Anusha Nathan
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View article: Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection
Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection Open
Memory lymphocytes are durable cells that persist in the absence of antigen, but few human B cell subsets have been characterized in terms of durability. The relative durability of eight non-overlapping human B cell sub-populations coverin…
View article: Deep learning enhances the prediction of HLA class I-presented CD8+ T cell epitopes in foreign pathogens
Deep learning enhances the prediction of HLA class I-presented CD8+ T cell epitopes in foreign pathogens Open
Accurate in silico determination of CD8 + T cell epitopes would greatly enhance T cell-based vaccine development, but current prediction models are not reliably successful. Here, motivated by recent successes applying machine learning to c…
View article: Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection
Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection Open
Memory lymphocytes are durable cells that persist in the absence of antigen, but few human B cell subsets have been characterized in terms of durability. The relative durability of eight non-overlapping human B cell sub-populations coverin…
View article: Structure-based network analysis predicts pathogenic variants in human proteins associated with inherited retinal disease
Structure-based network analysis predicts pathogenic variants in human proteins associated with inherited retinal disease Open
View article: Identification of mouse CD4+ T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers
Identification of mouse CD4+ T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers Open
Understanding adaptive immunity against SARS-CoV-2 is a major requisite for the development of effective vaccines and treatments for COVID-19. CD4 + T cells play an integral role in this process primarily by generating antiviral cytokines …
View article: Dynamic phenotypic switching and group behavior help non-small cell lung cancer cells evade chemotherapy
Dynamic phenotypic switching and group behavior help non-small cell lung cancer cells evade chemotherapy Open
Drug resistance, a major challenge in cancer therapy, is typically attributed to mutations and genetic heterogeneity. On the other hand, emerging evidence suggests that dynamic cellular interactions and group behavior also contribute to dr…
View article: SARS-CoV-2 viral clearance and evolution varies by type and severity of immunodeficiency
SARS-CoV-2 viral clearance and evolution varies by type and severity of immunodeficiency Open
Despite vaccination and antiviral therapies, immunocompromised individuals are at risk for prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but the immune defects that predispose an individual to persistent…
View article: Identification of mouse CD4<sup>+</sup>T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers
Identification of mouse CD4<sup>+</sup>T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers Open
Understanding adaptive immunity against SARS-CoV-2 is a major requisite for the development of effective vaccines and treatments for COVID-19. CD4 + T cells play an integral role in this process primarily by generating antiviral cytokines …
View article: SARS-CoV-2 Viral Clearance and Evolution Varies by Extent of Immunodeficiency
SARS-CoV-2 Viral Clearance and Evolution Varies by Extent of Immunodeficiency Open
Despite vaccination and antiviral therapies, immunocompromised individuals are at risk for prolonged SARS-CoV-2 infection, but the immune defects that predispose to persistent COVID-19 remain incompletely understood. In this study, we perf…
View article: Structure-based network analysis predicts mutations associated with inherited retinal disease
Structure-based network analysis predicts mutations associated with inherited retinal disease Open
With continued advances in gene sequencing technologies comes the need to develop better tools to understand which mutations cause disease. Here we validate structure-based network analysis (SBNA) 1, 2 in well-studied human proteins and re…
View article: T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals
T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals Open
(Cell 185, 1041–1051.e1–e6; March 17, 2022) In our originally published article, an error in production resulted in mistakes to the citations and references for Garcia-Beltran et al., 2021a, 2021b, and 2022. At publication, Garcia-Beltran …
View article: T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals
T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals Open
The SARS-CoV-2 Omicron variant (B.1.1.529) contains mutations that mediate escape from antibody responses, although the extent to which these substitutions in spike and non-spike proteins affect T cell recognition is unknown. In this study…
View article: T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all prior infected and vaccinated individuals
T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all prior infected and vaccinated individuals Open
The SARS-CoV-2 Omicron variant (B.1.1.529) contains mutations that mediate escape from infection and vaccine-induced antibody responses, although the extent to which these substitutions in spike and non-spike proteins affect T cell recogni…
View article: Preferential expansion upon boosting of cross-reactive “pre-existing” switched memory B cells that recognize the SARS-CoV-2 Omicron variant Spike protein
Preferential expansion upon boosting of cross-reactive “pre-existing” switched memory B cells that recognize the SARS-CoV-2 Omicron variant Spike protein Open
In previously unvaccinated and uninfected individuals, non-RBD SARS-CoV-2 spike-specific B cells were prominent in two distinct, durable, resting, cross-reactive, “pre-existing” switched memory B cell compartments. While pre-existing RBD-s…
View article: Dynamic Phenotypic Switching and Group Behavior Help Non-Small Cell Lung Cancer Cells Evade Chemotherapy
Dynamic Phenotypic Switching and Group Behavior Help Non-Small Cell Lung Cancer Cells Evade Chemotherapy Open
Drug resistance, a major challenge in cancer therapy, is typically attributed to mutations and genetic heterogeneity. Emerging evidence suggests that dynamic cellular interactions and group behavior also contribute to drug resistance. Howe…
View article: HLA class-I-peptide stability mediates CD8+ T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV
HLA class-I-peptide stability mediates CD8+ T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV Open
View article: Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses
Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses Open
View article: "Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses." Nathan and Rossin et al
"Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses." Nathan and Rossin et al Open
Supplemental Tables S3 and S4 for article titled "Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses." TABLE S3. List of SARS-CoV-2 epitopes tested by HLA class I-peptide stability assay. Each row indicates a…
View article: CRISPR amplicon sequencing of human TAP1 gene of CRISPR/Cas9-edited mono-allelic HLA class I-expressing cell lines
CRISPR amplicon sequencing of human TAP1 gene of CRISPR/Cas9-edited mono-allelic HLA class I-expressing cell lines Open
TAP-deficient monoallelic HLA class I-expressing cell lines were generated by sequential transduction of the HLA-null human B cell line 721.221 with lentiviral expression constructs encoding (i) Cas9 protein linked to blasticidin resistanc…
View article: A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer
A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer Open
[This corrects the article DOI: 10.1016/j.isci.2020.101496.].
View article: A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer
A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer Open
View article: Suppressing chemoresistance in lung cancer via dynamic phenotypic switching and intermittent therapy
Suppressing chemoresistance in lung cancer via dynamic phenotypic switching and intermittent therapy Open
A major challenge in cancer therapy is drug resistance, which is typically attributed to acquired mutations and tumor heterogeneity. However, emerging evidence suggests that dynamic cellular interactions and group behavior also contribute …
View article: Dynamic Phenotypic Switching and Group Behavior Help Cancer Cells Evade Chemotherapy
Dynamic Phenotypic Switching and Group Behavior Help Cancer Cells Evade Chemotherapy Open
View article: Monitoring and Determining Mitochondrial Network Parameters in Live Lung Cancer Cells
Monitoring and Determining Mitochondrial Network Parameters in Live Lung Cancer Cells Open
Mitochondria are dynamic organelles that constantly fuse and divide, forming dynamic tubular networks. Abnormalities in mitochondrial dynamics and morphology are linked to diverse pathological states, including cancer. Thus, alterations in…
View article: Phenotypic Switching of Naïve T Cells to Immune-Suppressive Treg-Like Cells by Mutant KRAS
Phenotypic Switching of Naïve T Cells to Immune-Suppressive Treg-Like Cells by Mutant KRAS Open
Oncogenic (mutant) Ras protein Kirsten rat sarcoma viral oncogene homolog (KRAS) promotes uncontrolled proliferation, altered metabolism, and loss of genome integrity in a cell-intrinsic manner. Here, we demonstrate that CD4+ T cells when …
View article: A Non-genetic Mechanism for Chemoresistance in Lung Cancer: The Role of Integrin β4/Paxillin Axis
A Non-genetic Mechanism for Chemoresistance in Lung Cancer: The Role of Integrin β4/Paxillin Axis Open
Summary Tumor heterogeneity and cisplatin resistance are a major cause of tumor relapse and poor survival. Here we show that in lung adenocarcinoma (LUAD), paxillin (PXN) and integrin beta 4 (ITGB4) are associated with tumor progression, a…
View article: Phenotypic Switching of Naïve T cells to Immune-suppressive Treg-like Cells by Mutant KRAS
Phenotypic Switching of Naïve T cells to Immune-suppressive Treg-like Cells by Mutant KRAS Open
Oncogenic (mutant) Ras protein Kirsten rat sarcoma viral oncogene homolog (KRAS) promotes uncontrolled proliferation, altered metabolism, and loss of genome integrity in a cell-intrinsic manner. Here, we demonstrate that CD4 + T cells when…