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  1. Article ; Online: Utility of immunohistochemical expression of H3.3K36M and DOG1 in the diagnosis of chondroblastomas: An experience from a tertiary cancer referral center.

    Rekhi, Bharat / Dave, Vinayak / Butle, Ashwin / Dutt, Amit

    Annals of diagnostic pathology

    2023  Volume 66, Page(s) 152174

    Abstract: Despite its characteristic clinicopathological features, chondroblastoma may pose a diagnostic challenge, given its morphological spectrum, potential for subdiagnostic appearances in limited biopsy specimens, and its potential mimicry of other entities. ... ...

    Abstract Despite its characteristic clinicopathological features, chondroblastoma may pose a diagnostic challenge, given its morphological spectrum, potential for subdiagnostic appearances in limited biopsy specimens, and its potential mimicry of other entities. Recently, a characteristic H3F3B mutation underlying most chondroblastomas was described, which led to the identification of H3.3K36M as the corresponding diagnostic immunohistochemical marker. The present study is an evaluation of immunohistochemical features of 26 chondroblastomas, including DOG1 and H3.3K36M immunostaining. H3.3K36M immunostaining was graded as 1+, 2+ and 3+ in terms of staining intensity. There were 17 males and 9 females (M:F = 1.8:1) with ages ranging from 7 to 34 years (average = 16.7, median = 16). The most common location was proximal humerus (8, 30.7 %) followed by proximal tibia (5, 19.2 %), distal femur (3, 11.5 %), proximal femur (3, 11.5 %), pelvis (2,), followed by distal tibia, calcaneum, upper sternum, scapula, and D9 vertebra, in a single case, respectively. Eighteen (69.23 %) tumors displayed all the classic histopathological features. Immunohistochemically, the tumor cells were positive for S-100 P (19/22, 86.3 %), DOG1 (focal to patchy) (21/23 91.3 %), and H3.3K36M (26/26, 100 %). H3.3K36M tested in other tumors, constituting diagnostic mimics of a chondroblastoma, such as giant cell tumor of bone, chondromyxoid fibroma, and tenosynovial giant cell tumors, showed negative staining. Six tumors, initially diagnosed as chondroblastomas were reclassified into other entities with the help of negative H3.3K36M immunostaining. The present study reinforces H3.3K36M as a highly sensitive and specific marker for diagnosing chondroblastoma, including small biopsies, and in uncommon tumor sites with variable histopathological features. DOG1 is also useful in reinforcing a diagnosis of chondroblastoma in a clinicoradiological context, especially in laboratories lacking H3.3K36M immunostain. However, its staining pattern is variable.
    MeSH term(s) Male ; Female ; Humans ; Histones/genetics ; Histones/metabolism ; Chondroblastoma/diagnosis ; Chondroblastoma/pathology ; Bone Neoplasms/pathology ; S100 Proteins ; Referral and Consultation
    Chemical Substances Histones ; S100 Proteins
    Language English
    Publishing date 2023-06-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1440011-x
    ISSN 1532-8198 ; 1092-9134
    ISSN (online) 1532-8198
    ISSN 1092-9134
    DOI 10.1016/j.anndiagpath.2023.152174
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Rare hybrid tumor of odontogenic fibromyxoma and central giant cell granuloma in maxilla: First reported case.

    Pandey, Narayan Dutt / Bagul, Sushilkumar Balasaheb / Talmohite, Rajeev Ramesh / Choudhary, Amit Kumar

    Indian journal of dental research : official publication of Indian Society for Dental Research

    2024  Volume 34, Issue 3, Page(s) 332–334

    Abstract: Fibromyxoma is a locally aggressive rare benign tumor of mesenchymal origin with or without odontogenic epithelium. The etiology of this tumor remains unknown and it is responsible for approximately 3-8% of all cysts and tumors. Another locally ... ...

    Abstract Fibromyxoma is a locally aggressive rare benign tumor of mesenchymal origin with or without odontogenic epithelium. The etiology of this tumor remains unknown and it is responsible for approximately 3-8% of all cysts and tumors. Another locally destructive benign lesion is central giant cell granuloma (CGCG) which contains osteoclast-like multinucleated giant cells. CGCG accounts for about 7% of all benign jaw tumors, which usually affects younger females. A hybrid lesion with histologic features of both central fibromyxoma and CGCG has not been reported in the literature so far. In the present article, we report the first case of a hybrid tumor comprising odontogenic fibromyxoma with CGCG in a female along with a brief review of its clinical presentation, radiographic features, histological features, and management.
    MeSH term(s) Female ; Humans ; Maxilla ; Granuloma, Giant Cell/diagnostic imaging ; Granuloma, Giant Cell/surgery ; Odontogenic Tumors/diagnostic imaging ; Odontogenic Tumors/surgery ; Fibroma/diagnostic imaging ; Fibroma/surgery
    Language English
    Publishing date 2024-01-10
    Publishing country India
    Document type Case Reports
    ZDB-ID 1354886-4
    ISSN 1998-3603 ; 0970-9290
    ISSN (online) 1998-3603
    ISSN 0970-9290
    DOI 10.4103/ijdr.ijdr_349_22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Singleton mutations in large-scale cancer genome studies: uncovering the tail of cancer genome.

    Desai, Sanket / Ahmad, Suhail / Bawaskar, Bhargavi / Rashmi, Sonal / Mishra, Rohit / Lakhwani, Deepika / Dutt, Amit

    NAR cancer

    2024  Volume 6, Issue 1, Page(s) zcae010

    Abstract: Singleton or low-frequency driver mutations are challenging to identify. We present a domain driver mutation estimator (DOME) to identify rare candidate driver mutations. DOME analyzes positions analogous to known statistical hotspots and resistant ... ...

    Abstract Singleton or low-frequency driver mutations are challenging to identify. We present a domain driver mutation estimator (DOME) to identify rare candidate driver mutations. DOME analyzes positions analogous to known statistical hotspots and resistant mutations in combination with their functional and biochemical residue context as determined by protein structures and somatic mutation propensity within conserved PFAM domains, integrating the CADD scoring scheme. Benchmarked against seven other tools, DOME exhibited superior or comparable accuracy compared to all evaluated tools in the prediction of functional cancer drivers, with the exception of one tool. DOME identified a unique set of 32 917 high-confidence predicted driver mutations from the analysis of whole proteome missense variants within domain boundaries across 1331 genes, including 1192 noncancer gene census genes, emphasizing its unique place in cancer genome analysis. Additionally, analysis of 8799 TCGA (The Cancer Genome Atlas) and in-house tumor samples revealed 847 potential driver mutations, with mutations in tyrosine kinase members forming the dominant burden, underscoring its higher significance in cancer. Overall, DOME complements current approaches for identifying novel, low-frequency drivers and resistant mutations in personalized therapy.
    Language English
    Publishing date 2024-03-12
    Publishing country England
    Document type Journal Article
    ISSN 2632-8674
    ISSN (online) 2632-8674
    DOI 10.1093/narcan/zcae010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A comparative study of conventional chemical deinking and environment-friendly bio-deinking of mixed office wastepaper

    Amit Kumar / Dharm Dutt

    Scientific African, Vol 12, Iss , Pp e00793- (2021)

    2021  

    Abstract: Bio-deinking is an environmentally friendly process that improves the pulp and paper properties and reduces chemical consumption during the recycling of waste paper. This study was performed to evaluate the efficacy of enzyme by Penicillium sp. AKB-24. ... ...

    Abstract Bio-deinking is an environmentally friendly process that improves the pulp and paper properties and reduces chemical consumption during the recycling of waste paper. This study was performed to evaluate the efficacy of enzyme by Penicillium sp. AKB-24. Chemical deinking of MOW showed freeness (CSF), pulp brightness (ISO), deinking efficiency, and dirt count by 426±4 ml, 75.55±0.1%, 82.13±0.7%, and 733±24 mm2/m2 respectively at optimum repulping parameters. The physical strength properties including burst index, tear index, tensile index and double fold numbers were found 2.97±0.14 kPa.m2/g, 11.14±0.61 mN.m2/g, 46.60±1.99 N.m/g, and 36±2 respectively during chemical deinking of MOW. The deinking chemicals including NaOH, Na2SiO3, and H2O2 were replaced with crude enzyme by Penicillium sp. AKB-24 during enzymatic deinking of MOW. Enzymatic deinking of MOW resulted in an improvement in pulp freeness by 18.30% compared to chemical deinking while the dirt count value decreased by 32.60% during enzymatic deinking of MOW. Physical strength properties such as burst index, tensile index, and double fold numbers were improved by 16.07%, 14.54% and 8.57% respectively while tear index was decreased by 11.61% during enzymatic deinking of MOW compared to chemical deinking.
    Keywords Cellulase deinking ; Recycling ; Deinking efficiency ; Brightness ; Repulping ; Science ; Q
    Subject code 660
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Cytomorphology of spindle cell/sclerosing rhabdomyosarcoma, including MYOD1 (LI22R) mutation result.

    Rekhi, Bharat / Dodd, Leslie / Dharavath, Bhaskar / Dutt, Amit

    Diagnostic cytopathology

    2022  Volume 50, Issue 12, Page(s) E367–E372

    Abstract: Spindle cell/sclerosing rhabdomyosarcoma (RMS), characterized by MYOD1 (L122R) mutation in a subset of cases is a newly described subtype of RMS. Presently, there is no documentation of cytomorphological features, especially of sclerosing RMS. Case 1: A ... ...

    Abstract Spindle cell/sclerosing rhabdomyosarcoma (RMS), characterized by MYOD1 (L122R) mutation in a subset of cases is a newly described subtype of RMS. Presently, there is no documentation of cytomorphological features, especially of sclerosing RMS. Case 1: A 24-year-old male presented with pain and swelling in his wrist for a one-year duration. MRI revealed a well-defined soft tissue lesion measuring 5.3 cm, encasing the lower end of the ulna. Fine-needle aspiration cytology (FNAC) smears revealed clusters of tumor cells with round to oval to spindle-shaped nuclei, scant to moderate amount of cytoplasm with the wisps of the metachromatic stroma. Histopathological examination revealed a malignant tumor comprising cells with polygonal to spindle-shaped nuclei, arranged in a sclerotic stroma. Immunohistochemically, the tumor cells were positive for desmin, myogenin, and MYOD1. A diagnosis of sclerosing RMS was offered. Furthermore, the tumor revealed MYOD1 (L122R) mutation. Case 2: A 43-year-old male presented with a 4-month history of "nasal stuffiness" and pressure. Imaging revealed a poorly defined infiltrative lesion in his nasal cavity. FNAC smears revealed loose and tightly cohesive clusters of malignant cells with oval to spindle-shaped nuclei, a moderate amount of ill-defined bluish to finely vacuolated cytoplasm, and focal streak artifact with interspersed stromal fragments. Histopathological examination revealed a malignant tumor composed of oval to spindle-shaped nuclei, embedded in a variably hyalinized stroma. Immunohistochemically, the tumor cells were positive for desmin, and myogenin. Diagnosis of spindle cell/sclerosing RMS was offered. The present study constitutes one of the first documentation of cytomorphological features of two rare cases of spindle cell/sclerosing RMS. The differential diagnoses and treatment-related implications are presented.
    MeSH term(s) Male ; Adult ; Child ; Humans ; Young Adult ; Myogenin/genetics ; MyoD Protein/genetics ; Desmin/genetics ; Rhabdomyosarcoma/genetics ; Rhabdomyosarcoma/pathology ; Mutation ; Rhabdomyosarcoma, Embryonal ; Biomarkers, Tumor
    Chemical Substances Myogenin ; MyoD Protein ; Desmin ; Biomarkers, Tumor
    Language English
    Publishing date 2022-08-05
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 632710-2
    ISSN 1097-0339 ; 8755-1039
    ISSN (online) 1097-0339
    ISSN 8755-1039
    DOI 10.1002/dc.25032
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Promises of Protein Kinase Inhibitors in Recalcitrant Small-Cell Lung Cancer: Recent Scenario and Future Possibilities.

    Tiwari, Aniket / Kumari, Beauty / Nandagopal, Srividhya / Mishra, Amit / Shukla, Kamla Kant / Kumar, Ashok / Dutt, Naveen / Ahirwar, Dinesh Kumar

    Cancers

    2024  Volume 16, Issue 5

    Abstract: SCLC is refractory to conventional therapies; targeted therapies and immunological checkpoint inhibitor (ICI) molecules have prolonged survival only marginally. In addition, ICIs help only a subgroup of SCLC patients. Different types of kinases play ... ...

    Abstract SCLC is refractory to conventional therapies; targeted therapies and immunological checkpoint inhibitor (ICI) molecules have prolonged survival only marginally. In addition, ICIs help only a subgroup of SCLC patients. Different types of kinases play pivotal roles in therapeutics-driven cellular functions. Therefore, there is a significant need to understand the roles of kinases in regulating therapeutic responses, acknowledge the existing knowledge gaps, and discuss future directions for improved therapeutics for recalcitrant SCLC. Here, we extensively review the effect of dysregulated kinases in SCLC. We further discuss the pharmacological inhibitors of kinases used in targeted therapies for recalcitrant SCLC. We also describe the role of kinases in the ICI-mediated activation of antitumor immune responses. Finally, we summarize the clinical trials evaluating the potential of kinase inhibitors and ICIs. This review overviews dysregulated kinases in SCLC and summarizes their potential as targeted therapeutic agents. We also discuss their clinical efficacy in enhancing anticancer responses mediated by ICIs.
    Language English
    Publishing date 2024-02-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers16050963
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Deciphering the mechanisms of action of progesterone in breast cancer.

    Chakravorty, Gaurav / Ahmad, Suhail / Godbole, Mukul S / Gupta, Sudeep / Badwe, Rajendra A / Dutt, Amit

    Oncotarget

    2023  Volume 14, Page(s) 660–667

    Abstract: A practice-changing, randomized, controlled clinical study established that preoperative hydroxyprogesterone administration improves disease-free and overall survival in patients with node-positive breast cancer. This research perspective summarizes ... ...

    Abstract A practice-changing, randomized, controlled clinical study established that preoperative hydroxyprogesterone administration improves disease-free and overall survival in patients with node-positive breast cancer. This research perspective summarizes evidences from our studies that preoperative hydroxyprogesterone administration may improve disease-free and overall survival in patients with node-positive breast cancer by modulating cellular stress response and negative regulation of inflammation. Non-coding RNAs, particularly
    MeSH term(s) Humans ; Female ; Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Progesterone/pharmacology ; Progesterone/therapeutic use ; Receptors, Progesterone/metabolism ; Signal Transduction ; Hydroxyprogesterones/therapeutic use
    Chemical Substances Progesterone (4G7DS2Q64Y) ; Receptors, Progesterone ; Hydroxyprogesterones
    Language English
    Publishing date 2023-07-01
    Publishing country United States
    Document type Randomized Controlled Trial ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2560162-3
    ISSN 1949-2553 ; 1949-2553
    ISSN (online) 1949-2553
    ISSN 1949-2553
    DOI 10.18632/oncotarget.28455
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Influence of mechanical operation on the biodelignification of

    Pandey, Laxman Kumar / Kumar, Amit / Dutt, Dharm / Singh, S P

    3 Biotech

    2021  Volume 12, Issue 1, Page(s) 20

    Abstract: This study aimed at energy reduction during pulping ... ...

    Abstract This study aimed at energy reduction during pulping of
    Language English
    Publishing date 2021-12-16
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-021-03024-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Recurrent UBE3C-LRP5 translocations in head and neck cancer with therapeutic implications.

    Dharavath, Bhasker / Butle, Ashwin / Chaudhary, Akshita / Pal, Ankita / Desai, Sanket / Chowdhury, Aniket / Thorat, Rahul / Upadhyay, Pawan / Nair, Sudhir / Dutt, Amit

    NPJ precision oncology

    2024  Volume 8, Issue 1, Page(s) 63

    Abstract: Head and neck cancer is a major cause of morbidity and mortality worldwide. The identification of genetic alterations in head and neck cancer may improve diagnosis and treatment outcomes. In this study, we report the identification and functional ... ...

    Abstract Head and neck cancer is a major cause of morbidity and mortality worldwide. The identification of genetic alterations in head and neck cancer may improve diagnosis and treatment outcomes. In this study, we report the identification and functional characterization of UBE3C-LRP5 translocation in head and neck cancer. Our whole transcriptome sequencing and RT-PCR analysis of 151 head and neck cancer tumor samples identified the LRP5-UBE3C and UBE3C-LRP5 fusion transcripts in 5.3% of patients of Indian origin (n = 151), and UBE3C-LRP5 fusion transcripts in 1.2% of TCGA-HNSC patients (n = 502). Further, whole genome sequencing identified the breakpoint of UBE3C-LRP5 translocation. We demonstrate that UBE3C-LRP5 fusion is activating in vitro and in vivo, and promotes the proliferation, migration, and invasion of head and neck cancer cells. In contrast, depletion of UBE3C-LRP5 fusion suppresses the clonogenic, migratory, and invasive potential of the cells. The UBE3C-LRP5 fusion activates the Wnt/β-catenin signaling by promoting nuclear accumulation of β-catenin, leading to upregulation of Wnt/β-catenin target genes, MYC, CCND1, TCF4, and LEF1. Consistently, treatment with the FDA-approved drug, pyrvinium pamoate, significantly reduced the transforming ability of cells expressing the fusion protein and improved survival in mice bearing tumors of fusion-overexpressing cells. Interestingly, fusion-expressing cells upon knockdown of CTNNB1, or LEF1 show reduced proliferation, clonogenic abilities, and reduced sensitivity to pyrvinium pamoate. Overall, our study suggests that the UBE3C-LRP5 fusion is a promising therapeutic target for head and neck cancer and that pyrvinium pamoate may be a potential drug candidate for treating head and neck cancer harboring this translocation.
    Language English
    Publishing date 2024-03-04
    Publishing country England
    Document type Journal Article
    ISSN 2397-768X
    ISSN 2397-768X
    DOI 10.1038/s41698-024-00555-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Immunohistochemical expression of H3.3 G34W in 100 giant cell tumors of bone and its diagnostic mimics, including its value in resolving uncommon diagnostic scenarios: A single institutional study at a tertiary cancer referral center, India.

    Rekhi, Bharat / Dave, Vinayak / Butle, Ashwin / Dharavath, Bhasker / Khetale, Sonali / Redhu, Archana K / Singh, Rudransh / Dutt, Amit

    Indian journal of pathology & microbiology

    2024  

    Abstract: Background: There can be a diagnostic challenge in differentiating giant cell tumor of bone (GCTB) from its mimics. Lately, histone H3F3A (Histone 3.3) G34W has been identified as a promising immunohistochemical marker.: Aims: This study was aimed at ...

    Abstract Background: There can be a diagnostic challenge in differentiating giant cell tumor of bone (GCTB) from its mimics. Lately, histone H3F3A (Histone 3.3) G34W has been identified as a promising immunohistochemical marker.
    Aims: This study was aimed at evaluating H3.3 G34W immunostaining in 100 GCTBs, including its value in resolving diagnostic dilemmas.
    Materials and methods: Immunohistochemical staining for H3.3 G34W was graded in terms of staining intensity (1+ to 3+) and the percentage of tumor cells showing crisp nuclear staining.
    Results: One hundred GCTBs occurred in 58 males and 42 females (M: F ratio = 1.3), of 7-66 years age (average = 31.3, median = 28), commonly in distal femur (26), followed by proximal tibia (17), distal radius (12), proximal humerus (7), metacarpals (7), sacrum (6), proximal fibula (6), and relatively unusual sites (19), including a single multicentric case. Out of 92 GCTBs, wherein H3.3 G34W immunostaining worked, 81 (88.1%) showed positive staining in the mononuclear cells, including tumors with fibrous histiocytoma-like areas, sparing osteoclast-like giant cells, with 3+ staining intensity in 65/81 (80%) tumors. All 7/7 (100%) malignant GCTBs showed positive staining, including the pleomorphic/sarcomatous cells. All 7/7 (100%) metastatic GCTBs showed positive immunostaining. Seven out of 10 post-denosumab treated GCTBs showed positive H3.3 G34W immunostaining in the residual mononuclear cells. None of the other 37 "giant cell-rich" lesions displayed H3.3 G34W immunostaining. Four of 9 GCTBs tested for H3.3 G34W mutation showed positive results.
    Conclusions: The diagnostic sensitivity and specificity of H3.3 G34W for GCTB were 88.1% and 100%, respectively. This constitutes one of the first reports from our country, further validating the diagnostic value of H3.3 G34W in differentiating GCTB, including metastatic and malignant forms from its mimics, including small biopsy samples. Its value in various diagnostic dilemmas is presented and utility in identifying residual tumor cells in post-denosumab treated GCTBs is worth exploring.
    Language English
    Publishing date 2024-02-12
    Publishing country India
    Document type Journal Article
    ZDB-ID 197621-7
    ISSN 0974-5130 ; 0377-4929
    ISSN (online) 0974-5130
    ISSN 0377-4929
    DOI 10.4103/ijpm.ijpm_886_23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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