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  1. Article: Culture and transfection: Two major bottlenecks in understanding

    Kumari, Sanju / Sinha, Abhinav

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1144453

    Abstract: ... The long ... ...

    Abstract The long term
    Language English
    Publishing date 2023-04-04
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1144453
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Pan-Cancer Analysis of Patient Tumor Single-Cell Transcriptomes Identifies Promising Selective and Safe Chimeric Antigen Receptor Targets in Head and Neck Cancer.

    Madan, Sanna / Sinha, Sanju / Chang, Tiangen / Gutkind, J Silvio / Cohen, Ezra E W / Schäffer, Alejandro A / Ruppin, Eytan

    Cancers

    2023  Volume 15, Issue 19

    Abstract: Chimeric antigen receptor (CAR) T cell therapies have yielded transformative clinical successes for patients with blood tumors, but their full potential remains to be unleashed against solid tumors. One challenge is ... ...

    Abstract Chimeric antigen receptor (CAR) T cell therapies have yielded transformative clinical successes for patients with blood tumors, but their full potential remains to be unleashed against solid tumors. One challenge is finding
    Language English
    Publishing date 2023-10-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers15194885
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The 2023 generation.

    Achinger-Kawecka, Joanna / Correa, Santiago / Hu, Jing / Li, Gaopeng / Lindeboom, Rik G H / Misale, Sandra / Monkkonen, Teresa / Nirmal, Ajit J / Prekovic, Stefan / Sinha, Sanju / Trigos, Anna S / Watson, Caroline J

    Nature cancer

    2023  Volume 4, Issue 12, Page(s) 1630–1635

    Language English
    Publishing date 2023-12-22
    Publishing country England
    Document type Journal Article
    ISSN 2662-1347
    ISSN (online) 2662-1347
    DOI 10.1038/s43018-023-00681-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Faculty Opinions recommendation of Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection.

    Ruppin, Eytan / Sinha, Sanju

    Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature

    2020  

    Keywords covid19
    Publisher Faculty Opinions Ltd
    Publishing country uk
    Document type Book ; Online
    DOI 10.3410/f.738159858.793575952
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Big data in basic and translational cancer research.

    Jiang, Peng / Sinha, Sanju / Aldape, Kenneth / Hannenhalli, Sridhar / Sahinalp, Cenk / Ruppin, Eytan

    Nature reviews. Cancer

    2022  Volume 22, Issue 11, Page(s) 625–639

    Abstract: Historically, the primary focus of cancer research has been molecular and clinical studies of a few essential pathways and genes. Recent years have seen the rapid accumulation of large-scale cancer omics data catalysed by breakthroughs in high-throughput ...

    Abstract Historically, the primary focus of cancer research has been molecular and clinical studies of a few essential pathways and genes. Recent years have seen the rapid accumulation of large-scale cancer omics data catalysed by breakthroughs in high-throughput technologies. This fast data growth has given rise to an evolving concept of 'big data' in cancer, whose analysis demands large computational resources and can potentially bring novel insights into essential questions. Indeed, the combination of big data, bioinformatics and artificial intelligence has led to notable advances in our basic understanding of cancer biology and to translational advancements. Further advances will require a concerted effort among data scientists, clinicians, biologists and policymakers. Here, we review the current state of the art and future challenges for harnessing big data to advance cancer research and treatment.
    MeSH term(s) Humans ; Artificial Intelligence ; Computational Biology ; Proteomics ; Translational Research, Biomedical ; Biomedical Research ; Neoplasms/genetics
    Language English
    Publishing date 2022-09-05
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Intramural
    ZDB-ID 2062767-1
    ISSN 1474-1768 ; 1474-175X
    ISSN (online) 1474-1768
    ISSN 1474-175X
    DOI 10.1038/s41568-022-00502-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Predicting tumor immune microenvironment and checkpoint therapy response of head & neck cancer patients from blood immune single-cell transcriptomics.

    Cao, Yingying / Chang, Tiangen / Schischlik, Fiorella / Wang, Kun / Sinha, Sanju / Hannenhalli, Sridhar / Jiang, Peng / Ruppin, Eytan

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The immune state of tumor microenvironment is crucial for determining immunotherapy response but is not readily accessible. Here we investigate if we can infer the tumor immune state from the blood and further predict immunotherapy response. First, we ... ...

    Abstract The immune state of tumor microenvironment is crucial for determining immunotherapy response but is not readily accessible. Here we investigate if we can infer the tumor immune state from the blood and further predict immunotherapy response. First, we analyze a dataset of head and neck squamous cell carcinoma (HNSCC) patients with matched scRNA-Seq of peripheral blood mononuclear cells (PBMCs) and tumor tissues. We find that the tumor immune cell fractions of different immune cell types and many of the genes they express can be inferred from the matched PBMC scRNA-Seq. Second, analyzing another HNSCC dataset with PBMC scRNA-Seq and immunotherapy response, we find that the inferred ratio between tumor memory B and regulatory T cell fractions is predictive of immunotherapy response and is superior to the well-established cytolytic and exhausted T-cell signatures. Overall, these results showcase the potential of scRNA-Seq liquid biopsies in cancer immunotherapy, calling for their larger-scale testing.
    Significance: This head and neck cancer study demonstrates the potential of using blood single-cell transcriptomics to (1) infer the tumor immune status and (2) predict immunotherapy response from the tumor immune status inferred from blood. These results showcase the potential of single-cell transcriptomics liquid biopsies for further advancing personalized cancer immunotherapy.
    Language English
    Publishing date 2023-01-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.17.524455
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Using a Recently Approved Tumor Mutational Burden Biomarker to Stratify Patients for Immunotherapy May Introduce a Sex Bias.

    Sinha, Neelam / Sinha, Sanju / Cheng, Kuoyuan / Madan, Sanna / Erez, Ayelet / Ryan, Bríd M / Schäffer, Alejandro A / Aldape, Kenneth / Ruppin, Eytan

    JCO precision oncology

    2021  Volume 5, Page(s) 1147–1150

    MeSH term(s) Biomarkers, Tumor/genetics ; Female ; Humans ; Immune Checkpoint Inhibitors/therapeutic use ; Immunotherapy ; Male ; Mutation ; Neoplasms/genetics ; Neoplasms/therapy ; Patient Selection ; Sexism
    Chemical Substances Biomarkers, Tumor ; Immune Checkpoint Inhibitors
    Language English
    Publishing date 2021-06-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ISSN 2473-4284
    ISSN (online) 2473-4284
    DOI 10.1200/PO.21.00168
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Speech evoked auditory brainstem response and gap detection threshold in middle-aged individual.

    Sanju, Himanshu Kumar / Bohra, Vaishnavi / Sinha, Sujeet Kumar

    European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery

    2017  Volume 274, Issue 4, Page(s) 2041–2048

    Abstract: This study aimed at characterizing the gap detection threshold (GDT) and speech evoked ABR (SABR) in younger and middle-aged individuals. Two groups of subjects were participated in the study which includes 15 young adults in the age range of 15-25 years ...

    Abstract This study aimed at characterizing the gap detection threshold (GDT) and speech evoked ABR (SABR) in younger and middle-aged individuals. Two groups of subjects were participated in the study which includes 15 young adults in the age range of 15-25 years and 15 middle-aged individuals in the age range of 40-60 years. SABR with stimulus/da/of 40 ms and GDT were investigated on both groups. For SABR, Mann-Whitney U test revealed that ageing has significantly adverse effect on the encoding of F1 and F2 at brainstem level. However, no significant effect of ageing (till middle age) on the encoding of F0 was observed in present study. Mann-Whitney U test also showed significant longer latency of wave V in middle-aged individuals compared to younger adults. Furthermore, GDT was significantly better in younger adults compared to middle-aged individuals according to Mann-Whitney U test. This study also revealed no significant correlation between GDT and F0, F1, F2 for younger as well as middle-aged individuals. The findings of this study showed poor encoding of certain aspects of speech at brainstem level in middle-aged individuals compared to younger adults. This study also revealed deterioration of auditory processes in middle-aged individuals.
    MeSH term(s) Acoustic Stimulation/methods ; Adolescent ; Adult ; Age Factors ; Audiometry, Speech/methods ; Auditory Threshold/physiology ; Evoked Potentials, Auditory, Brain Stem/physiology ; Female ; Humans ; Male ; Middle Aged ; Speech Perception/physiology ; Statistics as Topic
    Language English
    Publishing date 2017-04
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1017359-6
    ISSN 1434-4726 ; 0937-4477
    ISSN (online) 1434-4726
    ISSN 0937-4477
    DOI 10.1007/s00405-016-4402-x
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  9. Article ; Online: The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective

    Saba Ahmadi / Pattara Sukprasert / Rahulsimham Vegesna / Sanju Sinha / Fiorella Schischlik / Natalie Artzi / Samir Khuller / Alejandro A. Schäffer / Eytan Ruppin

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 17

    Abstract: Intra-tumor heterogeneity is often associated with resistance to targeted therapy, requiring the design of combinatorial therapies. Here, based on tumor single-cell transcriptomic datasets, the authors develop a computational approach to identify optimal ...

    Abstract Intra-tumor heterogeneity is often associated with resistance to targeted therapy, requiring the design of combinatorial therapies. Here, based on tumor single-cell transcriptomic datasets, the authors develop a computational approach to identify optimal combinatorial treatments targeting membrane receptors for cancer therapy.
    Keywords Science ; Q
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Immune Determinants of the Association between Tumor Mutational Burden and Immunotherapy Response across Cancer Types.

    Sinha, Neelam / Sinha, Sanju / Valero, Cristina / Schäffer, Alejandro A / Aldape, Kenneth / Litchfield, Kevin / Chan, Timothy A / Morris, Luc G T / Ruppin, Eytan

    Cancer research

    2022  Volume 82, Issue 11, Page(s) 2076–2083

    Abstract: The FDA has recently approved a high tumor mutational burden (TMB-high) biomarker, defined by ≥10 mutations/Mb, for the treatment of solid tumors with pembrolizumab, an immune checkpoint inhibitor (ICI) that targets PD1. However, recent studies have ... ...

    Abstract The FDA has recently approved a high tumor mutational burden (TMB-high) biomarker, defined by ≥10 mutations/Mb, for the treatment of solid tumors with pembrolizumab, an immune checkpoint inhibitor (ICI) that targets PD1. However, recent studies have shown that this TMB-high biomarker is only able to stratify ICI responders in a subset of cancer types, and the mechanisms underlying this observation have remained unknown. The tumor immune microenvironment (TME) may modulate the stratification power of TMB (termed TMB power), determining if it will be predictive of ICI response in a given cancer type. To systematically study this hypothesis, we inferred the levels of 31 immune-related factors characteristic of the TME of different cancer types in The Cancer Genome Atlas. Integration of this information with TMB and response data of 2,277 patients treated with anti-PD1 identified key immune factors that determine TMB power across 14 different cancer types. We find that high levels of M1 macrophages and low resting dendritic cells in the TME characterized cancer types with high TMB power. A model based on these two immune factors strongly predicted TMB power in a given cancer type during cross-validation and testing (Spearman Rho = 0.76 and 1, respectively). Using this model, we predicted the TMB power in nine additional cancer types, including rare cancers, for which TMB and ICI response data are not yet publicly available. Our analysis indicates that TMB-high may be highly predictive of ICI response in cervical squamous cell carcinoma, suggesting that such a study should be prioritized.
    Significance: This study uncovers immune-related factors that may modulate the relationship between high tumor mutational burden and ICI response, which can help prioritize cancer types for clinical trials.
    MeSH term(s) Biomarkers, Tumor/genetics ; Humans ; Immune Checkpoint Inhibitors/therapeutic use ; Immunologic Factors/therapeutic use ; Immunotherapy ; Mutation ; Neoplasms/drug therapy ; Neoplasms/therapy ; Tumor Microenvironment/genetics
    Chemical Substances Biomarkers, Tumor ; Immune Checkpoint Inhibitors ; Immunologic Factors
    Language English
    Publishing date 2022-03-31
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
    ZDB-ID 1432-1
    ISSN 1538-7445 ; 0008-5472
    ISSN (online) 1538-7445
    ISSN 0008-5472
    DOI 10.1158/0008-5472.CAN-21-2542
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