Publications by authors named "Saba Shafi"

Water scarcity is a foremost environmental concern and is expected to hasten in the forthcoming years due to severe fluctuations in weather patterns worldwide. The present work was designed to explore the potential role of alpha-tocopherol (α-Toc), a form of vitamin E, on the morphological, physio-biochemical, and cellular antioxidant responses of two radish genotypes grown under drought conditions (38 ± 3% of field capacity). The individual and combined applications of α-Toc (100 ppm) were used as T0- Control, T1- Control + TF (TF-alpha-tocopherol), T2- Drought (D), and T3- D + TF with three replications.

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  • Primary cutaneous sarcomatoid squamous cell carcinoma (PCSSCC) can be difficult to diagnose due to its similarities with other spindle cell tumors and atypical expressions of markers like smooth muscle actin (SMA).
  • A study of 16 cases showed that these tumors were high-grade and typically involved deeper skin layers, with most cases exhibiting atypical spindle and epithelioid cell patterns.
  • The research highlights the importance of using multiple epithelial markers for accurate diagnosis, while also noting that SMA expression can complicate the identification process.
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Tenosynovial giant cell tumors (TGCTs) arise from the synovium of joint, bursa, and tendon sheath. Diffuse type often affects large joints, has higher recurrence rates, metastases, and malignant transformation potential compared to the localized type. The cytopathology of TGCT, a fibrohistiocytic neoplasm distinct from other giant cell-rich soft tissue tumors, is rarely reported.

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  • Vitamin D deficiency is common and linked to allergic diseases due to its role in immune regulation; the study focuses on the role of vitamin D receptor (VDR) genetic variants in allergic rhinitis (AR).
  • Research examined three specific VDR variants (TaqI, FokI, and BsmI) among 550 participants, finding that FokI and BsmI variants are associated with higher susceptibility to AR.
  • The study revealed that AR patients had significantly lower VDR mRNA and serum vitamin D levels, indicating a complex relationship between VDR genetic variations and immune response in allergic conditions.
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  • Cancer is a leading cause of death globally, and traditional chemotherapy drugs have severe side effects and issues with drug resistance, highlighting the need for new treatments.
  • Steroidal saponins, natural compounds with significant anticancer potential, have not yet been effectively applied in clinical settings, prompting a thorough review of their antitumor effects, mechanisms, and challenges.
  • The review identifies over 40 steroidal saponin compounds, categorizes them by structure, and discusses their ability to induce cancer cell death and inhibit tumor growth, while also suggesting strategies to enhance their therapeutic effectiveness.
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Melanoma is an aggressive skin cancer with increasing incidence and mortality worldwide. For many years the therapeutic strategies were limited to surgery, radiotherapy, and chemotherapy. Recent advances in immunology and cancer biology have led to the discovery and development of novel therapeutics, such as immune checkpoint inhibitors (ICIs) and targeted therapies, which have revolutionized the clinical care of patients with metastatic melanoma.

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Background: The establishment of minimum standards for display selection for the whole slide image (WSI) interpretation has not been fully defined. Recently, pathologists have increasingly preferred using remote displays for clinical diagnostics. Our study aims to assess and compare the performance of three fixed work displays and one remote personal display in accurately identifying ten selected pathologic features integrated into WSIs.

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Digital pathology (DP) is being increasingly employed in cancer diagnostics, providing additional tools for faster, higher-quality, accurate diagnosis. The practice of diagnostic pathology has gone through a staggering transformation wherein new tools such as digital imaging, advanced artificial intelligence (AI) algorithms, and computer-aided diagnostic techniques are being used for assisting, augmenting and empowering the computational histopathology and AI-enabled diagnostics. This is paving the way for advancement in precision medicine in cancer.

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Glomus tumors are classified as members of the perivascular myoid family of tumors. Nearly half of these show NOTCH-gene fusions and a smaller subset has BRAF V600E mutations. Here, we report a novel ATG7::RAF1 fusion in malignant glomus tumor occurring in a 40-year-old female which has not been reported in the malignant glomus tumor before.

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Purpose: We conducted a phase II randomized noncomparative window of opportunity (WOO) trial to evaluate the inhibition of cellular proliferation and the modulation of immune microenvironment after treatment with olaparib alone or in combination with cisplatin or durvalumab in patients with operable head and neck squamous cell carcinoma (HNSCC).

Experimental Design: Forty-one patients with HNSCC were randomized to cisplatin plus olaparib (arm A), olaparib alone (arm B), no treatment (arm C) or durvalumab plus olaparib (arm D). The primary endpoint was to evaluate the percentage of patients in each arm that achieved a reduction of at least 25% in Ki67.

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. Whole slide imaging (WSI) represents a paradigm shift in pathology, serving as a necessary first step for a wide array of digital tools to enter the field. It utilizes virtual microscopy wherein glass slides are converted into digital slides and are viewed by pathologists by automated image analysis.

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The histogenesis of the rare primary cutaneous epithelioid rhabdomyosarcoma (PCERMS) remains unclear, with the morphological and immunophenotypic appearance of a rhabdomyosarcoma but a genomic profile consistent with sarcomatoid undifferentiated malignant melanoma (SUMM). Here, we provide comprehensive clinical, histopathological, and genomic analysis of a putative PCERMS presenting in an elderly patient. Histopathologic examination revealed an ulcerative tumefactive lesion with diffuse replacement of the dermis by sheets of malignant epithelioid cells with a rhabdoid appearance.

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Atypical fibroxanthoma and pleomorphic dermal sarcoma (PDS) are dermal malignant mesenchymal tumors that lie at the ends of the same disease spectrum. Clinically indistinguishable from atypical fibroxanthoma, PDS has a more aggressive course with significantly higher rate of local recurrence and metastases. Histological findings that favor a PDS include subcutaneous invasion, tumor necrosis, lymphovascular invasion, and/or perineural infiltration.

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We assessed the predictive value of an image analysis-based tumor-infiltrating lymphocytes (TILs) score for pathologic complete response (pCR) and event-free survival in breast cancer (BC). About 113 pretreatment samples were analyzed from patients with stage IIB-IIIC HER-2-negative BC randomized to neoadjuvant chemotherapy ± bevacizumab. TILs quantification was performed on full sections using QuPath open-source software with a convolutional neural network cell classifier (CNN11).

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Unlabelled: Programmed cell death protein-1 (PD-1)-targeted immunotherapy is approved for recurrent or metastatic head and neck squamous cell carcinoma (R/M HNSCC) treatment. Although its efficacy correlates with PD-L1 expression, response is limited even among positive cases. We employed digital spatial profiling (DSP) to discover potential biomarkers of immunotherapy outcomes in HNSCC.

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Unlabelled: Targeting the interaction of leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1) and its ligands has been shown to reinstate antitumor immunity. In addition, the introduction of the LAIR-1 decoy protein, LAIR-2, sensitizes previously resistant lung tumors to programmed death-1 (PD-1) blockade, indicating the potential of LAIR-1 as an alternative marker for anti-PD-1 resistance in lung cancer. Here, we assessed LAIR-1 as compared with programmed death-ligand 1 (PD-L1) expression in various tumors, with a focus on non-small cell lung cancer (NSCLC) and its histologic subtypes using multiplexed quantitative immunofluorescence (mQIF) in 287 (discovery cohort) and 144 (validation cohort) patients with NSCLC.

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Objectives: Human epidermal growth factor receptor 2 (HER2) status in endometrial cancer is usually determined by immunohistochemistry and/or in situ hybridization. We employed a novel HER2 gene protein assay (GPA) to simultaneously assesses HER2 gene amplification and protein expression in high-grade endometrial cancers.

Methods: We performed GPA in 180 endometrial cancers, including 106 serous carcinomas, 34 carcinosarcomas, and 40 mixed epithelial carcinomas.

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Wnt9b was recently identified as a highly sensitive and specific marker for breast carcinomas. Due to the limited number of triple-negative breast carcinomas (TNBCs) in previous study, we further explored Wnt9b's utility in breast carcinoma, especially in TNBCs including metaplastic carcinomas. We systematically evaluated Wnt9b expression on tissue microarrays (TMAs) from 413 breast carcinomas, 208 urothelial carcinomas, 102 endometrial carcinomas, 109 cholangiocarcinomas, 192 ovarian carcinomas, 48 lung adenocarcinomas, 69 colorectal adenocarcinomas, and 78 melanomas, and whole tissue section (WTS) from 20 human epidermal growth factor receptor 2-positive, 34 nonmetaplastic TNBCs, and 67 invasive metaplastic carcinomas.

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Treatment with immune checkpoint inhibitors has altered the course of malignant melanoma, with approximately half of the patients with advanced disease surviving for more than 5 years after diagnosis. Currently, there are no biomarker methods for predicting outcome from immunotherapy. Here, we obtained transcriptomic information from a total of 105 baseline tumor samples comprising two cohorts of patients with advanced melanoma treated with programmed cell death protein 1 (PD-1)-based immunotherapies.

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Background: The Visiopharm automated estrogen receptor (ER) digital imaging analysis (DIA) algorithm assesses digitized ER immunohistochemistry (IHC) by segmenting tumor nuclei and detecting stained nuclei automatically. We aimed to integrate and validate this algorithm in a digital pathology workflow for clinical use.

Design: The study cohort consisted of a serial collection of 97 invasive breast carcinoma specimens including 73 biopsies and 24 resections.

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Purpose: The recent WHO classification of breast cancer (2019) categorizes breast carcinoma with neuroendocrine (NE) differentiation into three morphologically distinct subtypes: well-differentiated neuroendocrine tumor (NET), poorly differentiated neuroendocrine carcinoma (NEC), and invasive breast carcinoma, no special type with neuroendocrine differentiation (IBC-NST-NE). Data regarding the prognostic significance of neuroendocrine differentiation are conflicting and an association, if any, between p53 mutation and neuroendocrine differentiation is largely unknown.

Methods: We examined p53 expression and other clinicopathologic characteristics in three types of invasive breast carcinoma with NE differentiation in a cohort of sixty-three patients, including 45 IBC-NST with NE differentiation, 10 NETs, and 8 NECs.

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Background: The prognostic value of tumor-infiltrating lymphocytes (TILs) assessed by machine learning algorithms in melanoma patients has been previously demonstrated but has not been widely adopted in the clinic. We evaluated the prognostic value of objective automated electronic TILs (eTILs) quantification to define a subset of melanoma patients with a low risk of relapse after surgical treatment.

Methods: We analyzed data for 785 patients from 5 independent cohorts from multiple institutions to validate our previous finding that automated TIL score is prognostic in clinically-localized primary melanoma patients.

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Synopsis of recent research by authors named "Saba Shafi"

  • - Saba Shafi's recent research primarily focuses on advancements in dermatopathology, exploring the complexities of diagnosing various skin cancers, such as folliculotropic mycosis fungoides and sarcomatoid carcinoma, with an emphasis on histological challenges and immunophenotypic profiles.
  • - Her work also investigates broader implications of immunology and genetics in health, including a study on vitamin D receptor variants and their association with allergic rhinitis, highlighting the gene-environment interactions in disease susceptibility.
  • - Additionally, Shafi contributes to the integration of technology in pathology, examining the role of artificial intelligence in diagnostic pathology and evaluating display technologies for interpreting whole slide images, thus bridging traditional methods with contemporary digital techniques.

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