TY - JOUR T1 - S. mediterranea ETS-1 regulates the function of cathepsin-positive cells and the epidermal lineage landscape via basement membrane remodeling. JF - J Cell Sci Y1 - 2022 A1 - Dubey, Vinay Kumar A1 - Sarkar, Souradeep R A1 - Lakshmanan, Vairavan A1 - Dalmeida, Rimple A1 - Gulyani, Akash A1 - Palakodeti, Dasaradhi KW - Animals KW - Basement Membrane KW - Cathepsins KW - Cell Differentiation KW - Epidermis KW - Humans KW - Matrix Metalloproteinases KW - Mediterranea KW - Planarians KW - Transcription Factors AB -

Extracellular matrix (ECM) is an important component of stem cell niche. Remodeling of ECM mediated by ECM regulators, such as matrix metalloproteinases (MMPs) plays a vital role in stem cell function. However, the mechanisms that modulate the function of ECM regulators in the stem cell niche are understudied. Here, we explored the role of the transcription factor (TF) ETS-1, which is expressed in the cathepsin-positive cell population, in regulating the expression of the ECM regulator, mt-mmpA, thereby modulating basement membrane thickness. In planarians, the basement membrane around the gut/inner parenchyma is thought to act as a niche for pluripotent stem cells. It has been shown that the early epidermal progenitors migrate outwards from this region and progressively differentiate to maintain the terminal epidermis. Our data shows that thickening of the basement membrane in the absence of ets-1 results in defective migration of stem cell progeny. Furthermore, the absence of ets-1 leads to a defective epidermal progenitor landscape, despite its lack of expression in those cell types. Together, our results demonstrate the active role of ECM remodeling in regulating tissue homeostasis and regeneration in the planarian Schmidtea mediterranea. This article has an associated First Person interview with one of the co-first authors of the paper.

VL - 135 IS - 20 ER - TY - JOUR T1 - Snail maintains the stem/progenitor state of skin epithelial cells and carcinomas through the autocrine effect of matricellular protein Mindin. JF - Cell Rep Y1 - 2022 A1 - Badarinath, Krithika A1 - Dam, Binita A1 - Kataria, Sunny A1 - Zirmire, Ravindra K A1 - Dey, Rakesh A1 - Kansagara, Gaurav A1 - Ajnabi, Johan A1 - Hegde, Akshay A1 - Singh, Randhir A1 - Masudi, Tafheem A1 - Sambath, Janani A1 - Sachithanandan, Sasikala P A1 - Kumar, Prashant A1 - Gulyani, Akash A1 - He, You-Wen A1 - Krishna, Sudhir A1 - Jamora, Colin KW - Carcinoma, Squamous Cell KW - Cell Line, Tumor KW - Epithelial Cells KW - Extracellular Matrix Proteins KW - Humans KW - Integrins KW - Neoplasm Proteins KW - Neoplasm Recurrence, Local KW - Neoplastic Stem Cells KW - Skin Neoplasms KW - Snail Family Transcription Factors AB -

Preservation of a small population of cancer stem cells (CSCs) within a heterogeneous carcinoma serves as a paradigm to understand how select cells in a tissue maintain their undifferentiated status. In both embryogenesis and cancer, Snail has been correlated with stemness, but the molecular underpinning of this phenomenon remains largely ill-defined. In models of cutaneous squamous cell carcinoma (cSCC), we discovered a non-epithelial-mesenchymal transition function for the transcription factor Snail in maintaining the stemness of epidermal keratinocytes. Snail-expressing cells secrete the matricellular protein Mindin, which functions in an autocrine fashion to activate a Src-STAT3 pathway to reinforce their stem/progenitor phenotype. This pathway is activated by the engagement of Mindin with the leukocyte-specific integrin, CD11b (ITGAM), which is also unexpectedly expressed by epidermal keratinocytes. Interestingly, disruption of this signaling module in human cSCC attenuates tumorigenesis, suggesting that targeting Mindin would be a promising therapeutic approach to hinder cancer recurrence.

VL - 40 IS - 12 ER - TY - JOUR T1 - Discovery of a body-wide photosensory array that matures in an adult-like animal and mediates eye-brain-independent movement and arousal. JF - Proc Natl Acad Sci U S A Y1 - 2021 A1 - Shettigar, Nishan A1 - Chakravarthy, Anirudh A1 - Umashankar, Suchitta A1 - Lakshmanan, Vairavan A1 - Palakodeti, Dasaradhi A1 - Gulyani, Akash AB -

The ability to respond to light has profoundly shaped life. Animals with eyes overwhelmingly rely on their visual circuits for mediating light-induced coordinated movements. Building on previously reported behaviors, we report the discovery of an organized, eye-independent (extraocular), body-wide photosensory framework that allows even a head-removed animal to move like an intact animal. Despite possessing sensitive cerebral eyes and a centralized brain that controls most behaviors, head-removed planarians show acute, coordinated ultraviolet-A (UV-A) aversive phototaxis. We find this eye-brain-independent phototaxis is mediated by two noncanonical rhabdomeric opsins, the first known function for this newly classified opsin-clade. We uncover a unique array of dual-opsin-expressing photoreceptor cells that line the periphery of animal body, are proximal to a body-wide nerve net, and mediate UV-A phototaxis by engaging multiple modes of locomotion. Unlike embryonically developing cerebral eyes that are functional when animals hatch, the body-wide photosensory array matures postembryonically in "adult-like animals." Notably, apart from head-removed phototaxis, the body-wide, extraocular sensory organization also impacts physiology of intact animals. Low-dose UV-A, but not visible light (ocular-stimulus), is able to arouse intact worms that have naturally cycled to an inactive/rest-like state. This wavelength selective, low-light arousal of resting animals is noncanonical-opsin dependent but eye independent. Our discovery of an autonomous, multifunctional, late-maturing, organized body-wide photosensory system establishes a paradigm in sensory biology and evolution of light sensing.

VL - 118 IS - 20 ER - TY - JOUR T1 - Engineered RNA biosensors enable ultrasensitive SARS-CoV-2 detection in a simple color and luminescence assay. JF - Life Sci Alliance Y1 - 2021 A1 - Chakravarthy, Anirudh A1 - Nandakumar, Anirudh A1 - George, Geen A1 - Ranganathan, Shyamsundar A1 - Umashankar, Suchitta A1 - Shettigar, Nishan A1 - Palakodeti, Dasaradhi A1 - Gulyani, Akash A1 - Ramesh, Arati KW - Biosensing Techniques KW - COVID-19 KW - Humans KW - Luminescence KW - Nucleic Acid Amplification Techniques KW - RNA KW - RNA, Viral KW - SARS-CoV-2 AB -

The continued resurgence of the COVID-19 pandemic with multiple variants underlines the need for diagnostics that are adaptable to the virus. We have developed toehold RNA-based sensors across the SARS-CoV-2 genome for direct and ultrasensitive detection of the virus and its prominent variants. Here, isothermal amplification of a fragment of SARS-CoV-2 RNA coupled with activation of our biosensors leads to a conformational switch in the sensor. This leads to translation of a reporter protein, for example, LacZ or nano-lantern that is easily detected using color/luminescence. By optimizing RNA amplification and biosensor design, we have generated a highly sensitive diagnostic assay that is capable of detecting as low as 100 copies of viral RNA with development of bright color. This is easily visualized by the human eye and quantifiable using spectrophotometry. Finally, this PHAsed NASBA-Translation Optical Method (PHANTOM) using our engineered RNA biosensors efficiently detects viral RNA in patient samples. This work presents a powerful and universally accessible strategy for detecting COVID-19 and variants. This strategy is adaptable to further viral evolution and brings RNA bioengineering center-stage.

VL - 4 IS - 12 ER - TY - JOUR T1 - Dynamic expression of tRNA-derived small RNAs define cellular states. JF - EMBO Rep Y1 - 2019 A1 - Krishna, Srikar A1 - Yim, Daniel Gr A1 - Lakshmanan, Vairavan A1 - Tirumalai, Varsha A1 - Koh, Judice Ly A1 - Park, Jung Eun A1 - Cheong, Jit Kong A1 - Low, Joo Leng A1 - Lim, Michelle Js A1 - Sze, Siu Kwan A1 - Shivaprasad, Padubidri A1 - Gulyani, Akash A1 - Raghavan, Srikala A1 - Palakodeti, Dasaradhi A1 - DasGupta, Ramanuj AB -

Transfer RNA (tRNA)-derived small RNAs (tsRNAs) have recently emerged as important regulators of protein translation and shown to have diverse biological functions. However, the underlying cellular and molecular mechanisms of tsRNA function in the context of dynamic cell-state transitions remain unclear. Expression analysis of tsRNAs in distinct heterologous cell and tissue models of stem vs. differentiated states revealed a differentiation-dependent enrichment of 5'-tsRNAs. We report the identification of a set of 5'-tsRNAs that is upregulated in differentiating mouse embryonic stem cells (mESCs). Notably, interactome studies with differentially enriched 5'-tsRNAs revealed a switch in their association with "effector" RNPs and "target" mRNAs in different cell states. We demonstrate that specific 5'-tsRNAs can preferentially interact with the RNA-binding protein, Igf2bp1, in the RA-induced differentiated state. This association influences the transcript stability and thereby translation of the pluripotency-promoting factor, c-Myc, thus providing a mechanistic basis for how 5'-tsRNAs can modulate stem cell states in mESCs. Together our study highlights the role of 5'-tsRNAs in defining distinct cell states.

VL - 20 IS - 7 ER - TY - JOUR T1 - Highly Responsive Fluorescent Assemblies Allow for Unique, Multiparametric Sensing of the Phospholipid Membrane Environment. JF - Chemistry Y1 - 2019 A1 - Gulyani, Akash A1 - Dey, Nilanjan A1 - Bhattacharya, Santanu KW - Fluorescence Polarization KW - Fluorescent Dyes KW - Lipid Bilayers KW - Phospholipids KW - Pyrenes KW - Spectrometry, Fluorescence KW - Water AB -

Despite decades-long extensive research, probes that provide a comprehensive description of the lipid membrane microenvironment are still lacking. Here, a "smart" pyrene-terpyridine probe for multiparametric sensing of lipid membranes is reported. The complexity of the associated local microenvironment can be described by the distinct features of the probe fluorescence. The self-assembly of the probe molecules in phospholipid bilayers was sensitive to membrane order and phase state. The self-assembled probes showed a unique emission, influenced by dye-dye interactions and excited-state charge transfer. Moreover, this emission was sensitive to interfacial hydration, with very specific changes in emission wavelengths and fluorescence lifetimes upon variation of lipid compositions and properties. In parallel, changes in the lipid order and hydration affected the ground-state interactions in the dye aggregates and, thus, could be measured through ratiometric changes in the excitation and emission readouts. In addition, fluorescence anisotropy measurements provided another way to study the nature of dye aggregates in lipid bilayers. Overall, this report demonstrates how multiple aspects of the membrane microenvironment can be sensed through the unique fluorescence signatures of this "smart" probe in lipid membranes, and it establishes a new paradigm in lipid-membrane sensing.

VL - 25 IS - 6 ER - TY - JOUR T1 - KMT1 family methyltransferases regulate heterochromatin-nuclear periphery tethering via histone and non-histone protein methylation. JF - EMBO Rep Y1 - 2019 A1 - Rao, Radhika Arasala A1 - Ketkar, Alhad Ashok A1 - Kedia, Neelam A1 - Krishnamoorthy, Vignesh K A1 - Lakshmanan, Vairavan A1 - Kumar, Pankaj A1 - Mohanty, Abhishek A1 - Kumar, Shilpa Dilip A1 - Raja, Sufi O A1 - Gulyani, Akash A1 - Chaturvedi, Chandra Prakash A1 - Brand, Marjorie A1 - Palakodeti, Dasaradhi A1 - Rampalli, Shravanti AB -

Euchromatic histone methyltransferases (EHMTs), members of the KMT1 family, methylate histone and non-histone proteins. Here, we uncover a novel role for EHMTs in regulating heterochromatin anchorage to the nuclear periphery (NP) via non-histone methylation. We show that EHMTs methylate and stabilize LaminB1 (LMNB1), which associates with the H3K9me2-marked peripheral heterochromatin. Loss of LMNB1 methylation or EHMTs abrogates heterochromatin anchorage at the NP We further demonstrate that the loss of EHMTs induces many hallmarks of aging including global reduction of H3K27methyl marks and altered nuclear morphology. Consistent with this, we observe a gradual depletion of EHMTs, which correlates with loss of methylated LMNB1 and peripheral heterochromatin in aging human fibroblasts. Restoration of EHMT expression reverts peripheral heterochromatin defects in aged cells. Collectively, our work elucidates a new mechanism by which EHMTs regulate heterochromatin domain organization and reveals their impact on fundamental changes associated with the intrinsic aging process.

ER - TY - JOUR T1 - FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation. JF - iScience Y1 - 2018 A1 - D'Souza, Michelle Ninochka A1 - Gowda, Naveen Kumar Chandappa A1 - Tiwari, Vishal A1 - Babu, Rosana Ottakandathil A1 - Anand, Praveen A1 - Dastidar, Sudhriti Ghosh A1 - Singh, Randhir A1 - James, Owen G A1 - Selvaraj, Bhuvaneish A1 - Pal, Rakhi A1 - Ramesh, Arati A1 - Chattarji, Sumantra A1 - Chandran, Siddharthan A1 - Gulyani, Akash A1 - Palakodeti, Dasaradhi A1 - Muddashetty, Ravi S AB -

FMRP is an RNA-binding protein that is known to localize in the cytoplasm and in the nucleus. Here, we have identified an interaction of FMRP with a specific set of C/D box snoRNAs in the nucleus. C/D box snoRNAs guide 2'O methylations of ribosomal RNA (rRNA) on defined sites, and this modification regulates rRNA folding and assembly of ribosomes. 2'O methylation of rRNA is partial on several sites in human embryonic stem cells, which results in ribosomes with differential methylation patterns. FMRP-snoRNA interaction affects rRNA methylation on several of these sites, and in the absence of FMRP, differential methylation pattern of rRNA is significantly altered. We found that FMRP recognizes ribosomes carrying specific methylation patterns on rRNA and the recognition of methylation pattern by FMRP may potentially determine the translation status of its target mRNAs. Thus, FMRP integrates its function in the nucleus and in the cytoplasm.

VL - 9 ER - TY - JOUR T1 - A unique self-assembly-driven probe for sensing a lipid bilayer: ratiometric probing of vesicle to micelle transition JF - Chem. Commun. Y1 - 2018 A1 - Gulyani, Akash A1 - Dey, Nilanjan A1 - Bhattacharya, Santanu AB -

An amphiphilic pyrene-terpyridine (Pytpy) probe forms novel{,} fluorescent nanoaggregates in phospholipid membranes. This unique membrane-driven self-assembly of Pytpy shows large Stokes shifts and long-lived fluorescent states and efficiently reports on vesicle-micelle transition through ratiometric changes. Strikingly{,} Pytpy can even distinguish between bilayer-like domains and more-dynamic micelle-like {'}rim{'} phases that co-exist in mixed assemblies (bicelles).

VL - 54 UR - http://dx.doi.org/10.1039/C8CC01635F ER - TY - JOUR T1 - Cytoplasmic poly (A)-binding protein critically regulates epidermal maintenance and turnover in the planarian . JF - Development Y1 - 2017 A1 - Bansal, Dhiru A1 - Kulkarni, Jahnavi A1 - Nadahalli, Kavana A1 - Lakshmanan, Vairavan A1 - Krishna, Srikar A1 - Sasidharan, Vidyanand A1 - Geo, Jini A1 - Dilipkumar, Shilpa A1 - Pasricha, Renu A1 - Gulyani, Akash A1 - Raghavan, Srikala A1 - Palakodeti, Dasaradhi KW - Animals KW - Cell Lineage KW - Cell Proliferation KW - Cytoplasm KW - Epidermis KW - Epithelium KW - Extracellular Matrix KW - Gene Knockdown Techniques KW - Homeostasis KW - Models, Biological KW - Planarians KW - Poly(A)-Binding Protein I KW - Regeneration KW - RNA, Messenger KW - Wound Healing AB -

Identifying key cellular events that facilitate stem cell function and tissue organization is crucial for understanding the process of regeneration. Planarians are powerful model system to study regeneration and stem cell (neoblast) function. Here, using planaria, we show that the initial events of regeneration, such as epithelialization and epidermal organization are critically regulated by a novel cytoplasmic poly A-binding protein, SMED-PABPC2. Knockdown leads to defects in epidermal lineage specification, disorganization of epidermis and ECM, and deregulated wound healing, resulting in the selective failure of neoblast proliferation near the wound region. Polysome profiling suggests that epidermal lineage transcripts, including , are translationally regulated by SMED-PABPC2 Together, our results uncover a novel role for SMED-PABPC2 in the maintenance of epidermal and ECM integrity, critical for wound healing and subsequent processes for regeneration.

VL - 144 IS - 17 ER - TY - JOUR T1 - Hierarchies in light sensing and dynamic interactions between ocular and extraocular sensory networks in a flatworm. JF - Sci Adv Y1 - 2017 A1 - Shettigar, Nishan A1 - Joshi, Asawari A1 - Dalmeida, Rimple A1 - Gopalkrishna, Rohini A1 - Chakravarthy, Anirudh A1 - Patnaik, Siddharth A1 - Mathew, Manoj A1 - Palakodeti, Dasaradhi A1 - Gulyani, Akash AB -

Light sensing has independently evolved multiple times under diverse selective pressures but has been examined only in a handful among the millions of light-responsive organisms. Unsurprisingly, mechanistic insights into how differential light processing can cause distinct behavioral outputs are limited. We show how an organism can achieve complex light processing with a simple "eye" while also having independent but mutually interacting light sensing networks. Although planarian flatworms lack wavelength-specific eye photoreceptors, a 25 nm change in light wavelength is sufficient to completely switch their phototactic behavior. Quantitative photoassays, eye-brain confocal imaging, and RNA interference/knockdown studies reveal that flatworms are able to compare small differences in the amounts of light absorbed at the eyes through a single eye opsin and convert them into binary behavioral outputs. Because planarians can fully regenerate, eye-brain injury-regeneration studies showed that this acute light intensity sensing and processing are layered on simple light detection. Unlike intact worms, partially regenerated animals with eyes can sense light but cannot sense finer gradients. Planarians also show a "reflex-like," eye-independent (extraocular/whole-body) response to low ultraviolet A light, apart from the "processive" eye-brain-mediated (ocular) response. Competition experiments between ocular and extraocular sensory systems reveal dynamic interchanging hierarchies. In intact worms, cerebral ocular response can override the reflex-like extraocular response. However, injury-regeneration again offers a time window wherein both responses coexist, but the dominance of the ocular response is reversed. Overall, we demonstrate acute light intensity-based behavioral switching and two evolutionarily distinct but interacting light sensing networks in a regenerating organism.

VL - 3 IS - 7 ER -