K in regulating PI3P levels in
MeSH term(s)	Animals ; Autophagy/genetics ; Cell Size ; Drosophila ; Endosomes
Chemical Substances	phosphatidylinositol 5-phosphate
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202301920
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