publications

2024

1. Tissue-of-origin for cancers determines HIF-1 activation induced phenotypic heterogeneity

   Shaofei Liu, Yamin Liu, Xihua Qiu, *Yasir Suhail^*, and  Kshitiz

   Molecular Carcinogenesis, 2024

   Abs

   

   Hypoxia-inducible factor-1 (HIF-1) is the master regulator of cellular response to hypoxia, and is activated in many cancers contributing to many steps in the metastatic cascade by acting as a key transcription co-regulator for a large number of downstream genes. Presence of hypoxia within a tumor is spatially nonuniform, and can also by dynamic. Further, although HIF-1 is primarily stabilized and activated by lack of molecular O2, its stability is also affected by other factors present in the tumor microenvironment. HIF-1 also crosstalks with other transcription factors in co-regulating gene expression. Consequently, it is nontrivial to predict the gene expression patterns in cells in response to hypoxia, or HIF-1 activation. Additionally, cancers originating from tissue origins with different basal level of partial oxygen tension may activate HIF-1 at different threshold of hypoxia. We analyzed large published single cell RNAseq data for colorectal, lung, and pancreatic cancers to investigate the phenotypic outcome of HIF-1 activation in cancer cells. We found that cancers from tissues with different partial O2 tension levels exhibit HIF-1 activation at different stages of metastasis, and phenotypically respond differently to HIF-1 activation, likely by contextual co-option of different transcription factors. We experimentally confirmed these predictions by using cell lines representative of colorectal, lung, and pancreatic cancers, finding that while hypoxia enhances growth of colorectal cancer, it induces increased invasion of lung, and pancreatic cancers. Our analysis suggest that HIF-1 activation may act as a rheostat regulating downstream gene expression towards phenotypic outcomes differently in various cancers.

2. Lactate in breast cancer cells is associated with evasion of hypoxia-induced cell cycle arrest and adverse patient outcome

   Yamin Liu, Yasir Suhail, Ashkan Novin, Junaid Afzal, Aditya Pant, and  Kshitiz

   Human Cell, 2024

   Abs

   Tumor hypoxia is a common microenvironmental factor in breast cancers, resulting in stabilization of Hypoxia-Inducible Factor 1 (HIF-1), the master regulator of hypoxic response in cells. Metabolic adaptation by HIF-1 results in inhibition of citric acid cycle, causing accumulation of lactate in large concentrations in hypoxic cancers. Lactate can therefore serve as a secondary microenvironmental factor influencing cellular response to hypoxia. Presence of lactate can alter the hypoxic response of breast cancers in many ways, sometimes in opposite manners. Lactate stabilizes HIF-1 in oxidative condition, as well as destabilizes HIF-1 in hypoxia, increases cellular acidification, and mitigates HIF-1-driven inhibition of cellular respiration. We therefore tested the effect of lactate in MDA-MB-231 under hypoxia, finding that lactate can activate pathways associated with DNA replication, and cell cycling, as well as tissue morphogenesis associated with invasive processes. Using a bioengineered nano-patterned stromal invasion assay, we also confirmed that high lactate and induced HIF-1α gene overexpression can synergistically promote MDA-MB-231 dissemination and stromal trespass. Furthermore, using The Cancer Genome Atlas, we also surprisingly found that lactate in hypoxia promotes gene expression signatures prognosticating low survival in breast cancer patients. Our work documents that lactate accumulation contributes to increased heterogeneity in breast cancer gene expression promoting cancer growth and reducing patient survival.

3. Oscillatory Hypoxia Can Induce Senescence of Adipose-Derived Mesenchymal Stromal Cells Potentiating Invasive Transformation of Breast Epithelial Cells

   Ashkan Novin, Khadija Wali, Aditya Pant, Shaofei Liu, Wenqiang Du, Yamin Liu, Lichao Wang, Ming Xu, Binsheng Wang, Yasir Suhail, and  Kshitiz

   Cancers, 2024

   Abs

   Obesity is strongly associated with occurrence, metastasis, and resistance to therapy in breast cancers, which also exhibit high adipose content in the tumor microenvironment. Adipose tissue-derived mesenchymal stromal cells (ASCs) are recruited to breast cancer by many mechanisms, including hypoxia, and contribute to metastatic transition of the cancer. Breast cancers are characterized by regions of hypoxia, which can be temporally unstable owing to a mismatch between oxygen supply and consumption. Using a high-sensitivity nanopatterned stromal invasion assay, we found that ASCs could promote stromal invasion of not only breast cancer cell lines but also MCF10A1, a cell line derived from untransformed breast epithelium. RNA sequencing of MCF10A1 cells conditioned with medium from ASCs revealed upregulation of genes associated with increased cell migration, chemotaxis, and metastasis. Furthermore, we found that fluctuating or oscillating hypoxia could induce senescence in ASCs, which could result in an increased invasive potential in the treated MCF10A1 cells. These findings highlight the complex interplay within the breast cancer microenvironment, hypoxia, and the role of ASCs in transforming even non-cancerous breast epithelium toward an invasive phenotype, providing insights into early metastatic events.

2022

1. Evolution of higher mesenchymal CD44 expression in the human lineage: A gene linked to cancer malignancy

   Xinghong Ma, Anasuya Dighe, Jamie Maziarz, Edwin Neumann, Eric Erkenbrack, Yuan Yuan Hei, Yansheng Liu, Yasir Suhail,  Kshitiz, Irene Pak, Andre Levchenko, and Günter P. Wagner

   Evolution, medicine, and public health, 2022

   Abs

   CD44 is an extracellular matrix receptor implicated in cancer progression. CD44 increases the invasibility of skin (SF) and endometrial stromal fibroblasts (ESF) by cancer and trophoblast cells. We reasoned that the evolution of CD44 expression can affect both, the fetal-maternal interaction through CD44 in ESF as well as vulnerability to malignant cancer through expression in SF. We studied the evolution of CD44 expression in mammalian SF and ESF and demonstrate that in the human lineage evolved higher CD44 expression. Isoform expression in cattle and human is very similar suggesting that differences in invasibility are not due to the nature of expressed isoforms. We then asked whether the concerted gene expression increase in both cell types is due to shared regulatory mechanisms or due to cell type-specific factors. Reporter gene experiments with cells and cis-regulatory elements from human and cattle show that the difference of CD44 expression is due to cis effects as well as cell type-specific trans effects. These results suggest that the concerted expression increase is likely due to selection acting on both cell types because the evolutionary change in cell type-specific factors requires selection on cell type-specific functions. This scenario implies that the malignancy enhancing effects of elevated CD44 expression in humans likely evolved as a side-effect of positive selection on a yet unidentified other function of CD44. A possible candidate is the anti-fibrotic effect of CD44 but there are no reliable data showing that humans and primates are less fibrotic than other mammals.

2. Evolution of higher mesenchymal CD44 expression in the human lineage

   Xinghong Ma, Anasuya Dighe, Jamie Maziarz, Edwin Neumann, Eric Erkenbrack, Yuan Yuan Hei, Yansheng Liu, Yasir Suhail,  Kshitiz, Irene Pak, Andre Levchenko, and Günter P. Wagner

   Evolution, Medicine and Public Health, 2022

   Abs

   CD44 is an extracellular matrix receptor implicated in cancer progression. CD44 increases the invasibility of skin (SF) and endometrial stromal fibroblasts (ESF) by cancer and trophoblast cells. We reasoned that the evolution of CD44 expression can affect both, the fetal-maternal interaction through CD44 in ESF as well as vulnerability to malignant cancer through expression in SF. We studied the evolution of CD44 expression in mammalian SF and ESF and demonstrate that in the human lineage evolved higher CD44 expression. Isoform expression in cattle and human is very similar suggesting that differences in invasibility are not due to the nature of expressed isoforms. We then asked whether the concerted gene expression increase in both cell types is due to shared regulatory mechanisms or due to cell type-specific factors. Reporter gene experiments with cells and cis-regulatory elements from human and cattle show that the difference of CD44 expression is due to cis effects as well as cell type-specific trans effects. These results suggest that the concerted expression increase is likely due to selection acting on both cell types because the evolutionary change in cell type-specific factors requires selection on cell type-specific functions. This scenario implies that the malignancy enhancing effects of elevated CD44 expression in humans likely evolved as a side-effect of positive selection on a yet unidentified other function of CD44. A possible candidate is the anti-fibrotic effect of CD44 but there are no reliable data showing that humans and primates are less fibrotic than other mammals.

3. Metastatic Transition of Pancreatic Ductal Cell Adenocarcinoma Is Accompanied by the Emergence of Pro-Invasive Cancer-Associated Fibroblasts

   Shaofei Liu, Yasir Suhail, Ashkan Novin, Lorrie Perpetua, and  Kshitiz

   Cancers, 2022

   Abs

   Cancer-associated fibroblasts (CAFs) are now appreciated as key regulators of cancer metastasis, particularly in cancers with high stromal content, e.g., pancreatic ductal cell carcinoma (PDAC). However, it is not yet well understood if fibroblasts are always primed to be cooperative in PDAC transition to metastasis, if they undergo transformation which ensures their cooperativity, and if such transformations are cancer-driven or intrinsic to fibroblasts. We performed a fibroblast-centric analysis of PDAC cancer, as it transitioned from the primary site to trespass stromal compartment reaching the lymph node using published single-cell RNA sequencing data by Peng et al. We have characterized the change in fibroblast response to cancer from a normal wound healing response in the initial stages to the emergence of subclasses with myofibroblast and inflammatory fibroblasts such as signatures. We have previously posited “Evolved Levels of Invasibility (ELI)”, a framework describing the evolution of stromal invasability as a selected phenotype, which explains the large and correlated reduction in stromal invasion by placental trophoblasts and cancer cells in certain mammals. Within PDAC samples, we found large changes in fibroblast subclasses at succeeding stages of PDAC progression, with the emergence of specific subclasses when cancer trespasses stroma to metastasize to proximal lymph nodes (stage IIA to IIB). Surprisingly, we found that the initial metastatic transition is accompanied by downregulation of ELI-predicted pro-resistive genes, and the emergence of a subclass of fibroblasts with ELI-predicted increased invasibility. Interestingly, this trend was also observed in stellate cells. Using a larger cohort of bulk RNAseq data from The Cancer Genome Atlas for PDAC cancers, we confirmed that genes describing this emergent fibroblast subclass are also correlated with lymph node metastasis of cancer cells. Experimental testing of selected genes characterizing pro-resistive and pro-invasive fibroblast clusters confirmed their contribution in regulating stromal invasability as a phenotype. Our data confirm that the complexity of stromal response to cancer is really a function of stage-wise emergence of distinct fibroblast clusters, characterized by distinct gene sets which confer initially a predominantly pro-resistive and then a pro-invasive property to the stroma. Stromal response therefore transitions from being tumor-limiting to a pro-metastatic state, facilitating stromal trespass and the onset of metastasis.

4. Recombinant Human Proteoglycan 4 (rhPRG4) Downregulates TNFα-Stimulated NFκB Activity and FAT10 Expression in Human Corneal Epithelial Cells

   Nikhil G. Menon, Yasir Suhail, Ruchi Goyal, Wenqiang Du, Adam P. Tanguay, Gregory D. Jay, Mallika Ghosh,  Kshitiz, and Tannin A. Schmidt

   International Journal of Molecular Sciences, 2022

   Abs

   Dry Eye Disease (DED) is a complex pathology affecting millions of people with significant impact on quality of life. Corneal inflammation, including via the nuclear factor kappa B (NFκB) pathway, plays a key etiological role in DED. Recombinant human proteoglycan 4 (rhPRG4) has been shown to be a clinically effective treatment for DED that has anti-inflammatory effects in corneal epithelial cells, but the underlying mechanism is still not understood. Our goal was to understand if rhPRG4 affects tumor necrosis factor α (TNFα)-stimulated inflammatory activity in corneal epithelial cells. We treated hTERT-immortalized corneal epithelial (hTCEpi) cells ± TNFα ± rhPRG4 and performed Western blotting on cell lysate and RNA sequencing. Bioinformatics analysis revealed that rhPRG4 had a significant effect on TNFα-mediated inflammation with potential effects on matricellular homeostasis. rhPRG4 reduced activation of key inflammatory pathways and decreased expression of transcripts for key inflammatory cytokines, interferons, interleukins, and transcription factors. TNFα treatment significantly increased phosphorylation and nuclear translocation of p65, and rhPRG4 significantly reduced both these effects. RNA sequencing identified human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10), a ubiquitin-like modifier protein which has not been studied in the context of DED, as a key pro-inflammatory transcript increased by TNFα and decreased by rhPRG4. These results were confirmed at the protein level. In summary, rhPRG4 is able to downregulate NFκB activity in hTCEpi cells, suggesting a potential biological mechanism by which it may act as a therapeutic for DED.

5. Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells

   Kshitiz, Junaid Afzal, Yasir Suhail, Hao Chang, Maimon E. Hubbi, Archer Hamidzadeh, Ruchi Goyal, Yamin Liu, Peng Sun, Stefania Nicoli, Chi V. Dang, and Andre Levchenko

   Cell Systems, 2022

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   Response to hypoxia is a highly regulated process, but little is known about single-cell responses to hypoxic conditions. Using fluorescent reporters of hypoxia response factor-1α (HIF-1α) activity in various cancer cell lines and patient-derived cancer cells, we show that hypoxic responses in individual cancer cells can be highly dynamic and variable. These responses fall into three classes, including oscillatory activity. We identify a molecular mechanism that can account for all three response classes, implicating reactive-oxygen-species-dependent chaperone-mediated autophagy of HIF-1α in a subset of cells. Furthermore, we show that oscillatory response is modulated by the abundance of extracellular lactate in a quorum-sensing-like mechanism. We show that oscillatory HIF-1α activity rescues hypoxia-mediated inhibition of cell division and causes broad suppression of genes downregulated in cancers and activation of genes upregulated in many cancers, suggesting a mechanism for aggressive growth in a subset of hypoxic tumor cells.

6. Cardiac ultrastructure inspired matrix induces advanced metabolic and functional maturation of differentiated human cardiomyocytes

   Junaid Afzal, Yamin Liu, Wenqiang Du, Yasir Suhail, Pengyu Zong, Jianlin Feng, Visar Ajeti, Wasim A. Sayyad, Joerg Nikolaus, Maya Yankova, Alix C. Deymier, Lixia Yue, and  Kshitiz

   Cell Reports, 2022

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   The vast potential of human induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs) in preclinical models of cardiac pathologies, precision medicine, and drug screening remains to be fully realized because hiPSC-CMs are immature without adult-like characteristics. Here, we present a method to accelerate hiPSC-CM maturation on a substrate, cardiac mimetic matrix (CMM), mimicking adult human heart matrix ligand chemistry, rigidity, and submicron ultrastructure, which synergistically mature hiPSC-CMs rapidly within 30 days. hiPSC-CMs matured on CMM exhibit systemic transcriptomic maturation toward an adult heart state, are aligned with high strain energy, metabolically rely on oxidative phosphorylation and fatty acid oxidation, and display enhanced redox handling capability, efficient calcium handling, and electrophysiological features of ventricular myocytes. Endothelin-1-induced pathological hypertrophy is mitigated on CMM, highlighting the role of a native cardiac microenvironment in withstanding hypertrophy progression. CMM is a convenient model for accelerated development of ventricular myocytes manifesting highly specialized cardiac-specific functions.

7. Tracing the cis-regulatory changes underlying the endometrial control of placental invasion

   Yasir Suhail, Jamie D. Maziarz, Ashkan Novin, Anasuya Dighe, Junaid Afzal, Gunter Wagner, and  Kshitiz

   Proceedings of the National Academy of Sciences of the United States of America, 2022

   Abs

   Among eutherian (placental) mammals, placental embedding into the maternal endometrium exhibits great differences, from being deeply invasive (e.g., humans) to noninvasive (e.g., cattle). The degree of invasion of placental trophoblasts is positively correlated with the rate of cancer malignancy. Previously, we have shown that fibroblasts from different species offer different levels of resistance to the invading trophoblasts as well as to cancer cell invasion. Here we present a comparative genomic investigation revealing cis-regulatory elements underlying these interspecies differences in invasibility. We identify transcription factors that regulate proinvasibility and antiinvasibility genes in stromal cells. Using an in vitro invasibility assay combined with CRISPR-Cas9 gene knockout, we found that the transcription factors GATA2 and TFDP1 strongly influence the invasibility of endometrial and skin fibroblasts. This work identifies genomic mechanisms explaining species differences in stromal invasibility, paving the way to therapies targeting stromal characteristics to regulate placental invasion, wound healing, and cancer dissemination.

2021

1. Diversity in cancer invasion phenotypes indicates specific stroma regulated programs

   Ashkan Novin, Yasir Suhail, Visar Ajeti, Ruchi Goyal, Khadija Wali, Atta Seck, Alex Jackson, and  Kshitiz

   Human Cell, 2021

   Abs

   Tumor dissemination into the surrounding stroma is the initial step in a metastatic cascade. Invasion into stroma is a non-autonomous process for cancer, and its progression depends upon the stage of cancer, as well as the cells residing in the stroma. However, a systems framework to understand how stromal fibroblasts resist, collude, or aid cancer invasion has been lacking, limiting our understanding of the role of stromal biology in cancer metastasis. We and others have shown that gene perturbation in stromal fibroblasts can modulate cancer invasion into the stroma, highlighting the active role stroma plays in regulating its own invasion. However, cancer invasion into stroma is a complex higher-order process and consists of various sub-phenotypes that together can result in an invasion. Stromal invasion exhibits a diversity of modalities in vivo. It is not well understood if these diverse modalities are correlated, or they emanate from distinct mechanisms and if stromal biology could regulate these characteristics. These characteristics include the extent of invasion, formation, and persistence of invasive forks by cancer as opposed to a collective frontal invasion, the persistence of invading velocity by leader cells at the tip of invasive forks, etc. We posit that quantifying distinct aspects of collective invasion can provide useful suggestions about the plausible mechanisms regulating these processes, including whether the process is regulated by mechanics or by intercellular communication between stromal cells and cancer. Here, we have identified the sub-characteristics of invasion, which might be indicative of broader mechanisms regulating these processes, developed methods to quantify these metrics, and demonstrated that perturbation of stromal genes can modulate distinct aspects of collective invasion. Our results highlight that the genetic state of stromal fibroblasts can regulate complex phenomena involved in cancer dissemination and suggest that collective cancer invasion into stroma is an outcome of the complex interplay between cancer and stromal fibroblasts.

2. Evolved resistance to placental invasion secondarily confers increased survival in melanoma patients

   Yasir Suhail, Junaid Afzal, and  Kshitiz

   Journal of Clinical Medicine, 2021

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   Mammals exhibit large differences in rates of cancer malignancy, even though the tumor formation rates may be similar. In placental mammals, rates of malignancy correlate with the extent of placental invasion. Our Evolved Levels of Invasibility (ELI) framework links these two phenomena identifying genes that potentially confer resistance in stromal fibroblasts to limit invasion, from trophoblasts in the endometrium, and from disseminating melanoma in the skin. Herein, using patient data from The Cancer Genome Atlas (TCGA), we report that these anti-invasive genes may be crucial in melanoma progression in human patients, and that their loss is correlated with increased cancer spread and lowered survival. Our results suggest that, surprisingly, these anti-invasive genes, which have lower expression in humans compared to species with non-invasive placentation, may potentially prevent stromal invasion, while a further reduction in their levels increases the malignancy and lethality of melanoma. Our work links evolution, comparative biology, and cancer progression across tissues, indicating new avenues for using evolutionary medicine to prognosticate and treat human cancers.

3. Incorporating and addressing testing bias within estimates of epidemic dynamics for SARS-CoV-2

   Yasir Suhail, Junaid Afzal, and  Kshitiz

   BMC Medical Research Methodology, 2021

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   Background: The disease burden of SARS-CoV-2 as measured by tests from various localities, and at different time points present varying estimates of infection and fatality rates. Models based on these acquired data may suffer from systematic errors and large estimation variances due to the biases associated with testing. An unbiased randomized testing to estimate the true fatality rate is still missing. Methods: Here, we characterize the effect of incidental sampling bias in the estimation of epidemic dynamics. Towards this, we explicitly modeled for sampling bias in an augmented compartment model to predict epidemic dynamics. We further calculate the bias from differences in disease prediction from biased, and randomized sampling, proposing a strategy to obtain unbiased estimates. Results: Our simulations demonstrate that sampling biases in favor of patients with higher disease manifestation could significantly affect direct estimates of infection and fatality rates calculated from the numbers of confirmed cases and deaths, and serological testing can partially mitigate these biased estimates. Conclusions: The augmented compartmental model allows the explicit modeling of different testing policies and their effects on disease estimates. Our calculations for the dependence of expected confidence on a randomized sample sizes, show that relatively small sample sizes can provide statistically significant estimates for SARS-CoV-2 related death rates.

4. Artificial Intelligence for radiographic image analysis

   Shivam Mehta, Yasir Suhail, John Nelson, and Madhur Upadhyay

   Seminars in Orthodontics, 2021

   Abs

   Automated identification of landmarks on lateral cephalogram and cone-beam computed tomography (CBCT) scans can save time for the clinicians and act as a second set of eyes for analysis of radiographic images in diagnosis and treatment planning. Several machine-learning techniques have been utilized for this purpose with varying accuracies. However, high degree of variability in the clinical presentation of orthodontic patients, limitations of the algorithms, lack of labelled data, high compute power, etc. are some drawbacks that have limited robust clinical application of such techniques. In recent years, artificial neural networks like deep learning and more specifically deep neural networks are making significant inroads in the true adoption of this technology. YOLOv3 and Single Shot Multibox Detector are some of the deep learning algorithms that have shown promising results. This paper is a theoretical review of the evolution of these technologies and the current state of the art in orthodontic image analysis.

2020

1. Machine learning for the diagnosis of orthodontic extractions: A computational analysis using ensemble learning

   Yasir Suhail, Madhur Upadhyay, Aditya Chhibber, and  Kshitiz

   Bioengineering, 2020

   Abs

   Extraction of teeth is an important treatment decision in orthodontic practice. An expert system that is able to arrive at suitable treatment decisions can be valuable to clinicians for verifying treatment plans, minimizing human error, training orthodontists, and improving reliability. In this work, we train a number of machine learning models for this prediction task using data for 287 patients, evaluated independently by five different orthodontists. We demonstrate why ensemble methods are particularly suited for this task. We evaluate the performance of the machine learning models and interpret the training behavior. We show that the results for our model are close to the level of agreement between different orthodontists.

2019

1. Cell Systems Review Systems Biology of Cancer Metastasis

   Yasir Suhail, Margo P Cain, Kiran Vanaja, Paul A Kurywchak, Andre Levchenko, and Raghu Kalluri

   Cell Systems, 2019

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   Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon. Introduction Cancer metastasis, the processes involving dissemination of cancer cells from a primary lesion to distal organs, is the principal cause of cancer lethality. Dissemination of cells from a primary tumor involves a variety of cellular mechanisms. These include invading through, or colluding with, stroma, escaping immune surveillance by inhibiting or co-opting their anti-tumor-igenic processes, evading and modulating the tissue microen-vironment, and evolving resistance to therapeutic intervention (Fischer et al., 2015; Kalluri, 2016; Li et al., 2016b; Massagué and Obenauf, 2016). Recent reports provide strong evidence that metastasis is non-linear and involves multiple parallel overlapping routes (Harper et al., 2016; Lambert et al., 2017; Te Boekhorst and Friedl, 2016). The reductive disease models that were necessary to establish the field of metastasis research and provide foundational concepts are limited in completely characterizing metastasis owing to the integrated and complex nature of its constituent processes. The multi-parametric and multiscale nature of cancer metastasis warrants a renewed focus on comprehensive experimental and computational approaches that provide systems-level insight, versus the investigation of isolated steps in a complex network of events. Systems biology approaches that result in predic-tive and testable models of complex phenotypes through integration of expertise from diverse fields including cancer biology, oncology, genetics, mathematics, bioinformatics, imaging , physics, and computer science could provide a more holistic understanding of the complete metastatic process. In this review, we present insights into the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of investigating the processes involved in invasive spread of cancer cells. We highlight the gaps in our understanding of steps involved in tumor metastasis and insights emerging from interdisciplinary systems biology approaches to this important cancer process.

2. Single-cell connectomic analysis of adult mammalian lungs

   Micha Sam, Brickman Raredon , Taylor Sterling Adams, Yasir Suhail, Jonas Christian Schupp, Sergio Poli, Nir Neumark, Katherine L Leiby, Allison Marie Greaney, Yifan Yuan, Corey Horien, George Linderman, Alexander J Engler, Daniel J Boffa, Yuval Kluger, Ivan O Rosas, Andre Levchenko, Naftali Kaminski, and Laura E Niklason

   Science Advances, 2019

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   Efforts to decipher chronic lung disease and to reconstitute functional lung tissue through regenerative medicine have been hampered by an incomplete understanding of cell-cell interactions governing tissue homeostasis. Because the structure of mammalian lungs is highly conserved at the histologic level, we hypothesized that there are evolutionarily conserved homeostatic mechanisms that keep the fine architecture of the lung in balance. We have leveraged single-cell RNA sequencing techniques to identify conserved patterns of cell-cell cross-talk in adult mammalian lungs, analyzing mouse, rat, pig, and human pulmonary tissues. Specific stereotyped functional roles for each cell type in the distal lung are observed, with alveolar type I cells having a major role in the regulation of tissue homeostasis. This paper provides a systems-level portrait of signaling between alveolar cell populations. These methods may be applicable to other organs, providing a roadmap for identifying key pathways governing pathophysiology and informing regenerative efforts.

3. Dynamic secretome of bone marrow-derived stromal cells reveals a cardioprotective biochemical cocktail

   Kshitiz, David D. Ellison, Yasir Suhail, Junaid Afzal, Laura Woo, Onur Kilic, Jeffrey Spees, and Andre Levchenko

   Proceedings of the National Academy of Sciences of the United States of America, 2019

   Abs

   Transplanted stromal cells have demonstrated considerable promise as therapeutic agents in diverse disease settings. Paracrine signaling can be an important mediator of these therapeutic effects at the sites of acute or persistent injury and inflammation. As many stromal cell types, including bone marrow-derived stromal cells (BMSCs), display tissue-specific responses, there is a need to explore their secretory dynamics in the context of tissue and injury type. Paracrine signals are not static, and could encode contextual dynamics in the kinetic changes of the concentrations of the secreted ligands. However, precise measurement of dynamic and context-specific cellular secretory signatures, particularly in adherent cells, remains challenging. Here, by creating an experimental and computational analysis platform, we reconstructed dynamic secretory signatures of cells based on a very limited number of time points. By using this approach, we demonstrate that the secretory signatures of CD133-positive BMSCs are uniquely defined by distinct biological contexts, including signals from injured cardiac cells undergoing oxidative stress, characteristic of cardiac infarction. Furthermore, we show that the mixture of recombinant factors reproducing the dynamics of BMSC-generated secretion can mediate a highly effective rescue of cells injured by oxidative stress and an improved cardiac output. These results support the importance of the dynamic multifactorial paracrine signals in mediating remedial effects of stromal stem cells, and pave the way for stem cell-inspired cell-free treatments of cardiac and other injuries.

4. E-cadherin is required for metastasis in multiple models of breast cancer

   Veena Padmanaban, Ilona Krol, Yasir Suhail, Barbara M. Szczerba, Nicola Aceto, Joel S. Bader, and Andrew J. Ewald

   Nature, 2019

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   Metastasis is the major driver of death in patients with cancer. Invasion of surrounding tissues and metastasis have been proposed to initiate following loss of the intercellular adhesion protein, E-cadherin1,2, on the basis of inverse correlations between in vitro migration and E-cadherin levels3. However, this hypothesis is inconsistent with the observation that most breast cancers are invasive ductal carcinomas and express E-cadherin in primary tumours and metastases4. To resolve this discrepancy, we tested the genetic requirement for E-cadherin in metastasis using mouse and human models of both luminal and basal invasive ductal carcinomas. Here we show that E-cadherin promotes metastasis in diverse models of invasive ductal carcinomas. While loss of E-cadherin increased invasion, it also reduced cancer cell proliferation and survival, circulating tumour cell number, seeding of cancer cells in distant organs and metastasis outgrowth. Transcriptionally, loss of E-cadherin was associated with upregulation of genes involved in transforming growth factor-β (TGFβ), reactive oxygen species and apoptosis signalling pathways. At the cellular level, disseminating E-cadherin-negative cells exhibited nuclear enrichment of SMAD2/3, oxidative stress and increased apoptosis. Colony formation of E-cadherin-negative cells was rescued by inhibition of TGFβ-receptor signalling, reactive oxygen accumulation or apoptosis. Our results reveal that E-cadherin acts as a survival factor in invasive ductal carcinomas during the detachment, systemic dissemination and seeding phases of metastasis by limiting reactive oxygen-mediated apoptosis. Identifying molecular strategies to inhibit E-cadherin-mediated survival in metastatic breast cancer cells may have potential as a therapeutic approach for breast cancer.

5. Single-cell connectomic analysis of adult mammalian lungs

   Micha Sam Brickman Raredon , Taylor Sterling Adams, Yasir Suhail, Jonas Christian Schupp, Sergio Poli, Nir Neumark, Katherine L. Leiby, Allison Marie Greaney, Yifan Yuan, Corey Horien, George Linderman, Alexander J. Engler, Daniel J. Boffa, Yuval Kluger, Ivan O. Rosas, Andre Levchenko, Naftali Kaminski, and Laura E. Niklason

   Science Advances, 2019

   Abs

   Efforts to decipher chronic lung disease and to reconstitute functional lung tissue through regenerative medicine have been hampered by an incomplete understanding of cell-cell interactions governing tissue homeostasis. Because the structure of mammalian lungs is highly conserved at the histologic level, we hypothesized that there are evolutionarily conserved homeostatic mechanisms that keep the fine architecture of the lung in balance. We have leveraged single-cell RNA sequencing techniques to identify conserved patterns of cell-cell cross-talk in adult mammalian lungs, analyzing mouse, rat, pig, and human pulmonary tissues. Specific stereotyped functional roles for each cell type in the distal lung are observed, with alveolar type I cells having a major role in the regulation of tissue homeostasis. This paper provides a systems-level portrait of signaling between alveolar cell populations. These methods may be applicable to other organs, providing a roadmap for identifying key pathways governing pathophysiology and informing regenerative efforts.

6. Systems Biology of Cancer Metastasis

   Yasir Suhail, Margo P. Cain, Kiran Vanaja, Paul A. Kurywchak, Andre Levchenko, Raghu Kalluri, and  Kshitiz

   2019

   Abs

   

   Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon. Cancer metastasis is a complex disease, arising from a growing tumor from which cells escape to other parts of the body. For long, cancer metastasis was considered as a combination of steps, which were studied separately, limiting our understanding of this complex disease. Here, we present the new developments and our perspective on how the new systems biology approach is changing our view of cancer metastasis as an integrated multiscale phenomenon comprising interlinked parts that allow tumors to metastasize.

2016

1. Molecular and systems approaches towards drought-tolerant canola crops

   Mengmeng Zhu, J. Grey Monroe, Yasir Suhail, Florent Villiers, Jack Mullen, Dianne Pater, Felix Hauser, Byeong Wook Jeon, Joel S. Bader, June M. Kwak, Julian I. Schroeder, John K. Mckay, and Sarah M. Assmann

   New Phytologist, 2016

   Abs

   Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.

2015

1. Control of the interface between heterotypic cell populations reveals the mechanism of intercellular transfer of signaling proteins

   Kshitiz, Junaid Afzal, Yasir Suhail, Eun Hyun Ahn, Ruchi Goyal, Maimon E. Hubbi, Qasim Hussaini, David D. Ellison, Jatinder Goyal, Benjamin Nacev, Deok Ho Kim, Justin Ho Lee, Sam Frankel, Kevin Gray, Rashmi Bankoti, Andy J. Chien, and Andre Levchenko

   Integrative Biology (United Kingdom), 2015

   Abs

   Direct intercellular transfer of cellular components is a recently described general mechanism of cell-cell communication. It is a more non-specific mode of intercellular communication that is not actively controlled by the participating cells. Though membrane bound proteins and small non-protein cytosolic components have been shown to be transferred between cells, the possibility of transfer of cytosolic proteins has not been clearly established, and its mechanism remains unexplained. Using a cell-cell pair of metastatic melanoma and endothelial cells, known to interact at various stages during cancer progression, we show that cytosolic proteins can indeed be transferred between heterotypic cells. Using precise relative cell patterning we provide evidence that this transfer depends on extent of the interface between heterotypic cell populations. This result is further supported by a mathematical model capturing various experimental conditions. We further demonstrate that cytosolic protein transfer can have important functional consequences for the tumor-stroma interactions, e.g., in heterotypic transfer of constitutively activated BRAF, a common melanoma associated mutation, leading to an enhanced activation of the downstream MAPK pathway. Our results suggest that cytosolic protein transfer can have important consequences for regulation of processes involving physical co-location of heterotypic cell types, particularly in invasive cancer growth.

2013

1. Modeling Intercellular Transfer of Biomolecules Through Tunneling Nanotubes

   Yasir Suhail,  Kshitiz, Justin Lee, Mark Walker, Deok Ho Kim, Matthew D. Brennan, Joel S. Bader, and Andre Levchenko

   Bulletin of Mathematical Biology, 2013

   Abs

   Tunneling nanotubes (TNTs) have previosly been observed as long and thin transient structures forming between cells and intercellular protein transfer through them has been experimentally verified. It is hypothesized that this may be a physiologically important means of cell-cell communication. This paper attempts to give a simple model for the rates of transfer of molecules across these TNTs at different distances. We describe the transfer of both cytosolic and membrane bound molecules between neighboring populations of cells and argue how the lifetime of the TNT, the diffusion rate, distance between cells, and the size of the molecules may affect their transfer. The model described makes certain predictions and opens a number of questions to be explored experimentally. © 2013 Society for Mathematical Biology.

2008

1. Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions

   Yan Qi, Yasir Suhail, Yu Yi Lin, Jef D. Boeke, and Joel S. Bader

   Genome Research, 2008

   Abs

   The yeast synthetic lethal genetic interaction network contains rich information about underlying pathways and protein complexes as well as new genetic interactions yet to be discovered. We have developed a graph diffusion kernel as a unified framework for inferring complex/pathway membership analogous to "friends" and genetic interactions analogous to "enemies" from the genetic interaction network. When applied to the Saccharomyces cerevisiae synthetic lethal genetic interaction network, we can achieve a precision around 50% with 20% to 50% recall in the genome-wide prediction of new genetic interactions, supported by experimental validation. The kernels show significant improvement over previous best methods for predicting genetic interactions and protein co-complex membership from genetic interaction data. ©2008 by Cold Spring Harbor Laboratory Press.

2007

1. Identifying neuronal assemblies with local and global connectivity with scale space spectral clustering

   Karim Oweiss, Rong Jin, and Yasir Suhail

   Neurocomputing, 2007

   Abs

   A nonparametric approach is proposed to identify clusters of functionally interdependent neurons, independent of the time scale at which they are maximally correlated. The neural point processes are represented in a N-dimensional scale space using the Haar wavelet transform. A similarity measure between any given pair of neurons is defined in the scale space. Clusters of "similar" neurons are identified by first reducing the N-dimensional scale space representation using principal components to obtain a Q-dimensional space. The weighted principal components are subsequently used to connect each neuron to the others in a graph representation. A probabilistic spectral clustering algorithm is used to perform graph partitioning by maximizing cluster compactness. Performance is compared to that of the k-means and the expectation-maximization algorithms for 120 neurons with time-varying intensity functions consisting of spontaneous background activity and phased response elicited at distinct time scales. © 2006 Elsevier B.V. All rights reserved.

2. A scalable wavelet transform VLSI architecture for real-time signal processing in high-density intra-cortical implants

   Karim G. Oweiss, Andrew Mason, Yasir Suhail, Awais M. Kamboh, and Kyle E. Thomson

   IEEE Transactions on Circuits and Systems I: Regular Papers, 2007

   Abs

   This paper describes an area and power-efficient VLSI approach for implementing the discrete wavelet transform on streaming multielectrode neurophysiological data in real time. The VLSI implementation is based on the lifting scheme for wavelet computation using the symmlet4 basis with quantized coefficients and integer fixed-point data precision to minimize hardware demands. The proposed design is driven by the need to compress neural signals recorded with high-density microelectrode arrays implanted in the cortex prior to data telemetry. Our results indicate that signal integrity is not compromised by quantization down to 5-bit filter coefficient and 10-bit data precision at intermediate stages. Furthermore, results from analog simulation and modeling show that a hardware-minimized computational core executing filter steps sequentially is advantageous over the pipeline approach commonly used in DWT implementations. The design is compared to that of a B-spline approach that minimizes the number of multipliers at the expense of increasing the number of adders. The performance demonstrates that in vivo real-time DWT computation is feasible prior to data telemetry, permitting large savings in bandwidth requirements and communication costs given the severe limitations on size, energy consumption and power dissipation of an implantable device. © 2007 IEEE.

3. Genetically encoded molecules for inducibly inactivating CaV channels

   Tingting Yang, Yasir Suhail, Stanislava Dalton, Timothy Kernan, and Henry M. Colecraft

   Nature Chemical Biology, 2007

   Abs

   Voltage-gated Ca2+ (CaV) channels are central to the biology of excitable cells, and therefore regulating their activity has widespread applications. We describe genetically encoded molecules for inducibly inhibiting CaV channels (GEMIICCs). GEMIICCs are derivatives of Rem, a Ras-like GTPase that constitutively inhibits Ca2+ currents (I Ca). C terminus-truncated Rem1-265 lost the ability to inhibit ICa owing to loss of membrane targeting. Fusing the C1 domain of protein kinase Cγ to yellow fluorescent protein (YFP)-Rem 1-265 generated a molecule that rapidly translocated from cytosol to plasma membrane with phorbol-12,13-dibutyrate in human embryonic kidney cells. Recombinant CaV2.2 and CaV1.2 channels were inhibited concomitantly with C1PKCγ-YFP-Rem1-265 membrane translocation. The generality of the approach was confirmed by creating a GEMIICC using rapamycin-dependent heterodimerization of YFP-FKBP-Rem 1-265 and a constitutively membrane-targeted rapamycin-binding domain. GEMIICCs reduced ICa without diminishing gating charge, thereby ruling out decreased number of surface channels and voltage-sensor immobilization as mechanisms for inhibition. We introduce small-molecule- regulated GEMIICCs as potent tools for rapidly manipulating Ca2+ signals in excitable cells. © 2007 Nature Publishing Group.

2006

1. A mixture model for spike train ensemble analysis using spectral clustering

   Rong Jin, Yasir Suhail, and Karim Oweiss

   In ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings, 2006

   Abs

   Identifying clusters of neurons with correlated spiking activity in large-size neuronal ensembles recorded with highdensity multielectrode array is an emerging problem in computational neuroscience. We propose a nonparametric approach that represents multiple neural spike trains by a mixed point process model. A spectral clustering algorithm is applied to identify the clusters of neurons through their correlated firing activities. The advantage of the proposed technique is its ability to efficiently identify large populations of neurons with correlated spiking activity independent of the temporal scale. We report the clustering performance of the algorithm applied to a complex synthesized data set and compare it to multiple clustering techniques. © 2006 IEEE.

2. B-Spline vs. Lifting architecture for neuroprosthetic devices

   Kyle E. Thomson, Theo Shlien, Yasir Suhail, Andrew Mason, and Karim G. Oweiss

   In 2006 IEEE International Conference on Electro Information Technology, 2006

   Abs

   Advances in high-density microelectrode arrays has created a need for high level signal processing to cope with the immense data throughput. The Discrete Wavelet Transform (DWT) has been shown to optimally reduce the amount of data throughput, while concisely preserving the information in the data. Two factorizations, Lifting and B-spline, have been proposed for implementing the DWT in hardware. A comparison based on critical path, memory requirements, and computational hardware is drawn. The context of this comparison focuses on multichannel and multiresolution neuroprosthetic devices.

3. Augmenting information channels in hearing aids and cochlear implants under adverse conditions

   Yasir Suhail, and Karim G. Oweiss

   In ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings, 2006

   Abs

   We conceptualize a new signal processing strategy to better represent the temporal and spectral cues in speech signals for Hearing Aid (HA) and Cochlear Implant (CI) applications under severe adverse conditions. The proposed approach rests on two well studied methods for signal separation and noise suppression, namely, the denoising and function approximation capabilities of the wavelet transform, blended with signal subspace decomposition through low rank approximation. The technique targets suppression of "competing voice" type noises. A cost function is defined to obtain a "best basis" representation of the desired speech signal for which an inherent invariance property of the signal subspace is observed. This allows better separation of the speech-like noise in contrast to classical bandpass filtering currently employed in CI and HA devices. We demonstrate the efficiency of the proposed method in capturing the rapid dynamics of speech signals, while minimizing the masking effects of noise, in addition to improved recognition rates in normal hearing listeners. The technique remains to be tested on actual patients. © 2006 IEEE.

2005

1. A scalable architecture for streaming neural information from implantable multichannel neuroprosthetic devices

   Kyle E. Thomson, Yasir Suhail, and Karim G. Oweiss

   In Proceedings - IEEE International Symposium on Circuits and Systems, 2005

   Abs

   Two hardware architectures for implementing lifting-based discrete wavelet transform (DWT) suitable for implantable, real-time operation of high-density sensor array neuroprosthetic devices. A core computational node (CN) is designed for use in both architectures to yield maximum processor usage. The first uses multiple pipelined replicas of the CN, requiring fewer clock cycles. The second architecture reuses a single CN, thus requires less chip area but longer time delay. By utilizing the difference between the data sampling rate and available computation bandwidth, the novelty of both designs lies in the scalability to an arbitrary number of channels by interleaving the DWT computation without affecting the real-time operability. Performance comparison and overall considerations of both designs are presented in details. © 2005 IEEE.