About

Sameer Shakir, MD, is an Assistant Professor of Surgery at the Children's Hospital of Philadelphia within the Department of Surgery. He completed his undergraduate studies with a BS in Economics, graduating summa cum laude from the University of Pittsburgh in 2010, and earned his MD from the University of Pittsburgh School of Medicine in 2015. His professional focus includes pediatric craniofacial surgery, with research contributions in areas such as mandibular distraction osteogenesis, cranial vault remodeling, and ear reconstruction. Dr. Shakir has authored multiple publications on these topics, contributing to the advancement of surgical techniques and outcomes in pediatric craniofacial procedures.

Research topics

• Medicine
• Surgery
• Dentistry
• Orthodontics
• General surgery

Selected publications

• Discussion: A Comparison of Surgical Techniques for Macroglossia in Beckwith-Wiedemann Syndrome

  Plastic & Reconstructive Surgery · 2026-03-25

  article1st authorCorresponding
  PublisherDOI

• Optimizing Release Dynamics Of Encapsulated Materials In Bone Derived Nanoparticles

  Zenodo (CERN European Organization for Nuclear Research) · 2026-05-08

  articleOpen accessSenior author

  Introduction: A lack of bone and a dearth of renewable autologous bone grafting sources introduce significant challenges in the treatment of orofacial clefts. Few bioengineered materials exist that can be dynamically modified to fit the variety of clinical scenarios encountered in the treatment of these craniofacial conditions. Our lab previously developed an indocyanine green encapsulated bone-based nanoparticle (ICG/BPs) capable of bone regeneration and real-time healing visualization using non-ionizing Near Infrared (NIR) fluorescence imaging in a small animal model. In this study, we sought to further modify the ICG/BPs and assess the spatial and temporal release kinetics of encapsulated ICG. We hypothesized that alteration of the ICG/BPs would affect the release kinetics of encapsulated ICG in vivo. Methods: Unmodified ICG/BPs were fabricated using previous methods; they are denoted in this study as uncrosslinked ICG/BPs (UnX ICG/BPs). Glutaraldehyde was used as a crosslinking agent in the fabrication process to create crosslinked ICG/BPs (X ICG/BPs). Non-healing maxillary alveolar cleft defects were created in adult rats and separated into 4 groups: 1) Control, 2) Defects with no treatment, 3) Defects with UnX ICG/BPs, and 4) Defects with X ICG/BPs. NIR imaging was conducted on days 1, 3, 7, 10, and 14 and weekly thereafter up to 8 weeks, after which alveolar tissues were dissected to evaluate regenerative efficacy grossly, using CT, and with histologic analysis. Results: Analysis of NIR imaging revealed a more rapid, burst-style release profile for the UnX ICG/BPs compared to X ICG/BPs. Fluorescent signal in the UnX group decreased rapidly to less than 65% of its original value within the first 7 days and was undetectable after day 42. While in the X group, a sustained, dynamic release rate was observed with the signal continuing to be detectable and localized to the defect site at day 42. Gross and microscopic observation demonstrated no signs of necrosis or abnormal tissue surrounding the defect site in treatment groups. The UnX group demonstrated moderate defect regeneration with limited hard tissue ingrowth. The X group exhibited the greatest regeneration, with substantial calcified bone and no surface fibrous tissue. Ex vivo, CT, histological, and immunofluorescent analysis supported these findings, showing the most calcified bone regeneration and vascular ingrowth in the X group. Conclusion: These results highlight the promising potential of the ICG/BPs to act as a modifiable alternative grafting strategy. The ability to alter the release kinetics of encapsulated materials within the BPs presents many opportunities, particularly in addressing challenges associated with the off-label use of osteogenic growth factors. This dual-therapeutic system can be designed to match the physiological requirements of healing while releasing growth factors in a precise manner. By encapsulating NIR-capable fluorophores, we can non-invasively monitor and quantify release kinetics of encapsulated materials, and model regenerative outcomes based on fluorescence outputs, obviating the need for ionizing-based imaging techniques. These results demonstrate that the BPs represent a promising theranostic material for bone regeneration in orofacial clefting that can be tailored to fit many clinical situations. *Source: https://ps-rc.org/meeting/Program/2026/AS53.cgi*

  PublisherDOI

• Optimizing release dynamics of bone-derived nanoparticles for enhanced <i>in vivo</i> fluorescence monitoring and bone regeneration in craniofacial repair

  Biofabrication · 2026-01-20

  article

  Craniofacial bone defects, particularly alveolar clefts, pose significant clinical challenges in pediatric patients due to complex anatomy and the limitations of current grafting options. Although autologous bone grafts remain the clinical gold standard, their use is restricted by donor-site morbidity, limited tissue availability, high cost, and risks such as infection, chronic pain, and functional impairment. Decellularized and demineralized bone matrix (DDBM) offers an attractive alternative but lacks controlled drug-release capability and cannot be monitored in real time in patients. To address these limitations, we developed indocyanine green-encapsulated bone-derived nanoparticles (ICG/BPs) from porcine DDBM, combining the intrinsic osteoinductive and osteoconductive properties of DDBM with near-infrared (NIR) imaging functionality. In this study, we fabricated two ICG/BP formulations , crosslinked (X-ICG/BP) and uncrosslinked (UnX-ICG/BP), and compared their in vitro degradation, release profiles, and in vivo performance in a rat model of cavity-type alveolar defects. Crosslinking improved particle stability and prolonged ICG release, and NIR imaging enabled real-time, non-invasive monitoring of particle degradation and retention within the defect. Additionally, both ICG/BP formulations supported bone regeneration, with X-ICG/BPs demonstrating greater regeneration, tissue organization, and vascularization. Overall, these findings highlight the tunability and theranostic potential of ICG/BPs and support their continued development as an image-guided functional biomaterial for craniofacial bone repair.

  PublisherDOI

• Optimizing Release Dynamics Of Encapsulated Materials In Bone Derived Nanoparticles

  Zenodo (CERN European Organization for Nuclear Research) · 2026-05-08

  articleOpen accessSenior author

  Introduction: A lack of bone and a dearth of renewable autologous bone grafting sources introduce significant challenges in the treatment of orofacial clefts. Few bioengineered materials exist that can be dynamically modified to fit the variety of clinical scenarios encountered in the treatment of these craniofacial conditions. Our lab previously developed an indocyanine green encapsulated bone-based nanoparticle (ICG/BPs) capable of bone regeneration and real-time healing visualization using non-ionizing Near Infrared (NIR) fluorescence imaging in a small animal model. In this study, we sought to further modify the ICG/BPs and assess the spatial and temporal release kinetics of encapsulated ICG. We hypothesized that alteration of the ICG/BPs would affect the release kinetics of encapsulated ICG in vivo. Methods: Unmodified ICG/BPs were fabricated using previous methods; they are denoted in this study as uncrosslinked ICG/BPs (UnX ICG/BPs). Glutaraldehyde was used as a crosslinking agent in the fabrication process to create crosslinked ICG/BPs (X ICG/BPs). Non-healing maxillary alveolar cleft defects were created in adult rats and separated into 4 groups: 1) Control, 2) Defects with no treatment, 3) Defects with UnX ICG/BPs, and 4) Defects with X ICG/BPs. NIR imaging was conducted on days 1, 3, 7, 10, and 14 and weekly thereafter up to 8 weeks, after which alveolar tissues were dissected to evaluate regenerative efficacy grossly, using CT, and with histologic analysis. Results: Analysis of NIR imaging revealed a more rapid, burst-style release profile for the UnX ICG/BPs compared to X ICG/BPs. Fluorescent signal in the UnX group decreased rapidly to less than 65% of its original value within the first 7 days and was undetectable after day 42. While in the X group, a sustained, dynamic release rate was observed with the signal continuing to be detectable and localized to the defect site at day 42. Gross and microscopic observation demonstrated no signs of necrosis or abnormal tissue surrounding the defect site in treatment groups. The UnX group demonstrated moderate defect regeneration with limited hard tissue ingrowth. The X group exhibited the greatest regeneration, with substantial calcified bone and no surface fibrous tissue. Ex vivo, CT, histological, and immunofluorescent analysis supported these findings, showing the most calcified bone regeneration and vascular ingrowth in the X group. Conclusion: These results highlight the promising potential of the ICG/BPs to act as a modifiable alternative grafting strategy. The ability to alter the release kinetics of encapsulated materials within the BPs presents many opportunities, particularly in addressing challenges associated with the off-label use of osteogenic growth factors. This dual-therapeutic system can be designed to match the physiological requirements of healing while releasing growth factors in a precise manner. By encapsulating NIR-capable fluorophores, we can non-invasively monitor and quantify release kinetics of encapsulated materials, and model regenerative outcomes based on fluorescence outputs, obviating the need for ionizing-based imaging techniques. These results demonstrate that the BPs represent a promising theranostic material for bone regeneration in orofacial clefting that can be tailored to fit many clinical situations. *Source: https://ps-rc.org/meeting/Program/2026/AS53.cgi*

  PublisherDOI

• A Comprehensive Approach to Robin Sequence

  Clinics in Plastic Surgery · 2025-01-08 · 2 citations

  review1st authorCorresponding
  PublisherDOI

• 112. Alternative Bone-grafting Nanomaterials: A Nanoparticle-based Treatment and Assessment Tool for Autologous Bone Grafting

  Plastic & Reconstructive Surgery Global Open · 2025-04-24

  articleOpen access

  PURPOSE: Autologous bone grafting in the immature craniofacial skeleton continues to be a challenge across a spectrum of disease processes. Limitations include a dearth of donor sites, donor site morbidity, potential resorption, and an immature diploic space in young children. Our laboratory’s recent work has demonstrated the feasibility of turning bone tissue into nanoparticles for tissue engineering applications in the craniofacial skeleton. The ICG/BPs, bone-based nanoparticles (BPs) with encapsulated indocyanine green dye (ICG), can be used as a therapeutic bone-grafting material with in-situ, real time monitoring using non-ionizing Near-Infrared fluorescence imaging (NIR). In this study, we sought to determine if this multi-functional treatment and assessment tool could serve as a viable substitute for repairing non-healing calvarial bone defects in a small animal model. We hypothesized that ICG/BPs allow for sustained calvarial bone healing that can be spatially and temporally controlled and inversely correlated with real-time fluorescence using NIR imaging. METHODS: ICG/BPs were synthesized using previously established methods, and to enhance therapeutic efficacy, bone morphogenetic protein 2 (BMP2) peptide was additionally encapsulated, creating ICG/BMP2/BPs. The regenerative efficacy and NIR monitoring capabilities were tested in vivo using 8-week-old rats with bilateral non-healing calvarial defects. The defects were divided into two groups: 1) one side untreated, the other treated with ICG/BPs, and 2) one side untreated, the other treated with ICG/BMP2/BPs. NIR imaging was conducted at various intervals over 10 weeks to assess material degradation, and post-euthanasia, skulls were analyzed for osteogenic capacity and bone growth. RESULTS: Over the course of 10 weeks, we found a robust NIR imaging capability of both the ICG/BPs and ICG/BMP2/BPs which enabled us to accurately measure and quantify the material degradation within the defect. Using this quantification method, we determined a difference in the degradation kinetics of each material, with the ICG/BPs degrading at a more rapid pace than the ICG/BMP2/BPs, having lost all fluorescence by days 35 and 56, respectively. Ex vivo analysis of the bone tissues using gross observations and computed tomography (CT) indicated the ICG/BPs were effective at stimulating bone growth when compared to a non-treated defect. However, the addition of BMP2 appeared to improve the therapeutic efficacy of the BPs, with the ICG/BMP2/BP group showing near-complete bone growth. CONCLUSION: Bone-based nanoparticles applied to a non-healing calvarial defect model were associated with bone regeneration that can be tracked in real time using non-ionizing fluorescence-based imaging. The nanoparticle functionality includes 1) robust imaging capabilities for in vivo monitoring that inversely correlates with bone healing, 2) spatial and temporal control of tissue regeneration, and 3) effective bone-stimulating capabilities. NIR imaging revealed varying release kinetics between regular BPs and BMP2/BPs, possibly contributing to the quality and quantity of bone tissue formed after 10 weeks. Future directions will include a thorough investigation into the kinetics of each material over time and how the degradation of the BPs, with subsequent ICG and BMP2 release, can be translated into a fully reliable treatment and assessment option for calvarial defect repair.

  PublisherDOI

• Long-Term Midfacial Growth and Speech Outcomes Following Modified Furlow Double-Opposing Z-Palatoplasty

  The Cleft Palate-Craniofacial Journal · 2025-07-15 · 1 citations

  article1st author

  Objective Modified Furlow palatoplasty shows favorable early speech results, however long-term outcomes of midfacial growth and speech have not been fully described. Design A retrospective cohort study was performed of subjects undergoing modified Furlow palatoplasty for primary repair of Veau III and IV cleft lip/palate during a 20-year period. Dentofacial and speech results were analyzed at skeletal maturity using cephalometrics and Pittsburgh Weighted Speech Scores, respectively. Results Subjects ( n = 186) presented with Veau III (62.9%) and IV (37.1%) clefts. Rates of oronasal fistula (ONF) and velopharyngeal dysfunction (VPD) indicating secondary surgery for speech following palatoplasty were 6.5% and 5.9% in the nonsyndromic cohort. Competent velopharyngeal mechanisms (Pittsburgh Weight Speech Score 0-2) in nonsyndromic subjects were noted in 88.3% postpalatoplasty; resonance deterioration was noted in 5.9% postorthodontic expansion and 14.7% postorthognathic surgery (cumulative VPD 27.8%). At skeletal maturity, 59.2% of nonsyndromic subjects (Veau III 51.4%, Veau IV 74.1%) demonstrated midface hypoplasia according to Steiner analysis and 54.0% ultimately underwent orthognathic surgery (OGS) (III 46.2%, IV 68.4%). Presence of midface hypoplasia correlated with Veau class ( P &lt; .003) and presurgical nasoalveolar molding ( P &lt; .02). Neither age at repair ( P &lt; .90), surgeon ( P &lt; 1.0), prior lip adhesion ( P &lt; .72), use of vomerine flaps at time of palate repair ( P &lt; .33), nor syndromic status ( P &lt; .074) correlated with midface hypoplasia. Veau IV clefts demonstrated the highest rate of midface hypoplasia ( P &lt; .004). Conclusions Speech outcomes in the long term indicate adequate velopharyngeal competency using the modified Furlow palatoplasty. OGS for midface hypoplasia was indicated in over half of patients presenting with severe Veau type cleft phenotypes.

  PublisherDOI

• Enhanced Recovery After Surgery in Patients With Cleft Lip and Palate Undergoing Alveolar Bone Grafting: A Review

  The Cleft Palate-Craniofacial Journal · 2025-09-18

  reviewSenior authorCorresponding

  IntroductionEnhanced Recovery After Surgery (ERAS) protocols are evidence-based perioperative management pathways designed to optimize surgical outcomes. The American Society of Craniofacial Surgeons (ASCFS) Presidential Task Force has developed a series of ERAS protocols for patients with cleft and craniofacial anomalies. We outline an ERAS protocol for secondary alveolar bone grafting using cancellous bone graft from the iliac crest for patients with cleft lip and palate.Design and settingThe authors extracted information from existing peer-reviewed literature and our institutional experience at a large, tertiary pediatric hospital through retrospective chart review to guide surgeons in the pre-hospitalization, preoperative, intraoperative, and postoperative phases of care of alveolar bone grafting.ResultsIn the pre-hospitalization phase, our ERAS protocol emphasizes family education and expectation management, as well as minimization of preoperative fasting. In the preoperative phase, oral midazolam is recommended to reduce patient anxiety. In the intraoperative phase, we emphasize multimodal pain control with regional nerve blocks, bupivacaine-soaked absorbable sponge in the iliac crest, and ketorolac to minimize postoperative narcotic use. To prevent postoperative nausea and vomiting, we emphasize the use of an oropharyngeal pack prior to incision and nasogastric tube evacuation of the gastric contents at the completion of surgery, as well as a combination of ondansetron with dexamethasone intraoperatively. In the postoperative phase, we recommend dexmedetomidine, early postoperative oral feeding and hydration, and early ambulation with Physical Therapy consultation.ConclusionsThe present study sought to outline an ERAS protocol for secondary alveolar bone grafting in pediatric patients with cleft lip and/or palate to optimize surgical outcomes.

  PublisherDOI

• Using Digested and Lyophilized Bone Matrices to Enhance Retention and Sustained Release of BMP-2 for Bone Regeneration

  Journal of Craniofacial Surgery · 2025-07-03 · 1 citations

  articleCorresponding

  BACKGROUND: Human recombinant bone morphogenetic protein 2 (rhBMP-2) is an FDA-approved growth factor that is shown to induce new bone formation but includes safety risks like inflammation and ectopic bone formation. Research indicates that a prolonged, controlled release of rhBMP-2 enhances bone healing with fewer side effects than short-term release. Collagen sponges, commonly used for this purpose, have drawbacks including poor structural stability and inadequate release profiles. Current research is focused on improving rhBMP-2 delivery strategies, particularly for pediatric patients where its use is considered off-label. METHODS: The authors' previous study developed a sponge-like gellable bone matrix from decellularized, demineralized, and enzymatically digested porcine bone that demonstrated both biocompatibility and bone regenerative capabilities. This study expands our previous work by infusing synthetic BMP2 (sBMP2) into digested and lyophilized bone matrix (DLBM) and stabilizing it with glutaraldehyde (GL) crosslinking, referred to as DLBM/sBMP2/GL scaffold. The authors evaluate the release of sBMP2 in vitro from within the DLBM post stabilization, and the overall effectiveness of the DLBM/sBMP2/GL scaffold at stimulating bone growth in vivo using a nonhealing, surgically created tibial defect in a small animal model. RESULTS: The DLBM/sBMP2/GL scaffold offers a prolonged and sustained release of sBMP2 in vitro and demonstrates biocompatibility and osteogenicity in vivo, resulting in substantial bone regeneration based on the gradual scaffold degradation with the sustained release of sBMP2. CONCLUSIONS: The resulting DLBM/sBMP2/GL scaffold provides a promising alternative grafting option for pediatric patients, offering improved safety and efficacy over existing methods. This innovative approach addresses the need for better rhBMP-2 delivery systems, potentially expanding its use in pediatric bone healing applications.

  PublisherDOI

• Comparative Outcomes Assessment of Velopharyngeal Dysfunction and Oronasal Fistula: Implications of Muscle Repair in Palatoplasty

  Journal of Craniofacial Surgery · 2025-08-20 · 1 citations

  article

  OBJECTIVE: To shed light on a clinical concern common to surgeries performed on muscles namely does more extensive muscle dissection during palatoplasty lead to excessive scarring, which would impair rather than improve subsequent muscle function? DESIGN: Retrospective cohort study. SETTING: Cleft lip and palate clinic within a single tertiary care academic institution. PARTICIPANTS: Nonsyndromic infants with cleft lip and palate or cleft palate only undergoing primary palatoplasty by 3 fellowship-trained craniofacial surgeons, assisted by plastic surgery resident physicians between 2001 and 2021 were reviewed. Inclusion criteria included primary surgery under 21 months of age, and at least 7 years of follow-up. INTERVENTIONS: A comparison of 2 palatoplasty techniques-the von Langenbeck (VL), which consisted of coaptation of the levator muscle with minimal dissection and no actual levator muscle reconstruction and the Bardach Two-Flap (BTF) with Intravelar Veloplasty (IVVP) and levator palatini suture muscle repair. MAIN OUTCOMES MEASURED: Incidence of velopharyngeal dysfunction (VPD), defined by preoperative and postoperative Velopharyngeal Function Assessment Score (VFAS), need for secondary VPD surgery, and incidence of Oronasal Fistula (ONF). RESULTS: One hundred fifty-seven patients were included, n=66 subjects underwent VL repair (mean age 12.5 mo) and n=91 subjects underwent BTF repair (mean age 12.8 mo), with similar age at surgery (P<0.33). Preoperative VFAS (8.8 VL versus 9.7 BTF, P<0.09) and postoperative VFAS (5.3 VL versus 4.2 BTF, P<0.10) did not differ significantly between groups. However, the VL group had significantly higher rates of adverse outcomes: VPD (59% VL versus 42% BTF, P<0.04), secondary speech surgery (59% VL versus 32% BTF, P<0.001), and postoperative ONF (64% VL versus 29% BTF, P<0.001). Analysis of surgeon factors showed that the single attending surgeon performing VL (without IVVP) had more years of experience than the BTF surgeons, yet the VL technique still yielded higher rates of secondary surgery and ONF (P<0.01, P<0.001). Resident physician experience level was similar across study groups. CONCLUSIONS: Levator muscle repair is associated with markedly improved outcomes after palatoplasty, challenging the notion that significant dissection and suture repair of the muscle would lead to subsequent scarring and compromise of clinical outcomes.

  PublisherDOI

Frequent coauthors

• Sanjay Naran

  University of Pittsburgh

  65 shared

• Joseph E. Losee

  University of Pittsburgh

  58 shared

• Evan B. Katzel

  VA Pittsburgh Healthcare System

  48 shared

• Zoe M. MacIsaac

  University of Pittsburgh Medical Center

  46 shared

• Jordan W. Swanson

  Children's Hospital of Philadelphia

  46 shared

• Scott P. Bartlett

  Children's Hospital of Philadelphia

  45 shared

• Stephen J. Kovach

  University of Pennsylvania

  43 shared

• Jesse A. Taylor

  Children's Hospital of Philadelphia

  43 shared

Education

• MD

  University of Pittsburgh

  2015

• BS

  University of Pittsburgh

  2010