Swarna Ganesh

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• Ganesh, S., Premachandran, S., Venkatakrishnan, K., & Tan, B. (2024). Enhancing the cancer metastasis diagnosis: Ultrasensitive nano sensors exploiting Cancer stem cell associated DNA methylation as a liquid biopsy marker. Sensors and Actuators B: Chemical, 403. doi:10.1016/j.snb.2023.135206
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  Cancer metastasis presents a significant clinical challenge due to its impact on patient survival rates. Early detection of metastasis is pivotal for effective intervention and improved patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, holds promise for cancer detection, yet its utility in metastasis detection remains underexplored. Stable and accurate, DNA methylation reflects early tumor stages and enables molecular characterization, providing valuable longitudinal information. Despite its potential, clinical translation of DNA methylation biomarkers is limited, partially due to technology constraints and tumor heterogeneity. To enable clinical translation, an assay is needed that 1) quantifies DNA methylation, 2) integrates seamlessly into clinical workflows, and 3) ensures accuracy and sensitivity. In this study, we introduce an ultrasensitive nanosensor, Methylprobe, for DNA methylation-based liquid biopsy of metastasis. Methylprobe, synthesized via ultrashort pulsed ionization, provides signal amplification, enabling direct detection of methylated DNA in plasma. The technology is scalable and adaptable for clinical settings. The assay comprises the Methylprobe, metastasis-specific biomarkers, and a machine-learning algorithm. Tumor heterogeneity is addressed by integrating DNA-methylation signatures from distinct cancer stem cell phenotypes, enhancing assay reliability. The Methylprobe assay is validated on breast, lung, and colorectal cancer samples, demonstrating 99.8% accuracy in metastasis detection. This innovative approach offers potential as a reliable, sensitive, and accurate platform for assessing metastasis-associated DNA methylation patterns in blood plasma. Integrating Methylprobe into clinical practice could revolutionize metastasis detection, providing comprehensive insights into metastatic phenotypes and informing tailored therapeutic strategies.
• Ganesh, S., Premachandran, S., Venkatakrishnan, K., & Tan, B. o. (2024). Enhancing the cancer metastasis diagnosis: Ultrasensitive nano sensors exploiting Cancer stem cell associated DNA methylation as a liquid biopsy marker. Sensors and Actuators B: Chemical, 403, 135206.
• Ganesh, S., Dharmalingam, P., Das, S., Venkatakrishnan, K., & Tan, B. (2023). Mapping Immune-Tumor Bidirectional Dialogue Using Ultrasensitive Nanosensors for Accurate Diagnosis of Lung Cancer. ACS Nano, 17(9). doi:10.1021/acsnano.2c09323
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  Lung cancer is one of the most common cancers with high mortality worldwide despite the development of molecularly targeted therapies and immunotherapies. A significant challenge in managing lung cancer is the accurate diagnosis of cancerous lesions owing to the lack of sensitive and specific biomarkers. The current procedure necessitates an invasive tissue biopsy for diagnosis and molecular subtyping, which presents patients with risk, morbidity, anxiety, and high false-positive rates. The high-risk diagnostic approach has highlighted the need to search for a reliable, low-risk noninvasive diagnostic approach to capture lung cancer heterogeneity precisely. The immune interaction profile of lung cancer is driven by immune cells’ distinctive, precise interactions with the tumor microenvironment. Here, we hypothesize that immune cells, particularly T cells, can be used for accurate lung cancer diagnosis by exploiting the distinctive immune-tumor interaction by detecting the immune-diagnostic signature. We have developed an ultrasensitive T-sense nanosensor to probe these specific diagnostic signatures using the physical synthesis process of multiphoton ionization. Our research employed predictive in vitro models of lung cancers, cancer-associated T cells (PCAT, MCAT) and CSC-associated T cells (PCSCAT, MCSCAT), from primary and metastatic lung cancer patients to reveal the immune-diagnostic signature and uncover the molecular, functional, and phenotypic separation between patient-derived T cells (PDT) and healthy samples. We demonstrated this by adopting a machine learning model trained with SERS data obtained using cocultured T cells with preclinical models (CAT, CSCAT) of primary (H69AR) and metastatic lung cancer (H1915). Interrogating these distinct signatures with PDT captured the complexity and diversity of the tumor-associated T cell signature across the patient population, exposing the clinical feasibility of immune diagnosis in an independent cohort of patient samples. Thus, our predictive approach using T cells from the patient peripheral blood showed a highly accurate diagnosis with a specificity and sensitivity of 94.1% and 100%, respectively, for primary lung cancer and 97.9% and 94.4% for metastatic lung cancer. Our results prove that the immune-diagnostic signature developed in this study could be used as a clinical technology for cancer diagnosis and determine the course of clinical management with T cells.
• Ganesh, S., Dharmalingam, P., Das, S., Venkatakrishnan, K., & Tan, B. o. (2023). Mapping Immune--Tumor Bidirectional Dialogue Using Ultrasensitive Nanosensors for Accurate Diagnosis of Lung Cancer. ACS nano, 17(9), 8026--8040.
• Ganesh, S., Dhinakaran, A. K., Premnath, P., Venkatakrishnan, K., & Tan, B. o. (2023). Label-free saliva test for rapid detection of coronavirus using nanosensor-enabled SERS. Bioengineering, 10(3), 391.
• Ganesh, S., Dhinakaran, A., Premnath, P., Venkatakrishnan, K., & Tan, B. (2023). Label-Free Saliva Test for Rapid Detection of Coronavirus Using Nanosensor-Enabled SERS. Bioengineering, 10(3). doi:10.3390/bioengineering10030391
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  The recent COVID-19 pandemic has highlighted the inadequacies of existing diagnostic techniques and the need for rapid and accurate diagnostic systems. Although molecular tests such as RT-PCR are the gold standard, they cannot be employed as point-of-care testing systems. Hence, a rapid, noninvasive diagnostic technique such as Surface-enhanced Raman scattering (SERS) is a promising analytical technique for rapid molecular or viral diagnosis. Here, we have designed a SERS- based test to rapidly diagnose SARS-CoV-2 from saliva. Physical methods synthesized the nanostructured sensor. It significantly increased the detection specificity and sensitivity by ~ten copies/mL of viral RNA (~femtomolar concentration of nucleic acids). Our technique combines the multiplexing capability of SERS with the sensitivity of novel nanostructures to detect whole virus particles and infection-associated antibodies. We have demonstrated the feasibility of the test with saliva samples from individuals who tested positive for SARS-CoV-2 with a specificity of 95%. The SERS—based test provides a promising breakthrough in detecting potential mutations that may come up with time while also preparing the world to deal with other pandemics in the future with rapid response and very accurate results.
• Ishwar, D., Ganesh, S., Haldavnekar, R., Venkatakrishnan, K., & Tan, B. (2023). Degradable intracellular self-functionalized nanoprobes for in vitro diagnosis and monitoring of cancer. Materials Today Chemistry, 27, 101310.
• Ishwar, D., Ganesh, S., Haldavnekar, R., Venkatakrishnan, K., & Tan, B. (2023). Degradable intracellular self-functionalized nanoprobes for in vitro diagnosis and monitoring of cancer. Materials Today Chemistry, 27, 101310. doi:10.1016/j.mtchem.2022.101310
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  Despite various attempts to accelerate nanoparticle clearance from the cell, considerable amounts of nanomaterials remain in the cell, impairing cellular activities and hence precluding reliable invitro diagnosis. Retention of nanoparticles in cellular organelles disturbs cellular equilibrium and induces long-term consequences such as change in cell phenotype, genotype, cell mobility, toxicity, and even cell death. As a result, it is necessary to produce nanoparticles that degrade promptly and are then safely expelled from the cell while remaining biocompatible and fully functional. Here, we present a metabolizable organic carbon probe functionalized for Raman and fluorescence that can be used to track and monitor metabolizable organic carbon probe breakdown in lysosomes while simultaneously performing molecular level probing for invitro cancer diagnosis. The probes were stable in medium and other fluids and degraded in cancer cells within a week. The probes demonstrated an excellent Raman signal, which allowed surface-enhanced Raman spectroscopy-based monitoring of the degradation. Additionally, the probes showed the property of fluorescence which can be attributed to the inherent fluorescence of the probe on quantum scale. Experimental evidence of self-metabolization of the probe was further demonstrated. We tested the ability of the probes for cancer diagnosis with two cancer cell lines (breast and lung) and experimentally demonstrated the ability to discriminate between breast cancer and lung cancer without any ambiguity. These findings establish a novel type of functionalized degradable nanostructure for intracellular sensing and imaging cancer cells in cellular nanomedicine.
• Premachandran, S., Haldavnekar, R., Ganesh, S., Das, S., Venkatakrishnan, K., & Tan, B. (2023). Self-Functionalized Superlattice Nanosensor Enables Glioblastoma Diagnosis Using Liquid Biopsy. ACS Nano, 17(20). doi:10.1021/acsnano.3c04118
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  Glioblastoma (GBM), the most aggressive and lethal brain cancer, is detected only in the advanced stage, resulting in a median survival rate of 15 months. Therefore, there is an urgent need to establish GBM diagnosis tools to identify the tumor accurately. The clinical relevance of the current liquid biopsy techniques for GBM diagnosis remains mostly undetermined, owing to the challenges posed by the blood-brain barrier (BBB) that restricts biomarkers entering the circulation, resulting in the unavailability of clinically validated circulating GBM markers. GBM-specific liquid biopsy for diagnosis and prognosis of GBM has not yet been developed. Here, we introduce extracellular vesicles of GBM cancer stem cells (GBM CSC-EVs) as a previously unattempted, stand-alone GBM diagnosis modality. As GBM CSCs are fundamental building blocks of tumor initiation and recurrence, it is desirable to investigate these reliable signals of malignancy in circulation for accurate GBM diagnosis. So far, there are no clinically validated circulating biomarkers available for GBM. Therefore, a marker-free approach was essential since conventional liquid biopsy relying on isolation methodology was not viable. Additionally, a mechanism capable of trace-level detection was crucial to detecting the rare GBM CSC-EVs from the complex environment in circulation. To break these barriers, we applied an ultrasensitive superlattice sensor, self-functionalized for surface-enhanced Raman scattering (SERS), to obtain holistic molecular profiling of GBM CSC-EVs with a marker-free approach. The superlattice sensor exhibited substantial SERS enhancement and ultralow limit of detection (LOD of attomolar 10-18 M concentration) essential for trace-level detection of invisible GBM CSC-EVs directly from patient serum (without isolation). We detected as low as 5 EVs in 5 μL of solution, achieving the lowest LOD compared to existing SERS-based studies. We have experimentally demonstrated the crucial role of the signals of GBM CSC-EVs in the precise detection of glioblastoma. This was evident from the unique molecular profiles of GBM CSC-EVs demonstrating significant variation compared to noncancer EVs and EVs of GBM cancer cells, thus adding more clarity to the current understanding of GBM CSC-EVs. Preliminary validation of our approach was undertaken with a small amount of peripheral blood (5 μL) derived from GBM patients with 100% sensitivity and 97% specificity. Identification of the signals of GBM CSC-EV in clinical sera specimens demonstrated that our technology could be used for accurate GBM detection. Our technology has the potential to improve GBM liquid biopsy, including real-time surveillance of GBM evolution in patients upon clinical validation. This demonstration of liquid biopsy with GBM CSC-EV provides an opportunity to introduce a paradigm potentially impacting the current landscape of GBM diagnosis.
• Premachandran, S., Haldavnekar, R., Ganesh, S., Das, S., Venkatakrishnan, K., & Tan, B. o. (2023). Self-functionalized superlattice nanosensor enables glioblastoma diagnosis using liquid biopsy. ACS nano, 17(20), 19832--19852.
• Verma, A. H., Ganesh, S., Venkatakrishnan, K., & Tan, B. o. (2023). Epigenetic reprogramming of cancer stem cells to tumor cells using ultrasmall gold nanoparticle. Applied Materials Today, 30, 101725.
• Verma, A., Ganesh, S., Venkatakrishnan, K., & Tan, B. (2023). Epigenetic reprogramming of cancer stem cells to tumor cells using ultrasmall gold nanoparticle. Applied Materials Today, 30. doi:10.1016/j.apmt.2022.101725
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  Epigenetic reprogramming of cancer stem-like cells (CSC) is crucial to the clinical implementation of efficient tumor management. Groups of methylation on genomic DNA are a relatively stable epigenetic component. They are key drivers in the formation and maintenance of CSCs. Hence, reprogramming the DNA methylation epigenetics can provide new insights into cancer therapeutic approaches. Nanoprobes can influence CSC epigenetics; however, existing nanoprobes induce epigenetic alterations in an unregulated manner, which might result in undesirable mutation accumulation, which can hinder the reprogramming process. Here we report an epigenetic reprogramming approach with an ultrasmall Au NP, which can demethylate the genomic DNA, thereby causing the reprogramming of CSCs to cancer cells. In vitro bench top verification on preclinical models of non-metastatic and metastatic lung CSC showed a significant decrease in genetic, phenotypic stemness, and cell cycle quiescence, validated with biological assays. Furthermore, the ultrasmall Au NP was shown to interact with the epigenetic environment of CSCs through gold-DNA affinity spectral analysis. The pilot clinical validation study established the potential of our approach for clinical implementation. To the best of our knowledge, this is the first study to demonstrate a CSC epigenetic reprogramming using nanoparticles. In summary, this paper demonstrated that the nanoprobe could actively modify epigenetics and, as a result, can be employed to mitigate CSC stemness. Our findings might pave the path for more effective anti-cancer treatments and precision nanomedicine in the future.
• Dhinakaran, A. K., Dharmalingam, P., Ganesh, S., Venkatakrishnan, K., Das, S., & Tan, B. o. (2022). Molecular crosstalk between T cells and tumor uncovers GBM-specific T cell signatures in blood: Noninvasive GBM diagnosis using immunosensors. ACS nano, 16(9), 14134--14148.
• Dhinakaran, A. K., Ganesh, S., Haldavnekar, R., Tan, B. o., Das, S., & Venkatakrishnan, K. (2022). Holistic Analysis of Glioblastoma Stem cell DNA using Nanoengineered Plasmonic Metasensor for Glioblastoma Diagnosis. Small Methods, 6(9), 2200547.
• Dhinakaran, A. K., Ganesh, S., Venkatakrishnan, K., & Tan, B. o. (2022). Reprogramming the navigation of quantum probes in cancer initiating cells-Unlocking the pathway for next generation nanomedicine. Applied Materials Today, 28, 101534.
• Dhinakaran, A., Dharmalingam, P., Ganesh, S., Venkatakrishnan, K., Das, S., & Tan, B. (2022). Molecular Crosstalk between T Cells and Tumor Uncovers GBM-Specific T Cell Signatures in Blood: Noninvasive GBM Diagnosis Using Immunosensors. ACS Nano, 16(9). doi:10.1021/acsnano.2c04160
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  Glioblastoma (GBM) is the most common and aggressive stage IV brain cancer with a poor prognosis and survival rate. The blood-brain barrier (BBB) in GBM prevents the entry and exit of biomarkers, limiting its treatment options. Hence, GBM diagnosis is pivotal for timely clinical management. Currently, there exists no clinically validated biomarker for GBM diagnosis. T cells exhibit the potential to escape a leaky BBB in GBM patients. These T cells infiltrating the GBM interact with the heterogeneous population of tumor cells, display a symbiotic interaction resulting in intertwined molecular crosstalk, and display a GBM-associated signature while entering the peripheral circulation. Therefore, we hypothesize that studying these distinct molecular changes is critical to enable T cells to be a diagnostic marker for accurate detection of GBM from patient blood. We demonstrated this by utilizing the phenotypic and immunological landscape changes in T cells associated with glioblastoma tumors. GBM exhibits a high level of heterogeneity with diverse subtypes of cells within the tumor, enabling immune infiltration and different degrees of interactions with the tumor. To accurately detect these subtle molecular differences in T cells, we designed an immunosensor with a high detection sensitivity and repeatability. Hence in this study, we investigated the characteristic behavior of T cells to establish two preclinically validated biomarkers: GBM-associated T cells (GBMAT) and GBM stem cell-associated T cells (GSCAT). A comprehensive investigation was conducted by mimicking the tumor microenvironment in vitro by coculturing T cells with cancer cells and cancer stem cells to study the distinct variation in GBMAT and GSCAT. Preclinical investigation of T cells from GBM patient blood shows similar characteristics to our established biomarkers (GBMAT, GSCAT). Further evaluating the relative attributes of T cells in patient blood and tissue biopsy confirms the infiltrating ability of T cells across the BBB. A pilot validation using a SERS-based machine learning algorithm was accomplished by training the model with GBMAT and GSCAT as diagnostic markers. Using GBMAT as a biomarker, we achieved a sensitivity and specificity of 93.3% and 97.4%, respectively, whereas applying GSCAT yielded a sensitivity and specificity of 100% and 98.7%, respectively. We also validated this diagnostic methodology by using conventional biological assays to study the change in expression levels of T cell surface markers (CD4 and CD8) and cytokine levels in T cells (IL6, IL10, TNFα, INFγ) from GBM patients. This study introduces T cells as GBM-specific immune biomarkers to diagnose GBM using patient liquid biopsy. This preclinical validation study presents a better translatability into clinical reality that will enable rapid and noninvasive glioblastoma detection from patient blood.
• Dhinakaran, A., Ganesh, S., Haldavnekar, R., Tan, B., Das, S., & Venkatakrishnan, K. (2022). Holistic Analysis of Glioblastoma Stem Cell DNA Using Nanoengineered Plasmonic Metasensor for Glioblastoma Diagnosis. Small Methods, 6(9). doi:10.1002/smtd.202200547
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  The clinical relevance of liquid biopsy for glioblastoma (GBM) remains undetermined due to practical and biological limitations such as absence of a reliable GBM-specific biomarker, trace levels in circulation due to the blood–brain–barrier, and lack of a sensitive method to detect the trace levels of biomarkers. It is hypothesized that GBM stem cell (GSC)-associated cell free DNA can function as reliable biomarker for GBM because it accounts for tumor heterogeneity and provide accurate molecular information about the cancer. An integrative methodology is used for GBM diagnosis by utilizing the sub-single molecular sensitivity of nanoengineered plasmonic metasensors for real-time genomic profiling of GSC DNA. The nanoengineered metasensors can detect the rare circulating GSC-DNA accurately from just 5 µL of blood and the test can be performed in under 10 min. Analysis of clinical serum samples from GBM patients and healthy volunteers demonstrates that the technology yielded an accurate classification of GBM in an independent validation cohort (accuracy 98.3%, specificity 100%). The methodology detects GBM-signatures from the patient blood rapidly within the half-life period of cfDNA in circulation, non-invasively and amplification-free with a high diagnostic accuracy. With clinical validation, this methodology can evolve as a clinically viable diagnostic tool for fatal and hard-to-detect cancer like GBM.
• Dhinakaran, A., Ganesh, S., Venkatakrishnan, K., & Tan, B. (2022). Reprogramming the navigation of quantum probes in cancer initiating cells - Unlocking the pathway for next generation nanomedicine. Applied Materials Today, 28. doi:10.1016/j.apmt.2022.101534
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  Nanomedicine possesses the immense potential to tackle cancer effectively. Cancer recurrence is predominantly due to this small subpopulation of cells with stem cell properties known as Cancer stem cells (CSCs). Studies have established a clear understanding of nanomaterial's uptake mechanism in cancer cells; however, the internalization pathway in cancer stem cells remains unclear. Given the scarcity and importance of CSCs, it is critical to emphasize the focus on the uptake of nanoparticles in CSC, which will pave the way for next-generation CSC nanomedicine. To the best of our knowledge, this study is the first to reveal the complex uptake mechanism of nanoparticles in CSC comprehensively. We successfully introduced the mechanism of nanomaterial uptake in preclinical models of CSCs derived from lung cancer and pancreatic cancer, which account for most cancer deaths. Tailoring the Quantum probes with favorable surface functional groups is a practical approach to predetermine the intracellular destination. We successfully programmed the uptake pathway by tuning the surface functional groups on the Quantum probes, enabling us to effectively direct the probes to distinct subcellular locations to perform specific functions. In this study, we achieved the Quantum probes' synthesis and surface functionalization by adopting a non-chemical approach using ultrashort laser pulses. We synthesized sub-10 nm Quantum probes and decorated them with favorable surface functional groups by manipulating the laser plume's ionic components. The Quantum probes enriched with specific functional groups determine their lysosomal escape and localization, which decides the potential applications such as diagnostic, therapeutic, and theranostics. In addition to the surface functionalization, maintaining the probe size down to 2 nm has provided additional functionality to increase the efficiency of delivering nanomedicine to the CSC. Our results have also shown that the quantum probes do not interfere with the cellular dynamics and are highly biocompatible, eliminating a dedicated biocompatible coating. These results present a whole new perception of the fundamental processes involved in the internalization of nanoparticles into the CSCs through a regulated pathway and subcellular fate for specific applications that could unlock a new frontier in the next generation of broad-spectrum CSC nanomedicine.
• Ganesh, S., Venkatakrishnan, K., & Tan, B. (2022). Early detection and prediction of cancer metastasis – Unravelling metastasis initiating cell as a dynamic marker using self- functionalized nanosensors. Sensors and Actuators B: Chemical, 361. doi:10.1016/j.snb.2022.131655
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  The ability of cancer to metastasize to distant organs is an urgent problem to be solved clinically and continue to pose a greater challenge to researchers. Current treatments for cancer are ineffective for metastatic cancer due to inability of conventional imaging techniques to detect at early stages. Additionally, the ability to predict the ability of cancer to metastasize in advance will prove to be a valuable tool to improve patient prognosis. However, current techniques of prediction rely on molecular expression profiles which are highly tumor- specific, patient-specific and does not account for tumor heterogeneity. These factors critically impede the ability to use molecular expression profiles for early diagnosis and prediction of cancer metastasis. Hence, there is a need to concentrate on using tumor cells' phenotypic heterogeneity, which can serve as a diagnostic and predictive marker for cancer metastasis. Here, we have identified a rare subpopulation of cells within the tumor, which can signal metastasis initiation, known as metastasis-initiating cells (MICs) which are cancer non-specific, independent of epigenetic makeup, thereby becoming an excellent, unprejudiced marker for cancer metastasis irrespective of cancer type, the tissue of origin, and cancer stage. However, it is challenging to use MICs as a cellular marker for metastasis from a clinical perspective due to their rare, undetectable nature and the lack of sensitive methods to detect this elusive population of cells. To provide the ultra-sensitivity necessary for the early detection and prediction of cancer metastasis using MICs here we have created a self- functionalised nanosensor which is highly SERS active. The self- functionalized nanosensor enabled the detection of MIC using properties of intracellular biological processes and characters of the tumor microenvironment. The nanosensor enabled a detection sensitivity of 98%. It was able to identify MIC in a heterogeneous population of TICs with an unparalleled specificity of 99.62%. Further, the accuracy of MIC as a predictive marker for metastasis in a heterogeneous population of tumor spheroids was found to be 84.6%. This work contributed to the utilization of cancer cell heterogeneity to identify MIC, which can serve as a universal marker for diagnosis, prediction, and prognosis of tumor metastasis. To the best of our knowledge, this study is the first to design a probe that can provide both the diagnostic signature and predictive signature of cancer metastasis as early as the single cellular stage. This approach holds immense potential in the early diagnosis of metastatic tumors in a clinical setting and considerably improve patient prognosis.
• Ganesh, S., Venkatakrishnan, K., & Tan, B. o. (2022). Early detection and prediction of cancer metastasis--Unravelling metastasis initiating cell as a dynamic marker using self-functionalized nanosensors. Sensors and Actuators B: Chemical, 361, 131655.
• Haldavnekar, R., Ganesh, S., Venkatakrishnan, K., & Tan, B. (2022). Cancer Stem Cell DNA Enabled Real-Time Genotyping with Self-Functionalized Quantum Superstructures—Overcoming the Barriers of Noninvasive cfDNA Cancer Diagnostics. Small Methods, 6(4), 2101467. doi:10.1002/smtd.202101467
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  Cancer diagnosis and determining its tissue of origin are crucial for clinical implementation of personalized medicine. Conventional diagnostic techniques such as imaging and tissue biopsy are unable to capture the dynamic tumor landscape. Although circulating tumor DNA (ctDNA) shows promise for diagnosis, the clinical relevance of ctDNA remains largely undetermined due to several biological and technical complexities. Here, cancer stem cell-ctDNA is used to overcome the biological complexities like the inability for molecular analysis of ctDNA and dependence on ctDNA concentration rather than the molecular profile. Ultrasensitive quantum superstructures overcome the technical complexities of trace-level detection and rapid diagnosis to detect ctDNA within its short half-life. Activation of multiple surface enhanced Raman scattering mechanisms of the quantum superstructures achieved a very high enhancement factor (1.35 × 1011) and detection at ultralow concentration (10−15 M) with very high reliability (RSD: 3–12%). Pilot validation with clinical plasma samples from an independent validation cohort achieved a diagnosis sensitivity of ≈95% and specificity of 83%. Quantum superstructures identified the tissue of origin with ≈75–86% sensitivity and ≈92–96% specificity. With large scale clinical validation, the technology can develop into a clinically useful liquid biopsy tool improving cancer diagnostics.
• Haldavnekar, R., Ganesh, S., Venkatakrishnan, K., & Tan, B. o. (2022). Cancer Stem Cell DNA Enabled Real-Time Genotyping with Self-Functionalized Quantum Superstructures—Overcoming the Barriers of Noninvasive cfDNA Cancer Diagnostics. Small Methods, 6(4), 2101467.
• Tan, B. o., Ganesh, S., Haldavnekar, R., & Venkatakrishnan, K. (2022). OncoProfiler-A Multi-Cancer Early Detection (MCED) Assay. 21st Century Pathology, 2(5), 1--4.
• Verma, A. H., Ganesh, S., Venkatakrishnan, K., & Tan, B. o. (2022). Self-functional gold nanoprobes for intra-nuclear epigenomic monitoring of cancer stem-like cells. Biosensors and Bioelectronics, 195, 113644.
• Verma, A., Ganesh, S., Venkatakrishnan, K., & Tan, B. (2022). Self-functional gold nanoprobes for intra-nuclear epigenomic monitoring of cancer stem-like cells. Biosensors and Bioelectronics, 195. doi:10.1016/j.bios.2021.113644
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  Cancer epigenomic-environment is a core center of a tumor's genetic and epigenetic configuration. Surveying epigenomic-environment of cancer stem-like cells (CSC) is vital for developing novel diagnostic methods and improving current therapies since CSCs are among the most challenging clinical hurdles. To date, there exists no technique which can successfully monitor the epigenomics of CSC. Here, we have developed unique sub-10 nm Self-functional Gold Nanoprobes (GNP) as a CSC epigenomic monitoring platform that can easily maneuver into the nucleus while not producing any conformal changes to the genomic DNA. The GNP was synthesized using physical synthesis method of pulsed laser multiphoton ionization, which enabled the shrinking of GNP to 2.69 nm which helped us achieve two critical parameters for epigenomics monitoring: efficient nuclear uptake (98%) without complex functionalization and no conformational nuclear changes. The GNP efficiently generated SERS for structural, functional, molecular epigenetics, and nuclear proteomics in preclinical models of breast and lung CSCs. To the best of knowledge, this study is first to utilize the intranuclear epigenomic signal to distinguish between CSC from different tissues with >99% accuracy and specificity. Our findings are anticipated to help advance real-time epigenomics surveillance technologies such as nucleus-targeted drug surveillance and epigenomic prognosis and diagnostics.
• Ganesh, S., Venkatakrishnan, K., & Tan, B. (2020). Detecting the Origin of Cancer-Mobile Quantum Probe for Single Cancer Stem Cell Detection. Advanced Functional Materials, 30(9). doi:10.1002/adfm.201907572
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  Cancer stem cells (CSC) are believed to be the driving force of cancer metastases and are a rare population of self-renewing cells that contribute majorly to the poor outcomes of cancer therapy. The detection of CSC is of utmost importance to shed light on the indestructible nature of certain solid tumors and their metastatic ability. However, tumors tend to harbor CSCs in a specialized niche, making the detection process difficult. Currently, there is no method available to detect CSCs. The significance of this work is twofold. First, to the best of the knowledge, it is the first time that the detection of CSC is demonstrated. This approach simultaneously detects both the phenotypic and the metabolic state of the cell, thus enabling universal detection of CSC with high accuracy. Second, to the best of the knowledge, for the first time, light is shed on cell chemistry of CSC in their dedicated niche to facilitate a better understanding of the key players involved in the metabolic rewiring of CSC. This work will enable a better understanding of the fundamentals of CSCs, which are critical for the early diagnosis of cancer and the development of therapies for the cure of cancer.
• Ganesh, S., Venkatakrishnan, K., & Tan, B. (2020). Quantum scale organic semiconductors for SERS detection of DNA methylation and gene expression. Nature Communications, 11(1). doi:10.1038/s41467-020-14774-3
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  Cancer stem cells (CSC) can be identified by modifications in their genomic DNA. Here, we report a concept of precisely shrinking an organic semiconductor surface-enhanced Raman scattering (SERS) probe to quantum size, for investigating the epigenetic profile of CSC. The probe is used for tag-free genomic DNA detection, an approach towards the advancement of single-molecule DNA detection. The sensor detected structural, molecular and gene expression aberrations of genomic DNA in femtomolar concentration simultaneously in a single test. In addition to pointing out the divergences in genomic DNA of cancerous and non-cancerous cells, the quantum scale organic semiconductor was able to trace the expression of two genes which are frequently used as CSC markers. The quantum scale organic semiconductor holds the potential to be a new tool for label-free, ultra-sensitive multiplexed genomic analysis.
• Ganesh, S., Venkatakrishnan, K., & Tan, B. (2020). Tailoring carbon for single molecule detection – Broad spectrum 3D quantum sensor. Sensors and Actuators, B: Chemical, 317. doi:10.1016/j.snb.2020.128216
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  Current single-molecule SERS sensing is mostly done by plasmonic materials like Gold and Silver due to higher enhancement efficiency. However, plasmonic materials suffer from inherent disadvantages, including inconsistent spectral signature and non-biocompatibility. Researchers are actively searching for a replacement with superior biocompatibility and a uniform spectral signature. Quantum scale Graphene-based SERS signifies a newfound frontier in this regard, owing to high surface area and tunable optical and electronic properties. The use of GQD as a SERS sensor is still critically impeded by low enhancement factor as well as inferior sensitivity due to wavelength-dependent fluorescence property. In this work, we introduce a 3-D Graphene Oxide Quantum sensor (GOQS) with an unmatched enhancement of 1014, enabling ultra-sensitive detection with a limit of detection down to single molecule sensitivity. With 3-D architecture, the interference of the inherent fluorescence of GQD is eliminated, thereby achieving a relatively high enhancement factor on par with plasmonic materials. The high enhancement factor is a combined effect of quantum confinement, edge effects, and charge transfer through molecular adsorption. The single molecule sensitivity (10 −15 M) was experimentally verified using a Raman Probe molecule (CV, R6 G) with excellent repeatability. As a distinct confirmation of single molecule sensitivity of GOQS, we have detected two Raman probe molecules (CV, R6 G) simultaneously, thereby systematically computing the probability of detecting at 10 -15 M level. The ability to detect and distinguish Raman probe molecules simultaneously down to femtomolar level is the lowest limit of detection reported in a non-plasmonic sensor thus far. GOQS was demonstrated for the detecting of disease biomarkers and using Tryptophan. An environmental contaminant Bisphenol-A was detected at a concentration of 10−15 M, corresponding to 2000 ppb. The experimental results indicate a new paradigm towards the activation of quantum scale graphene as a broad-spectrum SERS sensor for numerous ultra-trace analysis.
• Ganesh, S., Venkatakrishnan, K., & Tan, B. o. (2020). Detecting the Origin of Cancer-Mobile Quantum Probe for Single Cancer Stem Cell Detection. Advanced Functional Materials, 30(9), 1907572.
• Ganesh, S., Venkatakrishnan, K., & Tan, B. o. (2020). Quantum cytosensor for early detection of cancer. Medical Devices & Sensors, 3(1), e10058.
• Ganesh, S., Venkatakrishnan, K., & Tan, B. o. (2020). Quantum scale organic semiconductors for SERS detection of DNA methylation and gene expression. Nature communications, 11(1), 1135.
• Ganesh, S., Venkatakrishnan, K., & Tan, B. o. (2020). Tailoring carbon for single molecule detection--Broad spectrum 3D quantum sensor. Sensors and Actuators B: Chemical, 317, 128216.

Others

• Tan, B. o., Venkatakrishnan, K., Ganesh, S., & Ravindra, H. R. (2024). Apparatus and method for early cancer detection and cancer prognosis using a nanosensor with raman spectroscopy.
• Ganesh, S. (2020). Quantum Carbon: A New Approach Towards Label-Free Cancer Stem Cell Theranostics.